diff options
Diffstat (limited to 'api/macroapi.c')
| -rwxr-xr-x | api/macroapi.c | 3390 |
1 files changed, 2881 insertions, 509 deletions
diff --git a/api/macroapi.c b/api/macroapi.c index 7141726c..8d9975eb 100755 --- a/api/macroapi.c +++ b/api/macroapi.c @@ -29,7 +29,7 @@ * * Version Creation Date: 11/8/2007 * -* $Revision: 1.498 $ +* $Revision: 1.598 $ * * File Description: * @@ -64,6 +64,8 @@ #include <valid.h> #include <objvalid.h> #include <valapi.h> +#include <tax3api.h> +#include <tofasta.h> /* static void CollectNucBioseqCallback (BioseqPtr bsp, Pointer data); */ static void AddCommentDescriptorDestinationsForBioseq (BioseqPtr bsp, ValNodePtr PNTR dest_list); @@ -98,24 +100,6 @@ static ValNodePtr CollectNucBioseqs (SeqEntryPtr sep) return vnb.head; } -static Boolean IsAllDigits (CharPtr str) -{ - CharPtr cp; - - if (StringHasNoText (str)) return FALSE; - - cp = str; - while (*cp != 0 && isdigit (*cp)) { - cp++; - } - if (*cp == 0) { - return TRUE; - } else { - return FALSE; - } -} - - static Boolean IsAllCaps (CharPtr str) { CharPtr cp; @@ -171,6 +155,33 @@ static Boolean IsAllPunctuation (CharPtr str) } +static CharPtr PrintPartialOrCompleteDate(DatePtr date) +{ + CharPtr str = NULL; + Char year[5]; + Char result[15]; + + if (date == NULL) { + return NULL; + } + str = PrintDate(date); + if (str == NULL && date->data[0] > 0 && date->data[1]) { + if ((int) (date -> data[1]) < 30) { + sprintf(year, "%4d", (int) (date -> data[1] + 2000)); + } else { + sprintf(year, "%4d", (int) (date -> data[1] + 1900)); + } + if (date->data[2]) { + sprintf(result, "%s %s", NCBI_months[date->data[2] -1 ], year); + } else { + StringCpy (result, year); + } + str = StringSave (result); + } + return str; +} + + static Boolean DoesFeatureMatchRnaType (SeqFeatPtr sfp, RnaFeatTypePtr rt); static Int4 CompareRnaTypes (RnaFeatTypePtr rt1, RnaFeatTypePtr rt2); @@ -714,7 +725,7 @@ static int CompareSourceQuals (VoidPtr ptr1, VoidPtr ptr2) static int LIBCALLBACK SortVnpByChoiceAndIntvalue (VoidPtr ptr1, VoidPtr ptr2); -static int CompareFieldTypesEx (FieldTypePtr vnp1, FieldTypePtr vnp2, Boolean use_source_qual_sort) +NLM_EXTERN int CompareFieldTypesEx (FieldTypePtr vnp1, FieldTypePtr vnp2, Boolean use_source_qual_sort) { int rval = 0; FeatureFieldPtr field1, field2; @@ -1356,7 +1367,8 @@ static FeatTypeFeatDefData feattype_featdef[] = { { Macro_feature_type_oriT , FEATDEF_oriT , "oriT" } , { Macro_feature_type_ncRNA , FEATDEF_ncRNA , "ncRNA" } , { Macro_feature_type_tmRNA , FEATDEF_tmRNA , "tmRNA" } , - { Macro_feature_type_mobile_element, FEATDEF_mobile_element, "mobile_element" } + { Macro_feature_type_mobile_element, FEATDEF_mobile_element, "mobile_element" } , + { Macro_feature_type_regulatory, FEATDEF_regulatory, "regulatory" } }; #define NUM_feattype_featdef sizeof (feattype_featdef) / sizeof (FeatTypeFeatDefData) @@ -1477,6 +1489,7 @@ NLM_EXTERN void AddImportFeaturesToChoiceList (ValNodePtr PNTR feature_type_list for (i = 1; i < NUM_feattype_featdef; i++) { if (feattype_featdef[i].feattype == Macro_feature_type_gap) continue; if (feattype_featdef[i].feattype == Macro_feature_type_conflict) continue; + if (IsRegulatorySubtype(feattype_featdef[i].featdef)) continue; seqfeattype = FindFeatFromFeatDefType (feattype_featdef[i].featdef); if (seqfeattype == SEQFEAT_IMP) { featname = GetFeatureNameFromFeatureType (feattype_featdef[i].feattype); @@ -1549,6 +1562,7 @@ NLM_EXTERN void AddAllFeaturesToChoiceList (ValNodePtr PNTR feature_type_list) for (i = 1; i < NUM_feattype_featdef; i++) { if (feattype_featdef[i].feattype == Macro_feature_type_gap) continue; + if (IsRegulatorySubtype(feattype_featdef[i].featdef)) continue; featname = GetFeatureNameFromFeatureType (feattype_featdef[i].feattype); if (featname != NULL) { ValNodeAddPointer (&tmp_list, feattype_featdef[i].feattype, StringSave (featname)); @@ -1579,7 +1593,7 @@ static FeatQualGBQualData featqual_gbqual[] = { { Feat_qual_legal_db_xref , GBQUAL_db_xref , 0, "db-xref" } , { Feat_qual_legal_direction , GBQUAL_direction , 0, "direction" } , { Feat_qual_legal_ec_number , GBQUAL_EC_number , 0, "EC number" } , - { Feat_qual_legal_environmental_sample , 0, GBQUAL_environmental_sample , "environmental-sample" } , + { Feat_qual_legal_environmental_sample , GBQUAL_environmental_sample , 0, "environmental-sample" } , { Feat_qual_legal_evidence , GBQUAL_evidence , 0, "evidence" } , { Feat_qual_legal_exception , GBQUAL_exception , 0, "exception" } , { Feat_qual_legal_experiment , GBQUAL_experiment , 0, "experiment" } , @@ -1605,12 +1619,14 @@ static FeatQualGBQualData featqual_gbqual[] = { { Feat_qual_legal_organism , GBQUAL_organism , 0, "organism" } , { Feat_qual_legal_organelle , GBQUAL_organelle , 0, "organelle" } , { Feat_qual_legal_partial , GBQUAL_partial , 0, "partial" } , + { Feat_qual_legal_pcr_conditions, GBQUAL_PCR_conditions , 0, "pcr-conditions" } , { Feat_qual_legal_phenotype , GBQUAL_phenotype , 0, "phenotype" } , { Feat_qual_legal_plasmid , GBQUAL_plasmid , 0, "plasmid" } , { Feat_qual_legal_product , GBQUAL_product , 0, "product" } , { Feat_qual_legal_protein_id , GBQUAL_protein_id , 0, "protein-id" } , { Feat_qual_legal_pseudo , GBQUAL_pseudogene , 0, "pseudogene" } , { Feat_qual_legal_rearranged , GBQUAL_rearranged , 0, "rearranged" } , + { Feat_qual_legal_regulatory_class , GBQUAL_regulatory_class , 0, "regulatory-class" } , { Feat_qual_legal_replace , GBQUAL_replace , 0, "replace" } , { Feat_qual_legal_rpt_family , GBQUAL_rpt_family , 0, "rpt-family" } , { Feat_qual_legal_rpt_type , GBQUAL_rpt_type , 0, "rpt-type" } , @@ -2172,6 +2188,7 @@ typedef struct srcqualscqual { #define kAllNotesStr "All Notes" #define kAllQualsStr "All" +#define kAllPrimersStr "All Primers" static SrcQualSCQualData srcqual_scqual[] = { { Source_qual_acronym , ORGMOD_acronym , IS_ORGMOD , 0 , "acronym" } , @@ -2264,6 +2281,7 @@ static SrcQualSCQualData srcqual_scqual[] = { { Source_qual_transgenic , SUBSRC_transgenic , IS_SUBSRC , 0 , "transgenic" } , { Source_qual_transposon_name , SUBSRC_transposon_name , IS_SUBSRC , 0 , "transposon-name" } , { Source_qual_type , ORGMOD_type , IS_ORGMOD , 0 , "type" } , + { Source_qual_type_material , ORGMOD_type_material , IS_ORGMOD , 0 , "type-material" } , { Source_qual_variety , ORGMOD_variety , IS_ORGMOD , 0 , "variety" } , { Source_qual_all_notes , 255 , IS_OTHER , 0 , kAllNotesStr } , { Source_qual_all_quals , 0 , IS_OTHER , 0, kAllQualsStr } , @@ -2271,6 +2289,8 @@ static SrcQualSCQualData srcqual_scqual[] = { { Source_qual_linkage_group , SUBSRC_linkage_group , IS_SUBSRC , 0 , "linkage-group" } , { Source_qual_haplogroup , SUBSRC_haplogroup, IS_SUBSRC, 0, "haplogroup"} , { Source_qual_taxid , 0 , IS_OTHER , 0 , "taxid" } , + { Source_qual_all_primers , 0, IS_OTHER , 0, kAllPrimersStr } , + { Source_qual_altitude , SUBSRC_altitude, IS_SUBSRC , 0 , "altitude"} }; #define NUM_srcqual_scqual sizeof (srcqual_scqual) / sizeof (SrcQualSCQualData) @@ -2286,7 +2306,7 @@ static StringAliasData src_qual_alias_list[] = { }; -static Int4 GetSubSrcQualFromSrcQual (Int4 srcqual, Int4Ptr subfield) +NLM_EXTERN Int4 GetSubSrcQualFromSrcQual (Int4 srcqual, Int4Ptr subfield) { Int4 i; @@ -2411,6 +2431,11 @@ NLM_EXTERN Int4 GetSourceQualTypeByName (CharPtr qualname) return Source_qual_variety; } else if (StringICmp (qualname, "str.") == 0) { return Source_qual_strain; + } else if (StringICmp (qualname, "note") == 0) { + return Source_qual_orgmod_note; + } else if (Matchnamestring (qualname, "latitude-longitude") + || Matchnamestring (qualname, "lat-long")) { + return Source_qual_lat_lon; } return -1; } @@ -2424,10 +2449,12 @@ NLM_EXTERN ValNodePtr GetSourceQualList (Boolean for_remove) if (for_remove) { ValNodeAddPointer (&list, 0, StringSave (kAllQualsStr)); last = ValNodeAddPointer (&list, 0, StringSave (kAllNotesStr)); + last = ValNodeAddPointer (&list, 0, StringSave (kAllPrimersStr)); } for (i = 0; i < NUM_srcqual_scqual; i++) { if (srcqual_scqual[i].srcqual != Source_qual_all_notes - && srcqual_scqual[i].srcqual != Source_qual_all_quals) { + && srcqual_scqual[i].srcqual != Source_qual_all_quals + && srcqual_scqual[i].srcqual != Source_qual_all_primers) { ValNodeAddPointer (&tmp, 0, StringSave (srcqual_scqual[i].qualname)); } } @@ -2473,7 +2500,7 @@ NLM_EXTERN ValNodePtr GetSourceQualFieldListFromBioSource (BioSourcePtr biop) vnp->data.intvalue = Source_qual_lineage; ValNodeAddPointer (&list, FieldType_source_qual, vnp); } - if (!StringHasNoText (biop->org->orgname->lineage)) { + if (!StringHasNoText (biop->org->orgname->div)) { vnp = ValNodeNew (NULL); vnp->choice = SourceQualChoice_textqual; vnp->data.intvalue = Source_qual_division; @@ -2701,6 +2728,25 @@ NLM_EXTERN ValNodePtr GetLocationList (Boolean for_remove) } +static ValNodePtr SrcLocationFieldFromValue (CharPtr value) +{ + ValNodePtr field, sq; + Int4 genome; + + genome = GenomeFromLocName(value); + if (genome < 0) { + return NULL; + } + sq = ValNodeNew (NULL); + sq->choice = SourceQualValChoice_location; + sq->data.intvalue = genome; + field = ValNodeNew (NULL); + field->choice = FieldType_source_qual; + field->data.ptrvalue = sq; + return field; +} + + typedef struct srcorigorigin { Int4 srcorig; Int4 origin; @@ -3620,6 +3666,7 @@ static TechniqueTypeTechData techniquetype_tech[] = { { Technique_type_barcode, MI_TECH_barcode, "BARCODE" } , { Technique_type_composite_wgs_htgs, MI_TECH_composite_wgs_htgs, "composite WGS-HTGS" } , { Technique_type_tsa, MI_TECH_tsa, "TSA" } , + { Technique_type_targeted, MI_TECH_targeted, "targeted" } , { Technique_type_other, MI_TECH_other, "other" } }; @@ -4284,7 +4331,7 @@ NLM_EXTERN ValNodePtr GetSiteTypeList (void) /* Simple constraints */ static Boolean DisallowCharacter (Char ch, Boolean disallow_slash) { - if (isalpha ((Int4) ch) || isdigit ((Int4) ch) || ch == '_') + if (isalpha ((Int4) ch) || isdigit ((Int4) ch) || ch == '_' || ch == '-') { return TRUE; } @@ -4692,14 +4739,14 @@ NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstrain switch (scp->match_location) { case String_location_contains: - if (scp->case_sensitive) - { - pFound = StringSearch (search, pattern); - } - else - { - pFound = StringISearch (search, pattern); - } + if (scp->case_sensitive) + { + pFound = StringSearch (search, pattern); + } + else + { + pFound = StringISearch (search, pattern); + } if (pFound == NULL) { rval = FALSE; @@ -4709,14 +4756,14 @@ NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstrain rval = IsWholeWordMatch (search, pFound, StringLen (pattern)); while (!rval && pFound != NULL) { - if (scp->case_sensitive) - { - pFound = StringSearch (pFound + 1, pattern); - } - else - { - pFound = StringISearch (pFound + 1, pattern); - } + if (scp->case_sensitive) + { + pFound = StringSearch (pFound + 1, pattern); + } + else + { + pFound = StringISearch (pFound + 1, pattern); + } if (pFound != NULL) { rval = IsWholeWordMatch (search, pFound, StringLen (pattern)); @@ -4729,14 +4776,14 @@ NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstrain } break; case String_location_starts: - if (scp->case_sensitive) - { - pFound = StringSearch (search, pattern); - } - else - { - pFound = StringISearch (search, pattern); - } + if (scp->case_sensitive) + { + pFound = StringSearch (search, pattern); + } + else + { + pFound = StringISearch (search, pattern); + } if (pFound == search) { if (scp->whole_word) @@ -4750,16 +4797,16 @@ NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstrain } break; case String_location_ends: - if (scp->case_sensitive) - { - pFound = StringSearch (search, pattern); - } - else - { - pFound = StringISearch (search, pattern); - } + if (scp->case_sensitive) + { + pFound = StringSearch (search, pattern); + } + else + { + pFound = StringISearch (search, pattern); + } while (pFound != NULL && !rval) { - char_after = *(pFound + StringLen (pattern)); + char_after = *(pFound + StringLen (pattern)); if (char_after == 0) { if (scp->whole_word) @@ -4775,14 +4822,14 @@ NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstrain } else { - if (scp->case_sensitive) - { - pFound = StringSearch (pFound + 1, pattern); - } - else - { - pFound = StringISearch (pFound + 1, pattern); - } + if (scp->case_sensitive) + { + pFound = StringSearch (pFound + 1, pattern); + } + else + { + pFound = StringISearch (pFound + 1, pattern); + } } } break; @@ -4848,7 +4895,7 @@ NLM_EXTERN Boolean DoesSingleStringMatchConstraint (CharPtr str, StringConstrain pattern = MemFree (pattern); } scp->match_text = tmp_match; - return rval; + return rval; } @@ -5051,23 +5098,23 @@ NLM_EXTERN Boolean RemoveStringConstraintPortionFromString (CharPtr PNTR str, St rval = TRUE; pFound = NULL; } else { - if (scp->case_sensitive) - { - pFound = StringSearch (pFound + 1, scp->match_text); - } - else - { - pFound = StringISearch (pFound + 1, scp->match_text); - } + if (scp->case_sensitive) + { + pFound = StringSearch (pFound + 1, scp->match_text); + } + else + { + pFound = StringISearch (pFound + 1, scp->match_text); + } } break; } } - } + } if (rval && StringHasNoText (*str)) { *str = MemFree (*str); } - return rval; + return rval; } @@ -5671,6 +5718,11 @@ static CharPtr FindTextMarker(CharPtr str, Int4Ptr len, TextMarkerPtr marker, Bo CharPtr digits = "0123456789"; CharPtr letters = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"; + if (str == NULL) + { + return NULL; + } + if (marker == NULL) { if (len != NULL) @@ -6604,7 +6656,7 @@ static Boolean SetInt2ValueWithString (Int2Ptr val, CharPtr val_str, Uint2 exist sprintf (num, "%d", *val); tmp = StringSave (num); if (SetStringValue (&tmp, val_str, existing_text) - && IsAllDigits (tmp)) { + && StringIsAllDigits (tmp)) { *val = atoi (tmp); rval = TRUE; } @@ -6645,7 +6697,7 @@ NLM_EXTERN Boolean SetObjectIdString (ObjectIdPtr oip, CharPtr value, Uint2 exis if (SetStringValue (&tmp, value, existing_text)) { oip->str = MemFree (oip->str); oip->id = 0; - if (IsAllDigits (tmp)) { + if (StringIsAllDigits (tmp) && StringLen (tmp) < 8 && *tmp != '0') { oip->id = atoi (tmp); } else { oip->str = tmp; @@ -6677,9 +6729,20 @@ NLM_EXTERN CharPtr GetObjectIdString (ObjectIdPtr oip) } +static Boolean DoesNumberMatchStringConstraint (Int4 num, StringConstraintPtr scp) +{ + Char tmp[15]; + + if (IsStringConstraintEmpty (scp)) { + return TRUE; + } + sprintf (tmp, "%d", num); + return DoesStringMatchConstraint(tmp, scp); +} + + static Boolean DoesObjectIdMatchStringConstraint (ObjectIdPtr oip, StringConstraintPtr scp) { - Char num[15]; Boolean rval = FALSE; if (oip == NULL) { @@ -6687,8 +6750,7 @@ static Boolean DoesObjectIdMatchStringConstraint (ObjectIdPtr oip, StringConstra } else if (IsStringConstraintEmpty (scp)) { return TRUE; } else if (oip->id > 0) { - sprintf (num, "%d", oip->id); - rval = DoesStringMatchConstraint (num, scp); + rval = DoesNumberMatchStringConstraint (oip->id, scp); } else { rval = DoesStringMatchConstraint (oip->str, scp); } @@ -7185,7 +7247,7 @@ NLM_EXTERN CharPtr GetRNARefProductString (RnaRefPtr rrp, StringConstraintPtr sc if (rrp->ext.choice == 1) { str = StringSave (rrp->ext.value.ptrvalue); } else if (rrp->ext.choice == 2) { - str = GetTrnaProductString (rrp->ext.value.ptrvalue); + str = StringSaveNoNull (GetTrnaProductString (rrp->ext.value.ptrvalue)); } else if (rrp->ext.choice == 3 && (rgp = (RNAGenPtr) rrp->ext.value.ptrvalue) != NULL) { if (!StringHasNoText (rgp->product)) { str = StringSave (rgp->product); @@ -7306,7 +7368,7 @@ NLM_EXTERN Boolean SetRNARefProductString (RnaRefPtr rrp, StringConstraintPtr sc rgp = (RNAGenPtr) rrp->ext.value.ptrvalue; rval = SetStringValue (&(rgp->product), new_val, existing_text); } else if (rrp->ext.choice == 2) { - tmp = StringSave (GetTrnaProductString (rrp->ext.value.ptrvalue)); + tmp = StringSaveNoNull (GetTrnaProductString (rrp->ext.value.ptrvalue)); if (DoesStringMatchConstraint (tmp, scp) && SetStringValue (&tmp, new_val, existing_text)) { @@ -7534,6 +7596,87 @@ static Boolean RemovetRNACodons_Recognized (SeqFeatPtr sfp) } +/* +M A or C +R A or G +W A or T +S C or G +Y C or T +K G or T +V A or C or G +H A or C or T +D A or G or T +B C or G or T +X G or A or T or C +N G or A or T or C +*/ +typedef struct ambiguitychar { + Char ch; + CharPtr replacements; +} AmbiguityCharData, PNTR AmbiguityCharPtr; + + +static AmbiguityCharData s_AmbiguityChars[] = { + {'M', "AC"}, + {'R', "AG"}, + {'W', "AT"}, + {'S', "CG"}, + {'Y', "CT"}, + {'K', "GT"}, + {'V', "ACG"}, + {'H', "ACT"}, + {'D', "AGT"}, + {'B', "CGT"}, + {'X', "GATC"}, + {'N', "GATC"}, + {'\0', NULL} +}; + + +static ValNodePtr ExpandWobbleCodon (CharPtr codon) +{ + ValNodePtr list = NULL, vnp, new_list; + Int4 i, j, len; + CharPtr this_codon, cp, new_codon; + Boolean any; + + if (StringHasNoText (codon)) { + return NULL; + } + len = StringLen (codon); + ValNodeAddPointer (&list, 0, StringSave (codon)); + + for (j = 0; j < len; j++) { + new_list = NULL; + for (vnp = list; vnp != NULL; vnp = vnp->next) { + this_codon = vnp->data.ptrvalue; + any = FALSE; + for (i = 0; s_AmbiguityChars[i].ch != 0 && !any; i++) { + if (this_codon[j] == s_AmbiguityChars[i].ch) { + cp = s_AmbiguityChars[i].replacements; + while (*cp != 0) { + new_codon = StringSave (this_codon); + new_codon[j] = *cp; + ValNodeAddPointer (&new_list, 0, new_codon); + cp++; + } + any = TRUE; + } + } + if (!any) { + ValNodeAddPointer (&new_list, 0, StringSave (this_codon)); + } + } + list = ValNodeFreeData (list); + list = new_list; + } + + for (vnp = list; vnp != NULL; vnp = vnp->next) { + vnp->choice = IndexForCodon (vnp->data.ptrvalue, Seq_code_iupacna); + } + return list; +} + static Boolean ParseCodonsRecognizedFromCommaDelimitedList (CharPtr str, Uint1Ptr codons) { @@ -7541,7 +7684,7 @@ static Boolean ParseCodonsRecognizedFromCommaDelimitedList (CharPtr str, Uint1Pt Char ch; Boolean rval = TRUE; Uint1 codon[4]; - Uint1 code; + ValNodePtr wobble_list, vnp; if (StringHasNoText (str) || codons == NULL) { return FALSE; @@ -7580,12 +7723,19 @@ static Boolean ParseCodonsRecognizedFromCommaDelimitedList (CharPtr str, Uint1Pt if (rval) { codon [q] = 0; if (q == 3) { - code = IndexForCodon (codon, Seq_code_iupacna); - if (code == INVALID_RESIDUE) { + wobble_list = ExpandWobbleCodon(codon); + for (vnp = wobble_list; vnp != NULL && codon_num < 6 && rval; vnp = vnp->next) { + if (vnp->choice == INVALID_RESIDUE) { + rval = FALSE; + } else { + codons [codon_num++] = vnp->choice; + } + } + if (vnp != NULL) { + /* too many ambiguities */ rval = FALSE; - } else { - codons [codon_num++] = code; } + wobble_list = ValNodeFreeData (wobble_list); } str += 3; while (isspace (*str)) { @@ -7606,7 +7756,7 @@ static Boolean ParseCodonsRecognizedFromCommaDelimitedList (CharPtr str, Uint1Pt } -static Boolean SettRNACodons_Recognized (SeqFeatPtr sfp, StringConstraintPtr scp, CharPtr new_val, Uint2 existing_text) +NLM_EXTERN Boolean SettRNACodons_Recognized (SeqFeatPtr sfp, StringConstraintPtr scp, CharPtr new_val, Uint2 existing_text) { RnaRefPtr rrp; tRNAPtr trp; @@ -7719,12 +7869,12 @@ static CharPtr GettRNACodonsRecognized (SeqFeatPtr sfp, StringConstraintPtr scp) for (j = 0; j < 6; j++) { if (trp->codon [j] < 64) { - /* Note - it is important to set the fourth character in the codon array to NULL - * because CodonForIndex only fills in the three characters of actual codon, - * so if you StringCpy the codon array and the NULL character is not found after - * the three codon characters, you will write in memory you did not intend to. - */ - codon [3] = 0; + /* Note - it is important to set the fourth character in the codon array to NULL + * because CodonForIndex only fills in the three characters of actual codon, + * so if you StringCpy the codon array and the NULL character is not found after + * the three codon characters, you will write in memory you did not intend to. + */ + codon [3] = 0; if (CodonForIndex (trp->codon [j], Seq_code_iupacna, codon)) { if (buf[0] != 0) { StringCat (buf, ", "); @@ -8383,8 +8533,9 @@ static CharPtr GetQualFromFeatureAnyType (SeqFeatPtr sfp, ValNodePtr field, Stri } /* pseudo */ - if ((field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_pseudo) - || (field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("pseudogene", field->data.ptrvalue))) + if (str == NULL + && (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_pseudo) + || (field->choice == FeatQualChoice_illegal_qual && DoesStringMatchConstraint ("pseudogene", field->data.ptrvalue))) { str = GetFirstGBQualMatch (sfp->qual, "pseudogene", 0, scp); if (str == NULL && sfp->pseudo) { @@ -8512,13 +8663,16 @@ static CharPtr GetQualFromFeatureAnyType (SeqFeatPtr sfp, ValNodePtr field, Stri /* coding region fields */ /* transl_except */ - if (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_transl_except - && sfp->data.choice == SEQFEAT_CDREGION) + if (str == NULL + && field->choice == FeatQualChoice_legal_qual + && field->data.intvalue == Feat_qual_legal_transl_except + && sfp->data.choice == SEQFEAT_CDREGION) { str = GetCodeBreakString (sfp); } /* transl_table */ - if (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_transl_table + if (str == NULL + && field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_transl_table && sfp->data.choice == SEQFEAT_CDREGION && (crp = (CdRegionPtr) sfp->data.value.ptrvalue) != NULL) { @@ -8529,7 +8683,8 @@ static CharPtr GetQualFromFeatureAnyType (SeqFeatPtr sfp, ValNodePtr field, Stri } } /* translation */ - if (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_translation + if (str == NULL + && field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_translation && sfp->data.choice == SEQFEAT_CDREGION) { if (sfp->product != NULL) @@ -9085,6 +9240,7 @@ static SeqFeatPtr CreateGeneForFeature (SeqFeatPtr sfp) { BioseqPtr bsp; SeqFeatPtr gene = NULL; + SeqLocPtr slp_new; if (sfp == NULL || sfp->data.choice == SEQFEAT_GENE) { return NULL; @@ -9093,6 +9249,11 @@ static SeqFeatPtr CreateGeneForFeature (SeqFeatPtr sfp) if (bsp != NULL) { gene = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, sfp->location); if (gene != NULL) { + slp_new = SeqLocMerge (bsp, gene->location, NULL, TRUE, FALSE, FALSE); + if (slp_new != NULL && slp_new != gene->location) { + gene->location = SeqLocFree (gene->location); + gene->location = slp_new; + } gene->data.value.ptrvalue = GeneRefNew(); } } @@ -9121,7 +9282,7 @@ static Boolean SetCitationTextOnFeature (SeqFeatPtr sfp, StringConstraintPtr scp return FALSE; } - if (!IsAllDigits (value)) { + if (!StringIsAllDigits (value)) { return FALSE; } @@ -9365,14 +9526,18 @@ static Boolean SetQualOnFeatureAnyType (SeqFeatPtr sfp, ValNodePtr field, String gene->pseudo = TRUE; rval = TRUE; } - rval |= SetStringInGBQualList (&(gene->qual), field, scp, value, existing_text); + if (StringICmp (value, "Unqualified") != 0) { + rval |= SetStringInGBQualList (&(gene->qual), field, scp, value, existing_text); + } return rval; } else { if (!sfp->pseudo) { sfp->pseudo = TRUE; rval = TRUE; } - rval |= SetStringInGBQualList (&(sfp->qual), field, scp, value, existing_text); + if (StringICmp (value, "Unqualified") != 0) { + rval |= SetStringInGBQualList (&(sfp->qual), field, scp, value, existing_text); + } return rval; } } @@ -9551,7 +9716,7 @@ static Boolean SetQualOnFeatureAnyType (SeqFeatPtr sfp, ValNodePtr field, String if (field->choice == FeatQualChoice_legal_qual && field->data.intvalue == Feat_qual_legal_transl_table && sfp->data.choice == SEQFEAT_CDREGION && (crp = (CdRegionPtr) sfp->data.value.ptrvalue) != NULL - && IsAllDigits (value)) + && StringIsAllDigits (value)) { if (crp->genetic_code != NULL && existing_text == ExistingTextOption_leave_old) { matched_term = TRUE; @@ -10833,7 +10998,7 @@ NLM_EXTERN CharPtr GetSourceQualFromBioSource (BioSourcePtr biop, SourceQualChoi vn.data.intvalue = Source_qual_orgmod_note; str = GetSourceQualFromBioSource (biop, &vn, constraint); } - } else if (scp->data.intvalue == Source_qual_all_quals) { + } else if (scp->data.intvalue == Source_qual_all_quals || scp->data.intvalue == Source_qual_all_primers) { /* will not do */ } else if (scp->data.intvalue == Source_qual_fwd_primer_name || scp->data.intvalue == Source_qual_fwd_primer_seq @@ -10986,7 +11151,8 @@ NLM_EXTERN ValNodePtr GetMultipleSourceQualsFromBioSource (BioSourcePtr biop, So if (str != NULL) { ValNodeAddPointer (&val_list, 0, str); } - } else if (scp->data.intvalue == Source_qual_all_quals) { + } else if (scp->data.intvalue == Source_qual_all_quals + || scp->data.intvalue == Source_qual_all_primers) { /* will not do */ } else { orgmod_subtype = GetOrgModQualFromSrcQual (scp->data.intvalue, &subfield); @@ -11064,7 +11230,8 @@ static Boolean RemoveAllSourceQualsFromBioSource (BioSourcePtr biop, StringConst for (i = 0; i < NUM_srcqual_scqual; i++) { if (srcqual_scqual[i].srcqual != Source_qual_all_quals - && srcqual_scqual[i].srcqual != Source_qual_all_notes) { + && srcqual_scqual[i].srcqual != Source_qual_all_notes + && srcqual_scqual[i].srcqual != Source_qual_all_primers) { vn.data.intvalue = srcqual_scqual[i].srcqual; rval |= RemoveSourceQualFromBioSource (biop, &vn, constraint); } @@ -11163,6 +11330,17 @@ NLM_EXTERN Boolean RemoveSourceQualFromBioSource (BioSourcePtr biop, SourceQualC rval |= RemoveSourceQualFromBioSource (biop, &vn, constraint); vn.data.intvalue = Source_qual_orgmod_note; rval |= RemoveSourceQualFromBioSource (biop, &vn, constraint); + } else if (scp->data.intvalue == Source_qual_all_primers) { + vn.choice = SourceQualChoice_textqual; + vn.data.intvalue = Source_qual_fwd_primer_name; + vn.next = NULL; + rval |= RemoveSourceQualFromBioSource (biop, &vn, constraint); + vn.data.intvalue = Source_qual_rev_primer_name; + rval |= RemoveSourceQualFromBioSource (biop, &vn, constraint); + vn.data.intvalue = Source_qual_fwd_primer_seq; + rval |= RemoveSourceQualFromBioSource (biop, &vn, constraint); + vn.data.intvalue = Source_qual_rev_primer_seq; + rval |= RemoveSourceQualFromBioSource (biop, &vn, constraint); } else if (scp->data.intvalue == Source_qual_all_quals) { rval |= RemoveAllSourceQualsFromBioSource (biop, constraint); } else { @@ -11362,6 +11540,11 @@ NLM_EXTERN Boolean SetSourceQualInBioSource (BioSourcePtr biop, SourceQualChoice rval |= SetSourceQualInBioSource (biop, &vn, constraint, value, existing_text); vn.data.intvalue = Source_qual_orgmod_note; rval |= SetSourceQualInBioSource (biop, &vn, constraint, value, existing_text); + } else if (scp->data.intvalue == Source_qual_all_primers) { + rval = SetPrimerValueInBioSource (biop, Source_qual_fwd_primer_name, constraint, value, existing_text); + rval |= SetPrimerValueInBioSource (biop, Source_qual_fwd_primer_seq, constraint, value, existing_text); + rval |= SetPrimerValueInBioSource (biop, Source_qual_rev_primer_name, constraint, value, existing_text); + rval |= SetPrimerValueInBioSource (biop, Source_qual_rev_primer_seq, constraint, value, existing_text); } else if (scp->data.intvalue == Source_qual_fwd_primer_name || scp->data.intvalue == Source_qual_fwd_primer_seq || scp->data.intvalue == Source_qual_rev_primer_name @@ -11818,7 +12001,7 @@ static CharPtr GetFieldValueFromCGPSet (CGPSetPtr c, Uint2 field, StringConstrai for (vnp = c->gene_list; vnp != NULL && str == NULL; vnp = vnp->next) { sfp = (SeqFeatPtr) vnp->data.ptrvalue; if (sfp != NULL) { - str = GetFirstGBQualMatch (sfp->qual, "old-locus-tag", 0, scp); + str = GetFirstGBQualMatch (sfp->qual, "old_locus_tag", 0, scp); } } break; @@ -12064,7 +12247,7 @@ static Boolean RemoveFieldValueFromCGPSet (CGPSetPtr c, Uint2 field, StringConst for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) { sfp = (SeqFeatPtr) vnp->data.ptrvalue; if (sfp != NULL) { - rval |= RemoveGBQualMatch (&(sfp->qual), "old-locus-tag", 0, scp); + rval |= RemoveGBQualMatch (&(sfp->qual), "old_locus_tag", 0, scp); } } break; @@ -12213,7 +12396,6 @@ static Boolean RemoveFieldValueFromCGPSet (CGPSetPtr c, Uint2 field, StringConst static SeqFeatPtr CreateGeneForCGPSet (CGPSetPtr c) { SeqFeatPtr gene = NULL, sfp = NULL; - BioseqPtr bsp; ValNodePtr vnp; if (c == NULL) return NULL; @@ -12224,15 +12406,7 @@ static SeqFeatPtr CreateGeneForCGPSet (CGPSetPtr c) for (vnp = c->mrna_list; vnp != NULL && sfp == NULL; vnp = vnp->next) { sfp = vnp->data.ptrvalue; } - if (sfp != NULL) { - bsp = BioseqFindFromSeqLoc (sfp->location); - if (bsp != NULL) { - gene = CreateNewFeatureOnBioseq (bsp, SEQFEAT_GENE, sfp->location); - if (gene != NULL) { - gene->data.value.ptrvalue = GeneRefNew(); - } - } - } + gene = CreateGeneForFeature (sfp); return gene; } @@ -12337,12 +12511,14 @@ static Boolean SetFieldValueInCGPSet (CGPSetPtr c, Uint2 field, StringConstraint } break; case CDSGeneProt_field_gene_old_locus_tag: + ffield = FeatureFieldFromCDSGeneProtField (field); for (vnp = c->gene_list; vnp != NULL; vnp = vnp->next) { sfp = (SeqFeatPtr) vnp->data.ptrvalue; if (sfp != NULL) { - rval |= RemoveGBQualMatch (&(sfp->qual), "old-locus-tag", 0, scp); + rval |= SetStringInGBQualList (&(sfp->qual), ffield->field, scp, value, existing_text); } } + ffield = FeatureFieldFree (ffield); break; case CDSGeneProt_field_mrna_product: for (vnp = c->mrna_list; vnp != NULL; vnp = vnp->next) { @@ -12765,7 +12941,7 @@ static Boolean SetGenomeProjectIdOnBioseq (BioseqPtr bsp, StringConstraintPtr sc UserFieldPtr ufp; Boolean rval = FALSE; - if (bsp == NULL || !IsAllDigits (value)) { + if (bsp == NULL || !StringIsAllDigits (value)) { return FALSE; } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &context); @@ -12781,7 +12957,7 @@ static Boolean SetGenomeProjectIdOnBioseq (BioseqPtr bsp, StringConstraintPtr sc sprintf (buf, "%d", ufp->data.intvalue); if (IsStringConstraintEmpty (scp) || DoesStringMatchConstraint (buf, scp)) { tmp = StringSave (buf); - if (SetStringValue (&tmp, value, existing_text) && IsAllDigits (tmp)) { + if (SetStringValue (&tmp, value, existing_text) && StringIsAllDigits (tmp)) { ufp->data.intvalue = atoi (tmp); rval = TRUE; } @@ -12821,7 +12997,7 @@ NLM_EXTERN CharPtr GetBioProjectIdFromBioseq (BioseqPtr bsp, StringConstraintPtr { ufp = uop->data; while (ufp != NULL) { - if (ufp->label != NULL && StringCmp (ufp->label->str, "BioProject") == 0) + if (ufp->label != NULL && StringCmp (ufp->label->str, "BioProject") == 0) { if (ufp->choice == 1) { @@ -12830,15 +13006,15 @@ NLM_EXTERN CharPtr GetBioProjectIdFromBioseq (BioseqPtr bsp, StringConstraintPtr { return StringSave (val); } - } + } else if (ufp->choice == 7 && ufp->num > 0 && (cpp = (CharPtr PNTR) ufp->data.ptrvalue) != NULL) { - for (i = 0; i < ufp->num; i++) + for (i = 0; i < ufp->num; i++) { - if (IsStringConstraintEmpty (scp) || DoesStringMatchConstraint (cpp[i], scp)) + if (IsStringConstraintEmpty (scp) || DoesStringMatchConstraint (cpp[i], scp)) { - return StringSave (cpp[i]); - } + return StringSave (cpp[i]); + } } } } @@ -12925,7 +13101,7 @@ static CharPtr DbnameValFromPrefixOrSuffix (CharPtr val) } -static Boolean IsUserFieldStructuredCommentPrefixOrSuffix (UserFieldPtr ufp) +NLM_EXTERN Boolean IsUserFieldStructuredCommentPrefixOrSuffix (UserFieldPtr ufp) { if (ufp == NULL || ufp->label == NULL) { return FALSE; @@ -13170,8 +13346,10 @@ static Boolean SetStructuredCommentFieldOnUserObject (UserObjectPtr uop, Structu curr->data.ptrvalue = StringSave (""); if (last == NULL) { ufp = uop->data; - curr->next = ufp->next; - ufp->next = curr; + if (ufp != NULL) { + curr->next = ufp->next; + ufp->next = curr; + } } else { curr->next = last->next; last->next = curr; @@ -13193,7 +13371,8 @@ static DBLinkNameData dblink_names[] = { { DBLink_field_type_bio_sample , "BioSample" } , { DBLink_field_type_probe_db , "ProbeDB" } , { DBLink_field_type_sequence_read_archve , "Sequence Read Archive" } , - { DBLink_field_type_bio_project , "BioProject" } + { DBLink_field_type_bio_project , "BioProject" } , + { DBLink_field_type_assembly , "Assembly" } }; #define NUM_dblinkname sizeof (dblink_names) / sizeof (DBLinkNameData) @@ -13276,6 +13455,47 @@ static CharPtr GetDBLinkFieldFromUserObject (UserObjectPtr uop, Int4 field, Stri } +static ValNodePtr GetMultipleDBLinkFieldValuesFromUserObject (UserObjectPtr uop, Int4 field, StringConstraintPtr scp) +{ + UserFieldPtr curr; + ValNodePtr rval = NULL; + CharPtr field_name; + Char buf[15]; + CharPtr PNTR cpp; + Int4Ptr ipp; + Int4 i; + + if (!IsUserObjectDBLink(uop) || field < 1) { + return NULL; + } + + field_name = GetDBLinkNameFromDBLinkFieldType (field); + for (curr = uop->data; curr != NULL; curr = curr->next) { + if (curr->label != NULL && StringCmp (curr->label->str, field_name) == 0) { + if (curr->choice == 7) { + if (curr->num > 0 && (cpp = (CharPtr PNTR) curr->data.ptrvalue) != NULL) { + for (i = 0; i < curr->num; i++) { + if (IsStringConstraintEmpty (scp) || DoesStringMatchConstraint (cpp[i], scp)) { + ValNodeAddPointer (&rval, 0, StringSave (cpp[i])); + } + } + } + } else if (curr->choice == 8) { + if (curr->num > 0 && (ipp = (Int4Ptr) curr->data.ptrvalue) != NULL) { + for (i = 0; i < curr->num; i++) { + sprintf (buf, "%d", ipp[i]); + if (IsStringConstraintEmpty (scp) || DoesStringMatchConstraint (buf, scp)) { + ValNodeAddPointer (&rval, 0, StringSave (buf)); + } + } + } + } + } + } + return rval; +} + + static Boolean RemoveDBLinkFieldFromUserObject (UserObjectPtr uop, Int4 field, StringConstraintPtr scp) { UserFieldPtr curr, prev_type = NULL, next_type; @@ -13347,9 +13567,9 @@ static Boolean SetDBLinkFieldOnUserObject (UserObjectPtr uop, Int4 field, String Boolean rval = FALSE; CharPtr newval; CharPtr field_name; - CharPtr PNTR cpp; + CharPtr PNTR cpp = NULL; CharPtr PNTR new_cpp; - Int4Ptr ipp, new_ipp; + Int4Ptr ipp = NULL, new_ipp; Int4 i; Char buf[15]; @@ -13374,24 +13594,26 @@ static Boolean SetDBLinkFieldOnUserObject (UserObjectPtr uop, Int4 field, String } if (!rval && IsStringConstraintEmpty (scp)) { new_cpp = (CharPtr PNTR) MemNew (sizeof (CharPtr) * (curr->num + 1)); - for (i = 0; i < curr->num; i++) { - new_cpp[i] = cpp[i]; - cpp[i] = NULL; + if (cpp != NULL) { + for (i = 0; i < curr->num; i++) { + new_cpp[i] = cpp[i]; + cpp[i] = NULL; + } + new_cpp[i] = StringSave (value); } - new_cpp[i] = StringSave (value); cpp = MemFree (cpp); curr->data.ptrvalue = new_cpp; curr->num++; rval = TRUE; } - } else if (curr->choice == 8 && IsAllDigits (value)) { + } else if (curr->choice == 8 && StringIsAllDigits (value)) { if (curr->num > 0 && (ipp = (Int4Ptr) curr->data.ptrvalue) != NULL && existing_text != ExistingTextOption_add_qual) { for (i = 0; i < curr->num; i++) { sprintf (buf, "%d", ipp[i]); if (IsStringConstraintEmpty (scp) || DoesStringMatchConstraint (buf, scp)) { newval = StringSave (buf); SetStringValue (&newval, value, existing_text); - if (IsAllDigits (newval)) { + if (StringIsAllDigits (newval)) { ipp[i] = atoi (newval); rval = TRUE; } @@ -13401,10 +13623,12 @@ static Boolean SetDBLinkFieldOnUserObject (UserObjectPtr uop, Int4 field, String } if (!rval && IsStringConstraintEmpty (scp)) { new_ipp = (Int4Ptr) MemNew (sizeof (Int4) * (curr->num + 1)); - for (i = 0; i < curr->num; i++) { - new_ipp[i] = ipp[i]; + if (ipp != NULL) { + for (i = 0; i < curr->num; i++) { + new_ipp[i] = ipp[i]; + } + new_ipp[i] = atoi (value); } - new_ipp[i] = atoi (value); ipp = MemFree (ipp); curr->data.ptrvalue = new_ipp; curr->num++; @@ -13414,7 +13638,7 @@ static Boolean SetDBLinkFieldOnUserObject (UserObjectPtr uop, Int4 field, String } last = curr; } - if (!rval && IsStringConstraintEmpty (scp) && (field != DBLink_field_type_trace_assembly || IsAllDigits (value))) { + if (!rval && IsStringConstraintEmpty (scp) && (field != DBLink_field_type_trace_assembly || StringIsAllDigits (value))) { curr = UserFieldNew (); curr->label = ObjectIdNew (); curr->label->str = StringSave (field_name); @@ -13652,7 +13876,7 @@ static CharPtr GetAuthorListStringEx (AuthListPtr alp, StringConstraintPtr scp, } -static CharPtr GetAuthorListString (AuthListPtr alp, StringConstraintPtr scp) +NLM_EXTERN CharPtr GetAuthorListString (AuthListPtr alp, StringConstraintPtr scp) { return GetAuthorListStringEx (alp, scp, FALSE); } @@ -13823,7 +14047,7 @@ static NameStdPtr ReadNameFromString (CharPtr str, CharPtr PNTR next_name) } -static ValNodePtr ReadNameListFromString (CharPtr value) +NLM_EXTERN ValNodePtr ReadNameListFromString (CharPtr value) { ValNodePtr names = NULL; AuthorPtr ap; @@ -14217,52 +14441,52 @@ static Boolean SetAffilPubField (AffilPtr ap, Int4 field, StringConstraintPtr sc switch (field) { case Publication_field_affiliation: - if (!StringHasNoText (ap->affil) && DoesStringMatchConstraint (ap->affil, scp)) { + if (!StringHasNoText (ap->affil) || DoesStringMatchConstraint (ap->affil, scp)) { rval = SetStringValue (&(ap->affil), value, existing_text); } break; case Publication_field_affil_div: - if (!StringHasNoText (ap->div) && DoesStringMatchConstraint (ap->div, scp)) { + if (!StringHasNoText (ap->div) || DoesStringMatchConstraint (ap->div, scp)) { rval = SetStringValue (&(ap->div), value, existing_text); } break; case Publication_field_affil_city: - if (!StringHasNoText (ap->city) && DoesStringMatchConstraint (ap->city, scp)) { + if (!StringHasNoText (ap->city) || DoesStringMatchConstraint (ap->city, scp)) { rval = SetStringValue (&(ap->city), value, existing_text); } break; case Publication_field_affil_sub: - if (!StringHasNoText (ap->sub) && DoesStringMatchConstraint (ap->sub, scp)) { + if (!StringHasNoText (ap->sub) || DoesStringMatchConstraint (ap->sub, scp)) { rval = SetStringValue (&(ap->sub), value, existing_text); } break; case Publication_field_affil_country: - if (!StringHasNoText (ap->country) && DoesStringMatchConstraint (ap->country, scp)) { + if (!StringHasNoText (ap->country) || DoesStringMatchConstraint (ap->country, scp)) { rval = SetStringValue (&(ap->country), value, existing_text); } break; case Publication_field_affil_street: - if (!StringHasNoText (ap->street) && DoesStringMatchConstraint (ap->street, scp)) { + if (!StringHasNoText (ap->street) || DoesStringMatchConstraint (ap->street, scp)) { rval = SetStringValue (&(ap->street), value, existing_text); } break; case Publication_field_affil_email: - if (!StringHasNoText (ap->email) && DoesStringMatchConstraint (ap->email, scp)) { + if (!StringHasNoText (ap->email) || DoesStringMatchConstraint (ap->email, scp)) { rval = SetStringValue (&(ap->email), value, existing_text); } break; case Publication_field_affil_fax: - if (!StringHasNoText (ap->fax) && DoesStringMatchConstraint (ap->fax, scp)) { + if (!StringHasNoText (ap->fax) || DoesStringMatchConstraint (ap->fax, scp)) { rval = SetStringValue (&(ap->fax), value, existing_text); } break; case Publication_field_affil_phone: - if (!StringHasNoText (ap->phone) && DoesStringMatchConstraint (ap->phone, scp)) { + if (!StringHasNoText (ap->phone) || DoesStringMatchConstraint (ap->phone, scp)) { rval = SetStringValue (&(ap->phone), value, existing_text); } break; case Publication_field_affil_zipcode: - if (!StringHasNoText (ap->postal_code) && DoesStringMatchConstraint (ap->postal_code, scp)) { + if (!StringHasNoText (ap->postal_code) || DoesStringMatchConstraint (ap->postal_code, scp)) { rval = SetStringValue (&(ap->postal_code), value, existing_text); } break; @@ -14293,9 +14517,11 @@ static CharPtr GetPubFieldFromImprint (ImprintPtr imprint, Int4 field, StringCon } break; case Publication_field_date: - str = PrintDate (imprint->date); - if (StringHasNoText (str) || !DoesStringMatchConstraint (str, scp)) { - str = MemFree (str); + if (imprint->date != NULL) { + str = PrintPartialOrCompleteDate (imprint->date); + if (StringHasNoText (str) || !DoesStringMatchConstraint (str, scp)) { + str = MemFree (str); + } } break; } @@ -14312,7 +14538,7 @@ static Boolean RemovePubDate (DatePtr PNTR pDate, StringConstraintPtr scp) return FALSE; } - str = PrintDate (*pDate); + str = PrintPartialOrCompleteDate (*pDate); if (!StringHasNoText (str) && DoesStringMatchConstraint (str, scp)) { *pDate = DateFree (*pDate); rval = TRUE; @@ -14326,12 +14552,17 @@ static Boolean SetPubDate (DatePtr PNTR pDate, StringConstraintPtr scp, CharPtr { CharPtr tmp; DatePtr dp = NULL; + Boolean made_new_date = FALSE; Boolean rval = FALSE; if (pDate == NULL) { return FALSE; } - tmp = PrintDate (*pDate); + if (*pDate == NULL) { + *pDate = DateNew(); + made_new_date = TRUE; + } + tmp = PrintPartialOrCompleteDate (*pDate); if (DoesStringMatchConstraint (tmp, scp) && SetStringValue (&tmp, value, existing_text)) { dp = ReadDateFromString (tmp); @@ -14342,6 +14573,9 @@ static Boolean SetPubDate (DatePtr PNTR pDate, StringConstraintPtr scp, CharPtr } } tmp = MemFree (tmp); + if (!rval && made_new_date) { + *pDate = DateFree (*pDate); + } return rval; } @@ -14391,12 +14625,12 @@ static Boolean SetPubFieldOnImprint (ImprintPtr imprint, Int4 field, StringConst } break; case Publication_field_issue: - if (!StringHasNoText (imprint->issue) && DoesStringMatchConstraint (imprint->issue, scp)) { + if (StringHasNoText (imprint->issue) || DoesStringMatchConstraint (imprint->issue, scp)) { rval = SetStringValue (&(imprint->issue), value, existing_text); } break; case Publication_field_pages: - if (!StringHasNoText (imprint->pages) && DoesStringMatchConstraint (imprint->pages, scp)) { + if (StringHasNoText (imprint->pages) || DoesStringMatchConstraint (imprint->pages, scp)) { rval = SetStringValue (&(imprint->pages), value, existing_text); } break; @@ -14574,6 +14808,9 @@ static Boolean SetPubFieldOnCitBook (CitBookPtr cbp, Int4 field, StringConstrain SetValNodeChoices (cbp->title, 1); break; case Publication_field_authors: + if (cbp->authors == NULL) { + cbp->authors = AuthListNew(); + } rval = SetAuthorListFromString (cbp->authors, scp, value, existing_text); break; case Publication_field_affiliation: @@ -14586,14 +14823,21 @@ static Boolean SetPubFieldOnCitBook (CitBookPtr cbp, Int4 field, StringConstrain case Publication_field_affil_fax: case Publication_field_affil_phone: case Publication_field_affil_zipcode: - if (cbp->authors != NULL) { - rval = SetAffilPubField (cbp->authors->affil, field, scp, value, existing_text); + if (cbp->authors == NULL) { + cbp->authors = AuthListNew(); + } + if (cbp->authors->affil == NULL) { + cbp->authors->affil = AffilNew(); } + rval = SetAffilPubField (cbp->authors->affil, field, scp, value, existing_text); break; case Publication_field_volume: case Publication_field_issue: case Publication_field_pages: case Publication_field_date: + if (cbp->imp == NULL) { + cbp->imp = ImprintNew(); + } rval = SetPubFieldOnImprint (cbp->imp, field, scp, value, existing_text); break; } @@ -14613,6 +14857,10 @@ NLM_EXTERN CharPtr GetPubFieldFromPub (PubPtr the_pub, Int4 field, StringConstra CharPtr str = NULL; if (the_pub == NULL || the_pub->data.ptrvalue == NULL) return NULL; + + if (field == Publication_field_pub_class) { + return GetPubclassFromPub(the_pub); + } switch (the_pub->choice) { case PUB_Gen : @@ -14639,7 +14887,7 @@ NLM_EXTERN CharPtr GetPubFieldFromPub (PubPtr the_pub, Int4 field, StringConstra case Publication_field_affil_fax: case Publication_field_affil_phone: case Publication_field_affil_zipcode: - if (cgp->authors != NULL) { + if (cgp->authors != NULL && cgp->authors->affil != NULL) { str = GetPubFieldFromAffil (cgp->authors->affil, field, scp); } break; @@ -14663,7 +14911,7 @@ NLM_EXTERN CharPtr GetPubFieldFromPub (PubPtr the_pub, Int4 field, StringConstra break; case Publication_field_date: if (cgp->date != NULL) { - str = PrintDate (cgp->date); + str = PrintPartialOrCompleteDate (cgp->date); if (StringHasNoText (str) || !DoesStringMatchConstraint (str, scp)) { str = MemFree (str); } @@ -14708,7 +14956,7 @@ NLM_EXTERN CharPtr GetPubFieldFromPub (PubPtr the_pub, Int4 field, StringConstra } break; case Publication_field_date: - str = PrintDate (csp->date); + str = PrintPartialOrCompleteDate (csp->date); if (StringHasNoText (str) || !DoesStringMatchConstraint (str, scp)) { str = MemFree (str); } @@ -14789,6 +15037,12 @@ NLM_EXTERN CharPtr GetPubFieldFromPub (PubPtr the_pub, Int4 field, StringConstra break; } break; + case PUB_PMid: + if (field == Publication_field_pmid) { + str = (CharPtr) MemNew (sizeof (Char) * 15); + sprintf (str, "%d", the_pub->data.intvalue); + } + break; default : break; } @@ -14796,6 +15050,34 @@ NLM_EXTERN CharPtr GetPubFieldFromPub (PubPtr the_pub, Int4 field, StringConstra } +static Boolean RemovePMIDOnCitArt (CitArtPtr cap, StringConstraintPtr scp) +{ + Boolean rval = FALSE; + ValNodePtr vnp, vnp_prev = NULL, vnp_next; + + if (cap == NULL) { + return FALSE; + } + + for (vnp = cap->ids; vnp != NULL; vnp = vnp_next) { + vnp_next = vnp->next; + if (vnp->choice == ARTICLEID_PUBMED && DoesNumberMatchStringConstraint (vnp->data.intvalue, scp)) { + if (vnp_prev == NULL) { + cap->ids->next = vnp_next; + } else { + vnp_prev->next = vnp_next; + } + vnp->next = NULL; + vnp = ArticleIdFree (vnp); + rval = TRUE; + } else { + vnp_prev = vnp; + } + } + return rval; +} + + static Boolean RemovePubFieldFromPub (PubPtr the_pub, Int4 field, StringConstraintPtr scp) { CitGenPtr cgp; @@ -14807,6 +15089,10 @@ static Boolean RemovePubFieldFromPub (PubPtr the_pub, Int4 field, StringConstrai Char num[15]; if (the_pub == NULL) return FALSE; + + if (field == Publication_field_pub_class) { + return SetPubclassOnPub(the_pub, "unpublished"); + } switch (the_pub->choice) { case PUB_Gen : @@ -14910,6 +15196,9 @@ static Boolean RemovePubFieldFromPub (PubPtr the_pub, Int4 field, StringConstrai case PUB_Article : cap = (CitArtPtr) the_pub->data.ptrvalue; switch (field) { + case Publication_field_pmid: + rval = RemovePMIDOnCitArt (cap, scp); + break; case Publication_field_title: rval = RemoveValNodeStringMatch (&(cap->title), scp); break; @@ -14975,6 +15264,11 @@ static Boolean RemovePubFieldFromPub (PubPtr the_pub, Int4 field, StringConstrai break; } break; + case PUB_PMid: + if (field == Publication_field_pmid) { + the_pub->data.intvalue = 0; + } + break; default : break; } @@ -14982,6 +15276,32 @@ static Boolean RemovePubFieldFromPub (PubPtr the_pub, Int4 field, StringConstrai } +static Boolean SetPMIDOnCitArt (CitArtPtr cap, StringConstraintPtr scp, CharPtr value, Uint2 existing_text) +{ + Boolean found = FALSE, rval = FALSE; + ValNodePtr vnp; + + if (cap == NULL || !StringIsAllDigits(value)) { + return FALSE; + } + + for (vnp = cap->ids; vnp != NULL; vnp = vnp->next) { + if (vnp->choice == ARTICLEID_PUBMED) { + found = TRUE; + if (existing_text == ExistingTextOption_replace_old && DoesNumberMatchStringConstraint(vnp->data.intvalue, scp)) { + vnp->data.intvalue = atoi (value); + rval = TRUE; + } + } + } + if (!found && IsStringConstraintEmpty (scp)) { + ValNodeAddInt (&(cap->ids), ARTICLEID_PUBMED, atoi (value)); + rval = TRUE; + } + return rval; +} + + static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr scp, CharPtr value, Uint2 existing_text) { CitGenPtr cgp; @@ -14992,6 +15312,10 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr Boolean rval = FALSE; if (the_pub == NULL || value == NULL) return FALSE; + + if (field == Publication_field_pub_class) { + return SetPubclassOnPub(the_pub, value); + } switch (the_pub->choice) { case PUB_Gen : @@ -15003,6 +15327,9 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr } break; case Publication_field_authors: + if (cgp->authors == NULL) { + cgp->authors = AuthListNew(); + } rval = SetAuthorListFromString (cgp->authors, scp, value, existing_text); break; case Publication_field_affiliation: @@ -15015,9 +15342,13 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr case Publication_field_affil_fax: case Publication_field_affil_phone: case Publication_field_affil_zipcode: - if (cgp->authors != NULL) { - rval = SetAffilPubField (cgp->authors->affil, field, scp, value, existing_text); + if (cgp->authors == NULL) { + cgp->authors = AuthListNew(); + } + if (cgp->authors->affil == NULL) { + cgp->authors->affil = AffilNew(); } + rval = SetAffilPubField (cgp->authors->affil, field, scp, value, existing_text); break; case Publication_field_journal: rval = SetStringsInValNodeStringList (&(cgp->journal), scp, value, existing_text); @@ -15060,6 +15391,9 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr } break; case Publication_field_authors: + if (csp->authors == NULL) { + csp->authors = AuthListNew(); + } rval = SetAuthorListFromString (csp->authors, scp, value, existing_text); break; case Publication_field_affiliation: @@ -15072,9 +15406,13 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr case Publication_field_affil_fax: case Publication_field_affil_phone: case Publication_field_affil_zipcode: - if (csp->authors != NULL) { - rval = SetAffilPubField (csp->authors->affil, field, scp, value, existing_text); + if (csp->authors == NULL) { + csp->authors = AuthListNew(); + } + if (csp->authors->affil == NULL) { + csp->authors->affil = AffilNew(); } + rval = SetAffilPubField (csp->authors->affil, field, scp, value, existing_text); break; case Publication_field_date: rval = SetPubDate (&(csp->date), scp, value, existing_text); @@ -15084,11 +15422,17 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr case PUB_Article : cap = (CitArtPtr) the_pub->data.ptrvalue; switch (field) { + case Publication_field_pmid: + rval = SetPMIDOnCitArt (cap, scp, value, existing_text); + break; case Publication_field_title: rval = SetStringsInValNodeStringList (&(cap->title), scp, value, existing_text); SetValNodeChoices (cap->title, 1); break; case Publication_field_authors: + if (cap->authors == NULL) { + cap->authors = AuthListNew(); + } rval = SetAuthorListFromString (cap->authors, scp, value, existing_text); break; case Publication_field_affiliation: @@ -15101,9 +15445,13 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr case Publication_field_affil_fax: case Publication_field_affil_phone: case Publication_field_affil_zipcode: - if (cap->authors != NULL) { - rval = SetAffilPubField (cap->authors->affil, field, scp, value, existing_text); + if (cap->authors == NULL) { + cap->authors = AuthListNew(); } + if (cap->authors->affil == NULL) { + cap->authors->affil = AffilNew(); + } + rval = SetAffilPubField (cap->authors->affil, field, scp, value, existing_text); break; default: if (cap->from == 1) { @@ -15131,6 +15479,9 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr } break; case Publication_field_authors: + if (cpp->authors == NULL) { + cpp->authors = AuthListNew(); + } rval = SetAuthorListFromString (cpp->authors, scp, value, existing_text); break; case Publication_field_affiliation: @@ -15143,12 +15494,23 @@ static Boolean SetPubFieldOnPub (PubPtr the_pub, Int4 field, StringConstraintPtr case Publication_field_affil_fax: case Publication_field_affil_phone: case Publication_field_affil_zipcode: - if (cpp->authors != NULL) { - rval = SetAffilPubField (cpp->authors->affil, field, scp, value, existing_text); + if (cpp->authors == NULL) { + cpp->authors = AuthListNew(); } + if (cpp->authors->affil == NULL) { + cpp->authors->affil = AffilNew(); + } + rval = SetAffilPubField (cpp->authors->affil, field, scp, value, existing_text); break; } break; + case PUB_PMid: + if (field == Publication_field_pmid && StringIsAllDigits (value) && DoesNumberMatchStringConstraint(the_pub->data.intvalue, scp) + && existing_text == ExistingTextOption_replace_old) { + the_pub->data.intvalue = atoi (value); + rval = TRUE; + } + break; default : break; } @@ -15191,7 +15553,7 @@ static Boolean RemovePubFieldFromObject (Uint1 choice, Pointer data, Int4 field, { Boolean rval = FALSE; PubdescPtr pdp = NULL; - PubPtr pub; + PubPtr pub, pub_prev = NULL, pub_next; SeqFeatPtr sfp; SeqDescrPtr sdp; @@ -15210,8 +15572,22 @@ static Boolean RemovePubFieldFromObject (Uint1 choice, Pointer data, Int4 field, if (pdp == NULL) return FALSE; - for (pub = pdp->pub; pub != NULL; pub = pub->next) { + pub = pdp->pub; + while (pub != NULL) { + pub_next = pub->next; rval |= RemovePubFieldFromPub (pub, field, scp); + if (field == Publication_field_pmid && pub->choice == PUB_PMid && pub->data.intvalue == 0) { + if (pub_prev == NULL) { + pdp->pub = pub_next; + } else { + pub_prev->next = pub_next; + } + pub->next = NULL; + pub = PubFree (pub); + } else { + pub_prev = pub; + } + pub = pub->next; } return rval; } @@ -15223,7 +15599,7 @@ static Boolean SetPubFieldOnObject (Uint1 choice, Pointer data, Int4 field, Stri PubdescPtr pdp = NULL; PubPtr pub; SeqFeatPtr sfp; - SeqDescrPtr sdp; + SeqDescrPtr sdp = NULL; if (data == NULL) return FALSE; if (choice == OBJ_SEQFEAT) { @@ -15243,11 +15619,17 @@ static Boolean SetPubFieldOnObject (Uint1 choice, Pointer data, Int4 field, Stri for (pub = pdp->pub; pub != NULL; pub = pub->next) { rval |= SetPubFieldOnPub (pub, field, scp, value, existing_text); } + if (!rval && field == Publication_field_pmid && IsStringConstraintEmpty (scp) && StringIsAllDigits(value)) { + /* first, set pub class to published for pre-existing pub */ + if (pdp->pub != NULL && pdp->pub->choice == PUB_Gen) { + SetPubclassOnPub(pdp->pub, "journal"); + } + ValNodeAddInt (&pdp->pub, PUB_PMid, atoi (value)); + } return rval; } - NLM_EXTERN Uint1 FieldTypeFromAECRAction (AECRActionPtr action) { Uint1 field_type = 0; @@ -15381,7 +15763,7 @@ static void CaptureRefBlockSerialNumbers SeqMgrFeatContext fcontext; SeqMgrDescContext dcontext; PubSerialNumberPtr psn; - ValNodePtr ppr; + ValNodePtr ppr = NULL; PubdescPtr pdp = NULL; if (blocktype != REFERENCE_BLOCK || userdata == NULL) return; @@ -15712,6 +16094,12 @@ NLM_EXTERN CharPtr GetFieldValueForObjectEx (Uint1 choice, Pointer data, FieldTy if (sdp != NULL && sdp->choice == Seq_descr_user) { str = GetDBLinkFieldFromUserObject (sdp->data.ptrvalue, field->data.intvalue, scp); } + } else if (choice == OBJ_BIOSEQ) { + for (sdp = SeqMgrGetNextDescriptor ((BioseqPtr) data, NULL, Seq_descr_user, &context); + sdp != NULL && str == NULL; + sdp = SeqMgrGetNextDescriptor ((BioseqPtr) data, sdp, Seq_descr_user, &context)) { + str = GetDBLinkFieldFromUserObject (sdp->data.ptrvalue, field->data.intvalue, scp); + } } break; case FieldType_misc: @@ -15775,13 +16163,17 @@ NLM_EXTERN CharPtr GetFieldValueForObject (Uint1 choice, Pointer data, FieldType NLM_EXTERN ValNodePtr GetMultipleFieldValuesForObject (Uint1 choice, Pointer data, FieldTypePtr field, StringConstraintPtr scp, BatchExtraPtr batch_extra) { - CharPtr str = NULL; - ValNodePtr val_list = NULL; + CharPtr str = NULL; + ValNodePtr val_list = NULL; + SeqDescPtr sdp; if (data == NULL || field == NULL || field->data.ptrvalue == NULL) return FALSE; if (field->choice == FieldType_source_qual) { val_list = GetMultipleSourceQualsFromBioSource (GetBioSourceFromObject (choice, data), (SourceQualChoicePtr) field->data.ptrvalue, scp); + } else if (field->choice == FieldType_dblink && choice == OBJ_SEQDESC + && (sdp = (SeqDescPtr) data) != NULL && sdp->choice == Seq_descr_user) { + val_list = GetMultipleDBLinkFieldValuesFromUserObject ((UserObjectPtr) sdp->data.ptrvalue, field->data.intvalue, scp); } else { str = GetFieldValueForObjectEx (choice, data, field, scp, batch_extra); if (str != NULL) { @@ -15868,6 +16260,10 @@ static Boolean RemoveFieldValueForObject (Uint1 choice, Pointer data, FieldTypeP sdp = (SeqDescrPtr) data; if (sdp != NULL && sdp->choice == Seq_descr_user) { rval = RemoveDBLinkFieldFromUserObject (sdp->data.ptrvalue, field->data.intvalue, scp); + if (rval && IsEmptyDBLink (sdp->data.ptrvalue)) { + ovp = (ObjValNodePtr) sdp; + ovp->idx.deleteme = TRUE; + } } } break; @@ -15986,6 +16382,7 @@ NLM_EXTERN Boolean SetFieldValueForObjectEx (Uint1 choice, Pointer data, FieldTy sdp = (SeqDescrPtr) data; if (sdp->choice == Seq_descr_title) { rval = SetTextDescriptor (sdp, scp, value, existing_text); + RemoveAutodefObjectsForDesc(sdp); } } else if (choice == OBJ_SEQDESC && field->data.intvalue == Misc_field_keyword) { sdp = (SeqDescrPtr) data; @@ -16342,8 +16739,8 @@ static void LIBCALLBACK AsnWriteConstraintCallBack (AsnExpOptStructPtr pAEOS) ohsp = (ObjectHasStringPtr) pAEOS->data; if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) { - pchSource = (CharPtr) pAEOS->dvp->ptrvalue; - ohsp->found |= DoesSingleStringMatchConstraint (pchSource, ohsp->scp); + pchSource = (CharPtr) pAEOS->dvp->ptrvalue; + ohsp->found |= DoesSingleStringMatchConstraint (pchSource, ohsp->scp); } } @@ -17094,15 +17491,20 @@ static void UnmarkFeatureList (ValNodePtr list) static void FillOutCGPSetForGene (CGPSetPtr c, SeqFeatPtr gene) { SeqFeatPtr cds, mrna, prot; - SeqMgrFeatContext fcontext; + SeqMgrFeatContext fcontext, pcontext; BioseqPtr bsp, protbsp; Int4 left, right, tmp; + ValNodeBlock cds_list, mrna_list, prot_list; if (c == NULL || gene == NULL || (bsp = BioseqFindFromSeqLoc (gene->location)) == NULL) { return; } + InitValNodeBlock(&cds_list, c->cds_list); + InitValNodeBlock(&mrna_list, c->mrna_list); + InitValNodeBlock(&prot_list, c->prot_list); + left = SeqLocStart (gene->location); right = SeqLocStop (gene->location); if (left > right) { @@ -17116,11 +17518,11 @@ static void FillOutCGPSetForGene (CGPSetPtr c, SeqFeatPtr gene) cds = SeqMgrGetNextFeature (bsp, cds, SEQFEAT_CDREGION, 0, &fcontext)) { if (gene == GetGeneForFeature (cds)) { - ValNodeAddPointer (&(c->cds_list), 0, cds); + ValNodeAddPointerToEnd (&cds_list, 0, cds); mrna = GetmRNAforCDS (cds); if (mrna != NULL) { - ValNodeAddPointer (&(c->mrna_list), 0, mrna); + ValNodeAddPointerToEnd (&mrna_list, 0, mrna); } if (cds->product != NULL) @@ -17128,18 +17530,18 @@ static void FillOutCGPSetForGene (CGPSetPtr c, SeqFeatPtr gene) protbsp = BioseqFindFromSeqLoc (cds->product); if (protbsp != NULL) { - prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext); + prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &pcontext); if (prot != NULL) { - ValNodeAddPointer (&(c->prot_list), 0, prot); + ValNodeAddPointerToEnd (&prot_list, 0, prot); } /* also add in mat_peptides from protein feature */ - prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext); + prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &pcontext); while (prot != NULL) { - ValNodeAddPointer (&(c->prot_list), 0, prot); - prot = SeqMgrGetNextFeature (protbsp, prot, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &fcontext); + ValNodeAddPointerToEnd (&prot_list, 0, prot); + prot = SeqMgrGetNextFeature (protbsp, prot, SEQFEAT_PROT, FEATDEF_mat_peptide_aa, &pcontext); } } } @@ -17151,9 +17553,12 @@ static void FillOutCGPSetForGene (CGPSetPtr c, SeqFeatPtr gene) mrna = SeqMgrGetNextFeature (bsp, mrna, 0, FEATDEF_mRNA, &fcontext)) { if (gene == GetGeneForFeature (mrna)) { - ValNodeAddPointer (&(c->mrna_list), 0, mrna); + ValNodeAddPointerToEnd (&mrna_list, 0, mrna); } } + c->cds_list = cds_list.head; + c->mrna_list = mrna_list.head; + c->prot_list = prot_list.head; } @@ -17310,10 +17715,11 @@ static Boolean DoesTextMatchBankItId (SeqIdPtr sip, StringConstraintPtr scp) Char ch_orig = 0; DbtagPtr dbtag; - if (scp == NULL || (text = scp->match_text) == NULL || sip == NULL || sip->choice != SEQID_GENERAL - || (dbtag = (DbtagPtr) sip->data.ptrvalue) == NULL - || StringCmp (dbtag->db, "BankIt") != 0 - || dbtag->tag == NULL) { + if (scp == NULL || scp->match_text == NULL || sip == NULL || sip->choice != SEQID_GENERAL) { + return FALSE; + } + dbtag = (DbtagPtr) sip->data.ptrvalue; + if (dbtag == NULL || StringCmp (dbtag->db, "BankIt") != 0 || dbtag->tag == NULL) { return FALSE; } text = CopyListWithoutBankIt (scp->match_text); @@ -17336,8 +17742,8 @@ static Boolean DoesTextMatchBankItId (SeqIdPtr sip, StringConstraintPtr scp) rval = DoesStringMatchConstraint (partial_match, scp); partial_match = MemFree (partial_match); } - text = MemFree (text); scp->match_text = tmp; + text = MemFree (text); return rval; } @@ -17772,67 +18178,72 @@ static Boolean DoesObjectMatchSequenceConstraint (Uint1 choice, Pointer data, Se } +/* Pub fields */ +typedef struct pubfieldlabel { + Int4 pub_field; + CharPtr name; +} PubFieldLabelData, PNTR PubFieldLabelPtr; + + +static PubFieldLabelData pubfield_labels[] = { + { Publication_field_cit, "citation" } , + { Publication_field_authors, "authors" } , + { Publication_field_journal, "journal" } , + { Publication_field_volume, "volume" } , + { Publication_field_issue, "issue" } , + { Publication_field_pages, "pages" } , + { Publication_field_date, "date" } , + { Publication_field_serial_number, "serial number" } , + { Publication_field_title, "title" } , + { Publication_field_affiliation, "affiliation" } , + { Publication_field_affil_div, "department" } , + { Publication_field_affil_city, "city" } , + { Publication_field_affil_sub, "state" } , + { Publication_field_affil_country, "country" } , + { Publication_field_affil_street, "street" } , + { Publication_field_affil_email, "email" } , + { Publication_field_affil_fax, "fax" } , + { Publication_field_affil_phone, "phone" } , + { Publication_field_affil_zipcode, "postal code" } , + { Publication_field_pmid, "PMID"} , + { Publication_field_pub_class, "class" } +}; + +#define NUM_pubfield_labels sizeof (pubfield_labels) / sizeof (PubFieldLabelData) + + NLM_EXTERN CharPtr GetPubFieldLabel (Int4 pub_field) { CharPtr rval = NULL; - switch (pub_field) { - case Publication_field_cit: - rval = "citation"; - break; - case Publication_field_authors: - rval = "authors"; - break; - case Publication_field_journal: - rval = "journal"; - break; - case Publication_field_volume: - rval = "volume"; - break; - case Publication_field_issue: - rval = "issue"; - break; - case Publication_field_pages: - rval = "pages"; - break; - case Publication_field_date: - rval = "date"; - break; - case Publication_field_serial_number: - rval = "serial number"; - break; - case Publication_field_title: - rval = "title"; - break; - case Publication_field_affiliation: - rval = "affiliation"; - break; - case Publication_field_affil_div: - rval = "department"; - break; - case Publication_field_affil_city: - rval = "city"; - break; - case Publication_field_affil_sub: - rval = "state"; - break; - case Publication_field_affil_country: - rval = "country"; - break; - case Publication_field_affil_street: - rval = "street"; - break; - case Publication_field_affil_email: - rval = "email"; - break; - case Publication_field_affil_fax: - rval = "fax"; - break; - case Publication_field_affil_phone: - rval = "phone"; + Int4 i; + + for (i = 0; i < NUM_pubfield_labels; i++) { + if (pubfield_labels[i].pub_field == pub_field) { + rval = pubfield_labels[i].name; break; - case Publication_field_affil_zipcode: - rval = "postal code"; + } + } + return rval; +} + + +NLM_EXTERN Int4 GetPubFieldFromLabel(CharPtr label) +{ + Int4 rval = -1; + Int4 i; + + if (StringNICmp (label, "publication", 11) == 0) { + label = label + 11; + while (*label == '-' || *label == ' ') { + label++; + } + } + + for (i = 0; i < NUM_pubfield_labels; i++) { + if (StringsAreEquivalent(pubfield_labels[i].name, label)) { + rval = pubfield_labels[i].pub_field; break; + } } return rval; } @@ -17841,25 +18252,11 @@ NLM_EXTERN CharPtr GetPubFieldLabel (Int4 pub_field) NLM_EXTERN ValNodePtr GetPubFieldList (void) { ValNodePtr val_list = NULL; + Int4 i; - ValNodeAddPointer (&val_list, Publication_field_title, StringSave ("title")); - ValNodeAddPointer (&val_list, Publication_field_authors, StringSave ("authors")); - ValNodeAddPointer (&val_list, Publication_field_journal, StringSave ("journal")); - ValNodeAddPointer (&val_list, Publication_field_issue, StringSave ("issue")); - ValNodeAddPointer (&val_list, Publication_field_pages, StringSave ("pages")); - ValNodeAddPointer (&val_list, Publication_field_serial_number, StringSave ("serial number")); - ValNodeAddPointer (&val_list, Publication_field_date, StringSave ("date")); - ValNodeAddPointer (&val_list, Publication_field_cit, StringSave ("citation")); - ValNodeAddPointer (&val_list, Publication_field_affiliation, StringSave ("affiliation")); - ValNodeAddPointer (&val_list, Publication_field_affil_div, StringSave ("department")); - ValNodeAddPointer (&val_list, Publication_field_affil_city, StringSave ("city")); - ValNodeAddPointer (&val_list, Publication_field_affil_sub, StringSave ("state")); - ValNodeAddPointer (&val_list, Publication_field_affil_country, StringSave ("country")); - ValNodeAddPointer (&val_list, Publication_field_affil_street, StringSave ("street")); - ValNodeAddPointer (&val_list, Publication_field_affil_email, StringSave ("email")); - ValNodeAddPointer (&val_list, Publication_field_affil_fax, StringSave ("fax")); - ValNodeAddPointer (&val_list, Publication_field_affil_phone, StringSave ("phone")); - ValNodeAddPointer (&val_list, Publication_field_affil_zipcode, StringSave ("postal code")); + for (i = 0; i < NUM_pubfield_labels; i++) { + ValNodeAddPointer (&val_list, pubfield_labels[i].pub_field, StringSave (pubfield_labels[i].name)); + } return val_list; } @@ -17868,30 +18265,400 @@ NLM_EXTERN ValNodePtr GetPubFieldList (void) static ValNodePtr MakePubFieldTypeList (void) { ValNodePtr field_list = NULL; + Int4 i; - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_title); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_authors); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_journal); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_issue); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_pages); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_serial_number); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_date); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_cit); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affiliation); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_div); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_city); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_sub); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_country); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_street); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_email); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_fax); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_phone); - ValNodeAddInt (&field_list, FieldType_pub, Publication_field_affil_zipcode); + for (i = 0; i < NUM_pubfield_labels; i++) { + ValNodeAddInt (&field_list, FieldType_pub, pubfield_labels[i].pub_field); + } return field_list; } +typedef struct pub_class_qual { + Uint1 pub_choice; + Int4 status; + Uint1 art_from; + CharPtr name; +} PubClassQualData, PNTR PubClassQualPtr; + + +static PubClassQualData pub_class_quals[] = { + { PUB_Gen, Pub_type_unpublished, 0, "unpublished" } , + { PUB_Sub, Pub_type_in_press, 0, "in-press submission" } , + { PUB_Sub, Pub_type_published, 0, "submission" } , + { PUB_Article, Pub_type_in_press, 1, "in-press journal" } , + { PUB_Article, Pub_type_published, 1, "journal" } , + { PUB_Article, Pub_type_in_press, 2, "in-press book chapter" } , + { PUB_Article, Pub_type_published, 2, "book chapter" } , + { PUB_Article, Pub_type_in_press, 3, "in-press proceedings chapter" } , + { PUB_Article, Pub_type_published, 3, "proceedings chapter" } , + { PUB_Book, Pub_type_in_press, 0, "in-press book" } , + { PUB_Book, Pub_type_published, 0, "book" } , + { PUB_Man, Pub_type_in_press, 0, "in-press thesis" } , + { PUB_Man, Pub_type_published, 0, "thesis" } , + { PUB_Proc, Pub_type_in_press, 0, "in-press proceedings" } , + { PUB_Proc, Pub_type_published, 0, "proceedings" } , + { PUB_Patent, Pub_type_any, 0, "patent" } +}; + +#define NUM_pub_class_quals sizeof (pub_class_quals) / sizeof (PubClassQualData) + + + +NLM_EXTERN ValNodePtr GetPubClassList () +{ + ValNodePtr list = NULL; + Int4 i; + + for (i = 0; i < NUM_pub_class_quals; i++) { + ValNodeAddPointer (&list, Publication_field_pub_class, StringSave (pub_class_quals[i].name)); + } + + return list; +} + + +static PubClassQualPtr GetPubclassQualFromPub (PubPtr the_pub) +{ + CharPtr str = NULL; + CitArtPtr art; + Int4 ml_class; + Int4 art_from = 0; + Int4 i; + + if (the_pub == NULL) { + return NULL; + } + + ml_class = GetPubMLStatus(the_pub); + if (the_pub->choice == PUB_Article && (art = (CitArtPtr) the_pub->data.ptrvalue) != NULL) { + art_from = art->from; + } + + for (i = 0; i < NUM_pub_class_quals; i++) { + if (the_pub->choice == pub_class_quals[i].pub_choice + && (ml_class == pub_class_quals[i].status || ml_class == 0 || pub_class_quals[i].status == 0) + && (art_from == 0 || pub_class_quals[i].art_from == 0 || art_from == pub_class_quals[i].art_from)) { + return pub_class_quals + i; + } + } + + return NULL; +} + + +NLM_EXTERN CharPtr GetPubclassFromPub (PubPtr the_pub) +{ + PubClassQualPtr pq = GetPubclassQualFromPub (the_pub); + if (pq == NULL) { + return NULL; + } else { + return StringSave(pq->name); + } +} + + +static PubClassQualPtr GetPubclassFromString(CharPtr str) +{ + Int4 i; + PubClassQualPtr pq = NULL; + + for (i = 0; i < NUM_pub_class_quals; i++) { + if (StringsAreEquivalent (pub_class_quals[i].name, str)) { + pq = pub_class_quals + i; + break; + } + } + return pq; +} + + +static Boolean FreePubDataForConversion (PubPtr the_pub) +{ + Boolean rval = FALSE; + + if (the_pub == NULL) { + return FALSE; + } + + switch (the_pub->choice) { + case PUB_Gen: + the_pub->data.ptrvalue = CitGenFree (the_pub->data.ptrvalue); + rval = TRUE; + break; + case PUB_Sub: + the_pub->data.ptrvalue = CitSubFree (the_pub->data.ptrvalue); + rval = TRUE; + break; + case PUB_Article: + the_pub->data.ptrvalue = CitArtFree (the_pub->data.ptrvalue); + rval = TRUE; + break; + case PUB_Journal: + the_pub->data.ptrvalue = CitJourFree (the_pub->data.ptrvalue); + rval = TRUE; + break; + case PUB_Book: + case PUB_Man: + case PUB_Proc: + the_pub->data.ptrvalue = CitBookFree (the_pub->data.ptrvalue); + rval = TRUE; + break; + case PUB_Patent: + the_pub->data.ptrvalue = CitPatFree (the_pub->data.ptrvalue); + rval = TRUE; + break; + } + return rval; +} + + +static void SetArtFrom(PubPtr the_pub, Uint1 art_from) +{ + CitArtPtr cap; + CitJourPtr cjp; + CitBookPtr cbp; + + if (the_pub == NULL) { + return; + } + if (the_pub->choice == PUB_Article) { + if ((cap = (CitArtPtr)the_pub->data.ptrvalue) == NULL) { + cap = CitArtNew(); + the_pub->data.ptrvalue = cap; + } + cap->from = art_from; + switch (cap->from) { + case 1: + cjp = CitJourNew(); + cjp->imp = ImprintNew(); + cap->fromptr = cjp; + break; + case 2: + case 3: + cbp = CitBookNew(); + cbp->imp = ImprintNew(); + cap->fromptr = cbp; + break; + } + } +} + + +static Boolean NewPubDataForConversion (PubPtr the_pub, Uint1 art_from) +{ + CitBookPtr cbp; + Boolean rval = FALSE; + + if (the_pub == NULL) { + return FALSE; + } + + switch (the_pub->choice) { + case PUB_Gen: + the_pub->data.ptrvalue = CitGenNew(); + rval = TRUE; + break; + case PUB_Sub: + the_pub->data.ptrvalue = CitSubNew(); + rval = TRUE; + break; + case PUB_Article: + the_pub->data.ptrvalue = CitArtNew(); + SetArtFrom(the_pub, art_from); + rval = TRUE; + break; + case PUB_Journal: + the_pub->data.ptrvalue = CitJourNew(); + rval = TRUE; + break; + case PUB_Book: + case PUB_Man: + case PUB_Proc: + cbp = CitBookNew(); + cbp->imp = ImprintNew(); + cbp->imp->date = DateNew(); + the_pub->data.ptrvalue = cbp; + rval = TRUE; + break; + case PUB_Patent: + the_pub->data.ptrvalue = CitPatNew(); + rval = TRUE; + break; + } + return rval; +} + + +static ImprintPtr GetPubImprint (PubPtr the_pub) +{ + CitArtPtr cap; + CitBookPtr cbp; + CitJourPtr cjp; + ImprintPtr imp = NULL; + + if (the_pub == NULL || the_pub->data.ptrvalue == NULL) + { + return NULL; + } + + switch (the_pub->choice) + { + case PUB_Article : + cap = (CitArtPtr) the_pub->data.ptrvalue; + if (cap->from == 1) + { + cjp = (CitJourPtr) cap->fromptr; + if (cjp != NULL) + { + imp = cjp->imp; + } + } + else if (cap->from == 2 || cap->from == 3) + { + cbp = (CitBookPtr) cap->fromptr; + if (cbp != NULL) { + imp = cbp->imp; + } + } + break; + case PUB_Journal : + cjp = (CitJourPtr) the_pub->data.ptrvalue; + imp = cjp->imp; + case PUB_Book : + case PUB_Man : + cbp = (CitBookPtr) the_pub->data.ptrvalue; + imp = cbp->imp; + break; + default : + break; + + } + return imp; +} + + +static Boolean SetPubStatusOnPub (PubPtr the_pub, Int4 status) +{ + ImprintPtr imp; + CitGenPtr cgp; + Boolean rval = FALSE; + + imp = GetPubImprint(the_pub); + if (imp != NULL) { + switch (status) { + case Pub_type_unpublished: + imp->prepub = 255; + rval = TRUE; + break; + case Pub_type_published: + imp->prepub = 0; + rval = TRUE; + break; + case Pub_type_in_press: + imp->prepub = 2; + rval = TRUE; + break; + case Pub_type_submitter_block: + imp->prepub = 1; + rval = TRUE; + break; + } + } else if (the_pub->choice == PUB_Gen) { + if ((cgp = (CitGenPtr) the_pub->data.ptrvalue) == NULL) { + cgp = CitGenNew(); + the_pub->data.ptrvalue = cgp; + } + if (status == Pub_type_unpublished) { + cgp->cit = MemFree (cgp->cit); + cgp->cit = StringSave("unpublished"); + } else { + if (StringICmp (cgp->cit, "unpublished") == 0) { + cgp->cit = MemFree (cgp->cit); + } + } + } else { + + } + return rval; +} + + +static void CopyRelevantPubDetails (PubPtr orig_pub, PubPtr new_pub) +{ + Int4 i; + CharPtr val; + + if (orig_pub == NULL || new_pub == NULL) { + return; + } + + for (i = 0; i < NUM_pubfield_labels; i++) { + if (pubfield_labels[i].pub_field != Publication_field_pub_class /* field we are copying now */ + && pubfield_labels[i].pub_field != Publication_field_authors /* already copying this elsewhere */) { + val = GetPubFieldFromPub(orig_pub, pubfield_labels[i].pub_field, NULL); + if (!StringHasNoText (val)) { + SetPubFieldOnPub(new_pub, pubfield_labels[i].pub_field, NULL, val, ExistingTextOption_replace_old); + } + } + } +} + + +NLM_EXTERN Boolean SetPubclassOnPub (PubPtr the_pub, CharPtr pub_class) +{ + PubClassQualPtr orig_pq = NULL, new_pq = NULL; + AuthListPtr PNTR palp; + AuthListPtr PNTR new_palp; + Boolean rval = FALSE; + ValNode new_pub; + + if (the_pub == NULL) { + return FALSE; + } + + new_pq = GetPubclassFromString(pub_class); + orig_pq = GetPubclassQualFromPub(the_pub); + + if (new_pq == NULL || orig_pq == NULL || new_pq == orig_pq) { + return FALSE; + } + + if (new_pq->pub_choice == the_pub->choice && new_pq->art_from == orig_pq->art_from) { + /* only thing changing is in-press/published */ + if (new_pq->status != orig_pq->status) { + rval = SetPubStatusOnPub(the_pub, new_pq->status); + } + } else { + MemSet (&new_pub, 0, sizeof (ValNode)); + new_pub.choice = new_pq->pub_choice; + NewPubDataForConversion(&new_pub, new_pq->art_from); + + palp = GetAuthListForPub(the_pub); + new_palp = GetAuthListForPub(&new_pub); + if (palp && *palp && new_palp) { + *new_palp = AsnIoMemCopy (*palp, (AsnReadFunc) AuthListAsnRead, (AsnWriteFunc) AuthListAsnWrite); + } + /* TODO: Copy over other relevant details */ + CopyRelevantPubDetails(the_pub, &new_pub); + + SetPubStatusOnPub(&new_pub, new_pq->status); + rval = FreePubDataForConversion(the_pub); + if (rval) { + the_pub->choice = new_pub.choice; + the_pub->data.ptrvalue = new_pub.data.ptrvalue; + } else { + FreePubDataForConversion(&new_pub); + } + + } + + + return FALSE; +} + + NLM_EXTERN Boolean IsPublicationConstraintEmpty (PublicationConstraintPtr constraint) { Boolean rval = FALSE; @@ -17950,13 +18717,13 @@ NLM_EXTERN Int4 GetPubMLStatus (PubPtr the_pub) imp = cjp->imp; } } - else if (cap->from == 2 || cap->from == 3) - { + else if (cap->from == 2 || cap->from == 3) + { cbp = (CitBookPtr) cap->fromptr; - if (cbp != NULL) { + if (cbp != NULL) { imp = cbp->imp; - } - } + } + } break; case PUB_Journal : cjp = (CitJourPtr) the_pub->data.ptrvalue; @@ -18356,6 +19123,7 @@ static Boolean DoesObjectMatchFieldConstraint (Uint1 choice, Pointer data, Field } break; case FieldType_misc: + case FieldType_dblink: bsp = GetSequenceForObject (choice, data); if (bsp != NULL) { str = GetFieldValueForObjectEx (OBJ_BIOSEQ, bsp, constraint->field, constraint->string_constraint, NULL); @@ -18365,6 +19133,7 @@ static Boolean DoesObjectMatchFieldConstraint (Uint1 choice, Pointer data, Field str = MemFree (str); } break; + /* TODO LATER */ case FieldType_pub: break; @@ -18662,19 +19431,21 @@ static Boolean DoesCodingRegionMatchTranslationConstraint (SeqFeatPtr sfp, Trans cp1 = actual; cp2 = translation; - for (pos = 0; pos < comp_len && rval; pos++) { - if (*cp1 != *cp2) { - num++; - if (constraint->num_mismatches->choice == QuantityConstraint_equals - && num > constraint->num_mismatches->data.intvalue) { - rval = FALSE; - } else if (constraint->num_mismatches->choice == QuantityConstraint_less_than - && num >= constraint->num_mismatches->data.intvalue) { - rval = FALSE; + if (cp1 != NULL && cp2 != NULL) { + for (pos = 0; pos < comp_len && rval; pos++) { + if (*cp1 != *cp2) { + num++; + if (constraint->num_mismatches->choice == QuantityConstraint_equals + && num > constraint->num_mismatches->data.intvalue) { + rval = FALSE; + } else if (constraint->num_mismatches->choice == QuantityConstraint_less_than + && num >= constraint->num_mismatches->data.intvalue) { + rval = FALSE; + } } + cp1++; + cp2++; } - cp1++; - cp2++; } if (rval) { if (constraint->num_mismatches->choice == QuantityConstraint_greater_than @@ -19219,6 +19990,61 @@ static ValNodePtr CollectMiscObjectsForApply (SeqEntryPtr sep, Int4 misc_type, V } +static void AddDBLinkDescriptorDestinationsForBioseq (BioseqPtr bsp, ValNodePtr PNTR dest_list) +{ + SeqDescrPtr sdp; + UserObjectPtr uop; + SeqMgrDescContext context; + Boolean found = FALSE; + ObjValNodePtr ovp; + + if (bsp == NULL || dest_list == NULL) { + return; + } + + for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &context); + sdp != NULL; + sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &context)) { + if ((uop = sdp->data.ptrvalue) != NULL + && IsUserObjectDBLink (uop)) { + ValNodeAddPointer (dest_list, OBJ_SEQDESC, sdp); + found = TRUE; + } + } + if (!found) { + /* if no existing comment descriptor, create one, marked for delete. + * unmark it for deletion when it gets populated. + */ + sdp = CreateNewDescriptorOnBioseq (bsp, Seq_descr_user); + sdp->data.ptrvalue = CreateDBLinkUserObject (); + ovp = (ObjValNodePtr) sdp; + ovp->idx.deleteme = TRUE; + ValNodeAddPointer (dest_list, OBJ_SEQDESC, sdp); + } +} + + +static ValNodePtr CollectDBLinkObjectsForApply (SeqEntryPtr sep, Int4 misc_type, ValNodePtr constraint) +{ + ValNodePtr target_list = NULL, bsp_list = NULL, tmp_list = NULL, tmp_tail = NULL, vnp; + + if (sep == NULL) { + return NULL; + } + + /* VisitBioseqsInSep (sep, &bsp_list, CollectNucBioseqCallback); */ + bsp_list = CollectNucBioseqs (sep); + for (vnp = bsp_list; vnp != NULL; vnp = vnp->next) { + if (DoesObjectMatchConstraintChoiceSet (vnp->choice, vnp->data.ptrvalue, constraint)) { + AddDBLinkDescriptorDestinationsForBioseq (vnp->data.ptrvalue, &target_list); + } + } + bsp_list = ValNodeFree (bsp_list); + + return target_list; +} + + static void AddStructuredCommentDescriptorDestinationsForBioseq (BioseqPtr bsp, ValNodePtr PNTR dest_list, ValNodePtr PNTR dest_tail) { SeqDescrPtr sdp; @@ -19307,6 +20133,11 @@ NLM_EXTERN ValNodePtr GetObjectListForAECRActionEx (SeqEntryPtr sep, AECRActionP && action->action->choice == ActionChoice_apply && (apply = action->action->data.ptrvalue) != NULL) { ocd.object_list = CollectMiscObjectsForApply (sep, apply->field->data.intvalue, action->constraint); + } else if (field_type == FieldType_dblink + && action->action != NULL + && action->action->choice == ActionChoice_apply + && (apply = action->action->data.ptrvalue) != NULL) { + ocd.object_list = CollectDBLinkObjectsForApply (sep, apply->field->data.intvalue, action->constraint); } else if (field_type == FieldType_struc_comment_field) { ocd.object_list = CollectStructuredCommentsForApply (sep, action->constraint); } else { @@ -19436,7 +20267,11 @@ static CGPSetPtr BuildCGPSetFromCodingRegion (SeqFeatPtr cds, BoolPtr indexing_n protbsp = BioseqFindFromSeqLoc (cds->product); if (protbsp != NULL) { - prot = SeqMgrGetNextFeature (protbsp, NULL, SEQFEAT_PROT, FEATDEF_PROT, &fcontext); + prot = SeqMgrGetBestProteinFeature (protbsp, NULL); + if (prot == NULL) { + prot = GetBestProteinFeatureUnindexed (cds->product); + } + /* if there is no full-length protein feature, make one */ if (prot == NULL) { @@ -19777,34 +20612,47 @@ static ValNodePtr BuildCGPSetList (Uint2 entityID, AECRActionPtr act, BoolPtr cr } -static void AlsoChangeMrnaForObject (Uint1 choice, Pointer data) +static Boolean AlsoChangeMrnaForObject (Uint1 choice, Pointer data) { CharPtr str; - SeqFeatPtr sfp, mrna; + SeqFeatPtr sfp, mrna, cds; + BioseqPtr prot; FeatureField f; + Boolean rval = FALSE; if (choice == 0) { str = GetFieldValueFromCGPSet (data, CDSGeneProt_field_prot_name, NULL); - SetFieldValueInCGPSet (data, CDSGeneProt_field_mrna_product, NULL, str, ExistingTextOption_replace_old); + rval = SetFieldValueInCGPSet (data, CDSGeneProt_field_mrna_product, NULL, str, ExistingTextOption_replace_old); str = MemFree (str); } else if (choice == OBJ_SEQFEAT) { sfp = (SeqFeatPtr) data; - if (sfp != NULL && sfp->data.choice == SEQFEAT_CDREGION) { - mrna = GetmRNAforCDS (sfp); + if (sfp != NULL) { + if (sfp->data.choice == SEQFEAT_CDREGION) { + mrna = GetmRNAforCDS (sfp); + } else if (sfp->data.choice == SEQFEAT_PROT) { + prot = BioseqFindFromSeqLoc(sfp->location); + cds = SeqMgrGetCDSgivenProduct (prot, NULL); + mrna = GetmRNAforCDS (cds); + } if (mrna != NULL) { - f.type = Macro_feature_type_cds; + if (sfp->data.choice == SEQFEAT_CDREGION) { + f.type = Macro_feature_type_cds; + } else { + f.type = Macro_feature_type_prot; + } f.field = ValNodeNew(NULL); f.field->next = NULL; f.field->choice = FeatQualChoice_legal_qual; f.field->data.intvalue = Feat_qual_legal_product; str = GetQualFromFeature (sfp, &f, NULL); f.type = Macro_feature_type_mRNA; - SetQualOnFeature (mrna, &f, NULL, str, ExistingTextOption_replace_old); + rval = SetQualOnFeature (mrna, &f, NULL, str, ExistingTextOption_replace_old); str = MemFree (str); f.field = ValNodeFree (f.field); } } } + return rval; } @@ -19948,14 +20796,53 @@ static Boolean NoFieldChange (CharPtr new_val, ValNodePtr vnp, FieldTypePtr fiel } +static Boolean AddValuesToList(ValNodePtr apply, ValNodePtr PNTR current, Uint2 existing_text) +{ + ValNodePtr vnp_a, vnp_c; + Boolean rval = FALSE; + CharPtr str; + + if (apply == NULL) { + return FALSE; + } else if (existing_text == ExistingTextOption_leave_old && current != NULL && *current != NULL) { + return FALSE; + } else if (existing_text == ExistingTextOption_add_qual) { + for (vnp_a = apply; vnp_a != NULL; vnp_a = vnp_a->next) { + ValNodeAddPointer (current, vnp_a->choice, StringSave ((CharPtr)(vnp_a->data.ptrvalue))); + } + rval = TRUE; + } else if (existing_text == ExistingTextOption_replace_old) { + *current = ValNodeFreeData (*current); + for (vnp_a = apply; vnp_a != NULL; vnp_a = vnp_a->next) { + ValNodeAddPointer (current, vnp_a->choice, StringSave ((CharPtr)(vnp_a->data.ptrvalue))); + } + rval = TRUE; + } else { + for (vnp_a = apply; vnp_a != NULL; vnp_a = vnp_a->next) { + if (*current == NULL) { + ValNodeAddPointer (current, vnp_a->choice, StringSave ((CharPtr)(vnp_a->data.ptrvalue))); + rval = TRUE; + } else { + for (vnp_c = *current; vnp_c != NULL; vnp_c = vnp_c->next) { + str = (CharPtr)(vnp_c->data.ptrvalue); + rval |= SetStringValue(&str, (CharPtr)(vnp_a->data.ptrvalue), existing_text); + vnp_c->data.ptrvalue = str; + } + } + } + } + return rval; +} + + NLM_EXTERN Int4 DoConvertActionToObjectListEx (ConvertActionPtr action, ValNodePtr object_list, Boolean also_change_mrna, StringConstraintPtr scp, BatchExtraPtr batch_extra) { ValNodePtr vnp; - Int4 num_succeed = 0, num_fail = 0; + Int4 num_succeed = 0; CharPtr str, from_val, field_name = NULL; FieldTypePtr field_from, field_to; - StringConstraint remove_constraint; - Boolean fail; + Boolean already_added, field_change; + ValNodePtr val_list_from, val_list_to, val_vnp; if (action == NULL || object_list == NULL || action->fields == NULL) return 0; @@ -19979,37 +20866,36 @@ NLM_EXTERN Int4 DoConvertActionToObjectListEx (ConvertActionPtr action, ValNodeP } else { for (vnp = object_list; vnp != NULL; vnp = vnp->next) { /* there may be multiple qualifiers */ - MemSet (&remove_constraint, 0, sizeof (StringConstraint)); - remove_constraint.case_sensitive = TRUE; - remove_constraint.match_location = String_location_equals; - remove_constraint.not_present = FALSE; - remove_constraint.whole_word = FALSE; - fail = FALSE; - - while ((str = GetFieldValueForObjectEx (vnp->choice, vnp->data.ptrvalue, field_from, scp, batch_extra)) != NULL && !fail) { - remove_constraint.match_text = StringSave (str); + val_list_from = GetMultipleFieldValuesForObject (vnp->choice, vnp->data.ptrvalue, field_from, scp, batch_extra); + val_list_to = GetMultipleFieldValuesForObject (vnp->choice, vnp->data.ptrvalue, field_to, NULL, batch_extra); + for (val_vnp = val_list_from; val_vnp != NULL; val_vnp = val_vnp->next) { + str = (CharPtr)(val_vnp->data.ptrvalue); if (action->strip_name) { RemoveFieldNameFromString (field_name, str); } FixCapitalizationInString(&str, action->capitalization, NULL); - - if ((SetFieldValueForObjectEx (vnp->choice, vnp->data.ptrvalue, field_to, NULL, str, action->existing_text, batch_extra) - || (!action->keep_original && NoFieldChange(str, vnp, field_to, NULL, batch_extra))) - && (action->keep_original || RemoveFieldValueForObject (vnp->choice, vnp->data.ptrvalue, field_from, &remove_constraint))) { - if (also_change_mrna) { - AlsoChangeMrnaForObject (vnp->choice, vnp->data.ptrvalue); - } - num_succeed ++; - } else { - num_fail++; - fail = TRUE; + val_vnp->data.ptrvalue = str; + } + field_change = AddValuesToList(val_list_from, &val_list_to, action->existing_text); + if (field_change) { + if (!action->keep_original) { + RemoveFieldValueForObject(vnp->choice, vnp->data.ptrvalue, field_from, scp); } - str = MemFree (str); - remove_constraint.match_text = MemFree (remove_constraint.match_text); - if (action->keep_original) { - break; + RemoveFieldValueForObject(vnp->choice, vnp->data.ptrvalue, field_to, NULL); + for (val_vnp = val_list_to; val_vnp != NULL; val_vnp = val_vnp->next) { + SetFieldValueForObjectEx(vnp->choice, vnp->data.ptrvalue, field_to, + NULL, (CharPtr) (val_vnp->data.ptrvalue), + ExistingTextOption_add_qual, batch_extra); } } + if (also_change_mrna) { + field_change |= AlsoChangeMrnaForObject (vnp->choice, vnp->data.ptrvalue); + } + if (field_change) { + num_succeed++; + } + val_list_from = ValNodeFreeData(val_list_from); + val_list_to = ValNodeFreeData(val_list_to); } } @@ -20157,7 +21043,7 @@ NLM_EXTERN Int4 DoParseActionToObjectListEx (AECRParseActionPtr action, ValNodeP } } } - if (!IsTextMarkerEmpty (action->portion->right_marker) + if (action->portion != NULL && !IsTextMarkerEmpty (action->portion->right_marker) && action->remove_right && !action->portion->include_right && action->portion != NULL @@ -20207,13 +21093,27 @@ static Int4 ApplyAECRActionToSeqEntry (AECRActionPtr act, SeqEntryPtr sep, BoolP Int4 num_succeed = 0; FieldTypePtr field_from; BatchExtraPtr batch_extra; + AECRActionPtr act_cpy = NULL; + FeatureFieldPtr field_cpy; if (act == NULL || act->action == NULL) return 0; + field_type = FieldTypeFromAECRAction (act); + if (field_type == FieldType_cds_gene_prot) { + if (act->action->choice == ActionChoice_edit) { + act_cpy = AsnIoMemCopy (act, (AsnReadFunc) AECRActionAsnRead, (AsnWriteFunc) AECRActionAsnWrite); + e = (EditActionPtr)act_cpy->action->data.ptrvalue; + field_cpy = FeatureFieldFromCDSGeneProtField (e->field->data.intvalue); + e->field->choice = FieldType_feature_field; + e->field->data.ptrvalue = field_cpy; + act = act_cpy; + field_type = FieldTypeFromAECRAction (act); + } + } + batch_extra = BatchExtraNew (); InitBatchExtraForAECRAction (batch_extra, act, sep); - field_type = FieldTypeFromAECRAction (act); if (field_type == FieldType_cds_gene_prot) { entityID = ObjMgrGetEntityIDForChoice(sep); object_list = BuildCGPSetList (entityID, act, created_protein_features); @@ -20222,13 +21122,16 @@ static Int4 ApplyAECRActionToSeqEntry (AECRActionPtr act, SeqEntryPtr sep, BoolP object_list = GetObjectListForAECRActionEx (sep, act, batch_extra); } + if (object_list == NULL) { + return 0; + } switch (act->action->choice) { case ActionChoice_apply: a = (ApplyActionPtr) act->action->data.ptrvalue; scp = FindStringConstraintInConstraintSetForField (a->field, act->constraint); num_succeed = DoApplyActionToObjectListEx (act->action->data.ptrvalue, object_list, act->also_change_mrna, scp, batch_extra); - if (a->field->choice == FieldType_misc) { + if (a->field->choice == FieldType_misc || a->field->choice == FieldType_dblink) { DeleteMarkedObjects (ObjMgrGetEntityIDForChoice(sep), 0, NULL); } break; @@ -20268,6 +21171,8 @@ static Int4 ApplyAECRActionToSeqEntry (AECRActionPtr act, SeqEntryPtr sep, BoolP num_succeed = DoRemoveActionToObjectList (act->action->data.ptrvalue, object_list, act->also_change_mrna, scp); if (r->field->choice == FieldType_misc) { DeleteMarkedObjects (ObjMgrGetEntityIDForChoice(sep), 0, NULL); + } else if (r->field->choice == FieldType_dblink) { + DeleteMarkedObjects (ObjMgrGetEntityIDForChoice(sep), 0, NULL); } break; case ActionChoice_parse: @@ -20276,6 +21181,7 @@ static Int4 ApplyAECRActionToSeqEntry (AECRActionPtr act, SeqEntryPtr sep, BoolP } object_list = FreeObjectList (object_list); batch_extra = BatchExtraFree (batch_extra); + act_cpy = AECRActionFree (act_cpy); return num_succeed; } @@ -20529,7 +21435,7 @@ static int LIBCALLBACK SortVnpByChoiceAndIntvalue (VoidPtr ptr1, VoidPtr ptr2) /* Callback function used for sorting and uniqueing */ -static int LIBCALLBACK SortVnpByFieldType (VoidPtr ptr1, VoidPtr ptr2) +NLM_EXTERN int LIBCALLBACK SortVnpByFieldType (VoidPtr ptr1, VoidPtr ptr2) { ValNodePtr vnp1; @@ -20546,7 +21452,7 @@ static int LIBCALLBACK SortVnpByFieldType (VoidPtr ptr1, VoidPtr ptr2) } -static int LIBCALLBACK SortVnpByFieldTypeAndSourceQualifier (VoidPtr ptr1, VoidPtr ptr2) +NLM_EXTERN int LIBCALLBACK SortVnpByFieldTypeAndSourceQualifier (VoidPtr ptr1, VoidPtr ptr2) { ValNodePtr vnp1; @@ -20789,16 +21695,13 @@ static ValNodePtr GetRnaQualFieldList (SeqEntryPtr sep) } -static void GetStructuredCommentFieldsCallback (SeqDescrPtr sdp, Pointer data) +NLM_EXTERN ValNodePtr GetStructuredCommentFieldListFromUserObject (UserObjectPtr uop) { - UserObjectPtr uop; + ValNodePtr list = NULL; UserFieldPtr ufp; ValNodePtr vnp; - if (sdp != NULL && data != NULL && sdp->choice == Seq_descr_user - && (uop = sdp->data.ptrvalue) != NULL - && IsUserObjectStructuredComment (uop)) { - + if (uop != NULL && IsUserObjectStructuredComment (uop)) { ufp = uop->data; while (ufp != NULL) { if (ufp->label != NULL && ufp->label->str != NULL @@ -20807,15 +21710,28 @@ static void GetStructuredCommentFieldsCallback (SeqDescrPtr sdp, Pointer data) vnp = ValNodeNew (NULL); vnp->choice = StructuredCommentField_named; vnp->data.ptrvalue = StringSave (ufp->label->str); - ValNodeAddPointer ((ValNodePtr PNTR) data, FieldType_struc_comment_field, vnp); + ValNodeAddPointer (&list, FieldType_struc_comment_field, vnp); } ufp = ufp->next; } } + return list; +} + + +static void GetStructuredCommentFieldsCallback (SeqDescrPtr sdp, Pointer data) +{ + UserObjectPtr uop; + + if (sdp != NULL && data != NULL && sdp->choice == Seq_descr_user + && (uop = sdp->data.ptrvalue) != NULL + && IsUserObjectStructuredComment (uop)) { + ValNodeLink ((ValNodePtr PNTR) data, GetStructuredCommentFieldListFromUserObject(uop)); + } } -static ValNodePtr GetStructuredCommentFieldList (SeqEntryPtr sep) +NLM_EXTERN ValNodePtr GetStructuredCommentFieldList (SeqEntryPtr sep) { ValNodePtr field_list = NULL; ValNodePtr dbname, field_name; @@ -20953,40 +21869,6 @@ static void CollectStructuredCommentsCallback (SeqDescrPtr sdp, Pointer data) } -static void AddDBLinkDescriptorDestinationsForBioseq (BioseqPtr bsp, ValNodePtr PNTR dest_list) -{ - SeqDescrPtr sdp; - UserObjectPtr uop; - SeqMgrDescContext context; - Boolean found = FALSE; - ObjValNodePtr ovp; - - if (bsp == NULL || dest_list == NULL) { - return; - } - - for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &context); - sdp != NULL; - sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &context)) { - if ((uop = sdp->data.ptrvalue) != NULL - && IsUserObjectDBLink (uop)) { - ValNodeAddPointer (dest_list, OBJ_SEQDESC, sdp); - found = TRUE; - } - } - if (!found) { - /* if no existing comment descriptor, create one, marked for delete. - * unmark it for deletion when it gets populated. - */ - sdp = CreateNewDescriptorOnBioseq (bsp, Seq_descr_user); - sdp->data.ptrvalue = CreateDBLinkUserObject (); - ovp = (ObjValNodePtr) sdp; - ovp->idx.deleteme = TRUE; - ValNodeAddPointer (dest_list, OBJ_SEQDESC, sdp); - } -} - - static ValNodePtr CollectDBLinkDescriptors (SeqEntryPtr sep) { ValNodePtr seq_list = NULL, vnp, desc_list = NULL; @@ -21104,6 +21986,21 @@ static ValNodePtr CollectGenbankBlockDescriptors (SeqEntryPtr sep) } +static void CollectDblinkCallback (SeqDescPtr sdp, Pointer data) +{ + UserObjectPtr uop; + + if (sdp == NULL || data == NULL + || sdp->choice != Seq_descr_user + || (uop = (UserObjectPtr)sdp->data.ptrvalue) == NULL + || uop->type == NULL + || StringCmp (uop->type->str, "DBLink") != 0) { + return; + } else { + ValNodeAddPointer ((ValNodePtr PNTR) data, OBJ_SEQDESC, sdp); + } +} + NLM_EXTERN ValNodePtr GetObjectListForFieldType (Uint1 field_type, SeqEntryPtr sep) { @@ -21140,6 +22037,9 @@ NLM_EXTERN ValNodePtr GetObjectListForFieldType (Uint1 field_type, SeqEntryPtr s object_list = CollectNucBioseqs (sep); ValNodeLink (&object_list, CollectCommentDescriptors (sep)); break; + case FieldType_dblink: + VisitDescriptorsInSep (sep, &object_list, CollectDblinkCallback); + break; } return object_list; } @@ -21209,6 +22109,13 @@ NLM_EXTERN ValNodePtr GetFieldListForFieldType (Uint1 field_type, SeqEntryPtr se ValNodeAddInt (&fields, FieldType_misc, Misc_field_defline); ValNodeAddInt (&fields, FieldType_misc, Misc_field_keyword); break; + case FieldType_dblink: + ValNodeAddInt (&fields, FieldType_dblink, DBLink_field_type_trace_assembly); + ValNodeAddInt (&fields, FieldType_dblink, DBLink_field_type_bio_sample); + ValNodeAddInt (&fields, FieldType_dblink, DBLink_field_type_probe_db); + ValNodeAddInt (&fields, FieldType_dblink, DBLink_field_type_sequence_read_archve); + ValNodeAddInt (&fields, FieldType_dblink, DBLink_field_type_bio_project); + break; } return fields; } @@ -22898,6 +23805,7 @@ static Int4 SetFieldForDestList (ValNodePtr dest_list, ParseDestPtr field, CharP num_succeeded++; } sdp->data.ptrvalue = cp; + RemoveAutodefObjectsForDesc(sdp); } } } @@ -23732,7 +24640,8 @@ static Int4 ApplyRemoveFeatureActionToSeqEntry (RemoveFeatureActionPtr action, S ConvertAndRemoveFeatureCollectionData d; ValNodePtr vnp; SeqFeatPtr sfp; - Int4 num_deleted = 0; + Int4 num_deleted = 0, num_products_deleted = 0; + BioseqPtr bsp; if (action == NULL) return 0; @@ -23745,12 +24654,17 @@ static Int4 ApplyRemoveFeatureActionToSeqEntry (RemoveFeatureActionPtr action, S sfp = vnp->data.ptrvalue; if (sfp != NULL) { sfp->idx.deleteme = TRUE; + if (sfp->product != NULL && (bsp = BioseqFind(SeqLocId(sfp->product))) != NULL) { + bsp->idx.deleteme = TRUE; + num_products_deleted++; + } num_deleted ++; } } d.feature_list = ValNodeFree (d.feature_list); DeleteMarkedObjects (ObjMgrGetEntityIDForChoice(sep), 0, NULL); - return num_deleted; + RenormalizeNucProtSets (sep, TRUE); + return num_deleted + num_products_deleted; } @@ -23994,9 +24908,9 @@ static Boolean ConvertCommentToMiscFeat (SeqFeatPtr sfp, Int4 featdef_to, Conver } -static Boolean ConvertGeneToMiscFeat (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDstOptionsPtr dst_options) +static Boolean ConvertGeneToImpFeat (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDstOptionsPtr dst_options) { - return ConvertGeneToMiscFeatFunc (sfp, featdef_to); + return ConvertGeneToImpFeatFunc (sfp, featdef_to); } @@ -24112,7 +25026,7 @@ static Boolean ConvertRegionToProt (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeat static Boolean ConvertToBond (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDstOptionsPtr dst_options) { - SeqLocPtr slp; + SeqLocPtr slp = NULL; BioseqPtr bsp; SeqEntryPtr sep; Boolean no_cds = FALSE; @@ -24192,7 +25106,7 @@ static Boolean ConvertToBond (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDst static Boolean ConvertToSite (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDstOptionsPtr dst_options) { - SeqLocPtr slp; + SeqLocPtr slp = NULL; BioseqPtr bsp; SeqEntryPtr sep; Boolean no_cds = FALSE; @@ -24340,6 +25254,18 @@ static Boolean MiscFeatToCodingRegionConvertFunc (SeqFeatPtr sfp, Int4 featdef_t } +static Boolean mRNAToCodingRegionConvertFunc (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDstOptionsPtr dst_options) +{ + return ConvertmRNAToCodingRegion (sfp); +} + + +static Boolean tRNAToGeneConvertFunc(SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDstOptionsPtr dst_options) +{ + return ConverttRNAToGene (sfp); +} + + static Boolean MiscFeatToGeneConvertFunc (SeqFeatPtr sfp, Int4 featdef_to, ConvertFeatureDstOptionsPtr dst_options) { return ConvertMiscFeatToGene (sfp); @@ -24407,12 +25333,18 @@ static ConvertFeatTableData conversion_functions[] = { { SEQFEAT_COMMENT, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_misc_feature, ConvertCommentToMiscFeat, "Creates a misc_feature with the same note as the original. Note - the flatfile display for the feature is the same." }, - { SEQFEAT_GENE, FEATDEF_GENE, SEQFEAT_IMP, FEATDEF_misc_feature, - ConvertGeneToMiscFeat, - "Creates a misc_feature with the gene description and locus prepended to the original comment, separated by semicolons." }, + { SEQFEAT_GENE, FEATDEF_GENE, SEQFEAT_IMP, FEATDEF_ANY, + ConvertGeneToImpFeat, + "Creates an import feature with the gene description and locus prepended to the original comment, separated by semicolons." }, { SEQFEAT_RNA, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_ANY, ConvertRNAToImpFeatEx, "Creates an import feature of the specified subtype and adds the RNA product name to the comment." } , + { SEQFEAT_RNA, FEATDEF_mRNA, SEQFEAT_CDREGION, FEATDEF_CDS, + mRNAToCodingRegionConvertFunc, + "Convert mRNA to coding region, use mRNA product for protein feature" }, + { SEQFEAT_RNA, FEATDEF_tRNA, SEQFEAT_GENE, FEATDEF_GENE, + tRNAToGeneConvertFunc, + "Convert tRNA to gene, use tRNA product for gene description" }, { SEQFEAT_SITE, FEATDEF_ANY, SEQFEAT_IMP, FEATDEF_ANY, ConvertSiteToImpFeat, "Creates an import feature of the specified subtype with the site type name as a /note qualifier." } , @@ -24540,6 +25472,9 @@ static Int4 ApplyConvertFeatureActionToSeqEntry (ConvertFeatureActionPtr action, d.feature_list = NULL; VisitFeaturesInSep (sep, &d, ConvertAndRemoveFeatureCollectionCallback); + if (d.feature_list == NULL) { + return 0; + } for (vnp = d.feature_list; vnp != NULL; vnp = vnp->next) { sfp = vnp->data.ptrvalue; if (sfp != NULL) { @@ -24983,7 +25918,7 @@ static Boolean ApplyClear3PartialToSeqFeat (Int4 action, SeqFeatPtr sfp) clear_partial = !At3EndOfSequence(sfp->location, BioseqFindFromSeqLoc (sfp->location)); break; case Partial_3_clear_constraint_good_end: - clear_partial = !HasGoodStopCodon(sfp); + clear_partial = HasGoodStopCodon(sfp); break; } if (clear_partial) { @@ -25078,58 +26013,58 @@ static Boolean ApplyConvertLocationToSeqFeat (Int4 convert_location, SeqFeatPtr } CheckSeqLocForPartial (sfp->location, &partial5, &partial3); - hasNulls = LocationHasNullsBetween (sfp->location); - switch (convert_location) - { - case Convert_location_type_join : - if (hasNulls) - { - slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, FALSE, FALSE); - sfp->location = SeqLocFree (sfp->location); - sfp->location = slp; - if (bsp->repr == Seq_repr_seg) - { - slp = SegLocToPartsEx (bsp, sfp->location, FALSE); - sfp->location = SeqLocFree (sfp->location); - sfp->location = slp; - hasNulls = LocationHasNullsBetween (sfp->location); - sfp->partial = (sfp->partial || hasNulls); - } - FreeAllFuzz (sfp->location); - SetSeqLocPartial (sfp->location, partial5, partial3); + hasNulls = LocationHasNullsBetween (sfp->location); + switch (convert_location) + { + case Convert_location_type_join : + if (hasNulls) + { + slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, FALSE, FALSE); + sfp->location = SeqLocFree (sfp->location); + sfp->location = slp; + if (bsp->repr == Seq_repr_seg) + { + slp = SegLocToPartsEx (bsp, sfp->location, FALSE); + sfp->location = SeqLocFree (sfp->location); + sfp->location = slp; + hasNulls = LocationHasNullsBetween (sfp->location); + sfp->partial = (sfp->partial || hasNulls); + } + FreeAllFuzz (sfp->location); + SetSeqLocPartial (sfp->location, partial5, partial3); rval = TRUE; - } - break; - case Convert_location_type_order : - if (!hasNulls) - { - slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, FALSE, TRUE); + } + break; + case Convert_location_type_order : + if (!hasNulls) + { + slp = SeqLocMerge (bsp, sfp->location, NULL, FALSE, FALSE, TRUE); sfp->location = SeqLocFree (sfp->location); - sfp->location = slp; - if (bsp->repr == Seq_repr_seg) - { - slp = SegLocToPartsEx (bsp, sfp->location, TRUE); - sfp->location = SeqLocFree (sfp->location); - sfp->location = slp; - hasNulls = LocationHasNullsBetween (sfp->location); - sfp->partial = (sfp->partial || hasNulls); - } - FreeAllFuzz (sfp->location); - SetSeqLocPartial (sfp->location, partial5, partial3); + sfp->location = slp; + if (bsp->repr == Seq_repr_seg) + { + slp = SegLocToPartsEx (bsp, sfp->location, TRUE); + sfp->location = SeqLocFree (sfp->location); + sfp->location = slp; + hasNulls = LocationHasNullsBetween (sfp->location); + sfp->partial = (sfp->partial || hasNulls); + } + FreeAllFuzz (sfp->location); + SetSeqLocPartial (sfp->location, partial5, partial3); rval = TRUE; - } - break; - case Convert_location_type_merge : + } + break; + case Convert_location_type_merge : if (sfp->location->choice != SEQLOC_INT) { - slp = SeqLocMerge (bsp, sfp->location, NULL, TRUE, FALSE, FALSE); - sfp->location = SeqLocFree (sfp->location); - sfp->location = slp; - SetSeqLocPartial (sfp->location, partial5, partial3); + slp = SeqLocMerge (bsp, sfp->location, NULL, TRUE, FALSE, FALSE); + sfp->location = SeqLocFree (sfp->location); + sfp->location = slp; + SetSeqLocPartial (sfp->location, partial5, partial3); rval = TRUE; } - default: - break; - } + default: + break; + } return rval; } @@ -25535,6 +26470,7 @@ static Int4 ApplyEditFeatureLocationActionToSeqEntry (EditFeatureLocationActionP } retranslated = FALSE; if (sfp->data.choice == SEQFEAT_CDREGION && action->retranslate_cds) { + SeqMgrIndexFeatures(sfp->idx.entityID, NULL); retranslated = RetranslateOneCDS (sfp, sfp->idx.entityID, TRUE, TRUE); } num_affected++; @@ -25821,7 +26757,7 @@ NLM_EXTERN Boolean LatLonAutocorrectList (FILE *fp, ValNodePtr object_list) CharPtr fix, extra_text; Boolean any_change = FALSE; - if (fp == NULL || object_list == NULL) return FALSE; + if (object_list == NULL) return FALSE; for (vnp = object_list; vnp != NULL; vnp = vnp->next) { @@ -25846,19 +26782,25 @@ NLM_EXTERN Boolean LatLonAutocorrectList (FILE *fp, ValNodePtr object_list) extra_text++; } } - fprintf (fp, "Corrected %s to %s\n", bad_ssp->name, fix); + if (fp != NULL) { + fprintf (fp, "Corrected %s to %s\n", bad_ssp->name, fix); + } bad_ssp->name = MemFree (bad_ssp->name); bad_ssp->name = fix; if (extra_text != NULL) { AddAltitudeToSubSourceNote (biop, extra_text); - fprintf (fp, "Moved %s to subsource note\n", extra_text); + if (fp != NULL) { + fprintf (fp, "Moved %s to subsource note\n", extra_text); + } } any_change = TRUE; } else { - fprintf (fp, "Unable to correct %s\n", bad_ssp->name); + if (fp != NULL) { + fprintf (fp, "Unable to correct %s\n", bad_ssp->name); + } } } } @@ -26045,19 +26987,8 @@ static ReplacePairData macro_spell_fixes[] = { {"Agricultrual", "Agricultural"}, {"Agricultureal", "Agricultural"}, {"Agricultrure", "Agriculture"}, - {"univeristy", "University" }, - {"univerisity", "University" }, - {"univercity", "University" }, - {"uiniversity", "University" }, - {"uinversity", "University" }, - {"univesity", "University" }, - {"uviversity", "University" }, - {"universtiy", "University" }, - {"unvierstity", "University" }, - {"univiersity", "University" }, - {"universtity", "University" }, - {"Unversity", "University" }, - {"protien", "protein" }, + {"bioremidiation", "bioremediation"}, + {"Colledge", "College"}, {"Insitiute", "Institute" }, {"Instutite", "Institute" }, {"instute", "Institute" }, @@ -26079,6 +27010,8 @@ static ReplacePairData macro_spell_fixes[] = { {"hypothtical", "hypothetical" }, {"hypthetical", "hypothetical" }, {"hyptothetical", "hypothetical" }, + {"idendification", "identification" }, + {"protien", "protein" }, {"puatative", "putative" }, {"puative", "putative" }, {"puative", "putative" }, @@ -26089,6 +27022,20 @@ static ReplacePairData macro_spell_fixes[] = { {"putatitve", "putative" }, {"putitive", "putative" }, {"reseach", "research"}, + {"sequene", "sequence"}, + {"univeristy", "University" }, + {"univerisity", "University" }, + {"univercity", "University" }, + {"uiniversity", "University" }, + {"uinversity", "University" }, + {"univesity", "University" }, + {"uviversity", "University" }, + {"universtiy", "University" }, + {"unvierstity", "University" }, + {"univiersity", "University" }, + {"universtity", "University" }, + {"Unversity", "University" }, + {"Univresity", "University" }, {NULL, NULL}}; @@ -26278,6 +27225,9 @@ static Int4 ApplyRemoveDescriptorActionToSeqEntry (RemoveDescriptorActionPtr act d.obj_list = NULL; VisitDescriptorsInSep (sep, &d, RemoveDescriptorCollectionCallback); + if (d.obj_list == NULL) { + return 0; + } for (vnp = d.obj_list; vnp != NULL; vnp = vnp->next) { sdp = vnp->data.ptrvalue; if (sdp != NULL && sdp->extended != 0) { @@ -26291,6 +27241,79 @@ static Int4 ApplyRemoveDescriptorActionToSeqEntry (RemoveDescriptorActionPtr act } +static void TrimStopsFromCompleteCodingRegionsCallback (SeqFeatPtr sfp, Pointer data) +{ + Boolean p5, p3; + BioseqPtr protbsp; + CharPtr prot_str; + Int4 len; + /* variables for shortening protein features */ + SeqFeatPtr prot_sfp; + SeqMgrFeatContext fcontext; + SeqIntPtr sintp; + /* variables for logging */ + LogInfoPtr lip; + Char id_buf[100]; + + if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION || sfp->product == NULL) { + return; + } + + CheckSeqLocForPartial (sfp->location, &p5, &p3); + if (p3) { + return; + } + + protbsp = BioseqFindFromSeqLoc (sfp->product); + if (protbsp == NULL) { + return; + } + + prot_str = GetSequenceByBsp (protbsp); + if (prot_str == NULL || (len = StringLen (prot_str)) == 0 + || prot_str[len - 1] != '*') { + prot_str = MemFree (prot_str); + return; + } + + BSSeek ((ByteStorePtr) protbsp->seq_data, -1, SEEK_END); + BSDelete ((ByteStorePtr) protbsp->seq_data, 1); + protbsp->length -= 1; + prot_str = MemFree (prot_str); + + for (prot_sfp = SeqMgrGetNextFeature (protbsp, NULL, 0, 0, &fcontext); + prot_sfp != NULL; + prot_sfp = SeqMgrGetNextFeature (protbsp, prot_sfp, 0, 0, &fcontext)) { + if (prot_sfp->location != NULL + && prot_sfp->location->choice == SEQLOC_INT + && (sintp = (SeqIntPtr)prot_sfp->location->data.ptrvalue) != NULL) { + if (sintp->to > protbsp->length - 1) { + sintp->to = protbsp->length - 1; + } + } + } + + lip = (LogInfoPtr) data; + if (lip != NULL) { + if (lip->fp != NULL) { + SeqIdWrite (SeqIdFindBest (protbsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); + fprintf (lip->fp, "Trimmed trailing * from %s\n", id_buf); + } + lip->data_in_log = TRUE; + } +} + + +NLM_EXTERN Boolean TrimStopsFromCompleteCodingRegions (SeqEntryPtr sep, FILE *log_fp) +{ + LogInfoData lid; + MemSet (&lid, 0, sizeof (LogInfoData)); + lid.fp = log_fp; + VisitFeaturesInSep (sep, &lid, TrimStopsFromCompleteCodingRegionsCallback); + return lid.data_in_log; +} + + static DefLineType DefLineTypeFromAutodefListType(Uint2 list_type) { DefLineType deflinetype = DEFLINE_USE_FEATURES; @@ -26415,7 +27438,7 @@ static void ApplyFixPubCapsCallback (PubdescPtr pdp, Pointer data) CharPtr orig, tmp; ValNodePtr pub; AuthListPtr alp = NULL; - ValNodePtr names; + ValNodePtr names; AuthorPtr ap, ap_orig; AffilPtr affil_orig; @@ -26550,6 +27573,12 @@ static Boolean ApplyFixPubCapsToSeqEntry (FixPubCapsActionPtr action, SeqEntryPt SeqDescPtr sdp; CharPtr summ; Boolean rval = FALSE; + AuthListPtr alp; + ValNodePtr names; + AuthorPtr ap; + SeqSubmitPtr ssp; + SubmitBlockPtr sbp; + CitSubPtr csp; if (action == NULL || sep == NULL) return FALSE; @@ -26582,6 +27611,26 @@ static Boolean ApplyFixPubCapsToSeqEntry (FixPubCapsActionPtr action, SeqEntryPt ApplyFixPubCapsCallback (pdp, &f); } + ssp = FindSeqSubmitForSeqEntry (sep); + if (ssp != NULL) { + sbp = ssp->sub; + if (sbp != NULL) { + csp = sbp->cit; + if (csp != NULL) { + alp = csp->authors; + if (alp != NULL && alp->choice == 1) { + for (names = alp->names; names != NULL; names = names->next) { + ap = names->data.ptrvalue; + if (f.action->authors && !f.action->punct_only) { + FixCapitalizationInAuthor (ap); + f.num_sub_fields++; + } + } + } + } + } + } + f.orgnames = ValNodeFree (f.orgnames); if (f.num_sub_fields > 0 || f.num_pub_fields > 0) { @@ -26799,6 +27848,309 @@ static Int4 SortFieldsInSeqEntry (SortFieldsActionPtr action, SeqEntryPtr sep) } +static Boolean DoStringsMatch (CharPtr str1, CharPtr str2, Boolean case_sensitive) +{ + Boolean rval = FALSE; + + if (case_sensitive) { + if (StringCmp (str1, str2) == 0) { + rval = TRUE; + } + } else if (StringICmp (str1, str2) == 0) { + rval = TRUE; + } + return rval; +} + + +static Boolean DoGBQualListsMatch (GBQualPtr gbq1, GBQualPtr gbq2, Boolean case_sensitive) +{ + Boolean rval = TRUE; + + while (rval && gbq1 != NULL && gbq2 != NULL) { + if (!DoStringsMatch (gbq1->qual, gbq2->qual, case_sensitive)) { + rval = FALSE; + } else if (!DoStringsMatch (gbq1->val, gbq2->val, case_sensitive)) { + rval = FALSE; + } else { + gbq1 = gbq1->next; + gbq2 = gbq2->next; + } + } + if (gbq1 != NULL || gbq2 != NULL) { + rval = FALSE; + } + return rval; +} + + +static Boolean CheckBioseqForPartial (BioseqPtr bsp, BoolPtr partial5, BoolPtr partial3) +{ + SeqMgrDescContext context; + SeqDescrPtr sdp; + MolInfoPtr mip; + Boolean rval = FALSE; + + if (bsp == NULL) { + return FALSE; + } + if (partial5 != NULL) { + *partial5 = FALSE; + } + if (partial3 != NULL) { + *partial3 = FALSE; + } + sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context); + if (sdp != NULL && (mip = (MolInfoPtr) sdp->data.ptrvalue) != NULL) { + /* partial 5 */ + if (mip->completeness == 3 || mip->completeness == 5) { + if (partial5 != NULL) { + *partial5 = TRUE; + } + rval = TRUE; + } + /* partial 3 */ + if (mip->completeness == 4 || mip->completeness == 5) { + if (partial3 != NULL) { + *partial3 = TRUE; + } + rval = TRUE; + } + if (mip->completeness == 2) { + rval = TRUE; + } + } + return rval; +} + + +static Boolean ProductsMatch (SeqLocPtr slp1, SeqLocPtr slp2, Boolean case_sensitive, Boolean ignore_partial) +{ + BioseqPtr bsp1, bsp2; + Int2 ctr, pos1, pos2; + Char buf1[51]; + Char buf2[51]; + Int4 len = 50; + SeqFeatPtr sfp1, sfp2; + SeqMgrFeatContext fcontext1, fcontext2; + Boolean partial5_1, partial5_2, partial3_1, partial3_2; + + if (slp1 == NULL && slp2 == NULL) { + return TRUE; + } else if (slp1 == NULL || slp2 == NULL) { + return FALSE; + } else if (SeqLocCompare (slp1, slp2) == SLC_A_EQ_B) { + return TRUE; + } else { + bsp1 = BioseqFindFromSeqLoc (slp1); + bsp2 = BioseqFindFromSeqLoc (slp2); + if (bsp1 == NULL || bsp2 == NULL) { + /* can't compare, assume they don't match */ + return FALSE; + } else if (bsp1->length != bsp2->length) { + return FALSE; + } else { + CheckBioseqForPartial (bsp1, &partial5_1, &partial3_1); + CheckBioseqForPartial (bsp2, &partial5_2, &partial3_2); + if (!ignore_partial + && ((partial5_1 && !partial5_2) || (!partial5_1 && partial5_2) + || (partial3_1 && !partial3_2) || (!partial3_1 && partial3_2))) { + return FALSE; + } + /* check that translation sequences match */ + pos1 = 0; + pos2 = 0; + if (ignore_partial) { + if (partial5_1 || partial5_2) { + pos1++; + pos2++; + } + } + while (pos1 < bsp1->length && pos2 < bsp2->length) { + ctr = SeqPortStreamInt (bsp1, pos1, MIN(pos1 + len - 1, bsp1->length - 1), Seq_strand_plus, + STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, + (Pointer) buf1, NULL); + ctr = SeqPortStreamInt (bsp2, pos2, MIN(pos2 + len - 1, bsp2->length - 1), Seq_strand_plus, + STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, + (Pointer) buf2, NULL); + if (StringNCmp (buf1, buf2, ctr) != 0) { + return FALSE; + } + pos1 += len; + pos2 += len; + } + + /* now check that protein features match */ + sfp1 = SeqMgrGetNextFeature (bsp1, NULL, 0, 0, &fcontext1); + sfp2 = SeqMgrGetNextFeature (bsp2, NULL, 0, 0, &fcontext2); + while (sfp1 != NULL && sfp2 != NULL) { + if (!DoFeaturesMatch (sfp1, sfp2, TRUE, case_sensitive, ignore_partial)) { + return FALSE; + } + sfp1 = SeqMgrGetNextFeature (bsp1, sfp1, SEQFEAT_PROT, 0, &fcontext1); + sfp2 = SeqMgrGetNextFeature (bsp2, sfp2, SEQFEAT_PROT, 0, &fcontext2); + } + if (sfp1 != NULL || sfp2 != NULL) { + return FALSE; + } else { + return TRUE; + } + } + } +} + + +static Boolean DoLocationPartialsMatch (SeqLocPtr slp1, SeqLocPtr slp2) +{ + Boolean partial5_1, partial3_1, partial1; + Boolean partial5_2, partial3_2, partial2; + + partial1 = CheckSeqLocForPartial (slp1, &partial5_1, &partial3_1); + partial2 = CheckSeqLocForPartial (slp2, &partial5_2, &partial3_2); + if ((partial1 && !partial2) || (!partial1 && partial2)) { + return FALSE; + } + if ((partial5_1 && !partial5_2) || (!partial5_1 && partial5_2)) { + return FALSE; + } + if ((partial3_1 && !partial3_2) || (!partial3_1 && partial3_2)) { + return FALSE; + } + return TRUE; +} + + +static Boolean DoLocationsMatch (SeqLocPtr slp1, SeqLocPtr slp2, Boolean allow_different_sequences, Boolean ignore_partial) +{ + SeqLocPtr slp_tmp1, slp_tmp2; + + if (slp1 == NULL && slp2 == NULL) { + return TRUE; + } else if (slp1 == NULL || slp2 == NULL) { + return FALSE; + } + + if (!ignore_partial && !DoLocationPartialsMatch (slp1, slp2)) { + return FALSE; + } + if (allow_different_sequences) { + for (slp_tmp1 = SeqLocFindNext (slp1, NULL), slp_tmp2 = SeqLocFindNext (slp2, NULL); + slp_tmp1 != NULL && slp_tmp2 != NULL; + slp_tmp1 = SeqLocFindNext (slp1, slp_tmp1), slp_tmp2 = SeqLocFindNext (slp2, slp_tmp2)) { + if (SeqLocStart (slp_tmp1) != SeqLocStart (slp_tmp2) + || SeqLocStop (slp_tmp1) != SeqLocStop (slp_tmp2) + || (!ignore_partial && !DoLocationPartialsMatch (slp_tmp1, slp_tmp2))) { + return FALSE; + } + } + } else if (SeqLocCompare (slp1, slp2) != SLC_A_EQ_B) { + return FALSE; + } + return TRUE; +} + + +static Boolean DoCdRegionsMatch (CdRegionPtr crp1, CdRegionPtr crp2) +{ + if (crp1 == NULL && crp2 == NULL) { + return TRUE; + } else if (crp1 == NULL || crp2 == NULL) { + return FALSE; + } else if ((crp1->orf && !crp2->orf) || (!crp1->orf && crp2->orf)){ + return FALSE; + } else if ((crp1->conflict && !crp2->conflict) || (!crp1->conflict && crp2->conflict)){ + return FALSE; + } else if (crp1->gaps != crp2->gaps) { + return FALSE; + } else if (crp1->mismatch != crp2->mismatch) { + return FALSE; + } else if (crp1->stops != crp2->stops) { + return FALSE; + } else if ((crp1->genetic_code == NULL && crp2->genetic_code != NULL) + || (crp1->genetic_code != NULL && crp2->genetic_code == NULL) + || (crp1->genetic_code != NULL && crp2->genetic_code != NULL + && !AsnIoMemComp (crp1->genetic_code, crp2->genetic_code, (AsnWriteFunc) GeneticCodeAsnWrite))) { + return FALSE; + } else if ((crp1->code_break == NULL && crp2->code_break != NULL) + || (crp1->code_break != NULL && crp2->code_break == NULL) + || (crp1->code_break != NULL && crp2->code_break != NULL + && !AsnIoMemComp (crp1->code_break, crp2->code_break, (AsnWriteFunc) CodeBreakAsnWrite))) { + return FALSE; + } else if (crp1->frame != crp2->frame) { + if ((crp1->frame == 0 || crp1->frame == 1) && (crp2->frame == 0 || crp2->frame == 1)) { + /* both effectively frame 1, ignore this difference */ + } else { + return FALSE; + } + } + return TRUE; +} + + +static Boolean DoesSeqFeatDataMatch (ChoicePtr d1, ChoicePtr d2) +{ + if (d1 == NULL && d2 == NULL) { + return TRUE; + } else if (d1 == NULL || d2 == NULL) { + return FALSE; + } else if (d1->choice != d2->choice) { + return FALSE; + } else if (d1->choice == SEQFEAT_CDREGION) { + return DoCdRegionsMatch(d1->value.ptrvalue, d2->value.ptrvalue); + } else { + return AsnIoMemComp(d1, d2, (AsnWriteFunc) SeqFeatDataAsnWrite); + } +} + + +NLM_EXTERN Boolean DoFeaturesMatch (SeqFeatPtr sfp1, SeqFeatPtr sfp2, Boolean allow_different_sequences, Boolean case_sensitive, Boolean ignore_partial) +{ + if (sfp1 == NULL && sfp2 == NULL) { + return TRUE; + } else if (sfp1 == NULL || sfp2 == NULL) { + return FALSE; + } if (sfp1->data.choice != sfp2->data.choice) { + return FALSE; + } else if (sfp1->idx.subtype != sfp2->idx.subtype) { + return FALSE; + } else if (!ignore_partial && ((sfp1->partial && !sfp2->partial) || (!sfp1->partial && sfp2->partial))) { + return FALSE; + } else if ((sfp1->pseudo && !sfp2->pseudo) || (!sfp1->pseudo && sfp2->pseudo)) { + return FALSE; + } else if ((sfp1->excpt && !sfp2->excpt) || (!sfp1->excpt && sfp2->excpt)) { + return FALSE; + } else if (!DoLocationsMatch (sfp1->location, sfp2->location, allow_different_sequences, ignore_partial)) { + return FALSE; + } else if (!DoStringsMatch (sfp1->comment, sfp2->comment, case_sensitive)) { + return FALSE; + } else if (!DoStringsMatch (sfp1->title, sfp2->title, case_sensitive)) { + return FALSE; + } else if (sfp1->ext != NULL || sfp2->ext != NULL) { + return FALSE; + } else if (sfp1->exts != NULL || sfp2->exts != NULL) { + return FALSE; + } else if (!DoStringsMatch (sfp1->except_text, sfp2->except_text, case_sensitive)) { + return FALSE; + } else if (sfp1->exp_ev != sfp2->exp_ev) { + return FALSE; + } else if (!DoGBQualListsMatch (sfp1->qual, sfp2->qual, case_sensitive)) { + return FALSE; + } else if ((sfp1->cit != NULL || sfp2->cit != NULL) && PubMatch (sfp1->cit, sfp2->cit) != 0) { + return FALSE; + } else if (!DbxrefsMatch (sfp1->dbxref, sfp2->dbxref, case_sensitive)) { + return FALSE; + } else if (!DoesSeqFeatDataMatch(&(sfp1->data), &(sfp2->data))) { + return FALSE; + } else if (!XrefsMatch (sfp1->xref, sfp2->xref)) { + return FALSE; + } else if (!ProductsMatch (sfp1->product, sfp2->product, case_sensitive, ignore_partial)) { + return FALSE; + } else { + return TRUE; + } +} + + typedef struct dupfeats { ValNodePtr delete_list; RemoveDuplicateFeatureActionPtr action; @@ -26877,7 +28229,7 @@ NLM_EXTERN void RemoveDuplicateFeaturesInList (ValNodePtr delete_list, Uint2 ent DeleteMarkedObjects (entityID, 0, NULL); if (remove_proteins) { sep = GetTopSeqEntryForEntityID (entityID); - RenormalizeNucProtSets (sep, TRUE); + RenormalizeNucProtSets (sep, TRUE); } } @@ -27459,15 +28811,19 @@ static void GetPubsForAuthorFixFeat (SeqFeatPtr sfp, Pointer data) static Boolean ApplyAuthorFixToSeqEntry (SeqEntryPtr sep, AuthorFixActionPtr action, FILE *log_fp) { - PubCollectData p; - ValNodePtr vnp, pub; - PubdescPtr pdp; - SeqFeatPtr sfp; - SeqDescPtr sdp; - AuthListPtr alp; - ValNodePtr names; - AuthorPtr ap; - Int4 num_changed = 0; + PubCollectData p; + ValNodePtr vnp, pub; + PubdescPtr pdp; + SeqFeatPtr sfp; + SeqDescPtr sdp; + AuthListPtr alp; + ValNodePtr names; + AuthorPtr ap; + SeqSubmitPtr ssp; + SubmitBlockPtr sbp; + ContactInfoPtr cip; + CitSubPtr csp; + Int4 num_changed = 0; if (sep == NULL || action == NULL) { return FALSE; @@ -27518,6 +28874,63 @@ static Boolean ApplyAuthorFixToSeqEntry (SeqEntryPtr sep, AuthorFixActionPtr act } } } + ssp = FindSeqSubmitForSeqEntry (sep); + if (ssp != NULL) { + sbp = ssp->sub; + if (sbp != NULL) { + csp = sbp->cit; + if (csp != NULL) { + alp = csp->authors; + if (alp != NULL && alp->choice == 1) { + for (names = alp->names; names != NULL; names = names->next) { + ap = names->data.ptrvalue; + switch (action->fix_type) { + case Author_fix_type_truncate_middle_initials: + if (TruncateAuthorMiddleInitials(ap)) { + num_changed++; + } + break; + case Author_fix_type_strip_suffix: + if (StripSuffixFromAuthor(ap)) { + num_changed++; + } + break; + case Author_fix_type_move_middle_to_first: + if (MoveAuthorMiddleToFirst (ap)) { + num_changed++; + } + break; + } + } + } + } + cip = sbp->contact; + if (cip != NULL) { + ap = cip->contact; + if (ap != NULL) { + /* + switch (action->fix_type) { + case Author_fix_type_truncate_middle_initials: + if (TruncateAuthorMiddleInitials(ap)) { + num_changed++; + } + break; + case Author_fix_type_strip_suffix: + if (StripSuffixFromAuthor(ap)) { + num_changed++; + } + break; + case Author_fix_type_move_middle_to_first: + if (MoveAuthorMiddleToFirst (ap)) { + num_changed++; + } + break; + } + */ + } + } + } + } p.list = ValNodeFree (p.list); if (num_changed > 0) { @@ -28308,6 +29721,11 @@ static Boolean PerformApplyTableInSeqEntry fprintf (log_fp, "%s not recognized as qualifier name, unable to apply table from %s\n", (CharPtr) val->data.ptrvalue, action->filename); } + } else { + if (IsFieldTypeCDSProduct(t->field)) { + t->match_mrna = action->also_change_mrna; + } + t->skip_blank = action->skip_blanks; } } } @@ -28616,10 +30034,40 @@ static Boolean IsStructuredCommentWithPrefix (UserObjectPtr uop, CharPtr prefix) return FALSE; } - + +static Boolean TruncateAtLocalId (SeqIdPtr sip_local, CharPtr filename) +{ + Char id_buf[20]; + CharPtr cmp; + ObjectIdPtr oip; + Boolean removed_id = FALSE; + Int4 len, f_len; + + if (filename == NULL || sip_local == NULL + || (oip = (ObjectIdPtr) sip_local->data.ptrvalue) == NULL) { + return FALSE; + } + f_len = StringLen (filename); + + if (oip->id > 0) { + sprintf (id_buf, "%d", oip->id); + cmp = id_buf; + } else { + cmp = oip->str; + } + len = StringLen (cmp); + if (f_len > len + 1 && filename[f_len - len - 1] == '/' + && StringCmp (filename + (f_len - len), cmp) == 0) { + filename[f_len - len - 1] = 0; + removed_id = TRUE; + } + return removed_id; +} + + static void FindSeqTechBsp (BioseqPtr bsp, Pointer data) { - SeqIdPtr sip; + SeqIdPtr sip, sip_local = NULL; DbtagPtr dbtag; PropagateSeqTechPtr p; CharPtr cp; @@ -28638,12 +30086,21 @@ static void FindSeqTechBsp (BioseqPtr bsp, Pointer data) && (dbtag = (DbtagPtr) sip->data.ptrvalue) != NULL && (StringICmp (dbtag->db, "NCBIFILE") == 0)) { p->filename = StringSave (dbtag->tag->str); - cp = StringRChr (p->filename, '/'); - if (cp != NULL) { - *cp = 0; - } + } else if (sip->choice == SEQID_LOCAL) { + sip_local = sip; + } + } + if (p->filename == NULL) { + p = MemFree (p); + return; + } + if (!TruncateAtLocalId(sip_local, p->filename)) { + cp = StringRChr (p->filename, '/'); + if (cp != NULL) { + *cp = 0; } } + for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_user, &context); sdp != NULL && p->uop == NULL; sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_user, &context)) { @@ -28731,6 +30188,367 @@ static Boolean PerformPropagateSequenceTechnology } +typedef struct ecrepdata { + CharPtr before; + CharPtr after; +} EcRepData, PNTR EcRepPtr; + + +static EcRepPtr EcRepFree (EcRepPtr e) +{ + if (e != NULL) { + e->before = MemFree (e->before); + e->after = MemFree (e->after); + e = MemFree (e); + } + return e; +} + + +static int LIBCALLBACK SortVnpByEcBefore (VoidPtr ptr1, VoidPtr ptr2) + +{ + EcRepPtr erp1, erp2; + CharPtr str1, str2; + ValNodePtr vnp1, vnp2; + + if (ptr1 == NULL || ptr2 == NULL) return 0; + vnp1 = *((ValNodePtr PNTR) ptr1); + vnp2 = *((ValNodePtr PNTR) ptr2); + if (vnp1 == NULL || vnp2 == NULL) return 0; + erp1 = (EcRepPtr) vnp1->data.ptrvalue; + erp2 = (EcRepPtr) vnp2->data.ptrvalue; + if (erp1 == NULL || erp2 == NULL) return 0; + str1 = erp1->before; + str2 = erp2->before; + if (str1 == NULL || str2 == NULL) return 0; + return StringCmp (str1, str2); +} + +static EcRepPtr PNTR SetupECReplacementTable (CharPtr file, Int4Ptr len) + +{ + EcRepPtr erp; + FileCache fc; + FILE *fp = NULL; + Int4 i; + ValNodePtr last = NULL; + Char line [512]; + Char path [PATH_MAX]; + CharPtr ptr; + ErrSev sev; + CharPtr str; + ValNodePtr vnp; + ValNodePtr ec_rep_list = NULL; + EcRepPtr PNTR ec_rep_data = NULL; + Int4 ec_rep_len = 0; + + if (FindPath ("ncbi", "ncbi", "data", path, sizeof (path))) { + FileBuildPath (path, NULL, file); + sev = ErrSetMessageLevel (SEV_ERROR); + fp = FileOpen (path, "r"); + ErrSetMessageLevel (sev); + if (fp != NULL) { + FileCacheSetup (&fc, fp); + + str = FileCacheReadLine (&fc, line, sizeof (line), NULL); + while (str != NULL) { + if (StringDoesHaveText (str)) { + ptr = StringChr (str, '\t'); + if (ptr != NULL) { + *ptr = '\0'; + ptr++; + erp = (EcRepPtr) MemNew (sizeof (EcRepData)); + if (erp != NULL) { + erp->before = StringSave (str); + erp->after = StringSave (ptr); + vnp = ValNodeAddPointer (&last, 0, (Pointer) erp); + if (ec_rep_list == NULL) { + ec_rep_list = vnp; + } + last = vnp; + } + } + } + str = FileCacheReadLine (&fc, line, sizeof (line), NULL); + } + + FileClose (fp); + ec_rep_len = ValNodeLen (ec_rep_list); + if (ec_rep_len > 0) { + ec_rep_list = ValNodeSort (ec_rep_list, SortVnpByEcBefore); + ec_rep_data = (EcRepPtr PNTR) MemNew (sizeof (EcRepPtr) * (ec_rep_len + 1)); + if (ec_rep_data != NULL) { + for (vnp = ec_rep_list, i = 0; vnp != NULL; vnp = vnp->next, i++) { + erp = (EcRepPtr) vnp->data.ptrvalue; + ec_rep_data [i] = erp; + } + } + } + } + } + ec_rep_list = ValNodeFree (ec_rep_list); + *len = ec_rep_len; + return ec_rep_data; +} + + +static EcRepPtr PNTR FreeECReplacementTable (EcRepPtr PNTR ec_rep_data, Int4 ec_rep_len) +{ + Int4 i; + + if (ec_rep_data == NULL) { + return NULL; + } + for (i = 0; i < ec_rep_len; i++) { + ec_rep_data[i] = EcRepFree(ec_rep_data[i]); + } + ec_rep_data = MemFree (ec_rep_data); + return ec_rep_data; +} + + +static EcRepPtr GetEcReplacementFromTable (CharPtr str, EcRepPtr PNTR ec_rep_data, Int4 ec_rep_len) +{ + Int4 L, R, mid; + EcRepPtr erp = NULL; + + L = 0; + R = ec_rep_len - 1; + while (L < R) { + mid = (L + R) / 2; + erp = ec_rep_data [(int) mid]; + if (erp != NULL && StringCmp (erp->before, str) < 0) { + L = mid + 1; + } else { + R = mid; + } + } + erp = ec_rep_data [(int) R]; + return erp; +} + + +typedef struct replaceupdatedec { + FILE *log_fp; + UpdateReplacedEcNumbersActionPtr action; + EcRepPtr PNTR ec_rep_data; + Int4 ec_rep_len; + Int4 num_removed; + Int4 num_replaced; +} ReplaceUpdatedECData, PNTR ReplaceUpdatedEcPtr; + + +static Boolean GetLocusTagFromProtRef (SeqFeatPtr sfp, CharPtr PNTR p_locus_tag) + +{ + BioseqPtr bsp; + SeqFeatPtr cds; + SeqMgrFeatContext fcontext; + SeqFeatPtr gene; + GeneRefPtr grp; + + if (sfp == NULL || p_locus_tag == NULL) return FALSE; + grp = SeqMgrGetGeneXref (sfp); + if (grp != NULL) { + if (SeqMgrGeneIsSuppressed (grp)) return FALSE; + if (StringDoesHaveText (grp->locus_tag)) { + *p_locus_tag = StringSave (grp->locus_tag); + return TRUE; + } else if (StringDoesHaveText (grp->locus)) { + *p_locus_tag = StringSave (grp->locus); + return TRUE; + } + } + bsp = BioseqFindFromSeqLoc (sfp->location); + if (bsp == NULL) return FALSE; + cds = SeqMgrGetCDSgivenProduct (bsp, &fcontext); + if (cds == NULL) return FALSE; + grp = SeqMgrGetGeneXref (cds); + if (grp != NULL) { + if (SeqMgrGeneIsSuppressed (grp)) return FALSE; + if (StringDoesHaveText (grp->locus_tag)) { + *p_locus_tag = StringSave (grp->locus_tag); + return TRUE; + } else if (StringDoesHaveText (grp->locus)) { + *p_locus_tag = StringSave (grp->locus); + return TRUE; + } + } + gene = SeqMgrGetOverlappingGene (cds->location, &fcontext); + if (gene == NULL || gene->data.choice != SEQFEAT_GENE) return FALSE; + grp = (GeneRefPtr) gene->data.value.ptrvalue; + if (grp != NULL) { + if (SeqMgrGeneIsSuppressed (grp)) return FALSE; + if (StringDoesHaveText (grp->locus_tag)) { + *p_locus_tag = StringSave (grp->locus_tag); + return TRUE; + } else if (StringDoesHaveText (grp->locus)) { + *p_locus_tag = StringSave (grp->locus); + return TRUE; + } + } + return FALSE; +} + + +static void UpdateECCallback (SeqFeatPtr sfp, Pointer userdata) + +{ + ProtRefPtr prp; + CharPtr str; + ValNodePtr vnp; + CharPtr locus_tag = NULL; + ReplaceUpdatedEcPtr r; + EcRepPtr erp; + + if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT) return; + prp = (ProtRefPtr) sfp->data.value.ptrvalue; + if (prp == NULL || prp->ec == NULL) return; + r = (ReplaceUpdatedEcPtr) userdata; + if (r == NULL) { + return; + } + GetLocusTagFromProtRef (sfp, &locus_tag); + + for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { + str = (CharPtr) vnp->data.ptrvalue; + if (StringHasNoText (str)) continue; + if (ValidateECnumber (str)) { + erp = GetEcReplacementFromTable(str, r->ec_rep_data, r->ec_rep_len); + if (erp != NULL && StringCmp (erp->before, str) == 0) { + if (StringChr (erp->after, '\t') == NULL) { + if (r->log_fp != NULL) { + fprintf (r->log_fp, "%s:replaced %s with %s\n", locus_tag == NULL ? "No locus tag" : locus_tag, erp->before, erp->after); + } + vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); + vnp->data.ptrvalue = StringSave (erp->after); + r->num_replaced++; + } else if (r->action->delete_multiple_replacement) { + if (r->log_fp != NULL) { + fprintf (r->log_fp, "%s: removed %s\n", locus_tag == NULL ? "No locus tag" : locus_tag, erp->before); + } + vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); + r->num_removed++; + } + } + str = vnp->data.ptrvalue; + if ( str != NULL && r->action->delete_unrecognized && ECnumberNotInList (str)) { + if (r->log_fp != NULL) { + fprintf (r->log_fp, "%s: deleted %s\n", locus_tag == NULL ? "No locus tag" : locus_tag, str); + } + vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); + r->num_removed++; + } + } else { + if (r->action->delete_improper_format) { + if (r->log_fp != NULL) { + fprintf (r->log_fp, "%s: removed %s\n", locus_tag == NULL ? "No locus tag" : locus_tag, str); + } + vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); + r->num_removed++; + } + } + } + locus_tag = MemFree (locus_tag); +} + + +static Boolean ReplaceUpdatedECNumbers (SeqEntryPtr sep, UpdateReplacedEcNumbersActionPtr action, FILE *log_fp) +{ + ReplaceUpdatedECData r; + + MemSet (&r, 0, sizeof (ReplaceUpdatedECData)); + r.action = action; + r.log_fp = log_fp; + r.ec_rep_data = SetupECReplacementTable ("ecnum_replaced.txt", &(r.ec_rep_len)); + + VisitFeaturesInSep (sep, (Pointer) &r, UpdateECCallback); + + r.ec_rep_data = FreeECReplacementTable(r.ec_rep_data, r.ec_rep_len); + if (r.num_removed > 0 || r.num_replaced > 0) { + return TRUE; + } else { + return FALSE; + } +} + + +typedef struct retranslatecdscallback { + Int4 num_retranslated; + RetranslateCdsActionPtr action; +} RetranslateCDSCallbackData, PNTR RetranslateCDSCallbackPtr; + +static void PerformRetranslationsCallback (SeqFeatPtr sfp, Pointer data) +{ + RetranslateCDSCallbackPtr r; + + if (sfp != NULL && sfp->data.choice == SEQFEAT_CDREGION + && (r = (RetranslateCDSCallbackPtr) data) != NULL + && r->action != NULL + && RetranslateOneCDS (sfp, sfp->idx.entityID, !r->action->obey_stop_codon, r->action->obey_stop_codon)) { + r->num_retranslated++; + } +} + + +static Boolean PerformRetranslations (SeqEntryPtr sep, RetranslateCdsActionPtr action, FILE *log_fp) +{ + RetranslateCDSCallbackData r; + + MemSet (&r, 0, sizeof (RetranslateCDSCallbackData)); + r.action = action; + + VisitFeaturesInSep (sep, &r, PerformRetranslationsCallback); + if (r.num_retranslated > 0) { + if (log_fp != NULL) { + fprintf (log_fp, "Retranslated %d coding regions\n", r.num_retranslated); + } + return TRUE; + } else { + return FALSE; + } +} + + +typedef struct adjustfeaturesforgapscallback { + Int4 num_processed; + AdjustFeaturesForGapsActionPtr action; +} AdjustFeaturesForGapCallbackData, PNTR AdjustFeaturesForGapCallbackPtr; + +static void PerformAdjustFeaturesForGapsCallback (SeqFeatPtr sfp, Pointer data) +{ + AdjustFeaturesForGapCallbackPtr r; + + if (sfp != NULL + && (r = (AdjustFeaturesForGapCallbackPtr) data) != NULL + && r->action != NULL) { + + AdjustFeatureForGapsCallback (sfp, r->action); + r->num_processed++; + } +} + + +static Boolean PerformAdjustFeaturesForGaps (SeqEntryPtr sep, AdjustFeaturesForGapsActionPtr action, FILE *log_fp) +{ + AdjustFeaturesForGapCallbackData r; + + MemSet (&r, 0, sizeof (AdjustFeaturesForGapCallbackData)); + r.action = action; + + VisitFeaturesInSep (sep, &r, PerformAdjustFeaturesForGapsCallback); + if (r.num_processed > 0) { + if (log_fp != NULL) { + fprintf (log_fp, "Adjusted %d features for gaps\n", r.num_processed); + } + return TRUE; + } else { + return FALSE; + } +} + + NLM_EXTERN CharPtr SummarizePerformAutofixAction (AutofixActionPtr action) { DiscrepancyType test_type; @@ -29603,7 +31421,40 @@ NLM_EXTERN CharPtr SummarizeMacroAction (ValNodePtr vnp) case MacroActionChoice_autoapply_structured_comments: str = StringSave ("Autoapply structured comment prefixes"); break; - default: + case MacroActionChoice_reorder_structured_comments: + str = StringSave ("Reorder structured comment fields"); + break; + case MacroActionChoice_remove_duplicate_structured_comments: + str = StringSave ("Remove duplicate structured comments"); + break; + case MacroActionChoice_lookup_taxonomy: + str = StringSave ("Perform taxonomy lookup and correct genetic codes"); + break; + case MacroActionChoice_lookup_pubs: + str = StringSave ("Perform pubs lookup"); + break; + case MacroActionChoice_trim_terminal_ns: + str = StringSave ("Trim terminal Ns from nucleotide bioseqs"); + break; + case MacroActionChoice_update_replaced_ecnumbers: + str = StringSave ("Update Replaced EC_numbers"); + break; + case MacroActionChoice_instantiate_protein_titles: + str = StringSave ("Instantiate Protein Titles"); + break; + case MacroActionChoice_retranslate_cds: + str = StringSave ("Retranslate coding regions"); + break; + case MacroActionChoice_add_selenocysteine_except: + str = StringSave ("Replace selenocysteine stops"); + break; + case MacroActionChoice_join_short_trnas: + str = StringSave ("Join short tRNAs"); + break; + case MacroActionChoice_adjust_features_for_gaps: + str = StringSave ("Adjust features for gaps"); + break; + default: str = StringSave ("Invalid action"); break; } @@ -29622,6 +31473,7 @@ NLM_EXTERN Boolean ApplyMacroToSeqEntryExEx (SeqEntryPtr sep, ValNodePtr macro, Boolean any_change = FALSE; Boolean created_protein_features = FALSE; ValNodePtr list; + LogInfoData lid; entityID = SeqMgrGetEntityIDForSeqEntry(sep); if (pNumNoOp != NULL) { @@ -29695,6 +31547,9 @@ NLM_EXTERN Boolean ApplyMacroToSeqEntryExEx (SeqEntryPtr sep, ValNodePtr macro, num = ApplyEditFeatureLocationActionToSeqEntry ((EditFeatureLocationActionPtr) macro->data.ptrvalue, sep, log_fp); if (num > 0) { any_change = TRUE; + ObjMgrSetDirtyFlag (entityID, TRUE); + ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0); + needs_update = FALSE; } else if (pNumNoOp != NULL) { (*pNumNoOp)++; } @@ -29779,7 +31634,7 @@ NLM_EXTERN Boolean ApplyMacroToSeqEntryExEx (SeqEntryPtr sep, ValNodePtr macro, } break; case MacroActionChoice_adjust_for_consensus_splice: - if (AdjustSeqEntryForConsensusSpliceEx(sep, log_fp)) { + if (AdjustSeqEntryForConsensusSpliceEx(sep, log_fp, TRUE)) { ObjMgrSetDirtyFlag (entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, entityID, 0, 0); needs_update = FALSE; @@ -29971,7 +31826,7 @@ NLM_EXTERN Boolean ApplyMacroToSeqEntryExEx (SeqEntryPtr sep, ValNodePtr macro, if (PropagateMissingOldNames (list)) { any_change = TRUE; if (log_fp != NULL) { - fprintf (log_fp, "Propagated missing old name qualifiers"); + fprintf (log_fp, "Propagated missing old name qualifiers\n"); } } else if (pNumNoOp != NULL) { (*pNumNoOp)++; @@ -29984,6 +31839,102 @@ NLM_EXTERN Boolean ApplyMacroToSeqEntryExEx (SeqEntryPtr sep, ValNodePtr macro, (*pNumNoOp)++; } break; + case MacroActionChoice_reorder_structured_comments: + if (ReorderStructuredCommentsInSeqEntry (sep)) { + if (log_fp != NULL) { + fprintf (log_fp, "Reordered structured comment fields\n"); + } + any_change = TRUE; + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_remove_duplicate_structured_comments: + if (RemoveDuplicateStructuredCommentsInSeqEntry(sep)) { + if (log_fp != NULL) { + fprintf (log_fp, "Removed duplicate structured comments\n"); + } + any_change = TRUE; + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_lookup_taxonomy: + Taxon3ReplaceOrgInSeqEntry(sep, FALSE); + CorrectGenCodes (sep, entityID); + if (log_fp != NULL) { + fprintf (log_fp, "Performed TaxLookup and corrected genetic codes\n"); + } + any_change = TRUE; + break; + case MacroActionChoice_lookup_pubs: + MemSet (&lid, 0, sizeof (LogInfoData)); + lid.fp = log_fp; + num = LookupPubsInSeqEntry (sep, log_fp == NULL ? NULL : &lid); + if (num > 0) { + any_change = TRUE; + if (log_fp != NULL) { + fprintf (log_fp, "Replaced %d pubs during Pub Lookup\n", num); + } + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_trim_terminal_ns: + MemSet (&lid, 0, sizeof (LogInfoData)); + lid.fp = log_fp; + num = TrimNsFromNucsInSeqEntry (sep, log_fp == NULL ? NULL : &lid); + if (num > 0) { + any_change = TRUE; + if (log_fp != NULL) { + fprintf (log_fp, "Trimmed terminal Ns from %d sequences\n", num); + } + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_update_replaced_ecnumbers: + if (ReplaceUpdatedECNumbers(sep, macro->data.ptrvalue, log_fp)) { + any_change = TRUE; + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_instantiate_protein_titles: + InstantiateProteinTitles (entityID, NULL); + any_change = TRUE; + if (log_fp != NULL) { + fprintf (log_fp, "Instantiated protein titles\n", num); + } + break; + case MacroActionChoice_retranslate_cds: + if (PerformRetranslations (sep, macro->data.ptrvalue, log_fp)) { + any_change = TRUE; + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_add_selenocysteine_except: + if (ReplaceStopsWithSelenocysteineInSeqEntry(sep, log_fp)) { + any_change = TRUE; + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_join_short_trnas: + if (JoinShortTrnas(sep, log_fp)) { + any_change = TRUE; + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; + case MacroActionChoice_adjust_features_for_gaps: + if (PerformAdjustFeaturesForGaps (sep, macro->data.ptrvalue, log_fp)) { + any_change = TRUE; + } else if (pNumNoOp != NULL) { + (*pNumNoOp)++; + } + break; } macro = macro->next; } @@ -30253,6 +32204,9 @@ NLM_EXTERN CharPtr SummarizeFieldType (ValNodePtr vnp) case Publication_field_title: str = StringSave ("publication title"); break; + case Publication_field_pmid: + str = StringSave ("PMID"); + break; default: label = GetPubFieldLabel (vnp->data.intvalue); if (label == NULL) { @@ -30300,7 +32254,7 @@ NLM_EXTERN FieldTypePtr FieldTypeFromString (CharPtr str) Int4 qual_type, feat_type = -1; FieldTypePtr ft = NULL; FeatureFieldPtr ffp; - ValNodePtr vnp; + ValNodePtr vnp, molfield; CharPtr cpy, cp; RnaQualPtr rq; @@ -30376,6 +32330,51 @@ NLM_EXTERN FieldTypePtr FieldTypeFromString (CharPtr str) ft->choice = FieldType_misc; ft->data.intvalue = Misc_field_comment_descriptor; } + + /* try DBLink fields */ + if (ft == NULL) { + qual_type = GetDBLinkFieldTypeFromDBLinkName (str); + if (qual_type > -1) { + ft = ValNodeNew (NULL); + ft->choice = FieldType_dblink; + ft->data.intvalue = qual_type; + } + } + + /* try publication fields */ + if (ft == NULL) { + qual_type = GetPubFieldFromLabel(str); + if (qual_type > -1) { + ft = ValNodeNew (NULL); + ft->choice = FieldType_pub; + ft->data.intvalue = qual_type; + } + } + /* molinfo fields */ + if (ft == NULL) { + if (StringsAreEquivalent(str, "completeness")) { + molfield = ValNodeNew (NULL); + molfield->choice = MolinfoField_completedness; + ft = ValNodeNew (NULL); + ft->choice = FieldType_molinfo_field; + ft->data.ptrvalue = molfield; + } else if (StringsAreEquivalent(str, "topology")) { + molfield = ValNodeNew (NULL); + molfield->choice = MolinfoField_topology; + ft = ValNodeNew (NULL); + ft->choice = FieldType_molinfo_field; + ft->data.ptrvalue = molfield; + } + } + /* location/genome */ + if (ft == NULL && StringsAreEquivalent(str, "location") || StringsAreEquivalent(str, "genome")) { + vnp = ValNodeNew (NULL); + vnp->choice = SourceQualValChoice_location; + ft = ValNodeNew (NULL); + ft->choice = FieldType_source_qual; + ft->data.ptrvalue = vnp; + } + } return ft; } @@ -31739,7 +33738,7 @@ NLM_EXTERN CharPtr SummarizeWordSubstitution (WordSubstitutionPtr word) ValNodePtr vnp; CharPtr summ = NULL; - if (word == NULL && word->synonyms == NULL) { + if (word == NULL || word->synonyms == NULL) { return NULL; } @@ -33062,6 +35061,9 @@ NLM_EXTERN MatchTypePtr MatchTypeFromTableMatchType (TableMatchPtr t) case TableMatchType_protein_name: m->choice = eTableMatchProteinName; break; + case TableMatchType_bioproject: + m->choice = eTableMatchBioProject; + break; case TableMatchType_any: m->choice = eTableMatchAny; break; @@ -33114,6 +35116,9 @@ NLM_EXTERN TableMatchPtr TableMatchTypeFromMatchType (MatchTypePtr m) case eTableMatchProteinName: t->match_type->choice = TableMatchType_protein_name; break; + case eTableMatchBioProject: + t->match_type->choice = TableMatchType_bioproject; + break; case eTableMatchAny: t->match_type->choice = TableMatchType_any; break; @@ -33525,7 +35530,7 @@ static BioseqSearchItemPtr BioseqSearchItemNewStr (BioseqPtr bsp, CharPtr str, B bsi->bsp = bsp; bsi->str = str; bsi->free_str = need_free; - if (IsAllDigits (bsi->str)) { + if (StringIsAllDigits (bsi->str)) { bsi->num = atoi (bsi->str); } return bsi; @@ -33650,9 +35655,14 @@ NLM_EXTERN void ValNodeAddPointerToFront (ValNodeBlockPtr vnbp, Uint1 choice, Po NLM_EXTERN void ValNodeLinkToEnd (ValNodeBlockPtr vnbp, ValNodePtr list) { - if (vnbp->head == NULL) { + if (list == NULL) { + return; + } else if (vnbp->head == NULL) { vnbp->head = list; vnbp->tail = list; + while (vnbp->tail->next != NULL) { + vnbp->tail = vnbp->tail->next; + } } else { vnbp->tail->next = list; while (vnbp->tail->next != NULL) { @@ -33662,6 +35672,19 @@ NLM_EXTERN void ValNodeLinkToEnd (ValNodeBlockPtr vnbp, ValNodePtr list) } +NLM_EXTERN void ValNodeSortBlock (ValNodeBlockPtr vnbp, int (LIBCALLBACK *compar )PROTO ((Nlm_VoidPtr, Nlm_VoidPtr ))) +{ + if (vnbp == NULL || vnbp->head == NULL) { + return; + } + vnbp->head = ValNodeSort(vnbp->head, compar); + vnbp->tail = vnbp->head; + while (vnbp->tail->next != NULL) { + vnbp->tail = vnbp->tail->next; + } +} + + static SeqIdPtr FindLocalId (SeqIdPtr list) { while (list != NULL && list->choice != SEQID_LOCAL) { @@ -34001,7 +36024,7 @@ static BioseqPtr FindStringInIdListIndex (CharPtr str, BioseqSearchIndexPtr inde if (index == NULL) { return NULL; } - if (IsAllDigits (str)) { + if (StringIsAllDigits (str)) { match = atoi (str); imax = index->num_total - 1; imin = index->num_str; @@ -34051,6 +36074,7 @@ static ValNodePtr FindListInIdListIndex (Uint1 match_location, CharPtr match_str Int4 i; ValNodePtr list = NULL; StringConstraintPtr scp; + Char buf[5000]; if (StringHasNoText (match_str) || index == NULL) { return NULL; @@ -34063,6 +36087,12 @@ static ValNodePtr FindListInIdListIndex (Uint1 match_location, CharPtr match_str ValNodeAddPointer (&list, OBJ_BIOSEQ, index->items[i]->bsp); } } + for (i = index->num_str; i < index->num_str + index->num_int; i++) { + sprintf (buf, "%u", index->items[i]->num); + if (DoesStringMatchConstraint (buf, scp)) { + ValNodeAddPointer (&list, OBJ_BIOSEQ, index->items[i]->bsp); + } + } scp = StringConstraintFree (scp); list = ValNodeSort (list, SortVnpByChoiceAndPtrvalue); @@ -34115,7 +36145,7 @@ static void FindBioseqByProteinName(SeqEntryPtr sep, BioseqByMatchPtr bsp_m, Val } else if (IS_Bioseq_set(sep)) { for (tmp = ((BioseqSetPtr) sep->data.ptrvalue)->seq_set; tmp != NULL; tmp= tmp->next) { - FindBioseqByProteinName(tmp, bsp_m, match_list); + FindBioseqByProteinName(tmp, bsp_m, match_list); } } } /* FindBioseqByProteinName */ @@ -34129,6 +36159,40 @@ static void GetAllBioseqsCallback (BioseqPtr bsp, Pointer data) } +typedef struct stringlist { + CharPtr str; + ValNodePtr list; +} StringListData, PNTR StringListPtr; + + +static void GetBioseqsByBioProjectCallback(BioseqPtr bsp, Pointer data) +{ + StringListPtr s; + CharPtr bioproject; + + if (bsp == NULL || ISA_aa(bsp->mol) || (s = (StringListPtr) data) == NULL) { + return; + } + bioproject = GetBioProjectIdFromBioseq(bsp, NULL); + if (StringICmp (bioproject, s->str) == 0) { + ValNodeAddPointer (&(s->list), OBJ_BIOSEQ, bsp); + } + bioproject = MemFree (bioproject); +} + + +static ValNodePtr GetBioseqsByBioProject (SeqEntryPtr sep, CharPtr match_str) +{ + StringListData s; + + MemSet (&s, 0, sizeof (StringListData)); + s.str = match_str; + + VisitBioseqsInSep (sep, &s, GetBioseqsByBioProjectCallback); + return s.list; +} + + static ValNodePtr FindMatchForRowEx (MatchTypePtr match_type, @@ -34189,6 +36253,9 @@ FindMatchForRowEx case eTableMatchAny: VisitBioseqsInSep (sep, &match_list, GetAllBioseqsCallback); break; + case eTableMatchBioProject: + match_list = GetBioseqsByBioProject(sep, match_str); + break; } return match_list; } @@ -34233,6 +36300,7 @@ static ValNodePtr GetFeatureListForProteinBioseq (Uint1 featdef, BioseqPtr bsp) cds = SeqMgrGetCDSgivenProduct (bsp, NULL); if (cds != NULL) { + sfp = NULL; if (featdef == FEATDEF_CDS) { sfp = cds; @@ -34315,7 +36383,7 @@ static ValNodePtr GetFeaturesForGene (SeqFeatPtr gene, Uint1 featdef) sfp != NULL && fcontext.left < stop; sfp = SeqMgrGetNextFeature (bsp, sfp, 0, featdef, &fcontext)) { - if (fcontext.right >= start && gene == GetGeneForFeature (sfp)) + if (sfp != gene && fcontext.right >= start && gene == GetGeneForFeature (sfp)) { ValNodeAddPointer (&feat_list, OBJ_SEQFEAT, sfp); } @@ -34478,6 +36546,7 @@ static ValNodePtr GetFeatureListForRowAndColumn (MatchTypePtr match_type, ValNod break; case eTableMatchNucID: case eTableMatchAny: + case eTableMatchBioProject: for (vnp = match_list; vnp != NULL; vnp = vnp->next) { ValNodeLink (&feature_list, GetFeatureListForNucleotideBioseq (GetFeatdefFromFeatureType(field->type), vnp->data.ptrvalue)); } @@ -34553,6 +36622,7 @@ static ValNodePtr GetBioSourceListForRowAndColumn (MatchTypePtr match_type, ValN case eTableMatchProteinID: case eTableMatchNucID: case eTableMatchAny: + case eTableMatchBioProject: for (vnp = match_list; vnp != NULL; vnp = vnp->next) { if (vnp->choice == OBJ_BIOSEQ) { AddBioSourcesForBioseq (vnp->data.ptrvalue, &feature_list); @@ -34575,6 +36645,51 @@ static ValNodePtr GetBioSourceListForRowAndColumn (MatchTypePtr match_type, ValN } +Boolean PropagateThisDescriptor (SeqDescPtr sdp, Pointer extradata) +{ + if (sdp == (SeqDescPtr) extradata) { + return TRUE; + } else { + return FALSE; + } +} + + +static void PrePropagatePubs (BioseqPtr bsp) +{ + ValNodePtr pub_list = NULL, vnp; + SeqEntryPtr sep; + SeqDescPtr sdp; + SeqMgrDescContext dcontext; + ObjValNodePtr ovp; + BioseqSetPtr bssp; + + if (bsp == NULL) { + return; + } + for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pub, &dcontext); + sdp != NULL; + sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_pub, &dcontext)) { + if (sdp->extended && (ovp = (ObjValNodePtr) sdp) != NULL + && ovp->idx.parenttype == OBJ_BIOSEQSET + && (bssp = (BioseqSetPtr) ovp->idx.parentptr) != NULL + && bssp->_class != BioseqseqSet_class_nuc_prot) { + ValNodeAddPointer (&pub_list, OBJ_SEQDESC, sdp); + } + } + if (pub_list != NULL) { + sep = GetTopSeqEntryForEntityID(bsp->idx.entityID); + for (vnp = pub_list; vnp != NULL; vnp = vnp->next) { + PropagateSomeDescriptors (sep, PropagateThisDescriptor, vnp->data.ptrvalue); + } + DeleteMarkedObjects (bsp->idx.entityID, 0, NULL); + ObjMgrSetDirtyFlag (bsp->idx.entityID, TRUE); + ObjMgrSendMsg (OM_MSG_UPDATE, bsp->idx.entityID, 0, 0); + pub_list = ValNodeFree (pub_list); + } +} + + static void AddPubsForBioseq (BioseqPtr bsp, ValNodePtr PNTR feature_list) { SeqDescrPtr sdp; @@ -34584,6 +36699,9 @@ static void AddPubsForBioseq (BioseqPtr bsp, ValNodePtr PNTR feature_list) if (bsp == NULL || feature_list == NULL) return; + /* pre-propagate publications descriptors */ + PrePropagatePubs(bsp); + for (sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pub, &dcontext); sdp != NULL; sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_pub, &dcontext)) { @@ -34684,6 +36802,7 @@ static ValNodePtr GetPubListForRowAndColumn (MatchTypePtr match_type, ValNodePtr case eTableMatchProteinID: case eTableMatchNucID: case eTableMatchAny: + case eTableMatchBioProject: for (vnp = match_list; vnp != NULL; vnp = vnp->next) { if (vnp->choice == OBJ_BIOSEQ) { AddPubsForBioseq (vnp->data.ptrvalue, &feature_list); @@ -34784,6 +36903,7 @@ static ValNodePtr GetSequenceListForRowAndColumn (MatchTypePtr match_type, ValNo case eTableMatchProteinName: /* J. Chen */ case eTableMatchProteinID: case eTableMatchNucID: + case eTableMatchBioProject: for (vnp = match_list; vnp != NULL; vnp = vnp->next) { if (vnp->choice == OBJ_BIOSEQ) { ValNodeAddPointer (&seq_list, OBJ_BIOSEQ, vnp->data.ptrvalue); @@ -35048,9 +37168,17 @@ NLM_EXTERN Boolean AdjustmRNAProductToMatchProteinProduct (SeqFeatPtr sfp) ProtRefPtr prp; RnaRefPtr rrp; - if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT) return FALSE; - - prp = (ProtRefPtr) sfp->data.value.ptrvalue; + if (sfp == NULL) { + return FALSE; + } + + if (sfp->data.choice == SEQFEAT_PROT) { + prp = (ProtRefPtr) sfp->data.value.ptrvalue; + } else if (sfp->data.choice == SEQFEAT_CDREGION) { + prp = GetProtRefForFeature(sfp); + } else { + return FALSE; + } mrna = GetmRNAForFeature (sfp); if (mrna == NULL) return FALSE; @@ -35084,11 +37212,14 @@ NLM_EXTERN Boolean IsFieldTypeCDSProduct (FieldTypePtr ft) if (ft == NULL) return FALSE; if (ft->choice == FieldType_feature_field) { field = (FeatureFieldPtr) ft->data.ptrvalue; - if (field != NULL && field->type == Macro_feature_type_cds - && field->field != NULL - && field->field->choice == FeatQualChoice_legal_qual - && field->field->data.intvalue == Feat_qual_legal_product) { - rval = TRUE; + if (field != NULL && field->field != NULL && field->field->choice == FeatQualChoice_legal_qual) { + if (field->type == Macro_feature_type_cds + && field->field->data.intvalue == Feat_qual_legal_product) { + rval = TRUE; + } else if (field->type == Macro_feature_type_prot + && field->field->data.intvalue == Feat_qual_legal_product) { + rval = TRUE; + } } } else if (ft->choice == FieldType_cds_gene_prot) { if (ft->data.intvalue == CDSGeneProt_field_prot_name) { @@ -35159,7 +37290,7 @@ NLM_EXTERN ValNodePtr ValidateTabTableValues (ValNodePtr table, ValNodePtr colum ValNodePtr line_vnp, col_vnp, val_vnp; Int4 line_num, col_num; TabColumnConfigPtr t; - ValNodePtr locus_tag_values = NULL, bad_locus_tags = NULL, vnp, tmp_field; + ValNodePtr locus_tag_values = NULL, bad_locus_tags = NULL, vnp, tmp_field, sq; CharPtr bad_format_fmt = "Locus tag %s has incorrect format"; CharPtr dup_fmt = "Locus tag %s appears in the table more than once"; CharPtr inconsistent_fmt = "Locus tag prefix for %s is inconsistent"; @@ -35205,6 +37336,17 @@ NLM_EXTERN ValNodePtr ValidateTabTableValues (ValNodePtr table, ValNodePtr colum sprintf (err_msg, bad_molinfo_fmt, val_vnp->data.ptrvalue); ValNodeAddPointer (&err_list, 0, err_msg); } + tmp_field = MolinfoFieldFree(tmp_field); + } else if (t->field != NULL && t->field->choice == FieldType_source_qual + && (sq = (ValNodePtr)(t->field->data.ptrvalue)) != NULL + && sq->choice == SourceQualValChoice_location) { + tmp_field = SrcLocationFieldFromValue(val_vnp->data.ptrvalue); + if (tmp_field == NULL) { + err_msg =(CharPtr) MemNew (sizeof (Char) * (StringLen(bad_molinfo_fmt) + StringLen (val_vnp->data.ptrvalue))); + sprintf (err_msg, bad_molinfo_fmt, val_vnp->data.ptrvalue); + ValNodeAddPointer (&err_list, 0, err_msg); + } + tmp_field = FieldTypeFree (tmp_field); } } } @@ -35390,7 +37532,7 @@ NLM_EXTERN ValNodePtr GetObjectTableForTabTable (SeqEntryPtr sep, ValNodePtr tab match_type = FindMatchTypeInHeader (columns); if (match_type == NULL) { ValNodeAddPointerToEnd (&vnb, 0, StringSave ("No Match Type")); - } else if (match_type->choice == eTableMatchAny && table->next != NULL) { + } else if (match_type->choice == eTableMatchAny && table != NULL && table->next != NULL) { if (table->next->next != NULL) { ValNodeAddPointerToEnd (&vnb, 0, StringSave ("Too many rows for apply to all")); } else { @@ -35670,7 +37812,7 @@ NLM_EXTERN ValNodePtr ApplyTableValuesToObjectTable (SeqEntryPtr sep, ValNodePtr ValNodePtr target_vnp, tmp_field; TabColumnConfigPtr t; CharPtr val, qual_name; - ValNodePtr err_list = NULL, count_list, count_affected_list = NULL, count_vnp, count_tot_vnp; + ValNodePtr err_list = NULL, count_list, count_affected_list = NULL, count_vnp, count_tot_vnp, sq; CharPtr err_msg; CharPtr bad_col_val_fmt = "Did not set value for column %d, line %d"; CharPtr num_affected_fmt = "%d fields affected"; @@ -35713,6 +37855,7 @@ NLM_EXTERN ValNodePtr ApplyTableValuesToObjectTable (SeqEntryPtr sep, ValNodePtr success = RemoveFieldValueForObject (target_vnp->choice, target_vnp->data.ptrvalue, t->field, NULL); } else { if (t->field != NULL && t->field->choice == FieldType_molinfo_field) { + /* adjust molinfo fields */ success = FALSE; if (target_vnp->choice == OBJ_BIOSEQ) { tmp_field = MolinfoFieldFromFieldAndStringValue (t->field->data.ptrvalue, val_vnp->data.ptrvalue); @@ -35721,6 +37864,17 @@ NLM_EXTERN ValNodePtr ApplyTableValuesToObjectTable (SeqEntryPtr sep, ValNodePtr tmp_field = MolinfoFieldFree(tmp_field); } } + } else if (t->field != NULL && t->field->choice == FieldType_source_qual + && (sq = (ValNodePtr)(t->field->data.ptrvalue)) != NULL + && sq->choice == SourceQualValChoice_location) { + /* adjust for source location */ + success = FALSE; + tmp_field = SrcLocationFieldFromValue(val_vnp->data.ptrvalue); + if (tmp_field != NULL) { + success = SetFieldValueForObject (target_vnp->choice, target_vnp->data.ptrvalue, tmp_field, NULL, + val_vnp->data.ptrvalue, t->existing_text); + tmp_field = FieldTypeFree (tmp_field); + } } else { success = SetFieldValueForObject (target_vnp->choice, target_vnp->data.ptrvalue, t->field, NULL, val_vnp->data.ptrvalue, t->existing_text); @@ -36105,7 +38259,7 @@ NLM_EXTERN ValNodePtr ApplyTableToFeatures (SeqEntryPtr sep, ValNodePtr table, V match_type = FindMatchTypeInHeader (columns); - if (match_type->choice == eTableMatchAny && table->next != NULL) { + if (match_type->choice == eTableMatchAny && table != NULL && table->next != NULL) { /* skip first row, must contain header */ table = table->next; } @@ -36219,7 +38373,7 @@ NLM_EXTERN ValNodePtr CheckTableForExistingText (SeqEntryPtr sep, ValNodePtr tab entityID = SeqMgrGetEntityIDForSeqEntry (sep); - if (match_type->choice == eTableMatchAny && table->next != NULL) { + if (match_type->choice == eTableMatchAny && table != NULL && table->next != NULL) { /* skip first row, must contain header */ table = table->next; } @@ -36458,8 +38612,10 @@ static void MergePCRPrimersCallback (BioSourcePtr biop, Pointer data) } else { pp_f_last->next = ps->forward; } - while (pp_f_last->next != NULL) { - pp_f_last = pp_f_last->next; + if (pp_f_last != NULL) { + while (pp_f_last->next != NULL) { + pp_f_last = pp_f_last->next; + } } ps->forward = NULL; } @@ -36469,8 +38625,10 @@ static void MergePCRPrimersCallback (BioSourcePtr biop, Pointer data) } else { pp_r_last->next = ps->reverse; } - while (pp_r_last->next != NULL) { - pp_r_last = pp_r_last->next; + if (pp_r_last != NULL) { + while (pp_r_last->next != NULL) { + pp_r_last = pp_r_last->next; + } } ps->reverse = NULL; } @@ -36794,8 +38952,10 @@ NLM_EXTERN CharPtr SummarizeSuspectRuleEx (SuspectRulePtr rule, Boolean short_ve { CharPtr find = NULL, replace = NULL, fix_type = NULL, feat_constraint = NULL, except = NULL; CharPtr summ = NULL; + CharPtr tmp = NULL; CharPtr butnot = " but not "; CharPtr desc = " Description: "; + CharPtr fatal = "(FATAL)"; Int4 len; if (rule == NULL) { @@ -36817,6 +38977,14 @@ NLM_EXTERN CharPtr SummarizeSuspectRuleEx (SuspectRulePtr rule, Boolean short_ve StringCat (summ, fix_type); StringCat (summ, ")"); } + if (rule->fatal) { + len = StringLen (summ) + StringLen (fatal) + 1; + tmp = (CharPtr) MemNew (sizeof (Char) * len); + StringCpy (tmp, summ); + StringCat (tmp, fatal); + summ = (CharPtr) MemFree (summ); + summ = tmp; + } return summ; } @@ -36848,6 +39016,9 @@ NLM_EXTERN CharPtr SummarizeSuspectRuleEx (SuspectRulePtr rule, Boolean short_ve if (except != NULL) { len += StringLen (butnot); } + if (rule->fatal) { + len += StringLen(fatal); + } summ = (CharPtr) MemNew (sizeof (Char) * len); StringCpy (summ, find); if (except != NULL) { @@ -36875,6 +39046,9 @@ NLM_EXTERN CharPtr SummarizeSuspectRuleEx (SuspectRulePtr rule, Boolean short_ve StringCat (summ, desc); StringCat (summ, rule->description); } + if (rule->fatal) { + StringCat (summ, fatal); + } find = MemFree (find); except = MemFree (except); @@ -38755,3 +40929,201 @@ NLM_EXTERN ValNodePtr ShuffleUpdateBioseqListWithIndex (ValNodePtr PNTR update_b return unmatched_list; } + + +static int LIBCALLBACK SortVnpByInt (VoidPtr ptr1, VoidPtr ptr2) + +{ + ValNodePtr vnp1; + ValNodePtr vnp2; + + if (ptr1 == NULL || ptr2 == NULL) return 0; + vnp1 = *((ValNodePtr PNTR) ptr1); + vnp2 = *((ValNodePtr PNTR) ptr2); + if (vnp1 == NULL || vnp2 == NULL) return 0; + + if (vnp1->data.intvalue > vnp2->data.intvalue) { + return 1; + } else if (vnp1->data.intvalue < vnp2->data.intvalue) { + return -1; + } + + return 0; +} + + +static void AddGeneQualifiersToNote (SeqFeatPtr gene, CharPtr PNTR note) +{ + GeneRefPtr grp; + GBQualPtr gbq; + + if (gene == NULL || note == NULL || gene->data.choice != SEQFEAT_GENE) { + return; + } + + grp = (GeneRefPtr) gene->data.value.ptrvalue; + if (!StringHasNoText(grp->locus)) { + SetStringValue(note, grp->locus, ExistingTextOption_prefix_semi); + } + if (!StringHasNoText(grp->allele)) { + SetStringValue(note, grp->allele, ExistingTextOption_prefix_semi); + } + if (!StringHasNoText(grp->desc)) { + SetStringValue(note, grp->desc, ExistingTextOption_prefix_semi); + } + if (!StringHasNoText(grp->maploc)) { + SetStringValue(note, grp->maploc, ExistingTextOption_prefix_semi); + } + if (!StringHasNoText(grp->locus_tag)) { + SetStringValue(note, grp->locus_tag, ExistingTextOption_prefix_semi); + } + if (!StringHasNoText(gene->comment)) { + SetStringValue(note, gene->comment, ExistingTextOption_prefix_semi); + } + for (gbq = gene->qual; gbq != NULL; gbq = gbq->next) { + if (!StringHasNoText (gbq->val)) { + SetStringValue(note, gbq->val, ExistingTextOption_prefix_semi); + } + } + +} + + +static void LogCDSConversion (LogInfoPtr lip, SeqFeatPtr sfp, SeqFeatPtr gene, ProtRefPtr prp) +{ + GeneRefPtr grp; + CharPtr desc = NULL; + CharPtr loc; + + if (lip == NULL || lip->fp == NULL) { + return; + } + if (gene != NULL && (grp = gene->data.value.ptrvalue) != NULL) { + if (!StringHasNoText (grp->locus_tag)) { + desc = grp->locus_tag; + } else if (!StringHasNoText (grp->locus)) { + desc = grp->locus; + } + } + if (desc == NULL && prp != NULL) { + if (prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) { + desc = prp->name->data.ptrvalue; + } + } + if (desc == NULL) { + desc = "Unknown"; + } + loc = SeqLocPrint (sfp->location); + fprintf (lip->fp, "%s CDS at %s converted to misc_feature", desc, loc); + loc = MemFree (loc); + lip->data_in_log = TRUE; +} + + +static void LogrRNAConversion (LogInfoPtr lip, SeqFeatPtr sfp, SeqFeatPtr gene) +{ + GeneRefPtr grp; + CharPtr desc = NULL, loc; + + if (lip == NULL || lip->fp == NULL) { + return; + } + if (gene != NULL && (grp = gene->data.value.ptrvalue) != NULL) { + if (!StringHasNoText (grp->locus_tag)) { + desc = StringSave(grp->locus_tag); + } else if (!StringHasNoText (grp->locus)) { + desc = StringSave(grp->locus); + } + } + if (desc == NULL) { + desc = GetRNAProductString(sfp, NULL); + } + if (desc == NULL) { + desc = StringSave("unknown"); + } + loc = SeqLocPrint (sfp->location); + fprintf (lip->fp, "%s rRNA at %s converted to misc_feature", desc, loc); + loc = MemFree (loc); + desc = MemFree (desc); + lip->data_in_log = TRUE; +} + + +/* for cleaning up bad features identified by validator or asndisc */ +NLM_EXTERN void ConvertListToMiscFeat (ValNodePtr list, Boolean remove_gene, LogInfoPtr lip) +{ + ValNodePtr vnp, other_list; + SeqFeatPtr sfp, gene; + ProtRefPtr prp; + BioseqPtr pbsp; + ImpFeatPtr ifp; + CharPtr rna_name; + ValNodePtr entityIDList = NULL; + SeqEntryPtr sep; + Boolean converted; + + for (vnp = list; vnp != NULL; vnp = vnp->next) { + sfp = (SeqFeatPtr) vnp->data.ptrvalue; + gene = GetGeneForFeature(sfp); + converted = FALSE; + if (sfp->data.choice == SEQFEAT_CDREGION) { + prp = GetProtRefForFeature (sfp); + LogCDSConversion(lip, sfp, gene, prp); + if (prp != NULL && prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) { + SetStringValue(&(sfp->comment), prp->name->data.ptrvalue, ExistingTextOption_prefix_semi); + } + pbsp = BioseqFindFromSeqLoc (sfp->product); + if (pbsp != NULL) { + pbsp->idx.deleteme = TRUE; + } + sfp->data.value.ptrvalue = CdRegionFree (sfp->data.value.ptrvalue); + sfp->data.choice = SEQFEAT_IMP; + ifp = ImpFeatNew(); + ifp->key = StringSave("misc_feature"); + sfp->data.value.ptrvalue = ifp; + sfp->product = SeqLocFree (sfp->product); + sfp->idx.subtype = 0; + ValNodeAddInt (&entityIDList, 0, sfp->idx.entityID); + converted = TRUE; + } else if (sfp->data.choice == SEQFEAT_RNA) { + LogrRNAConversion(lip, sfp, gene); + rna_name = GetRNAProductString(sfp, NULL); + SetStringValue(&(sfp->comment), rna_name, ExistingTextOption_prefix_semi); + sfp->data.value.ptrvalue = RnaRefFree (sfp->data.value.ptrvalue); + sfp->data.choice = SEQFEAT_IMP; + ifp = ImpFeatNew(); + ifp->key = StringSave("misc_feature"); + sfp->data.value.ptrvalue = ifp; + sfp->idx.subtype = 0; + ValNodeAddInt (&entityIDList, 0, sfp->idx.entityID); + converted = TRUE; + } + if (converted && remove_gene && gene != NULL) { + other_list = GetFeaturesForGene(gene, 0); + if (ValNodeLen (other_list) < 2) { + AddGeneQualifiersToNote(gene, &(sfp->comment)); + gene->idx.deleteme = TRUE; + if (lip != NULL && lip->fp != NULL) { + fprintf (lip->fp, ", gene deleted"); + } + } + other_list = ValNodeFree (other_list); + } + if (converted && lip != NULL && lip->fp != NULL) { + fprintf (lip->fp, "\n"); + } + } + entityIDList = ValNodeSort (entityIDList, SortVnpByInt); + ValNodeUnique (&entityIDList, SortVnpByInt, ValNodeFree); + for (vnp = entityIDList; vnp != NULL; vnp = vnp->next) { + /* remove any protein sequences or genes that were marked for deletion */ + DeleteMarkedObjects (vnp->data.intvalue, 0, NULL); + sep = GetTopSeqEntryForEntityID(vnp->data.intvalue); + RenormalizeNucProtSets (sep, TRUE); + SeqMgrIndexFeatures (vnp->data.intvalue, NULL); + } + entityIDList = ValNodeFree (entityIDList); +} + + + |