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authorAaron M. Ucko <ucko@debian.org>2005-03-24 18:32:05 +0000
committerAaron M. Ucko <ucko@debian.org>2005-03-24 18:32:05 +0000
commitf06fc23cbc179836f402001f24176fc9d5725482 (patch)
tree39e97ad8f13a33296b32a3907f3409b056cf851b /sequin
parentccba467ae4f393d7acce357a9847bfe1fb77ccc7 (diff)
Load ncbi (6.1.20040616) into ncbi-tools6/branches/upstream/current.
Diffstat (limited to 'sequin')
-rw-r--r--sequin/sequin.h10
-rw-r--r--sequin/sequin1.c297
-rw-r--r--sequin/sequin10.c446
-rw-r--r--sequin/sequin2.c200
-rw-r--r--sequin/sequin3.c112
-rw-r--r--sequin/sequin4.c98
-rw-r--r--sequin/sequin5.c12
-rw-r--r--sequin/sequin6.c762
-rw-r--r--sequin/sequin7.c202
-rw-r--r--sequin/sequin8.c36
-rw-r--r--sequin/sequin9.c75
11 files changed, 1894 insertions, 356 deletions
diff --git a/sequin/sequin.h b/sequin/sequin.h
index 5458109f..bed4357a 100644
--- a/sequin/sequin.h
+++ b/sequin/sequin.h
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.134 $
+* $Revision: 6.138 $
*
* File Description:
*
@@ -228,6 +228,8 @@ extern void ConsolidateOrganismNotes (IteM i);
extern void ConsolidateLikeModifiersWithSemicolons (IteM i);
extern void ConsolidateLikeModifiersWithoutSemicolons (IteM i);
+extern void CountryLookup (IteM i);
+
extern void ExtendPartialFeatures (IteM i);
extern void TrimOrganismName (IteM i);
@@ -485,6 +487,8 @@ extern void SetupEditSecondary (MenU m, BaseFormPtr bfp);
extern void EditLocusProc (IteM i);
extern void ConvertToLocalProc (IteM i);
+extern ValNodePtr BuildDescriptorValNodeList (void);
+
extern void RemoveFeature (IteM i);
extern void RemoveDescriptor (IteM i);
@@ -499,6 +503,8 @@ extern void MakeExonsFromMRNAIntervals (IteM i);
extern Int2 LIBCALLBACK CreateDeleteByTextWindow (Pointer data);
extern Int2 LIBCALLBACK CreateSegregateByTextWindow (Pointer data);
+extern Int2 LIBCALLBACK CreateSegregateByFeatureWindow (Pointer data);
+extern Int2 LIBCALLBACK CreateSegregateByDescriptorWindow (Pointer data);
extern Int2 LIBCALLBACK RemoveExtraneousSets (Pointer data);
extern void RemoveOrphanProteins (Uint2 entityID, SeqEntryPtr sep);
extern void ParseAsnOrFlatfileToAnywhere (IteM i);
@@ -552,6 +558,7 @@ extern void DownloadAndExtendProc (ButtoN b);
extern void UpdateSeqAfterDownload (BaseFormPtr bfp, BioseqPtr oldbsp, BioseqPtr newbsp);
extern void ExtendSeqAfterDownload (BaseFormPtr bfp, BioseqPtr oldbsp, BioseqPtr newbsp);
extern void NewUpdateSequence (IteM i);
+extern void NewUpdateSequenceNewBlast (IteM i);
extern void NewExtendSequence (IteM i);
extern void FastaNucDirectToSeqEdProc (IteM i);
@@ -562,6 +569,7 @@ extern void ParseAntiCodonsFromtRNAComment (IteM i);
extern void RemoveAlignment (IteM i);
extern void RemoveGraph (IteM i);
extern void RemoveProteins (IteM i);
+extern void RemoveProteinsAndRenormalize (IteM i);
extern void GlobalAddTranslExcept (IteM i);
diff --git a/sequin/sequin1.c b/sequin/sequin1.c
index d5f65dd5..a768978d 100644
--- a/sequin/sequin1.c
+++ b/sequin/sequin1.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.450 $
+* $Revision: 6.458 $
*
* File Description:
*
@@ -129,7 +129,7 @@ static char *time_of_compilation = "now";
#include <Gestalt.h>
#endif
-#define SEQ_APP_VER "5.22"
+#define SEQ_APP_VER "5.25"
#ifndef CODECENTER
static char* sequin_version_binary = "Sequin Indexer Services Version " SEQ_APP_VER " " __DATE__ " " __TIME__;
@@ -1099,7 +1099,7 @@ static void SmartResetProc (IteM i)
status = sm_usr_data->header->status;
sm_usr_data->header->status = SMStatClosed;
SMSendMsgToClient(sm_usr_data);
- sm_usr_data->header->status = status;
+ sm_usr_data->header->status = (SMStatusCode)status;
return;
}
}
@@ -3084,7 +3084,7 @@ static void PrintExtraErrorInstructions (FILE *fp, CharPtr message)
"\nMiddle gap characters are used to maintain the spacing "
"inside an alignment. These are not nucleotides and will "
"not appear as part of your sequence file.\n"
-"Missing characters are used to represent indeterminate/ambiguous "
+"Ambiguous/unknown characters are used to represent indeterminate/ambiguous "
"nucleotides. These will appear in your sequence file as 'n'.\n"
"Match characters are used to indicate positions where "
"sequences are identical to the first sequence. These will be "
@@ -3131,9 +3131,25 @@ static void WalkErrorList (TErrorInfoPtr list, FILE *fp)
}
+static Int4 CountNucleotides (CharPtr sequence)
+{
+ Int4 num = 0;
+ CharPtr cp;
+
+ if (sequence == NULL) return 0;
+ for (cp = sequence; *cp != 0; cp++)
+ {
+ if (*cp != '-')
+ {
+ num++;
+ }
+ }
+ return num;
+}
+
static void PrintAlignmentSummary (TAlignmentFilePtr afp, FILE *fp)
{
- Int4 index;
+ Int4 index;
if (fp == NULL) return;
@@ -3142,18 +3158,35 @@ static void PrintAlignmentSummary (TAlignmentFilePtr afp, FILE *fp)
} else {
fprintf (fp, "Found %d sequences\n", afp->num_sequences);
fprintf (fp, "Found %d organisms\n", afp->num_organisms);
- for (index = 0; index < afp->num_sequences; index++)
+ if (afp->num_sequences == afp->num_segments * afp->num_organisms)
{
- fprintf (fp, "\t%s\t", afp->ids [index]);
- if (index < afp->num_organisms) {
- fprintf (fp, "%s\n", afp->organisms [index]);
- } else {
- fprintf (fp, "No organism information\n");
- }
+ for (index = 0; index < afp->num_sequences; index++)
+ {
+ fprintf (fp, "\t%s\t%d nucleotides\t", afp->ids [index],
+ CountNucleotides (afp->sequences[index]));
+ if (index / afp->num_segments < afp->num_organisms) {
+ fprintf (fp, "%s\n", afp->organisms [index / afp->num_segments]);
+ } else {
+ fprintf (fp, "No organism information\n");
+ }
+ }
}
- while (index < afp->num_organisms) {
- fprintf (fp, "Unclaimed organism: %s\n", afp->organisms [index]);
- index++;
+ else
+ {
+ for (index = 0; index < afp->num_sequences; index++)
+ {
+ fprintf (fp, "\t%s\t%d nucleotides\t", afp->ids [index],
+ CountNucleotides (afp->sequences[index]));
+ if (index < afp->num_organisms) {
+ fprintf (fp, "%s\n", afp->organisms [index]);
+ } else {
+ fprintf (fp, "No organism information\n");
+ }
+ }
+ while (index < afp->num_organisms) {
+ fprintf (fp, "Unclaimed organism: %s\n", afp->organisms [index]);
+ index++;
+ }
}
}
}
@@ -3194,19 +3227,33 @@ typedef struct alphabetformdata {
static Boolean DoSequenceLengthsMatch (TAlignmentFilePtr afp)
{
- int seq_index;
- Int4 seq_len;
+ int seq_index;
+ int curr_seg;
+ Int4Ptr seq_len;
+ Boolean rval;
if (afp == NULL || afp->sequences == NULL || afp->num_sequences == 0) {
return TRUE;
}
- seq_len = StringLen (afp->sequences[0]);
- for (seq_index = 1; seq_index < afp->num_sequences; seq_index++) {
- if (StringLen (afp->sequences[seq_index]) != seq_len) {
- return FALSE;
+
+ seq_len = (Int4Ptr) MemNew (sizeof (Int4) * afp->num_segments);
+ if (seq_len == NULL) return FALSE;
+ for (seq_index = 0; seq_index < afp->num_segments; seq_index ++)
+ {
+ seq_len [seq_index] = StringLen (afp->sequences[seq_index]);
+ }
+
+ curr_seg = 0;
+ rval = TRUE;
+ for (seq_index = afp->num_segments; seq_index < afp->num_sequences && rval; seq_index++) {
+ if (StringLen (afp->sequences[seq_index]) != seq_len[curr_seg]) {
+ rval = FALSE;
}
+ curr_seg ++;
+ if (curr_seg >= afp->num_segments) curr_seg = 0;
}
- return TRUE;
+ MemFree (seq_len);
+ return rval;
}
extern SeqEntryPtr
@@ -3260,7 +3307,7 @@ SeqEntryFromAlignmentFile
if (afp != NULL) {
if (afp->num_organisms == 0 && no_org_err_msg != NULL) {
Message (MSG_ERROR, no_org_err_msg);
- } else if (afp->num_organisms != 0 && afp->num_organisms != afp->num_sequences) {
+ } else if (afp->num_organisms != 0 && afp->num_organisms != afp->num_sequences && afp->num_organisms * afp->num_segments != afp->num_sequences) {
Message (MSG_ERROR, "Number of organisms must match number of sequences!");
} else {
ans = ANS_YES;
@@ -3405,16 +3452,16 @@ static void BuildGetAlphabetDialog (IteM i)
SetGroupSpacing (h, 10, 10);
g = HiddenGroup (h, 2, 4, NULL);
- StaticPrompt (g, "Missing", 0, dialogTextHeight, programFont, 'c');
- afp->missing = DialogText (g, "?", 5, NULL);
+ StaticPrompt (g, "Ambiguous/Unknown", 0, dialogTextHeight, programFont, 'c');
+ afp->missing = DialogText (g, "?Nn", 5, NULL);
StaticPrompt (g, "Match", 0, dialogTextHeight, programFont, 'c');
afp->match = DialogText (g, ".", 5, NULL);
StaticPrompt (g, "Beginning Gap", 0, dialogTextHeight, programFont, 'c');
- afp->beginning_gap = DialogText (g, "-.nN", 5, NULL);
+ afp->beginning_gap = DialogText (g, "-.?nN", 5, NULL);
StaticPrompt (g, "Middle Gap", 0, dialogTextHeight, programFont, 'c');
- afp->middle_gap = DialogText (g, "-nN", 5, NULL);
+ afp->middle_gap = DialogText (g, "-", 5, NULL);
StaticPrompt (g, "End Gap", 0, dialogTextHeight, programFont, 'c');
- afp->end_gap = DialogText (g, "-?", 5, NULL);
+ afp->end_gap = DialogText (g, "-.?nN", 5, NULL);
StaticPrompt (g, "Sequence Type", 0, dialogTextHeight, programFont, 'c');
afp->sequence_type = PopupList (g, TRUE, NULL);
PopupItem (afp->sequence_type, "Nucleotide");
@@ -4356,8 +4403,6 @@ static void CloseProc (BaseFormPtr bfp)
OMUserDataPtr omudp;
ObjMgrDataPtr tmp;
#ifdef USE_SMARTNET
- ObjMgrDataPtr PNTR omdp;
- int fd;
SMUserDataPtr sm_usr_data = NULL;
#endif
@@ -9801,15 +9846,20 @@ static void s_GetTpaInfo (SequencesFormPtr sqfp)
Update ();
}
+static CharPtr tpaString = NULL;
+
static void FinishPuttingTogether (ForM f)
{
- BaseFormPtr bfp;
- BioseqSetPtr bssp;
- Uint2 entityID = 0;
- Int2 handled;
- SeqEntryPtr sep = NULL;
+ BaseFormPtr bfp;
+ BioseqSetPtr bssp;
+ Uint2 entityID = 0;
+ Int2 handled;
+ ObjMgrDataPtr omdp;
+ SubmitBlockPtr sbp;
+ SeqEntryPtr sep = NULL;
SequencesFormPtr sqfp;
+ SeqSubmitPtr ssp;
bfp = (BaseFormPtr) GetObjectExtra (f);
if (bfp != NULL) {
@@ -9821,6 +9871,22 @@ static void FinishPuttingTogether (ForM f)
}
/*#endif*/
entityID = PackageFormResults (globalsbp, sep, TRUE);
+ sqfp = (SequencesFormPtr) bfp;
+ if (SEQ_TPA_SUBMISSION == sqfp->submType && entityID > 0) {
+ omdp = ObjMgrGetData (entityID);
+ if (omdp != NULL && omdp->datatype == OBJ_SEQSUB) {
+ ssp = (SeqSubmitPtr) omdp->dataptr;
+ if (ssp != NULL && ssp->datatype == 1) {
+ sbp = ssp->sub;
+ if (sbp != NULL) {
+ if (sbp->comment == NULL && StringDoesHaveText (tpaString)) {
+ sbp->comment = tpaString;
+ tpaString = NULL;
+ }
+ }
+ }
+ }
+ }
globalsbp = NULL;
WatchCursor ();
seqviewprocs.forceSeparateViewer = TRUE;
@@ -9931,24 +9997,13 @@ static void BackToFormat (ButtoN b)
}
}
-static void GetOrgAndSeq (ButtoN b)
+static void FinishOrgAndSeq (void)
{
- FormatBlockPtr fbp;
- MonitorPtr mon;
- ForM w;
+ MonitorPtr mon;
+ ForM w;
WatchCursor ();
- Hide (formatForm);
- fbp = (FormatBlockPtr) FormToPointer (formatForm);
- if (fbp != NULL) {
- globalFormatBlock.seqPackage = fbp->seqPackage;
- globalFormatBlock.seqFormat = fbp->seqFormat;
- globalFormatBlock.numSeqs = fbp->numSeqs;
- globalFormatBlock.submType = fbp->submType;
- }
- MemFree (fbp);
- WatchCursor ();
mon = MonitorStrNewEx ("Sequin New Submission", 30, FALSE);
MonitorStrValue (mon, "Creating Sequences Form");
Update ();
@@ -9970,6 +10025,27 @@ static void GetOrgAndSeq (ButtoN b)
Update ();
}
+static void BackToSubmitter (ButtoN b)
+
+{
+ MsgAnswer ans;
+
+ ans = Message (MSG_OKC, "Are you sure? Format information will be lost.");
+ if (ans == ANS_CANCEL) return;
+ Hide (formatForm);
+ Update ();
+ PointerToForm (initSubmitForm, globalsbp);
+ globalsbp = SequinBlockFree (globalsbp);
+ Show (initSubmitForm);
+ Select (initSubmitForm);
+ SendHelpScrollMessage (helpForm, "Submitting Authors Form", NULL);
+ Update ();
+ globalFormatBlock.seqPackage = SEQ_PKG_SINGLE;
+ globalFormatBlock.seqFormat = SEQ_FMT_FASTA;
+ globalFormatBlock.numSeqs = 0;
+ globalFormatBlock.submType = SEQ_ORIG_SUBMISSION;
+}
+
static void GetFormat (ButtoN b)
{
@@ -9995,25 +10071,118 @@ static void GetFormat (ButtoN b)
Update ();
}
-static void BackToSubmitter (ButtoN b)
+static WindoW tpaWindow = NULL;
+static TexT tpaText = NULL;
+static ButtoN tpaNext = NULL;
+/* tpaString defined above FinishPuttingTogether */
+
+static void TpaPrev (ButtoN b)
{
- MsgAnswer ans;
+ Hide (tpaWindow);
+ tpaString = MemFree (tpaString);
+ SetTitle (tpaText, "");
+ Show (formatForm);
+ Select (formatForm);
+ SendHelpScrollMessage (helpForm, "Sequence Format Form", NULL);
+ Update ();
+}
+
+static void TpaNext (ButtoN b)
+
+{
+ tpaString = MemFree (tpaString);
+ tpaString = SaveStringFromText (tpaText);
+ if (StringHasNoText (tpaString)) {
+ Message (MSG_OK, "The requested information is required in order for you to be able to proceed with a TPA submission");
+ return;
+ }
+ Hide (tpaWindow);
+ WatchCursor ();
+ FinishOrgAndSeq ();
+}
+
+static void TpaText (TexT t)
+
+{
+ if (TextHasNoText (t)) {
+ SafeDisable (tpaNext);
+ } else {
+ SafeEnable (tpaNext);
+ }
+}
+
+static CharPtr tpaMssg = "\
+Third party annotation records require a publication describing the biological \
+experiments used as evidence for the annotation. Please provide information \
+regarding the nature of these experiments.";
+
+static void DoTpaForm (void)
+
+{
+ GrouP c, h, p;
+
+ if (tpaWindow == NULL) {
+ tpaWindow = FixedWindow (-50, -33, -10, -10, "TPA Evidence", NULL);
+ h = HiddenGroup (tpaWindow, -1, 0, NULL);
+ SetGroupSpacing (h, 10, 10);
+
+ p = MultiLinePrompt (h, tpaMssg, 30 * stdCharWidth, programFont);
+
+ tpaText = ScrollText (h, 30, 5, programFont, TRUE, TpaText);
+
+ c = HiddenGroup (h, 2, 0, NULL);
+ PushButton (c, "<< Prev Form", TpaPrev);
+ tpaNext = PushButton (c, "Next Form >>", TpaNext);
+
+ AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) tpaText, (HANDLE) c, NULL);
+
+ RealizeWindow (tpaWindow);
+ }
+ tpaString = MemFree (tpaString);
+ SafeSetTitle (tpaText, "");
+ SafeDisable (tpaNext);
+ Show (tpaWindow);
+ Select (tpaWindow);
+}
+
+static void GetOrgAndSeq (ButtoN b)
+
+{
+ /*
+ MsgAnswer ans;
+ */
+ FormatBlockPtr fbp;
+ Boolean is_tpa = FALSE;
- ans = Message (MSG_OKC, "Are you sure? Format information will be lost.");
- if (ans == ANS_CANCEL) return;
Hide (formatForm);
- Update ();
- PointerToForm (initSubmitForm, globalsbp);
- globalsbp = SequinBlockFree (globalsbp);
- Show (initSubmitForm);
- Select (initSubmitForm);
- SendHelpScrollMessage (helpForm, "Submitting Authors Form", NULL);
- Update ();
- globalFormatBlock.seqPackage = SEQ_PKG_SINGLE;
- globalFormatBlock.seqFormat = SEQ_FMT_FASTA;
- globalFormatBlock.numSeqs = 0;
- globalFormatBlock.submType = SEQ_ORIG_SUBMISSION;
+ fbp = (FormatBlockPtr) FormToPointer (formatForm);
+ if (fbp != NULL) {
+ globalFormatBlock.seqPackage = fbp->seqPackage;
+ globalFormatBlock.seqFormat = fbp->seqFormat;
+ globalFormatBlock.numSeqs = fbp->numSeqs;
+ globalFormatBlock.submType = fbp->submType;
+ is_tpa = (Boolean) (globalFormatBlock.submType == SEQ_TPA_SUBMISSION);
+ }
+ MemFree (fbp);
+ if (is_tpa) {
+ DoTpaForm ();
+ /*
+ ans = Message (MSG_YN, "%s", tpaMssg);
+ if (ans == ANS_YES) {
+ WatchCursor ();
+ FinishOrgAndSeq ();
+ } else {
+ Show (formatForm);
+ Select (formatForm);
+ SendHelpScrollMessage (helpForm, "Sequence Format Form", NULL);
+ Update ();
+ }
+ */
+ } else {
+ WatchCursor ();
+ FinishOrgAndSeq ();
+ }
}
static void BackToStartup (ButtoN b)
diff --git a/sequin/sequin10.c b/sequin/sequin10.c
index a27aa03d..36bc94d2 100644
--- a/sequin/sequin10.c
+++ b/sequin/sequin10.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 9/3/2003
*
-* $Revision: 1.213 $
+* $Revision: 1.217 $
*
* File Description:
*
@@ -69,16 +69,16 @@ static void ListClauses (
Boolean suppress_final_and
);
-static void LabelClauses (
- ValNodePtr clause_list,
- Uint1 biomol,
- BioseqPtr bsp
-);
+static void LabelClauses
+( ValNodePtr clause_list,
+ Uint1 biomol,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag);
-static CharPtr GetProductName (
- SeqFeatPtr cds,
- BioseqPtr bsp
-);
+static CharPtr GetProductName
+( SeqFeatPtr cds,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag);
#define DEFLINE_FEATLIST 1
#define DEFLINE_CLAUSEPLUS 2
@@ -112,8 +112,8 @@ typedef struct featureclause {
FeatureClausePtr NewFeatureClause (
SeqFeatPtr sfp,
- BioseqPtr bsp
-);
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag);
static void PluralizeConsolidatedClauseDescription (
FeatureClausePtr fcp
@@ -126,7 +126,8 @@ typedef Boolean (LIBCALLBACK *ShouldRemoveFunction) (
BioseqPtr bsp,
Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
);
/* This section of the code contains some functions for dealing with
@@ -344,6 +345,8 @@ static ModifierItemGlobalData DefLineModifiers[] = {
{ "Isolation-source" , FALSE, SUBSRC_isolation_source , FALSE },
{ "Lab-host" , FALSE, SUBSRC_lab_host , FALSE },
{ "Map" , FALSE, SUBSRC_map , FALSE },
+ { "Note-OrgMod" , TRUE, ORGMOD_other , FALSE },
+ { "Note-SubSrc" , FALSE, SUBSRC_other , FALSE },
{ "Old-lineage" , TRUE , ORGMOD_old_lineage , FALSE },
{ "Old-name" , TRUE , ORGMOD_old_name , FALSE },
{ "Pathovar" , TRUE , ORGMOD_pathovar , FALSE },
@@ -407,6 +410,8 @@ typedef enum {
DEFLINE_POS_Isolation_source,
DEFLINE_POS_Lab_host,
DEFLINE_POS_Map,
+ DEFLINE_POS_Note_orgmod,
+ DEFLINE_POS_Note_subsrc,
DEFLINE_POS_Old_lineage,
DEFLINE_POS_Old_name,
DEFLINE_POS_Pathovar,
@@ -2316,16 +2321,15 @@ static Boolean LIBCALLBACK IsGene (
return TRUE;
}
-static CharPtr GetGeneName (
-GeneRefPtr grp
-)
+static CharPtr GetGeneName (GeneRefPtr grp, Boolean suppress_locus_tag)
{
ValNodePtr syn;
if (grp == NULL) return NULL;
if (SeqMgrGeneIsSuppressed (grp)) return NULL;
if (StringDoesHaveText (grp->locus)) return grp->locus;
- if (StringDoesHaveText (grp->locus_tag)) return grp->locus_tag;
+ if (! suppress_locus_tag && StringDoesHaveText (grp->locus_tag))
+ return grp->locus_tag;
if (StringDoesHaveText (grp->desc)) return grp->desc;
for (syn = grp->syn; syn != NULL; syn = syn->next)
{
@@ -2335,9 +2339,7 @@ GeneRefPtr grp
return NULL;
}
-static CharPtr GetAlleleName (
-GeneRefPtr grp
-)
+static CharPtr GetAlleleName (GeneRefPtr grp, Boolean suppress_locus_tag)
{
size_t lenallele;
size_t lengenename;
@@ -2346,7 +2348,7 @@ GeneRefPtr grp
if (grp == NULL) return NULL;
if (StringHasNoText (grp->allele)) return NULL;
- gene_name = GetGeneName (grp);
+ gene_name = GetGeneName (grp, suppress_locus_tag);
if (StringHasNoText (gene_name)) return NULL;
lenallele = StringLen (grp->allele);
lengenename = StringLen (gene_name);
@@ -2378,20 +2380,20 @@ GeneRefPtr grp
/* This function compares the gene names and allele names of the gene
* to see if they match.
*/
-static Boolean DoGenesMatch (
- GeneRefPtr grp1,
- GeneRefPtr grp2
-)
+static Boolean DoGenesMatch
+(GeneRefPtr grp1,
+ GeneRefPtr grp2,
+ Boolean suppress_locus_tag)
{
CharPtr name1;
CharPtr name2;
- name1 = GetGeneName (grp1);
- name2 = GetGeneName (grp2);
+ name1 = GetGeneName (grp1, suppress_locus_tag);
+ name2 = GetGeneName (grp2, suppress_locus_tag);
if (StringCmp (name1, name2) != 0) return FALSE;
- name1 = GetAlleleName (grp1);
- name2 = GetAlleleName (grp2);
+ name1 = GetAlleleName (grp1, suppress_locus_tag);
+ name2 = GetAlleleName (grp2, suppress_locus_tag);
if ((name1 == NULL && name2 != NULL)
|| (name1 != NULL && name2 == NULL))
{
@@ -3710,8 +3712,8 @@ static void GroupAltSplicedExons (
*/
static void ExpandAltSplicedExons (
ValNodePtr clause_list,
- BioseqPtr bsp
-)
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
ValNodePtr clause, rest_of_list, featlist, new_clause;
FeatureClausePtr fcp, new_fcp;
@@ -3744,7 +3746,7 @@ static void ExpandAltSplicedExons (
{
new_clause = ValNodeNew (clause);
if (new_clause == NULL) return;
- new_fcp = NewFeatureClause (featlist->data.ptrvalue, bsp);
+ new_fcp = NewFeatureClause (featlist->data.ptrvalue, bsp, suppress_locus_tag);
if (new_fcp == NULL) return;
new_fcp->grp = fcp->grp;
new_fcp->is_alt_spliced = fcp->is_alt_spliced;
@@ -3765,7 +3767,7 @@ static void ExpandAltSplicedExons (
}
else
{
- ExpandAltSplicedExons (fcp->featlist, bsp);
+ ExpandAltSplicedExons (fcp->featlist, bsp, suppress_locus_tag);
}
}
}
@@ -3777,11 +3779,11 @@ static void ExpandAltSplicedExons (
* than one clause, while other features should really only belong to
* one clause.
*/
-static Boolean AddGeneToClauses (
- SeqFeatPtr gene,
+static Boolean AddGeneToClauses
+( SeqFeatPtr gene,
CharPtr gene_productname,
- ValNodePtr clause_list
-)
+ ValNodePtr clause_list,
+ Boolean suppress_locus_tag)
{
ValNodePtr clause;
FeatureClausePtr fcp;
@@ -3817,7 +3819,7 @@ static Boolean AddGeneToClauses (
}
}
- if (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp))
+ if (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp, suppress_locus_tag))
{
used_gene = TRUE;
if (gene_productname != NULL
@@ -3849,9 +3851,7 @@ static Boolean AddGeneToClauses (
/* This function iterates through the list of features and calls
* AddGeneToClauses for each gene feature it finds.
*/
-static void GroupGenes (
- ValNodePtr PNTR clause_list
-)
+static void GroupGenes (ValNodePtr PNTR clause_list, Boolean suppress_locus_tag)
{
ValNodePtr vnp;
ValNodePtr featlist;
@@ -3870,7 +3870,7 @@ static void GroupGenes (
{
AddGeneToClauses (featlist->data.ptrvalue,
fcp->feature_label_data.productname,
- vnp->next);
+ vnp->next, suppress_locus_tag);
}
}
}
@@ -3883,11 +3883,11 @@ static void GroupGenes (
* mRNA can apply to more than one clause, while other features should
* really only belong to one clause.
*/
-static Boolean AddmRNAToClauses (
- SeqFeatPtr mRNA,
+static Boolean AddmRNAToClauses
+( SeqFeatPtr mRNA,
ValNodePtr clause_list,
- BioseqPtr bsp
-)
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
ValNodePtr clause;
FeatureClausePtr fcp;
@@ -3900,7 +3900,7 @@ static Boolean AddmRNAToClauses (
if (clause_list == NULL) return FALSE;
used_mRNA = FALSE;
- productname = GetProductName (mRNA, bsp);
+ productname = GetProductName (mRNA, bsp, suppress_locus_tag);
if (productname == NULL) return TRUE;
for (clause = clause_list; clause != NULL; clause = clause->next)
@@ -3953,7 +3953,8 @@ static Boolean AddmRNAToClauses (
*/
static void GroupmRNAs (
ValNodePtr PNTR clause_list,
- BioseqPtr bsp
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag
)
{
ValNodePtr vnp;
@@ -3971,7 +3972,7 @@ static void GroupmRNAs (
&& featlist->choice == DEFLINE_FEATLIST
&& IsmRNA (featlist->data.ptrvalue))
{
- if (AddmRNAToClauses (featlist->data.ptrvalue, *clause_list, bsp))
+ if (AddmRNAToClauses (featlist->data.ptrvalue, *clause_list, bsp, suppress_locus_tag))
{
fcp->delete_me = TRUE;
}
@@ -4130,10 +4131,10 @@ static CharPtr GetFeatureTypeWord (
* If none of the above conditions apply, the sequence indexing context label
* will be used to obtain the product name for the feature.
*/
-static CharPtr GetProductName (
- SeqFeatPtr cds,
- BioseqPtr bsp
-)
+static CharPtr GetProductName
+( SeqFeatPtr cds,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
CharPtr protein_name;
CharPtr semicolon;
@@ -4172,7 +4173,7 @@ static CharPtr GetProductName (
{
grp = (GeneRefPtr) cds->data.value.ptrvalue;
if (grp == NULL) return NULL;
- gene_name = GetGeneName (grp);
+ gene_name = GetGeneName (grp, suppress_locus_tag);
if (grp->desc != NULL
&& StringCmp (grp->desc, gene_name) != 0)
{
@@ -4222,8 +4223,8 @@ static CharPtr GetProductName (
static FeatureClausePtr FindProductInFeatureList (
FeatureClausePtr fcp,
ValNodePtr clause_list,
- matchFunction itemmatch
-)
+ matchFunction itemmatch,
+ Boolean suppress_locus_tag)
{
ValNodePtr vnp;
FeatureClausePtr vnp_fcp;
@@ -4233,7 +4234,7 @@ static FeatureClausePtr FindProductInFeatureList (
if (vnp->choice == DEFLINE_CLAUSEPLUS && vnp->data.ptrvalue != NULL)
{
vnp_fcp = vnp->data.ptrvalue;
- if (DoGenesMatch (vnp_fcp->grp, fcp->grp)
+ if (DoGenesMatch (vnp_fcp->grp, fcp->grp, suppress_locus_tag)
&& vnp_fcp->featlist != NULL
&& vnp_fcp->featlist->choice == DEFLINE_FEATLIST
&& itemmatch (vnp_fcp->featlist->data.ptrvalue))
@@ -4242,7 +4243,8 @@ static FeatureClausePtr FindProductInFeatureList (
}
else
{
- vnp_fcp = FindProductInFeatureList (fcp, vnp_fcp->featlist, itemmatch);
+ vnp_fcp = FindProductInFeatureList (fcp, vnp_fcp->featlist,
+ itemmatch, suppress_locus_tag);
if (vnp_fcp != NULL) return vnp_fcp;
}
}
@@ -4258,10 +4260,10 @@ static FeatureClausePtr FindProductInFeatureList (
* If there is a gene and a product, the description will be the name of
* the product followed by the name of the gene in parentheses.
*/
-static CharPtr GetGeneProtDescription (
- FeatureClausePtr fcp,
- BioseqPtr bsp
-)
+static CharPtr GetGeneProtDescription
+( FeatureClausePtr fcp,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
SeqFeatPtr sfp;
CharPtr protein_name;
@@ -4285,7 +4287,7 @@ static CharPtr GetGeneProtDescription (
}
else
{
- protein_name = GetProductName (sfp, bsp);
+ protein_name = GetProductName (sfp, bsp, suppress_locus_tag);
if (protein_name == NULL && IsGene (sfp))
{
@@ -4296,7 +4298,7 @@ static CharPtr GetGeneProtDescription (
description_length += StringLen (protein_name);
}
- gene_name = GetGeneName (fcp->grp);
+ gene_name = GetGeneName (fcp->grp, suppress_locus_tag);
if (gene_name != NULL)
{
description_length += StringLen (gene_name);
@@ -4339,10 +4341,10 @@ static matchFunction productfeatures[] = {
/* This function finds gene features without products and looks for
* features that might provide products for them.
*/
-static void FindGeneProducts (
- ValNodePtr clause_list,
- BioseqPtr bsp
-)
+static void FindGeneProducts
+( ValNodePtr clause_list,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
ValNodePtr vnp;
FeatureClausePtr fcp, productfcp;
@@ -4364,7 +4366,8 @@ static void FindGeneProducts (
for (i=0; i < NumProductFeatureTypes && productfcp == NULL; i++)
{
productfcp = FindProductInFeatureList (fcp, clause_list,
- productfeatures[i]);
+ productfeatures[i],
+ suppress_locus_tag);
}
if (productfcp != NULL)
{
@@ -4377,7 +4380,8 @@ static void FindGeneProducts (
else
{
fcp->feature_label_data.productname
- = GetProductName (productfcp->featlist->data.ptrvalue, bsp);
+ = GetProductName (productfcp->featlist->data.ptrvalue,
+ bsp, suppress_locus_tag);
}
if (fcp->feature_label_data.description != NULL)
{
@@ -4385,12 +4389,12 @@ static void FindGeneProducts (
fcp->feature_label_data.description = NULL;
}
fcp->feature_label_data.description =
- GetGeneProtDescription (fcp, bsp);
+ GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
}
}
else
{
- FindGeneProducts (fcp->featlist, bsp);
+ FindGeneProducts (fcp->featlist, bsp, suppress_locus_tag);
}
}
}
@@ -4434,10 +4438,10 @@ static CharPtr GetExonDescription (
return label;
}
-static CharPtr GetFeatureDescription (
- FeatureClausePtr fcp,
- BioseqPtr bsp
-)
+static CharPtr GetFeatureDescription
+( FeatureClausePtr fcp,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
SeqFeatPtr sfp;
@@ -4488,7 +4492,7 @@ static CharPtr GetFeatureDescription (
}
else
{
- return GetGeneProtDescription (fcp, bsp);
+ return GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
}
}
@@ -4548,11 +4552,11 @@ static void LIBCALLBACK GetPromoterFeatureLabel (
* subfeatures of the clause, or the interval could be a combination of the
* last two items if the feature is a CDS.
*/
-static CharPtr GetGenericInterval (
- FeatureClausePtr fcp,
- Uint1 biomol,
- BioseqPtr bsp
-)
+static CharPtr GetGenericInterval
+( FeatureClausePtr fcp,
+ Uint1 biomol,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
CharPtr interval;
Boolean partial5, partial3;
@@ -4589,7 +4593,7 @@ static CharPtr GetGenericInterval (
{
suppress_final_and = TRUE;
}
- LabelClauses (featlist, biomol, bsp);
+ LabelClauses (featlist, biomol, bsp, suppress_locus_tag);
ListClauses (featlist, &strings, FALSE, suppress_final_and);
subfeatlist = MergeValNodeStrings (strings, FALSE);
ValNodeFreeData (strings);
@@ -4647,12 +4651,12 @@ static CharPtr GetGenericInterval (
* for more of the specific feature types, to reduce the number of times
* that the feature must be identified as being a certain type.
*/
-static void LIBCALLBACK GetGenericFeatureLabel (
- FeatureClausePtr fcp,
- BioseqPtr bsp,
- Uint1 biomol,
- FeatureLabelPtr flp
-)
+static void LIBCALLBACK GetGenericFeatureLabel
+( FeatureClausePtr fcp,
+ BioseqPtr bsp,
+ Uint1 biomol,
+ FeatureLabelPtr flp,
+ Boolean suppress_locus_tag)
{
SeqFeatPtr main_feat;
@@ -4673,13 +4677,13 @@ static void LIBCALLBACK GetGenericFeatureLabel (
}
if (flp->productname == NULL)
{
- flp->productname = GetProductName (main_feat, bsp);
+ flp->productname = GetProductName (main_feat, bsp, suppress_locus_tag);
}
if (flp->description == NULL
&& (! IsMiscRNA (main_feat)
|| StringStr (flp->productname, "spacer") == NULL ))
{
- flp->description = GetFeatureDescription (fcp, bsp);
+ flp->description = GetFeatureDescription (fcp, bsp, suppress_locus_tag);
}
}
@@ -4711,11 +4715,11 @@ typedef enum {
NumDefLineFeatLabels
} DefLineFeatLabel;
-static void LabelFeature (
- BioseqPtr bsp,
- Uint1 biomol,
- FeatureClausePtr new_clauseplus
-)
+static void LabelFeature
+( BioseqPtr bsp,
+ Uint1 biomol,
+ FeatureClausePtr new_clauseplus,
+ Boolean suppress_locus_tag)
{
Int4 i;
SeqFeatPtr main_feat;
@@ -4726,11 +4730,12 @@ static void LabelFeature (
{
main_feat = (SeqFeatPtr) new_clauseplus->featlist->data.ptrvalue;
- new_clauseplus->allelename = GetAlleleName (new_clauseplus->grp);
+ new_clauseplus->allelename = GetAlleleName (new_clauseplus->grp,
+ suppress_locus_tag);
if (new_clauseplus->interval == NULL)
{
new_clauseplus->interval =
- GetGenericInterval (new_clauseplus, biomol, bsp);
+ GetGenericInterval (new_clauseplus, biomol, bsp, suppress_locus_tag);
}
for (i=0; i < NumDefLineFeatLabels; i++)
@@ -4745,7 +4750,7 @@ static void LabelFeature (
}
GetGenericFeatureLabel ( new_clauseplus, bsp, biomol,
- &new_clauseplus->feature_label_data);
+ &new_clauseplus->feature_label_data, suppress_locus_tag);
return;
}
}
@@ -4919,11 +4924,11 @@ static void TrimUnwantedWordsFromAltSpliceProductName (
* must have the same gene, must share a complete interval, and must have
* similarly named products.
*/
-static CharPtr MeetAltSpliceRules (
- FeatureClausePtr cdsfcp1,
+static CharPtr MeetAltSpliceRules
+( FeatureClausePtr cdsfcp1,
FeatureClausePtr cdsfcp2,
- BioseqPtr bsp
-)
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
SeqFeatPtr cds1, cds2;
CharPtr match_string;
@@ -4937,7 +4942,7 @@ static CharPtr MeetAltSpliceRules (
cds1 = cdsfcp1->featlist->data.ptrvalue;
cds2 = cdsfcp2->featlist->data.ptrvalue;
- if (! DoGenesMatch (cdsfcp1->grp, cdsfcp2->grp))
+ if (! DoGenesMatch (cdsfcp1->grp, cdsfcp2->grp, suppress_locus_tag))
return NULL;
if ( (res = TestFeatOverlap (cds1, cds2, COMMON_INTERVAL)) != -1)
@@ -5048,10 +5053,10 @@ static void MoveSubclauses (
/* a comment and a data.choice value that indicates alt splicing */
/* we remove the second alternatively spliced CDS feature from the list */
-static void FindAltSplices (
- ValNodePtr clause_list,
- BioseqPtr bsp
-)
+static void FindAltSplices
+( ValNodePtr clause_list,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
FeatureClausePtr fcp1, fcp2;
ValNodePtr cdsclause1, cdsclause2;
@@ -5069,7 +5074,7 @@ static void FindAltSplices (
if (fcp1->feature_label_data.productname == NULL)
{
fcp1->feature_label_data.productname =
- GetProductName (fcp1->featlist->data.ptrvalue, bsp);
+ GetProductName (fcp1->featlist->data.ptrvalue, bsp, suppress_locus_tag);
}
searchclause = cdsclause1->next;
cdsclause2 = FindNextCDSClause (searchclause);
@@ -5079,9 +5084,9 @@ static void FindAltSplices (
if (fcp2->feature_label_data.productname == NULL)
{
fcp2->feature_label_data.productname =
- GetProductName (fcp2->featlist->data.ptrvalue, bsp);
+ GetProductName (fcp2->featlist->data.ptrvalue, bsp, suppress_locus_tag);
}
- combined_protein_name = MeetAltSpliceRules (fcp1, fcp2, bsp);
+ combined_protein_name = MeetAltSpliceRules (fcp1, fcp2, bsp, suppress_locus_tag);
if (combined_protein_name != NULL)
{
/* get rid of variant, splice variant, splice product, isoform, etc.*/
@@ -5134,18 +5139,18 @@ static void FindAltSplices (
DeleteFeatureClauses (&clause_list);
}
-static void LabelClauses (
- ValNodePtr clause_list,
- Uint1 biomol,
- BioseqPtr bsp
-)
+static void LabelClauses
+( ValNodePtr clause_list,
+ Uint1 biomol,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
ValNodePtr clause;
clause = clause_list;
while (clause != NULL)
{
- LabelFeature ( bsp, biomol, clause->data.ptrvalue);
+ LabelFeature ( bsp, biomol, clause->data.ptrvalue, suppress_locus_tag);
clause = clause->next;
}
}
@@ -5176,10 +5181,10 @@ static CharPtr separators [] = {
#define num_separators 3
-static ValNodePtr GetMiscRNAelements (
- SeqFeatPtr misc_rna,
- BioseqPtr bsp
-)
+static ValNodePtr GetMiscRNAelements
+( SeqFeatPtr misc_rna,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
CharPtr buffer;
Int4 i, best_i;
@@ -5198,7 +5203,7 @@ static ValNodePtr GetMiscRNAelements (
to_free = NULL;
if (misc_rna == NULL) return NULL;
- buffer = GetProductName (misc_rna, bsp);
+ buffer = GetProductName (misc_rna, bsp, suppress_locus_tag);
to_free = buffer;
if (buffer == NULL)
{
@@ -5265,7 +5270,7 @@ static ValNodePtr GetMiscRNAelements (
word_i++) {}
if (word_i < NUM_MISC_RNA_WORDS)
{
- fcp = NewFeatureClause ( misc_rna, bsp);
+ fcp = NewFeatureClause ( misc_rna, bsp, suppress_locus_tag);
if (fcp == NULL) return NULL;
if (word_i == MISC_RNA_WORD_INTERNAL_SPACER
|| word_i == MISC_RNA_WORD_EXTERNAL_SPACER
@@ -5345,8 +5350,8 @@ static ValNodePtr GetMiscRNAelements (
*/
static void ReplaceRNAClauses (
ValNodePtr PNTR clause_list,
- BioseqPtr bsp
-)
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
FeatureClausePtr fcp;
SeqFeatPtr main_feat;
@@ -5368,7 +5373,7 @@ static void ReplaceRNAClauses (
if (IsrRNA (main_feat) || IsMiscRNA (main_feat))
{
- replacement_clauses = GetMiscRNAelements ( main_feat, bsp );
+ replacement_clauses = GetMiscRNAelements ( main_feat, bsp, suppress_locus_tag );
if (replacement_clauses != NULL)
{
for (vnp = replacement_clauses; vnp->next != NULL; vnp = vnp->next) {}
@@ -6309,7 +6314,7 @@ static void ListClauses (
"pseudogene mRNA")==0)
&& clause_len > StringLen ("precursor")
&& StringCmp ( thisclause->feature_label_data.description
- + clause_len - StringLen ("precursor"),
+ + clause_len - StringLen ("precursor") - 1,
"precursor") == 0)
{
print_comma_between_description_and_typeword = TRUE;
@@ -6483,7 +6488,8 @@ static Boolean LIBCALLBACK ShouldRemoveExon (
BioseqPtr bsp,
Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
)
{
Boolean partial3, partial5;
@@ -6513,13 +6519,13 @@ static Boolean LIBCALLBACK ShouldRemoveCDS (
BioseqPtr bsp,
Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
-)
+ Boolean isSegment,
+ Boolean suppress_locus_tag)
{
CharPtr description;
Boolean retval = FALSE;
- description = GetGeneProtDescription (this_fcp, bsp);
+ description = GetGeneProtDescription (this_fcp, bsp, suppress_locus_tag);
if (StringHasNoText (description))
{
retval = TRUE;
@@ -6534,7 +6540,8 @@ static Boolean LIBCALLBACK ShouldRemoveNoncodingProductFeat (
FeatureClausePtr this_fcp,
BioseqPtr bsp, Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
)
{
if (isRequested) return FALSE;
@@ -6547,7 +6554,8 @@ static Boolean LIBCALLBACK ShouldRemovePromoter (
FeatureClausePtr this_fcp,
BioseqPtr bsp, Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
)
{
if (isLonely || isRequested) return FALSE;
@@ -6561,7 +6569,8 @@ static Boolean LIBCALLBACK ShouldRemoveLTR (
BioseqPtr bsp,
Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
)
{
if (isLonely || isRequested)
@@ -6577,7 +6586,8 @@ static Boolean LIBCALLBACK ShouldRemove3UTR (
BioseqPtr bsp,
Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
)
{
if (isLonely || isRequested)
@@ -6593,7 +6603,8 @@ static Boolean LIBCALLBACK ShouldRemove5UTR (
BioseqPtr bsp,
Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
)
{
if (isLonely || isRequested)
@@ -6608,28 +6619,29 @@ static Boolean LIBCALLBACK ShouldRemoveIntron (
FeatureClausePtr this_fcp,
BioseqPtr bsp, Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
+ Boolean isSegment,
+ Boolean suppress_locus_tag
)
{
if (isLonely || isRequested) return FALSE;
else return TRUE;
}
-static Boolean LIBCALLBACK ShouldRemoveGeneric (
- SeqFeatPtr sfp,
+static Boolean LIBCALLBACK ShouldRemoveGeneric
+( SeqFeatPtr sfp,
FeatureClausePtr parent_fcp,
FeatureClausePtr this_fcp,
BioseqPtr bsp,
Boolean isLonely,
Boolean isRequested,
- Boolean isSegment
-)
+ Boolean isSegment,
+ Boolean suppress_locus_tag)
{
CharPtr productname;
Boolean rval;
rval = FALSE;
- if (IsMiscRNA (sfp) && ( productname = GetProductName (sfp, bsp)) != NULL)
+ if (IsMiscRNA (sfp) && ( productname = GetProductName (sfp, bsp, suppress_locus_tag)) != NULL)
{
if (StringStr (productname, "trans-spliced leader") != NULL)
{
@@ -6688,6 +6700,7 @@ typedef struct deflinefeaturerequestlist {
Boolean remove_subfeatures;
DefLineType feature_list_type;
Int4 misc_feat_parse_rule;
+ Boolean suppress_locus_tags;
} DeflineFeatureRequestList, PNTR DeflineFeatureRequestListPtr;
static void InitFeatureRequests (
@@ -6704,6 +6717,7 @@ static void InitFeatureRequests (
feature_requests->remove_subfeatures = FALSE;
feature_requests->feature_list_type = DEFLINE_USE_FEATURES;
feature_requests->misc_feat_parse_rule = 2;
+ feature_requests->suppress_locus_tags = FALSE;
}
static Boolean RemoveCondition (
@@ -6722,17 +6736,19 @@ static Boolean RemoveCondition (
{
if (remove_items[i].itemmatch (sfp))
return remove_items[i].ShouldRemove (sfp, parent_fcp, this_fcp, bsp,
- isLonely, feature_requests->items[i].keep, isSegment);
+ isLonely, feature_requests->items[i].keep,
+ isSegment,
+ feature_requests->suppress_locus_tags);
}
return ShouldRemoveGeneric(sfp, parent_fcp, this_fcp, bsp, isLonely, FALSE,
- isSegment);
+ isSegment, feature_requests->suppress_locus_tags);
}
-static Boolean FindOtherGeneClause (
- ValNodePtr feature_list,
+static Boolean FindOtherGeneClause
+( ValNodePtr feature_list,
ValNodePtr me,
- GeneRefPtr grp
-)
+ GeneRefPtr grp,
+ Boolean suppress_locus_tag)
{
ValNodePtr vnp;
FeatureClausePtr fcp;
@@ -6747,11 +6763,11 @@ static Boolean FindOtherGeneClause (
fcp = vnp->data.ptrvalue;
if (fcp->delete_me) continue;
if ( fcp->grp == grp
- || (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp)))
+ || (fcp->grp != NULL && DoGenesMatch (fcp->grp, grp, suppress_locus_tag)))
{
return TRUE;
}
- if ( FindOtherGeneClause (fcp->featlist, me, grp))
+ if ( FindOtherGeneClause (fcp->featlist, me, grp, suppress_locus_tag))
{
return TRUE;
}
@@ -6760,11 +6776,11 @@ static Boolean FindOtherGeneClause (
return FALSE;
}
-static void RemoveGenesMentionedElsewhere (
- ValNodePtr PNTR feature_list,
- ValNodePtr search_list,
- Boolean delete_now
-)
+static void RemoveGenesMentionedElsewhere
+( ValNodePtr PNTR feature_list,
+ ValNodePtr search_list,
+ Boolean delete_now,
+ Boolean suppress_locus_tag)
{
ValNodePtr vnp;
FeatureClausePtr fcp;
@@ -6780,13 +6796,13 @@ static void RemoveGenesMentionedElsewhere (
}
if ( IsGene (fcp->featlist->data.ptrvalue)
&& fcp->featlist->next == NULL
- && FindOtherGeneClause ( search_list, vnp, fcp->grp))
+ && FindOtherGeneClause ( search_list, vnp, fcp->grp, suppress_locus_tag))
{
fcp->delete_me = TRUE;
}
else
{
- RemoveGenesMentionedElsewhere ( &(fcp->featlist), search_list, FALSE);
+ RemoveGenesMentionedElsewhere ( &(fcp->featlist), search_list, FALSE, suppress_locus_tag);
}
}
}
@@ -7295,8 +7311,8 @@ static void ConsolidateClauses (
ValNodePtr PNTR list,
BioseqPtr bsp,
Uint1 biomol,
- Boolean delete_now
-)
+ Boolean delete_now,
+ Boolean suppress_locus_tag)
{
ValNodePtr vnp;
FeatureClausePtr fcp;
@@ -7317,14 +7333,14 @@ static void ConsolidateClauses (
continue;
}
- ConsolidateClauses (&(fcp->featlist), bsp, biomol, FALSE);
+ ConsolidateClauses (&(fcp->featlist), bsp, biomol, FALSE, suppress_locus_tag);
if (last_cds_fcp == NULL)
{
last_cds_fcp = fcp;
if (fcp->feature_label_data.description == NULL)
{
- last_desc = GetGeneProtDescription (fcp, bsp);
+ last_desc = GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
}
else
{
@@ -7344,7 +7360,7 @@ static void ConsolidateClauses (
{
if (fcp->feature_label_data.description == NULL)
{
- new_desc = GetGeneProtDescription (fcp, bsp);
+ new_desc = GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
}
else
{
@@ -7385,7 +7401,7 @@ static void ConsolidateClauses (
MemFree (last_cds_fcp->interval);
}
last_cds_fcp->interval =
- GetGenericInterval (last_cds_fcp, biomol, bsp);
+ GetGenericInterval (last_cds_fcp, biomol, bsp, suppress_locus_tag);
MemFree (new_desc);
}
else
@@ -7405,8 +7421,8 @@ static void ConsolidateClauses (
static void CountUnknownGenes (
ValNodePtr PNTR clause_list,
- BioseqPtr bsp
-)
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
FeatureClausePtr fcp, new_fcp;
ValNodePtr vnp, new_vnp;
@@ -7423,8 +7439,8 @@ static void CountUnknownGenes (
&& (fcp = vnp->data.ptrvalue) != NULL
&& ! fcp->is_unknown)
{
- CountUnknownGenes (&(fcp->featlist), bsp);
- gene_name = GetGeneProtDescription (fcp, bsp);
+ CountUnknownGenes (&(fcp->featlist), bsp, suppress_locus_tag);
+ gene_name = GetGeneProtDescription (fcp, bsp, suppress_locus_tag);
if (StringCmp (gene_name, "unknown") == 0
&& fcp->featlist != NULL
&& fcp->featlist->choice == DEFLINE_FEATLIST)
@@ -7433,7 +7449,8 @@ static void CountUnknownGenes (
{
new_vnp = ValNodeNew (*clause_list);
if (new_vnp == NULL) return;
- new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue, bsp);
+ new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue,
+ bsp, suppress_locus_tag);
new_fcp->is_unknown = TRUE;
new_vnp->choice = DEFLINE_CLAUSEPLUS;
new_vnp->data.ptrvalue = new_fcp;
@@ -7481,10 +7498,10 @@ static void ReplaceDefinitionLine (
MemFree (defline);
}
-FeatureClausePtr NewFeatureClause (
- SeqFeatPtr sfp,
- BioseqPtr bsp
-)
+FeatureClausePtr NewFeatureClause
+( SeqFeatPtr sfp,
+ BioseqPtr bsp,
+ Boolean suppress_locus_tag)
{
FeatureClausePtr fcp;
Boolean partial5, partial3;
@@ -7530,7 +7547,7 @@ FeatureClausePtr NewFeatureClause (
}
if (IsCDS (sfp))
{
- fcp->feature_label_data.productname = GetProductName (sfp, bsp);
+ fcp->feature_label_data.productname = GetProductName (sfp, bsp, suppress_locus_tag);
}
fcp->featlist = ValNodeNew (NULL);
if (fcp->featlist == NULL)
@@ -7545,9 +7562,7 @@ FeatureClausePtr NewFeatureClause (
return fcp;
}
-static ValNodePtr GetFeatureList (
- BioseqPtr bsp
-)
+static ValNodePtr GetFeatureList (BioseqPtr bsp, Boolean suppress_locus_tag)
{
ValNodePtr head, vnp;
SeqFeatPtr sfp;
@@ -7563,7 +7578,7 @@ static ValNodePtr GetFeatureList (
{
if (IsRecognizedFeature (sfp))
{
- fcp = NewFeatureClause (sfp, bsp);
+ fcp = NewFeatureClause (sfp, bsp, suppress_locus_tag);
if (fcp == NULL) return NULL;
fcp->numivals = fcontext.numivals;
fcp->ivals = fcontext.ivals;
@@ -7834,7 +7849,8 @@ static Boolean IntervalIntersectsIvals
static ValNodePtr GrabTraversingGenes
(ValNodePtr parent_feature_list,
SeqMgrSegmentContextPtr context,
- BioseqPtr parent_bsp)
+ BioseqPtr parent_bsp,
+ Boolean suppress_locus_tag)
{
FeatureClausePtr fcp, new_fcp;
ValNodePtr clause;
@@ -7855,7 +7871,8 @@ static ValNodePtr GrabTraversingGenes
&& fcp->ivals != NULL && fcp->numivals > 0)
{
if (IntervalIntersectsIvals (fcp->numivals, fcp->ivals, context)) {
- new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue, parent_bsp);
+ new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue, parent_bsp,
+ suppress_locus_tag);
if (new_fcp == NULL) return FALSE;
vnp = ValNodeNew (segment_feature_list);
if (vnp == NULL) return FALSE;
@@ -7883,8 +7900,7 @@ static CharPtr BuildFeatureClauses (
static Boolean LIBCALLBACK GetFeatureClauseForSeg (
SeqLocPtr slp,
- SeqMgrSegmentContextPtr context
-)
+ SeqMgrSegmentContextPtr context)
{
SegmentDefLineFeatureClausePtr sdlp;
ValNodePtr clause, tmp_parent_list;
@@ -7932,7 +7948,8 @@ static Boolean LIBCALLBACK GetFeatureClauseForSeg (
&& stop >= context->cumOffset)
{
new_fcp = NewFeatureClause (fcp->featlist->data.ptrvalue,
- sdlp->parent_bsp);
+ sdlp->parent_bsp,
+ sdlp->feature_requests->suppress_locus_tags);
if (new_fcp == NULL) return FALSE;
vnp = ValNodeNew (segment_feature_list);
if (vnp == NULL) return FALSE;
@@ -7945,7 +7962,8 @@ static Boolean LIBCALLBACK GetFeatureClauseForSeg (
if (segment_feature_list == NULL) {
segment_feature_list = GrabTraversingGenes (sdlp->parent_feature_list,
- context, sdlp->parent_bsp);
+ context, sdlp->parent_bsp,
+ sdlp->feature_requests->suppress_locus_tags);
}
entityID = ObjMgrGetEntityIDForPointer (bsp);
@@ -7996,15 +8014,15 @@ static CharPtr BuildFeatureClauses (
if (feature_requests->feature_list_type == DEFLINE_USE_FEATURES
&& ( ! isSegment || (seg_feature_list != NULL && *seg_feature_list != NULL)))
{
- GroupmRNAs (feature_list, bsp);
+ GroupmRNAs (feature_list, bsp, feature_requests->suppress_locus_tags);
/* genes are added to other clauses */
- GroupGenes (feature_list);
+ GroupGenes (feature_list, feature_requests->suppress_locus_tags);
if (! feature_requests->suppress_alt_splice_phrase)
{
/* find alt-spliced CDSs */
- FindAltSplices (*feature_list, bsp);
+ FindAltSplices (*feature_list, bsp, feature_requests->suppress_locus_tags);
}
GroupAltSplicedExons (feature_list, bsp, TRUE);
@@ -8012,9 +8030,9 @@ static CharPtr BuildFeatureClauses (
/* now group clauses */
GroupAllClauses ( feature_list, bsp );
- ExpandAltSplicedExons (*feature_list, bsp);
+ ExpandAltSplicedExons (*feature_list, bsp, feature_requests->suppress_locus_tags);
- FindGeneProducts (*feature_list, bsp);
+ FindGeneProducts (*feature_list, bsp, feature_requests->suppress_locus_tags);
if (seg_feature_list != NULL && *seg_feature_list != NULL)
{
@@ -8027,7 +8045,8 @@ static CharPtr BuildFeatureClauses (
/* remove exons and other unwanted features */
RemoveUnwantedFeatures (feature_list, bsp, isSegment, feature_requests);
- RemoveGenesMentionedElsewhere (feature_list, *feature_list, TRUE);
+ RemoveGenesMentionedElsewhere (feature_list, *feature_list, TRUE,
+ feature_requests->suppress_locus_tags);
if (feature_requests->remove_subfeatures)
{
@@ -8036,7 +8055,7 @@ static CharPtr BuildFeatureClauses (
DeleteOperonSubfeatures (feature_list, TRUE);
- CountUnknownGenes (feature_list, bsp);
+ CountUnknownGenes (feature_list, bsp, feature_requests->suppress_locus_tags);
if (feature_requests->misc_feat_parse_rule == 1)
{
@@ -8047,7 +8066,7 @@ static CharPtr BuildFeatureClauses (
RemoveUnwantedMiscFeats (feature_list, TRUE);
}
- ReplaceRNAClauses (feature_list, bsp);
+ ReplaceRNAClauses (feature_list, bsp, feature_requests->suppress_locus_tags);
/* take any exons on the minus strand */
/* and reverse their order within the clause */
@@ -8055,9 +8074,11 @@ static CharPtr BuildFeatureClauses (
RenameExonSequences ( feature_list, bsp, TRUE);
- LabelClauses (*feature_list, molecule_type, bsp);
+ LabelClauses (*feature_list, molecule_type, bsp,
+ feature_requests->suppress_locus_tags);
- ConsolidateClauses (feature_list, bsp, molecule_type, TRUE);
+ ConsolidateClauses (feature_list, bsp, molecule_type, TRUE,
+ feature_requests->suppress_locus_tags);
/* this allows genes to be listed together even if they are from */
/* separate sequences */
@@ -8096,17 +8117,26 @@ static Int2 GetProductFlagFromCDSProductNames (BioseqPtr bsp)
SeqFeatPtr cds = NULL;
Int2 product_flag;
Int2 i;
+ CharPtr found;
+ Char ch;
product_flag = 0;
- for (cds = SeqMgrGetNextFeature (bsp, cds, SEQFEAT_CDREGION, 0, &context); cds != NULL && product_flag == 0; cds = cds->next)
+ for (cds = SeqMgrGetNextFeature (bsp, cds, SEQFEAT_CDREGION, 0, &context);
+ cds != NULL && product_flag == 0;
+ cds = cds->next)
{
- for (i = 1; organelleByPopup[i] != NULL && product_flag == 0; i++)
- {
- if (StringStr (context.label, organelleByPopup[i]))
- {
- product_flag = i;
- }
- }
+ for (i = 1; organelleByPopup[i] != NULL && product_flag == 0; i++)
+ {
+ found = StringStr (context.label, organelleByPopup[i]);
+ if (found != NULL)
+ {
+ ch = *(found + StringLen (organelleByPopup[i]));
+ if (ch == 0 || ch == ' ')
+ {
+ product_flag = i;
+ }
+ }
+ }
}
return product_flag;
@@ -8162,7 +8192,8 @@ static void BuildDefLineFeatClauseList (
sdld.parent_bsp = bsp;
sdld.molecule_type = GetMoleculeType (bsp, entityID);
- sdld.parent_feature_list = GetFeatureList (bsp);
+ sdld.parent_feature_list = GetFeatureList (bsp,
+ feature_requests->suppress_locus_tags);
sdld.feature_requests = feature_requests;
sdld.product_flag = product_flag;
@@ -8201,7 +8232,7 @@ static void BuildDefLineFeatClauseList (
if (bsp == NULL) return;
if ( SpecialHandlingForSpecialTechniques (bsp)) return;
molecule_type = GetMoleculeType (bsp, entityID);
- head = GetFeatureList (bsp);
+ head = GetFeatureList (bsp, feature_requests->suppress_locus_tags);
/* get default product flag if necessary */
if (product_flag == -1 || product_flag == DEFAULT_ORGANELLE_CLAUSE) {
@@ -8280,6 +8311,7 @@ typedef struct deflineformdata {
GrouP featureOptsGrp;
PopuP misc_feat_parse_rule;
ButtoN alternate_splice_flag;
+ ButtoN suppress_locus_tags;
} DefLineFormData, PNTR DefLineFormPtr;
static void DefLineFormMessageProc (ForM f, Int2 mssg)
@@ -8435,6 +8467,9 @@ static void DoAutoDefLine (ButtoN b)
dlfp->feature_requests.remove_subfeatures =
GetStatus (dlfp->remove_subfeatures);
+ dlfp->feature_requests.suppress_locus_tags =
+ GetStatus (dlfp->suppress_locus_tags);
+
dlfp->feature_requests.misc_feat_parse_rule =
GetValue (dlfp->misc_feat_parse_rule);
@@ -8796,6 +8831,10 @@ static GrouP CreateDefLineFormFeatureOptionsGroup (
"Suppress transposon and insertion sequence subfeatures", NULL);
SetStatus (dlfp->remove_subfeatures, FALSE);
+ dlfp->suppress_locus_tags = CheckBox (dlfp->featureOptsGrp,
+ "Suppress locus tags", NULL);
+ SetStatus (dlfp->suppress_locus_tags, FALSE);
+
g = NormalGroup (dlfp->featureOptsGrp, 3, 0,
"Optional Features", programFont, NULL);
@@ -8824,6 +8863,7 @@ static GrouP CreateDefLineFormFeatureOptionsGroup (
(HANDLE) dlfp->alternate_splice_flag,
(HANDLE) dlfp->suppress_alt_splice_phrase,
(HANDLE) dlfp->remove_subfeatures,
+ (HANDLE) dlfp->suppress_locus_tags,
(HANDLE) g,
(HANDLE) r,
NULL);
diff --git a/sequin/sequin2.c b/sequin/sequin2.c
index c7302c3b..16d97958 100644
--- a/sequin/sequin2.c
+++ b/sequin/sequin2.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.168 $
+* $Revision: 6.172 $
*
* File Description:
*
@@ -1095,7 +1095,7 @@ End Gap: When some of the sequences in an alignment are shorter \
or longer than others, end gap characters are added to the end \
of the sequence to maintain the correct spacing. These will \
not appear in your sequence file.\n\
-Missing: These characters are used to represent \
+Ambiguous/Unknown: These characters are used to represent \
indeterminate/ambiguous nucleotides. These will appear in your \
sequence file as 'n'.\n\
Match: These characters are used to indicate positions where \
@@ -1187,6 +1187,7 @@ static Boolean ImportPhylipDialog (DialoG d, CharPtr filename)
CountTitlesWithoutOrganisms (sep);
} else {
+ SendHelpScrollMessage (helpForm, "Organism and Sequences Form", "Nucleotide Page");
SetPhylipDocInstructions (ppp);
}
} else {
@@ -1259,7 +1260,7 @@ static DialoG CreatePhylipDialog (GrouP h, CharPtr title, CharPtr text,
a = NormalGroup (m, 4, 0, "Sequence Characters", systemFont, NULL);
StaticPrompt (a, "Beginning Gap", 0, dialogTextHeight, systemFont, 'c');
ppp->beginning_gap = DialogText (a, "-.Nn?", 5, NULL);
- StaticPrompt (a, "Missing", 0, dialogTextHeight, systemFont, 'c');
+ StaticPrompt (a, "Ambiguous/Unknown", 0, dialogTextHeight, systemFont, 'c');
ppp->missing = DialogText (a, "?Nn", 5, NULL);
StaticPrompt (a, "Middle Gap", 0, dialogTextHeight, systemFont, 'c');
ppp->middle_gap = DialogText (a, "-.", 5, NULL);
@@ -7848,6 +7849,8 @@ extern void SqnNewAlign (BioseqPtr bsp1, BioseqPtr bsp2, SeqAlignPtr PNTR salp)
}
+/* This section of code is for the Remove Sequences From Alignments function. */
+
typedef struct alignmentsequencelist {
SeqIdPtr sip;
Char descr[255];
@@ -7860,12 +7863,70 @@ typedef struct removeseqfromaligndata {
SeqEntryPtr sep;
} RemoveSeqFromAlignData, PNTR RemoveSeqFromAlignPtr;
-static void RemoveOneSequenceFromAlignment (SeqIdPtr sip, SeqAlignPtr salp)
+/* This function will remove DenDiag and pairwise alignments if they contain
+ * the sequence identified by sip, otherwise it will remove the sequence from
+ * the alignment.
+ */
+static SeqAlignPtr RemoveOneSequenceFromAlignment (SeqIdPtr sip, SeqAlignPtr salphead)
{
- if (FindSeqIdinSeqAlign (salp, sip)) {
- SeqAlignIDCache (salp, sip);
+ Uint4 seqid_order;
+ SeqIdPtr tmpsip;
+ SeqAlignPtr salp, salp_next, prev_salp, remove_salp, last_remove;
+
+ if (!FindSeqIdinSeqAlign (salphead, sip)) return;
+
+ salp = salphead;
+ prev_salp = NULL;
+ remove_salp = NULL;
+ last_remove = NULL;
+ while (salp != NULL)
+ {
+ salp_next = salp->next;
+ tmpsip = SeqIdPtrFromSeqAlign (salp);
+ seqid_order = SeqIdOrderInBioseqIdList(sip, tmpsip);
+ if (seqid_order == 0)
+ {
+ /* do nothing for this subalignment */
+ prev_salp = salp;
+ }
+ else if (salp->dim == 2 || salphead->segtype ==1)
+ {
+ /* This is for a pairwise alignment or a DENDIAG alignment */
+ if (prev_salp == NULL)
+ {
+ salphead = salp->next;
+ }
+ else
+ {
+ prev_salp->next = salp->next;
+ }
+ /* save the alignments that we want to free in a list and get rid of them
+ * at the end - freeing them beforehand causes problems with listing the
+ * IDs in the alignment.
+ */
+ salp->next = NULL;
+ if (remove_salp == NULL)
+ {
+ remove_salp = salp;
+ }
+ else
+ {
+ last_remove->next = salp;
+ }
+ last_remove = salp;
+ }
+ else
+ {
+ SeqAlignBioseqDeleteById (salphead, sip);
+ prev_salp = salp;
+ }
+ salp = salp_next;
}
+ /* Now we can free the alignment */
+ SeqAlignFree (remove_salp);
+ return salphead;
}
+
static void RemoveSequenceFromAlignmentsCallback (SeqAnnotPtr sap, Pointer userdata)
{
SeqAlignPtr salp;
@@ -7875,19 +7936,94 @@ static void RemoveSequenceFromAlignmentsCallback (SeqAnnotPtr sap, Pointer userd
salp = (SeqAlignPtr) sap->data;
if (salp == NULL) return;
sip = (SeqIdPtr) userdata;
- RemoveOneSequenceFromAlignment (sip, salp);
+ sap->data = RemoveOneSequenceFromAlignment (sip, salp);
+ /* if we've deleted all of the alignments, get rid of the annotation as well */
+ if (sap->data == NULL)
+ {
+ sap->idx.deleteme = TRUE;
+ }
+}
+
+typedef struct checkforremovesequencefromalignments
+{
+ Boolean found_problem;
+ SeqIdPtr sip;
+} CheckForRemoveSequenceFromAlignmentsData, PNTR CheckForRemoveSequenceFromAlignmentsPtr;
+
+/* This is the callback function for looking for pairwise alignments.
+/* If we delete the first sequence in a pairwise alignment, we end up deleting
+ * the entire alignment because that sequence is paired with every other sequence.
+ */
+static void CheckForRemoveSequenceFromAlignmentsProblemsCallback (SeqAnnotPtr sap, Pointer userdata)
+{
+ CheckForRemoveSequenceFromAlignmentsPtr p;
+ SeqAlignPtr salphead, salp;
+ Uint4 seqid_order;
+ SeqIdPtr tmpsip;
+
+ if (sap == NULL || sap->type != 2
+ || (p = (CheckForRemoveSequenceFromAlignmentsPtr)userdata) == NULL
+ || p->found_problem)
+ {
+ return;
+ }
+ salphead = (SeqAlignPtr) sap->data;
+ if (salphead == NULL) return;
+
+ if (!FindSeqIdinSeqAlign (salphead, p->sip))
+ {
+ return;
+ }
+ for (salp = salphead; salp != NULL; salp = salp->next)
+ {
+ tmpsip = SeqIdPtrFromSeqAlign (salp);
+ seqid_order = SeqIdOrderInBioseqIdList(p->sip, tmpsip);
+ if (seqid_order == 0)
+ {
+ continue;
+ }
+ else if (seqid_order == 1 && salp->dim == 2)
+ {
+ p->found_problem = TRUE;
+ }
+ }
}
static void DoRemoveSequencesFromAlignment (ButtoN b)
{
RemoveSeqFromAlignPtr rp;
+ WindoW w;
ValNodePtr vnp;
Int2 val;
AlignmentSequenceListPtr aslp;
-
+ CheckForRemoveSequenceFromAlignmentsData data;
+
if (b == NULL) return;
rp = (RemoveSeqFromAlignPtr) GetObjectExtra (b);
if (rp == NULL) return;
+
+ w = (WindoW) rp->form;
+ Hide (w);
+ /* first, check for pairwise alignments */
+ val = 1;
+ for (vnp = rp->sequence_list; vnp != NULL; vnp = vnp->next) {
+ aslp = vnp->data.ptrvalue;
+ if (aslp == NULL) continue;
+ if (GetItemStatus (rp->sequence_list_ctrl, val)) {
+ data.sip = aslp->sip;
+ data.found_problem = FALSE;
+ VisitAnnotsInSep (rp->sep, (Pointer) &data, CheckForRemoveSequenceFromAlignmentsProblemsCallback);
+ if (data.found_problem)
+ {
+ Message (MSG_ERROR, "One of the selected sequences is the first in a pairwise alignment."
+ " You must convert the alignment to a multiple alignment before trying to remove this sequence.");
+ Remove (rp->form);
+ return;
+ }
+ }
+ val++;
+ }
+
val = 1;
for (vnp = rp->sequence_list; vnp != NULL; vnp = vnp->next) {
aslp = vnp->data.ptrvalue;
@@ -7897,11 +8033,39 @@ static void DoRemoveSequencesFromAlignment (ButtoN b)
}
val++;
}
+
+ ValNodeFree (rp->sequence_list);
+ rp->sequence_list = NULL;
+ DeleteMarkedObjects (rp->input_entityID, 0, NULL);
ObjMgrSetDirtyFlag (rp->input_entityID, TRUE);
ObjMgrSendMsg (OM_MSG_UPDATE, rp->input_entityID, 0, 0);
Remove (rp->form);
}
+/* This function is used so that a sequence ID will only appear once in the list,
+ * even if it appears in more than one alignment or subalignment.
+ */
+static Boolean IsIDAlreadyInList (SeqIdPtr sip, ValNodePtr list)
+{
+ ValNodePtr vnp;
+ AlignmentSequenceListPtr aslp;
+
+ if (sip == NULL) return FALSE;
+
+ for (vnp = list; vnp != NULL; vnp = vnp->next)
+ {
+ aslp = (AlignmentSequenceListPtr) vnp->data.ptrvalue;
+ if (aslp != NULL && SeqIdComp (aslp->sip, sip) == SIC_YES)
+ {
+ return TRUE;
+ }
+ }
+ return FALSE;
+}
+
+/* This function creates the list of sequence IDs and descriptions to use in
+ * the Remove Sequences From Alignments dialog.
+ */
static void ListSequencesInAlignmentsCallback (SeqAnnotPtr sap, Pointer userdata)
{
SeqAlignPtr salp;
@@ -7914,11 +8078,13 @@ static void ListSequencesInAlignmentsCallback (SeqAnnotPtr sap, Pointer userdata
if (sap == NULL || sap->type != 2 || userdata == NULL) return;
salp = (SeqAlignPtr) sap->data;
- if (salp == NULL) return;
- list = (ValNodePtr PNTR)userdata;
- sip_list = SeqAlignIDList (salp);
- if (sip_list == NULL) return;
- for (sip = sip_list; sip != NULL; sip = sip->next) {
+ while (salp != NULL)
+ {
+ list = (ValNodePtr PNTR)userdata;
+ sip_list = SeqAlignIDList (salp);
+ if (sip_list == NULL) return;
+ for (sip = sip_list; sip != NULL; sip = sip->next) {
+ if (IsIDAlreadyInList (sip, *list)) continue;
aslp = (AlignmentSequenceListPtr) MemNew (sizeof (AlignmentSequenceListData));
if (aslp == NULL) return;
aslp->sip = sip;
@@ -7933,7 +8099,7 @@ static void ListSequencesInAlignmentsCallback (SeqAnnotPtr sap, Pointer userdata
offset ++;
}
SeqIdWrite (bsp_sip, aslp->descr + offset, PRINTID_TEXTID_ACCESSION, 254 - offset);
- offset += StringLen (aslp->descr);
+ offset = StringLen (aslp->descr);
}
} else {
SeqIdWrite (sip, aslp->descr, PRINTID_TEXTID_ACCESSION, 254);
@@ -7942,7 +8108,9 @@ static void ListSequencesInAlignmentsCallback (SeqAnnotPtr sap, Pointer userdata
vnp->data.ptrvalue = aslp;
if (*list == NULL) {
*list = vnp;
- }
+ }
+ }
+ salp = salp->next;
}
}
@@ -7992,6 +8160,7 @@ extern void RemoveSequencesFromAlignment (IteM i)
rp = (RemoveSeqFromAlignPtr) MemNew (sizeof (RemoveSeqFromAlignData));
if (rp == NULL) return;
+ rp->input_entityID = bfp->input_entityID;
rp->sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
if (rp->sep == NULL) {
MemFree (rp);
@@ -8035,4 +8204,5 @@ extern void RemoveSequencesFromAlignment (IteM i)
Update ();
}
+/* End of Remove Sequences From Alignments function code. */
diff --git a/sequin/sequin3.c b/sequin/sequin3.c
index c574dd52..912199c2 100644
--- a/sequin/sequin3.c
+++ b/sequin/sequin3.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/22/95
*
-* $Revision: 6.377 $
+* $Revision: 6.384 $
*
* File Description:
*
@@ -1074,6 +1074,57 @@ static void RemoveAllGeneXrefs (IteM i)
ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
}
+static void DoRefreshGeneXrefs (SeqFeatPtr sfp, Pointer userdata)
+
+{
+ SeqFeatXrefPtr curr;
+ GeneRefPtr grp, grpfeat;
+ SeqFeatPtr gene;
+ SeqMgrFeatContext fcontext;
+ BioseqPtr bsp;
+
+ if (sfp == NULL) return;
+
+ for (curr = sfp->xref; curr != NULL; curr = curr->next)
+ {
+ if (curr->data.choice == SEQFEAT_GENE) {
+ grp = (GeneRefPtr) curr->data.value.ptrvalue;
+ if (grp != NULL)
+ {
+ bsp = BioseqFindFromSeqLoc (sfp->location);
+ gene = SeqMgrGetFeatureByLabel (bsp, grp->locus, SEQFEAT_GENE, 0, &fcontext);
+ if (gene != NULL && gene->data.choice == SEQFEAT_GENE) {
+ grpfeat = (GeneRefPtr) gene->data.value.ptrvalue;
+ if (grpfeat != NULL) {
+ GeneRefFree (grp);
+ grp = GeneRefDup (grpfeat);
+ curr->data.value.ptrvalue = grp;
+ }
+ }
+ }
+ }
+ }
+}
+
+static void RefreshGeneXRefs (IteM i)
+
+{
+ BaseFormPtr bfp;
+ SeqEntryPtr sep;
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+ if (bfp == NULL) return;
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+ if (sep == NULL) return;
+ VisitFeaturesInSep (sep, NULL, DoRefreshGeneXrefs);
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
static ValNodePtr RemoveDbxrefList (ValNodePtr vnp)
{
@@ -1634,7 +1685,47 @@ static void RawSeqToDeltaSeq (IteM i)
if (bfp == NULL) return;
sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
if (sep == NULL) return;
- VisitBioseqsInSep (sep, (Pointer) bfp, ConvertNsToGaps);
+ VisitBioseqsInSep (sep, NULL, ConvertNsToGaps);
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+static void RawSeqToDeltaSeqUnknownLengthGaps (IteM i)
+
+{
+ BaseFormPtr bfp;
+ SeqEntryPtr sep;
+ Int4 unknown_gap_size = 100;
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+ if (bfp == NULL) return;
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+ if (sep == NULL) return;
+ VisitBioseqsInSep (sep, &unknown_gap_size, ConvertNsToGaps);
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
+static void RawSeqToDeltaSeqUnknown100LengthGaps (IteM i)
+
+{
+ BaseFormPtr bfp;
+ SeqEntryPtr sep;
+ Int4 unknown_gap_size = -1;
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+ if (bfp == NULL) return;
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+ if (sep == NULL) return;
+ VisitBioseqsInSep (sep, &unknown_gap_size, ConvertNsToGaps);
ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
}
@@ -10314,6 +10405,9 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
i = CommandItem (s, "Genus-Species Fixup", GenSpecTaxonFixup);
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
+ i = CommandItem (s, "Country Fixup", CountryLookup);
+ SetObjectExtra (i, bfp, NULL);
+ SeparatorItem (s);
i = CommandItem (s, "Set Source Focus", SetSourceFocus);
SetObjectExtra (i, bfp, NULL);
i = CommandItem (s, "Clear Source Focus", ClearSourceFocus);
@@ -10371,6 +10465,8 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
i = CommandItem (s, "Remove Proteins", RemoveProteins);
SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (s, "Remove Proteins and Renormalize Nuc-Prot Sets", RemoveProteinsAndRenormalize);
+ SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
i = CommandItem (s, "Remove Source Qual", RemoveSource);
SetObjectExtra (i, bfp, NULL);
@@ -10566,6 +10662,9 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
i = CommandItem (s, "Resolve Colliding Local IDs", ResolveExistingLocalIDs);
SetObjectExtra (i, bfp, NULL);
}
+ SeparatorItem (s);
+ i = CommandItem (s, "Refresh Gene Xrefs", RefreshGeneXRefs);
+ SetObjectExtra (i, bfp, NULL);
s = SubMenu (m, "Edit/ E");
i = CommandItem (s, "Edit Qualifiers", EditQualifier);
@@ -10624,7 +10723,7 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
s = SubMenu (m, "Transform/ T");
i = CommandItem (s, "Correct CDS Genetic Codes", CorrectCDSGenCodes);
SetObjectExtra (i, bfp, NULL);
- i = CommandItem (s, "Correct CDS Propagate Crud", FixCdsAfterPropagate);
+ i = CommandItem (s, "Cleanup CDS partials after propagation", FixCdsAfterPropagate);
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
i = CommandItem (s, "Trim Ns from Bioseqs", TrimNsFromNucs);
@@ -10799,7 +10898,12 @@ extern void SetupSpecialMenu (MenU m, BaseFormPtr bfp)
SetObjectExtra (i, bfp, NULL);
SeparatorItem (s);
}
- i = CommandItem (s, "Raw Sequence with Ns to Delta Sequence", RawSeqToDeltaSeq);
+ x = SubMenu (s, "Raw Sequence with Ns to Delta Sequence");
+ i = CommandItem (x, "All Known Length Gaps", RawSeqToDeltaSeq);
+ SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "Unknown Length Gaps for 100 Ns", RawSeqToDeltaSeqUnknownLengthGaps);
+ SetObjectExtra (i, bfp, NULL);
+ i = CommandItem (x, "Unknown Length 100 Gaps for All Ns", RawSeqToDeltaSeqUnknown100LengthGaps);
SetObjectExtra (i, bfp, NULL);
s = SubMenu (m, "Misc/ M");
diff --git a/sequin/sequin4.c b/sequin/sequin4.c
index d21e8e4c..457c5add 100644
--- a/sequin/sequin4.c
+++ b/sequin/sequin4.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 6/28/96
*
-* $Revision: 6.210 $
+* $Revision: 6.214 $
*
* File Description:
*
@@ -74,6 +74,7 @@
#include <aliparse.h>
#include <spidey.h>
#include <ent2api.h>
+#include <valid.h>
#define REGISTER_UPDATESEGSET ObjMgrProcLoadEx (OMPROC_FILTER,"Update Segmented Set","UpdateSegSet",0,0,0,0,NULL,UpdateSegSet,PROC_PRIORITY_DEFAULT, "Indexer")
@@ -97,6 +98,10 @@
#define REGISTER_SEGREGATE_BY_TEXT ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Text","SegregateByText",0,0,0,0,NULL,CreateSegregateByTextWindow,PROC_PRIORITY_DEFAULT, "Indexer")
+#define REGISTER_SEGREGATE_BY_FEATURE ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Feature","SegregateByFeature",0,0,0,0,NULL,CreateSegregateByFeatureWindow,PROC_PRIORITY_DEFAULT, "Indexer")
+
+#define REGISTER_SEGREGATE_BY_DESCRIPTOR ObjMgrProcLoadEx (OMPROC_FILTER, "Segregate By Descriptor","SegregateByDescriptor",0,0,0,0,NULL,CreateSegregateByDescriptorWindow,PROC_PRIORITY_DEFAULT, "Indexer")
+
#define REGISTER_CONVERTSEQALIGN ObjMgrProcLoadEx (OMPROC_FILTER,"Convert SeqAlign","ConvertSeqAlign",0,0,0,0,NULL,ConvertToTrueMultipleAlignment,PROC_PRIORITY_DEFAULT, "Alignment")
#define REGISTER_MAKESEQALIGN ObjMgrProcLoadEx (OMPROC_FILTER,"Make SeqAlign","CreateSeqAlign",0,0,0,0,NULL,GenerateSeqAlignFromSeqEntry,PROC_PRIORITY_DEFAULT, "Alignment")
@@ -6509,6 +6514,8 @@ extern void SetupSequinFilters (void)
if (indexerVersion) {
REGISTER_DELETE_BY_TEXT;
+ REGISTER_SEGREGATE_BY_FEATURE;
+ REGISTER_SEGREGATE_BY_DESCRIPTOR;
REGISTER_SEGREGATE_BY_TEXT;
REGISTER_FIND_NON_ACGT;
REGISTER_BSP_INDEX;
@@ -8148,3 +8155,92 @@ extern void ConsolidateOrganismNotes (IteM i)
ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
}
+static void CountryLookupProc (BioSourcePtr biop, Pointer userdata)
+{
+ CharPtr PNTR list;
+ CharPtr PNTR ptr;
+ SubSourcePtr ssp;
+ CharPtr cp, before, newname;
+ Int4 len_cntry, len_qual, len_name;
+
+ if (biop == NULL || (list = (CharPtr PNTR)userdata) == NULL)
+ {
+ return;
+ }
+
+ for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next)
+ {
+ if (ssp->subtype != SUBSRC_country || ssp->name == NULL) continue;
+ for (ptr = list; ptr != NULL && *ptr != NULL; ptr++)
+ {
+ len_cntry = StringLen (*ptr);
+ cp = StringStr (ssp->name, *ptr);
+ if (cp != NULL && !isalpha (cp [len_cntry]))
+ {
+ len_qual = StringLen (ssp->name);
+ if (cp == ssp->name)
+ {
+ if (len_cntry == len_qual || ssp->name [len_cntry] == ':')
+ {
+ /* exact match, don't need to do anything */
+ return;
+ }
+ ssp->name [len_cntry] = ':';
+ return;
+ }
+ else
+ {
+ if (isalpha (*(cp - 1)))
+ {
+ /* not really a match, part of another word */
+ continue;
+ }
+ else
+ {
+ newname = (CharPtr) MemNew (len_qual + 3);
+ *(cp - 1) = 0;
+ before = StringSave (ssp->name);
+ StringNCpy (newname, *ptr, len_cntry);
+ newname [len_cntry] = ':';
+ newname [len_cntry + 1] = ' ';
+ StringNCpy (newname + len_cntry + 2, before, StringLen (before));
+ StringCpy (newname + len_cntry + 2 + StringLen (before), cp + len_cntry);
+ len_name = StringLen (newname);
+ while (isspace (newname[len_name - 1]) || ispunct (newname [len_name - 1]))
+ {
+ newname [len_name - 1] = 0;
+ len_name --;
+ }
+ before = MemFree (before);
+ MemFree (ssp->name);
+ ssp->name = newname;
+ }
+ }
+ }
+ }
+ }
+}
+
+extern void CountryLookup (IteM i)
+{
+ BaseFormPtr bfp;
+ SeqEntryPtr sep;
+ CharPtr PNTR list;
+
+
+#ifdef WIN_MAC
+ bfp = currentFormDataPtr;
+#else
+ bfp = GetObjectExtra (i);
+#endif
+ if (bfp == NULL) return;
+ sep = GetTopSeqEntryForEntityID (bfp->input_entityID);
+ if (sep == NULL) return;
+
+ list = GetValidCountryList ();
+ if (list == NULL) return;
+ VisitBioSourcesInSep (sep, list, CountryLookupProc);
+ ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
+}
+
diff --git a/sequin/sequin5.c b/sequin/sequin5.c
index db716219..2e45fc3c 100644
--- a/sequin/sequin5.c
+++ b/sequin/sequin5.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 8/26/97
*
-* $Revision: 6.169 $
+* $Revision: 6.171 $
*
* File Description:
*
@@ -3266,7 +3266,7 @@ static void BlastCDD (BioseqPtr bsp, Pointer userdata)
/* do blast search */
- salp = BlastBioseqNet (bl3hp, bsp, "blastp", "oasis_sap", options,
+ salp = BlastBioseqNet (bl3hp, bsp, "blastp", "cdd", options,
NULL, &error_returns, NULL);
/* BlastErrorPrintExtra (error_returns, TRUE, stdout); */
@@ -3314,7 +3314,7 @@ extern void SimpleCDDBlastProc (IteM i)
/* blast fetch enable needed to retrieve by general SeqID */
- BlastNetBioseqFetchEnable (bl3hp, "oasis_sap", FALSE, TRUE);
+ BlastNetBioseqFetchEnable (bl3hp, "cdd", FALSE, TRUE);
bf.bl3hp = bl3hp;
bf.options = options;
@@ -3330,7 +3330,7 @@ extern void SimpleCDDBlastProc (IteM i)
BlastFini (bl3hp);
options = BLASTOptionDelete (options);
- BlastNetBioseqFetchDisable (bl3hp, "oasis_sap", FALSE);
+ BlastNetBioseqFetchDisable (bl3hp, "cdd", FALSE);
ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
@@ -9301,14 +9301,14 @@ static void ProcessBioSourceFunc (BioSourcePtr biop, SourceFormPtr sfp, Boolean
if (ssp != NULL) {
foundit = StringISearch (ssp->name, sfp->findStr);
while (foundit != NULL) {
- offset = foundit - ssp->name;
+ offset = foundit - ssp->name + 1;
EditSourceString (&(ssp->name), sfp, foundit);
foundit = StringISearch (ssp->name + offset, sfp->findStr);
}
} else if (mod != NULL) {
foundit = StringISearch (mod->subname, sfp->findStr);
while (foundit != NULL) {
- offset = foundit - mod->subname;
+ offset = foundit - mod->subname + 1;
EditSourceString (&(mod->subname), sfp, foundit);
foundit = StringISearch (mod->subname + offset, sfp->findStr);
}
diff --git a/sequin/sequin6.c b/sequin/sequin6.c
index 4a0f4b4e..33c8c607 100644
--- a/sequin/sequin6.c
+++ b/sequin/sequin6.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 11/12/97
*
-* $Revision: 6.162 $
+* $Revision: 6.164 $
*
* File Description:
*
@@ -75,6 +75,7 @@ END_ENUM_ALIST
#define IMPORT_FEAT_TYPE 7
#define DEFLINE_TYPE 8
#define FEATURE_NOTE_TYPE 9
+#define PUBLICATION_TYPE 10
#define NUMBER_OF_TYPES 7
#define NUMBER_OF_TYPES_WITH_DEFLINE 8
@@ -91,7 +92,9 @@ static ENUM_ALIST(target_field_alist)
{"DefLine", DEFLINE_TYPE},
END_ENUM_ALIST
-#define NUMBER_OF_SEGREGATE_TYPES 9
+#define NUMBER_OF_SEGREGATE_TYPES 10
+#define NUMBER_OF_PARSE_TYPES 9
+
static ENUM_ALIST(segregate_target_field_alist)
{" ", 0},
{"Gene", GENE_TYPE},
@@ -103,8 +106,34 @@ static ENUM_ALIST(segregate_target_field_alist)
{"Import Feature", IMPORT_FEAT_TYPE},
{"DefLine", DEFLINE_TYPE},
{"Feature Note", FEATURE_NOTE_TYPE},
+ {"Publication", PUBLICATION_TYPE},
+END_ENUM_ALIST
+
+#define NUMBER_OF_PARSE_TYPES 9
+
+static ENUM_ALIST(parse_target_field_alist)
+ {" ", 0},
+ {"Gene", GENE_TYPE},
+ {"CDS", CDS_TYPE},
+ {"Prot", PROT_TYPE},
+ {"RNA", RNA_TYPE},
+ {"BioSource", BIOSOURCE_TYPE},
+ {"OrgMod and SubSource", ORGMOD_SUBSOURCE_TYPE},
+ {"Import Feature", IMPORT_FEAT_TYPE},
+ {"DefLine", DEFLINE_TYPE},
+ {"Feature Note", FEATURE_NOTE_TYPE},
END_ENUM_ALIST
+#define PUBLICATION_PUBLISHED_FIELD 1
+#define PUBLICATION_INPRESS_FIELD 2
+#define PUBLICATION_UNPUB_FIELD 3
+
+static ENUM_ALIST (publication_field_alist)
+ {" ", 0},
+ {"Published", PUBLICATION_PUBLISHED_FIELD},
+ {"In Press", PUBLICATION_INPRESS_FIELD},
+ {"Unpublished", PUBLICATION_UNPUB_FIELD},
+END_ENUM_ALIST
#define EXT_NUMBER_OF_TYPES 7
@@ -350,7 +379,7 @@ static ENUM_ALIST (subsource_subtype_and_note_alist)
END_ENUM_ALIST
-#define NUM_SUBTARGET_POPUPS 10
+#define NUM_SUBTARGET_POPUPS 11
static GbFeatName ParseQualifierList[] = {
{"allele", Class_text}, {"anticodon", Class_pos_aa},
@@ -1618,6 +1647,246 @@ static Boolean DoFeaturesContainText_Callback
return found;
}
+typedef struct objstringdata
+{
+ CharPtr match;
+ Boolean found;
+} ObjStringData, PNTR ObjStringPtr;
+
+static void LIBCALLBACK AsnWriteRemoveForDCallBack (AsnExpOptStructPtr pAEOS)
+
+{
+ CharPtr pchFind;
+ CharPtr pchSource;
+ ObjStringPtr osp;
+
+ osp = (ObjStringPtr) pAEOS->data;
+ if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) {
+ pchSource = (CharPtr) pAEOS->dvp->ptrvalue;
+ pchFind = osp->match;
+ if (StringSearch (pchSource, pchFind) != NULL) {
+ osp->found = TRUE;
+ }
+ }
+}
+
+static Boolean ObjectHasSubstring (ObjMgrTypePtr omtp, AsnIoPtr aip, Pointer ptr, ObjStringPtr osp)
+
+{
+ osp->found = FALSE;
+ (omtp->asnwrite) (ptr, aip, NULL);
+ return osp->found;
+}
+
+static Uint1 GetPubStatus (PubdescPtr pdp)
+{
+ ValNodePtr vnp;
+ CitGenPtr cgp;
+ CitArtPtr cap;
+ CitJourPtr cjp;
+ CitBookPtr cbp;
+ CitSubPtr csp;
+ MedlineEntryPtr mlp;
+ ImprintPtr ip = NULL;
+ Uint1 status = 255; /* 255 is currently not a valid status */
+
+ if (pdp == NULL) return status;
+
+ for (vnp = pdp->pub; vnp != NULL && ip == NULL; vnp = vnp->next)
+ {
+ switch (vnp->choice)
+ {
+ case PUB_Gen:
+ cgp = (CitGenPtr) vnp->data.ptrvalue;
+ if (cgp != NULL && StringICmp (cgp->cit, "Unpublished"))
+ {
+ return PUB_STATUS_UNPUBLISHED;
+ }
+ break;
+ case PUB_Article:
+ case PUB_Medline:
+ if (vnp->choice == PUB_Article)
+ {
+ cap = (CitArtPtr) vnp->data.ptrvalue;
+ }
+ else
+ {
+ cap = NULL;
+ mlp = (MedlineEntryPtr) vnp->data.ptrvalue;
+ if (mlp != NULL)
+ {
+ cap = mlp->cit;
+ }
+ }
+ if (cap != NULL && cap->from == 1)
+ {
+ cjp = (CitJourPtr) cap->fromptr;
+ if (cjp != NULL)
+ {
+ ip = cjp->imp;
+ }
+ }
+ break;
+ case PUB_Man:
+ case PUB_Book:
+ cbp = (CitBookPtr) vnp->data.ptrvalue;
+ if (cbp != NULL)
+ {
+ ip = cbp->imp;
+ }
+ break;
+ case PUB_Sub:
+ csp = (CitSubPtr) vnp->data.ptrvalue;
+ if (csp != NULL)
+ {
+ ip = csp->imp;
+ }
+ break;
+ }
+ }
+ if (ip != NULL)
+ {
+ status = ip->prepub;
+ }
+ return status;
+}
+
+static Boolean DoesPubStatusMatch (PubdescPtr pdp, ConvertFormPtr cfp)
+{
+ Uint1 pub_status;
+
+ if (pdp == NULL || cfp == NULL) return FALSE;
+ if (cfp->subtype == 0) return TRUE;
+
+ pub_status = GetPubStatus (pdp);
+
+ if (cfp->subtype == PUBLICATION_PUBLISHED_FIELD
+ && pub_status == PUB_STATUS_PUBLISHED)
+ {
+ return TRUE;
+ }
+ else if (cfp->subtype == PUBLICATION_INPRESS_FIELD
+ && pub_status == PUB_STATUS_IN_PRESS)
+ {
+ return TRUE;
+ }
+ else if (cfp->subtype == PUBLICATION_UNPUB_FIELD
+ && pub_status == PUB_STATUS_UNPUBLISHED)
+ {
+ return TRUE;
+ }
+ else
+ {
+ return FALSE;
+ }
+}
+
+static Boolean DoesSequenceHavePubWithText (BioseqPtr bsp, ConvertFormPtr cfp)
+{
+ AsnExpOptPtr aeop;
+ AsnIoPtr aip;
+ ObjStringData osd;
+ SeqMgrDescContext dcontext;
+ SeqDescrPtr sdp;
+ SeqMgrFeatContext fcontext;
+ SeqFeatPtr sfp;
+ Boolean rval = FALSE;
+ ObjMgrPtr omp;
+ ObjMgrTypePtr omtp;
+ PubdescPtr pdp;
+
+ if (bsp == NULL || cfp == NULL) return FALSE;
+ omp = ObjMgrGet ();
+ if (omp == NULL) return FALSE;
+ omtp = ObjMgrTypeFind (omp, OBJ_SEQDESC, NULL, NULL);
+ if (omtp == NULL) return FALSE;
+
+ aip = AsnIoNullOpen ();
+ aeop = AsnExpOptNew (aip, NULL, NULL, AsnWriteRemoveForDCallBack);
+ if (aeop != NULL) {
+ aeop->user_data = (Pointer) &osd;
+ }
+ osd.match = cfp->deleteStr;
+
+ /* look for publication descriptors */
+ sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_pub, &dcontext);
+ while (sdp != NULL && !rval) {
+ if (ObjectHasSubstring (omtp, aip, (Pointer) sdp, &osd)) {
+ pdp = (PubdescPtr) sdp->data.ptrvalue;
+ if (DoesPubStatusMatch (pdp, cfp))
+ {
+ rval = TRUE;
+ }
+ }
+ sdp = SeqMgrGetNextDescriptor (bsp, sdp, Seq_descr_pub, &dcontext);
+ }
+
+ if (!rval)
+ {
+ omtp = ObjMgrTypeFind (omp, OBJ_SEQFEAT, NULL, NULL);
+ if (omtp != NULL)
+ {
+ /* look for publication features */
+ sfp = SeqMgrGetNextFeature (bsp, NULL, 0, FEATDEF_PUB, &fcontext);
+ while (sfp != NULL && !rval)
+ {
+ if (ObjectHasSubstring (omtp, aip, (Pointer) sfp, &osd))
+ {
+ pdp = (PubdescPtr) sfp->data.value.ptrvalue;
+ if (DoesPubStatusMatch (pdp, cfp))
+ {
+ rval = TRUE;
+ }
+ }
+ sfp = SeqMgrGetNextFeature (bsp, sfp, 0, FEATDEF_PUB, &fcontext);
+ }
+ }
+ }
+
+ AsnIoClose (aip);
+ return rval;
+}
+
+static Boolean DoesNucProtSetHavePubWithText (BioseqSetPtr bssp, ConvertFormPtr cfp)
+{
+ AsnExpOptPtr aeop;
+ AsnIoPtr aip;
+ ObjStringData osd;
+ SeqDescrPtr sdp;
+ Boolean rval = FALSE;
+ ObjMgrPtr omp;
+ ObjMgrTypePtr omtp;
+ PubdescPtr pdp;
+
+ if (bssp == NULL || cfp == NULL) return FALSE;
+ omp = ObjMgrGet ();
+ if (omp == NULL) return FALSE;
+ omtp = ObjMgrTypeFind (omp, OBJ_SEQDESC, NULL, NULL);
+ if (omtp == NULL) return FALSE;
+
+ aip = AsnIoNullOpen ();
+ aeop = AsnExpOptNew (aip, NULL, NULL, AsnWriteRemoveForDCallBack);
+ if (aeop != NULL) {
+ aeop->user_data = (Pointer) &osd;
+ }
+ osd.match = cfp->deleteStr;
+
+ /* look for publication descriptors */
+ sdp = bssp->descr;
+ while (sdp != NULL && !rval) {
+ if (sdp->choice == Seq_descr_pub && ObjectHasSubstring (omtp, aip, (Pointer) sdp, &osd)) {
+ pdp = (PubdescPtr) sdp->data.ptrvalue;
+ if (DoesPubStatusMatch (pdp, cfp))
+ {
+ rval = TRUE;
+ }
+ }
+ sdp = sdp->next;
+ }
+
+ AsnIoClose (aip);
+ return rval;
+}
static Boolean DoesSequenceContainText (BioseqPtr bsp, ConvertFormPtr cfp)
{
@@ -1659,6 +1928,9 @@ static Boolean DoesSequenceContainText (BioseqPtr bsp, ConvertFormPtr cfp)
found = TRUE;
}
break;
+ case PUBLICATION_TYPE :
+ found = DoesSequenceHavePubWithText (bsp, cfp);
+ break;
default:
break;
}
@@ -1671,6 +1943,10 @@ static Boolean DoesNucProtSetContainText (BioseqSetPtr bssp, ConvertFormPtr cfp)
BioseqPtr bsp;
if (bssp == NULL) return FALSE;
+ if (cfp->type == PUBLICATION_TYPE && DoesNucProtSetHavePubWithText (bssp, cfp))
+ {
+ return TRUE;
+ }
for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
if (IS_Bioseq (sep)) {
bsp = (BioseqPtr) sep->data.ptrvalue;
@@ -1879,8 +2155,13 @@ static void SegregateByText_Callback (ButtoN b)
}
else
cfp->type = (Int2) val;
-
- if (cfp->type != DEFLINE_TYPE && cfp->type != FEATURE_NOTE_TYPE) {
+
+ if (cfp->type == PUBLICATION_TYPE)
+ {
+ GetEnumPopup (cfp->subtarget [cfp->type], cfp->alists [cfp->type], &val);
+ cfp->subtype = (Int2) val;
+ }
+ else if (cfp->type != DEFLINE_TYPE && cfp->type != FEATURE_NOTE_TYPE) {
GetEnumPopup (cfp->subtarget [cfp->type], cfp->alists [cfp->type], &val);
if (0 == val) {
Remove (cfp->form);
@@ -1957,7 +2238,7 @@ static void SetSegregateAcceptButton (Handle a)
SafeDisable (cfp->accept);
return;
}
- } else if (val != DEFLINE_TYPE) {
+ } else if (val != DEFLINE_TYPE && val != PUBLICATION_TYPE) {
cfp->type = (Int2) val;
if (!GetEnumPopup (cfp->subtarget [cfp->type],
@@ -2125,6 +2406,7 @@ extern Int2 LIBCALLBACK CreateSegregateByTextWindow (Pointer data)
cfp->alists [BIOSOURCE_TYPE] = orgref_field_alist;
cfp->alists [ORGMOD_SUBSOURCE_TYPE] = subsource_and_orgmod_note_subtype_alist;
cfp->alists [IMPORT_FEAT_TYPE] = impfeat_field_alist;
+ cfp->alists [PUBLICATION_TYPE] = publication_field_alist;
cfp->feature_list = BuildFeatureValNodeList (TRUE, "All", 255, TRUE, FALSE);
x = HiddenGroup (p, 0, 0, NULL);
@@ -2177,6 +2459,468 @@ extern Int2 LIBCALLBACK CreateSegregateByTextWindow (Pointer data)
return OM_MSG_RET_OK;
}
+
+typedef struct segregatefeatdata {
+ FEATURE_FORM_BLOCK
+
+ PopuP type_popup;
+ ValNodePtr type_list;
+ ButtoN accept;
+
+ BioseqSetPtr target_set;
+ Uint2 segregate_type;
+ Boolean is_feat;
+} SegregateFeatData, PNTR SegregateFeatPtr;
+
+static void CleanupSegregateFeatPage (GraphiC g, VoidPtr data)
+
+{
+ SegregateFeatPtr sfp;
+
+ sfp = (SegregateFeatPtr) data;
+ MemFree (sfp);
+ StdCleanupFormProc (g, data);
+}
+
+static Boolean DoesSequenceContainFeatureType (BioseqPtr bsp, SegregateFeatPtr sfp)
+{
+ SeqMgrFeatContext context;
+ SeqFeatPtr feat;
+
+ feat = NULL;
+ while ((feat = SeqMgrGetNextFeature (bsp, feat, 0, 0, &context)) != NULL)
+ {
+ if (feat->idx.subtype == sfp->segregate_type)
+ {
+ return TRUE;
+ }
+ }
+ return FALSE;
+}
+
+static Boolean DoesNucProtSetContainFeatureType (BioseqSetPtr bssp, SegregateFeatPtr sfp)
+{
+ SeqEntryPtr sep;
+ BioseqPtr bsp;
+
+ if (bssp == NULL) return FALSE;
+ for (sep = bssp->seq_set; sep != NULL; sep = sep->next) {
+ if (IS_Bioseq (sep)) {
+ bsp = (BioseqPtr) sep->data.ptrvalue;
+ if (DoesSequenceContainFeatureType (bsp, sfp)) {
+ return TRUE;
+ }
+ }
+ }
+ return FALSE;
+}
+
+static Boolean DoesSequenceContainDescriptorType (BioseqPtr bsp, SegregateFeatPtr sfp)
+{
+ SeqMgrDescContext context;
+ SeqDescPtr desc;
+
+ if((desc = SeqMgrGetNextDescriptor (bsp, NULL, sfp->segregate_type, &context)) != NULL)
+ {
+ return TRUE;
+ }
+ return FALSE;
+}
+
+typedef struct checkdescdata {
+ Uint2 segregate_type;
+ Boolean found;
+} CheckDescData, PNTR CheckDescPtr;
+
+static void DoesSetContainDescriptorType_Callback (SeqDescPtr sdp, Pointer userdata)
+{
+ CheckDescPtr p;
+
+ if (sdp == NULL || userdata == NULL) return;
+ p = (CheckDescPtr) userdata;
+ if (p->found) return;
+ if (sdp->choice == p->segregate_type) p->found = TRUE;
+}
+
+static Boolean DoesNucProtSetContainDescriptorType (BioseqSetPtr bssp, SegregateFeatPtr sfp)
+{
+ CheckDescData d;
+
+ if (bssp == NULL) return FALSE;
+ d.found = FALSE;
+ d.segregate_type = sfp->segregate_type;
+ VisitDescriptorsInSet (bssp, &d, DoesSetContainDescriptorType_Callback);
+ return d.found;
+}
+
+static Boolean WantToSegregateSequence (BioseqPtr bsp, SegregateFeatPtr sfp)
+{
+ if (bsp == NULL || sfp == NULL) return FALSE;
+ if (sfp->is_feat)
+ {
+ return DoesSequenceContainFeatureType (bsp, sfp);
+ }
+ else
+ {
+ return DoesSequenceContainDescriptorType (bsp, sfp);
+ }
+}
+
+static Boolean WantToSegregateNucProtSet (BioseqSetPtr bssp, SegregateFeatPtr sfp)
+{
+ if (bssp == NULL || sfp == NULL) return FALSE;
+ if (sfp->is_feat)
+ {
+ return DoesNucProtSetContainFeatureType (bssp, sfp);
+ }
+ else
+ {
+ return DoesNucProtSetContainDescriptorType (bssp, sfp);
+ }
+}
+
+/*=========================================================================*/
+/* */
+/* SegregateItemsByFeature () - Given a feature type, move bioseqs */
+/* containing those features to a new popset. */
+/* */
+/*=========================================================================*/
+
+static void SegregateItemsByFeatureOrDescriptor
+(SeqEntryPtr seqlist,
+ SegregateFeatPtr sfp,
+ BioseqSetPtr set1,
+ BioseqSetPtr set2)
+{
+
+ BioseqPtr bsp;
+ BioseqSetPtr this_bssp;
+ SeqEntryPtr this_list;
+ SeqEntryPtr sep, next_sep;
+ SeqEntryPtr set1last, set2last;
+
+
+ if (sfp == NULL || set1 == NULL || set2 == NULL || seqlist == NULL)
+ return;
+
+ set1last = set1->seq_set;
+ while (set1last != NULL && set1last->next != NULL) {
+ set1last = set1last->next;
+ }
+ set2last = set2->seq_set;
+ while (set2last != NULL && set2last->next != NULL) {
+ set2last = set2last->next;
+ }
+
+ sep = seqlist;
+ while (sep != NULL) {
+ next_sep = sep->next;
+ if (IS_Bioseq_set (sep)) {
+ this_bssp = (BioseqSetPtr) sep->data.ptrvalue;
+ if (this_bssp->_class == BioseqseqSet_class_nuc_prot) {
+ if (WantToSegregateNucProtSet (this_bssp, sfp)) {
+ if (set2last == NULL) {
+ set2->seq_set = sep;
+ } else {
+ set2last->next = sep;
+ }
+ set2last = sep;
+ } else {
+ if (set1last == NULL) {
+ set1->seq_set = sep;
+ } else {
+ set1last->next = sep;
+ }
+ set1last = sep;
+ }
+ sep->next = NULL;
+ } else {
+ this_list = this_bssp->seq_set;
+ this_bssp->seq_set = NULL;
+ SegregateItemsByFeatureOrDescriptor (this_list, sfp, set1, set2);
+ }
+ } else if (IS_Bioseq (sep)) {
+ bsp = (BioseqPtr) sep->data.ptrvalue;
+ if (WantToSegregateSequence (bsp, sfp)) {
+ if (set2last == NULL) {
+ set2->seq_set = sep;
+ } else {
+ set2last->next = sep;
+ }
+ set2last = sep;
+ } else {
+ if (set1last == NULL) {
+ set1->seq_set = sep;
+ } else {
+ set1last->next = sep;
+ }
+ set1last = sep;
+ }
+ sep->next = NULL;
+ }
+ sep = next_sep;
+ }
+}
+
+
+/*=========================================================================*/
+/* */
+/* SegregateByFeatureOrDescriptor_Callback () - Segregates sequences that */
+/* contain a selected feature. */
+/* */
+/*=========================================================================*/
+
+static void SegregateByFeatureOrDescriptor_Callback (ButtoN b)
+{
+ SegregateFeatPtr sfp;
+ SeqEntryPtr sep;
+ SeqEntryPtr tmp1, tmp2;
+ UIEnum val;
+ BioseqSetPtr bssp;
+ BioseqSetPtr parent_set;
+ SeqEntryPtr seqlist;
+ BioseqSetPtr newset1, newset2;
+ ObjMgrDataPtr omdptop;
+ ObjMgrData omdata;
+ Uint2 parenttype;
+ Pointer parentptr;
+ SeqEntryPtr last_sep;
+ ValNodePtr vnp;
+
+ /* Check the initial conditions and get the sequence */
+ sfp = (SegregateFeatPtr) GetObjectExtra (b);
+ if (sfp == NULL || sfp->input_entityID == 0 || sfp->target_set == NULL) {
+ Remove (sfp->form);
+ return;
+ }
+
+ sep = GetTopSeqEntryForEntityID (sfp->input_entityID);
+ if (sep == NULL) {
+ Remove (sfp->form);
+ return;
+ }
+
+ SaveSeqEntryObjMgrData (sep, &omdptop, &omdata);
+ GetSeqEntryParent (sep, &parentptr, &parenttype);
+
+ bssp = sfp->target_set;
+
+ parent_set = (BioseqSetPtr)(bssp->idx.parentptr);
+ seqlist = bssp->seq_set;
+ bssp->seq_set = NULL;
+
+ if (parent_set == NULL || parent_set->seq_set == NULL) {
+ newset1 = BioseqSetNew ();
+ if (newset1 == NULL) return;
+ newset2 = BioseqSetNew ();
+ if (newset2 == NULL) return;
+ newset1->_class = bssp->_class;
+ newset2->_class = bssp->_class;
+ tmp1 = SeqEntryNew ();
+ if (tmp1 == NULL) return;
+ tmp1->choice = 2;
+ tmp1->data.ptrvalue = (Pointer) newset1;
+ tmp2 = SeqEntryNew ();
+ if (tmp2 == NULL) return;
+ tmp2->choice = 2;
+ tmp2->data.ptrvalue = (Pointer) newset2;
+ bssp->seq_set = tmp1;
+ tmp1->next = tmp2;
+ bssp->_class = BioseqseqSet_class_genbank;
+ /* Propagate descriptors down */
+ ValNodeLink (&(newset1->descr),
+ AsnIoMemCopy ((Pointer) bssp->descr,
+ (AsnReadFunc) SeqDescrAsnRead,
+ (AsnWriteFunc) SeqDescrAsnWrite));
+ ValNodeLink (&(newset2->descr),
+ AsnIoMemCopy ((Pointer) bssp->descr,
+ (AsnReadFunc) SeqDescrAsnRead,
+ (AsnWriteFunc) SeqDescrAsnWrite));
+ bssp->descr = SeqDescrFree (bssp->descr);
+ } else {
+ last_sep = parent_set->seq_set;
+ newset1 = bssp;
+ newset2 = BioseqSetNew ();
+ if (newset2 == NULL) return;
+ newset2->_class = newset1->_class;
+ tmp1 = SeqEntryNew ();
+ if (tmp1 == NULL) return;
+ tmp1->choice = 2;
+ tmp1->data.ptrvalue = (Pointer) newset2;
+ while (last_sep != NULL && last_sep->next != NULL) {
+ last_sep = last_sep->next;
+ }
+ if (last_sep == NULL) return;
+ last_sep->next = tmp1;
+ /* copy descriptors horizontally */
+ ValNodeLink (&(newset2->descr),
+ AsnIoMemCopy ((Pointer) bssp->descr,
+ (AsnReadFunc) SeqDescrAsnRead,
+ (AsnWriteFunc) SeqDescrAsnWrite));
+ }
+
+ /* Get the feature to look for */
+ val = GetValue (sfp->type_popup);
+ for (vnp = sfp->type_list; vnp != NULL && val > 1; vnp = vnp->next, val--)
+ {
+ }
+ if (vnp == NULL || val != 1)
+ {
+ Remove (sfp->form);
+ return;
+ }
+ sfp->segregate_type = vnp->choice;
+
+ /* Display the 'working' cursor */
+
+ WatchCursor ();
+ Update ();
+
+ /* Do the search and move sequences */
+ SegregateItemsByFeatureOrDescriptor (seqlist, sfp, newset1, newset2);
+
+ /* Remove the window and update things */
+ SeqMgrLinkSeqEntry (sep, parenttype, parentptr);
+ RestoreSeqEntryObjMgrData (sep, omdptop, &omdata);
+ ObjMgrSetDirtyFlag (sfp->input_entityID, TRUE);
+ ObjMgrSendMsg (OM_MSG_UPDATE, sfp->input_entityID, 0, 0);
+
+ ArrowCursor ();
+ Update ();
+ Remove (sfp->form);
+
+ /* Return successfully */
+ return;
+}
+
+
+/*=========================================================================*/
+/* */
+/* CreateSegregateByFeatureWindow () - Creates and then displays the window*/
+/* for getting segregate by text info from the user.*/
+/* */
+/*=========================================================================*/
+
+static Int2 LIBCALLBACK CreateSegregateByFeatureOrDescriptorWindow (Pointer data, Boolean is_feat)
+{
+ GrouP c;
+ SegregateFeatPtr sfp;
+ GrouP g;
+ GrouP h;
+ OMProcControlPtr ompcp;
+ StdEditorProcsPtr sepp;
+ WindoW w;
+ ValNodePtr vnp;
+
+ /* Check parameters and get a pointer to the current data */
+
+ ompcp = (OMProcControlPtr) data;
+ if (ompcp == NULL)
+ return OM_MSG_RET_ERROR;
+
+ if (ompcp->input_itemtype != OBJ_BIOSEQSET || ompcp->input_data == NULL) {
+ Message (MSG_ERROR, "Must select Bioseq Set!");
+ return OM_MSG_RET_ERROR;
+ }
+
+ /* Create a new window, and a struct */
+ /* to pass around the data in. */
+
+ sfp = (SegregateFeatPtr) MemNew (sizeof (SegregateFeatData));
+ if (sfp == NULL)
+ return OM_MSG_RET_ERROR;
+ sfp->is_feat = is_feat;
+
+ if (sfp->is_feat)
+ {
+ w = FixedWindow (-50, -33, -10, -10, "Segregate By Feature",
+ StdCloseWindowProc);
+ }
+ else
+ {
+ w = FixedWindow (-50, -33, -10, -10, "Segregate By Descriptor",
+ StdCloseWindowProc);
+ }
+
+ SetObjectExtra (w, sfp, CleanupSegregateFeatPage);
+ sfp->form = (ForM) w;
+
+ sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
+ if (sepp != NULL) {
+ SetActivate (w, sepp->activateForm);
+ sfp->appmessage = sepp->handleMessages;
+ }
+
+ sfp->input_entityID = ompcp->input_entityID;
+ sfp->input_itemID = ompcp->input_itemID;
+ sfp->input_itemtype = ompcp->input_itemtype;
+ sfp->target_set = (BioseqSetPtr)ompcp->input_data;
+
+ sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
+ if (sepp != NULL) {
+ SetActivate (w, sepp->activateForm);
+ sfp->appmessage = sepp->handleMessages;
+ }
+
+ /* Add the popup lists */
+
+ h = HiddenGroup (w, -1, 0, NULL);
+ SetGroupSpacing (h, 10, 10);
+
+ g = HiddenGroup (h, 3, 0, NULL);
+
+ if (sfp->is_feat)
+ {
+ StaticPrompt (g, "Segregate sequences with the feature", 0, dialogTextHeight,
+ programFont, 'l');
+ sfp->type_list = BuildFeatureValNodeList (TRUE, NULL, 0, TRUE, FALSE);
+ }
+ else
+ {
+ StaticPrompt (g, "Segregate sequences with the descriptor", 0, dialogTextHeight,
+ programFont, 'l');
+ sfp->type_list = BuildDescriptorValNodeList ();
+ }
+
+ sfp->type_popup = PopupList (g, TRUE, NULL);
+ SetObjectExtra (sfp->type_popup, sfp, NULL);
+ for (vnp = sfp->type_list; vnp != NULL; vnp = vnp->next)
+ {
+ PopupItem (sfp->type_popup, (CharPtr) vnp->data.ptrvalue);
+ }
+ SetValue (sfp->type_popup, 1);
+
+ /* Add Accept and Cancel buttons */
+
+ c = HiddenGroup (h, 4, 0, NULL);
+ sfp->accept = DefaultButton (c, "Accept", SegregateByFeatureOrDescriptor_Callback);
+ SetObjectExtra (sfp->accept, sfp, NULL);
+ PushButton (c, "Cancel", StdCancelButtonProc);
+
+ /* Line things up nicely */
+
+ AlignObjects (ALIGN_LEFT, (HANDLE) g, (HANDLE) c, (HANDLE) h, NULL);
+
+ /* Display the window now */
+
+ RealizeWindow (w);
+ Show (w);
+ Select (w);
+ Select (sfp->accept);
+ Update ();
+ return OM_MSG_RET_OK;
+}
+
+extern Int2 LIBCALLBACK CreateSegregateByFeatureWindow (Pointer data)
+{
+ return CreateSegregateByFeatureOrDescriptorWindow (data, TRUE);
+}
+
+extern Int2 LIBCALLBACK CreateSegregateByDescriptorWindow (Pointer data)
+{
+ return CreateSegregateByFeatureOrDescriptorWindow (data, FALSE);
+}
+
static CharPtr SaveOrReplaceStringCopy (ConvertFormPtr cfp, CharPtr str, CharPtr current)
{
@@ -2919,7 +3663,7 @@ static void ConvertFromFlatFile (Uint2 entityID, SeqEntryPtr sep, ConvertFormPtr
bssp = (BioseqSetPtr) sep->data.ptrvalue;
} else return;
- ajp = asn2gnbk_setup (bsp, bssp, NULL, format, SEQUIN_MODE, NORMAL_STYLE, 0, 0, 0, NULL);
+ ajp = asn2gnbk_setup (bsp, bssp, NULL, (FmtType)format, SEQUIN_MODE, NORMAL_STYLE, 0, 0, 0, NULL);
if (ajp != NULL) {
goOn = TRUE;
for (index = 0; index < ajp->numParagraphs && goOn; index++) {
@@ -3618,7 +4362,7 @@ static void BuildParseToAnywhereDialog (IteM i, Int4 parsetype)
SetObjectExtra (w, cfp, CleanupParseForm);
cfp->form = (ForM) w;
cfp->formmessage = ConvertMessageProc;
- cfp->target_alist = segregate_target_field_alist;
+ cfp->target_alist = parse_target_field_alist;
cfp->set_accept_proc = (PupActnProc) SetSegregateAcceptButton;
sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm");
@@ -3688,7 +4432,7 @@ static void BuildParseToAnywhereDialog (IteM i, Int4 parsetype)
x = HiddenGroup (p, 0, 0, NULL);
- for (j = 1; j <= NUMBER_OF_SEGREGATE_TYPES; j++) {
+ for (j = 1; j <= NUMBER_OF_PARSE_TYPES; j++) {
if (j == ORGMOD_SUBSOURCE_TYPE) {
cfp->subtarget [j] = (PopuP) SingleList (x, 10, 8, (LstActnProc) cfp->set_accept_proc);
SetObjectExtra (cfp->subtarget [j], cfp, NULL);
diff --git a/sequin/sequin7.c b/sequin/sequin7.c
index 7b8c7e92..63218505 100644
--- a/sequin/sequin7.c
+++ b/sequin/sequin7.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 1/3/98
*
-* $Revision: 6.144 $
+* $Revision: 6.148 $
*
* File Description:
*
@@ -7195,9 +7195,11 @@ static Boolean CDSMeetsStringConstraint (SeqFeatPtr sfp,
extern Boolean MeetsStringConstraint (SeqFeatPtr sfp,
CharPtr findThisStr)
{
- GBQualPtr gbqp;
- GeneRefPtr grp;
- RnaRefPtr rrp;
+ GBQualPtr gbqp;
+ GeneRefPtr grp;
+ RnaRefPtr rrp;
+ SeqMgrFeatContext context;
+ Boolean have_context = FALSE;
/* If no string constraint, then everyone matches */
@@ -7226,6 +7228,15 @@ extern Boolean MeetsStringConstraint (SeqFeatPtr sfp,
gbqp = gbqp->next;
}
+ if (SeqMgrGetDesiredFeature (sfp->idx.entityID, NULL, 0, 0, sfp, &context) != NULL)
+ {
+ if (StringISearch (context.label, findThisStr))
+ {
+ return TRUE;
+ }
+ have_context = TRUE;
+ }
+
if (sfp->data.choice == SEQFEAT_GENE)
{
grp = sfp->data.value.ptrvalue;
@@ -7250,6 +7261,15 @@ extern Boolean MeetsStringConstraint (SeqFeatPtr sfp,
if (StringISearch ((CharPtr) rrp->ext.value.ptrvalue, findThisStr))
return TRUE;
}
+ else if (rrp->type == 3 && rrp->ext.choice == 2 && have_context)
+ {
+ /* look for the label as it appears to the user */
+ if (StringNCmp(findThisStr, "tRNA-", 5) == 0
+ && StringISearch (context.label, findThisStr + 5))
+ {
+ return TRUE;
+ }
+ }
}
/* If we got to here, then the string constraint was not found */
@@ -8123,7 +8143,7 @@ static void MarkProteinCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, In
}
}
-extern void RemoveProteins (IteM i)
+extern void RemoveProteinsAndOptionallyRenormalize (IteM i, Boolean renormalize)
{
BaseFormPtr bfp;
@@ -8167,12 +8187,26 @@ extern void RemoveProteins (IteM i)
ValNodeFree (vnp);
SeqMgrLinkSeqEntry (sep, parenttype, parentptr);
RestoreSeqEntryObjMgrData (sep, omdptop, &omdata);
+ if (renormalize)
+ {
+ RenormalizeNucProtSets (sep, TRUE);
+ }
ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE);
ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0);
ObjMgrDeSelect (0, 0, 0, 0, NULL);
Update ();
}
+extern void RemoveProteins (IteM i)
+{
+ RemoveProteinsAndOptionallyRenormalize (i, FALSE);
+}
+
+extern void RemoveProteinsAndRenormalize (IteM i)
+{
+ RemoveProteinsAndOptionallyRenormalize (i, TRUE);
+}
+
#define EDIT_FIVE_PRIME 1
#define EDIT_THREE_PRIME 2
@@ -9009,7 +9043,7 @@ WriteAlignmentInterleaveToFile
MemSet (printed_line, ' ', printed_line_len - 2);
label_pos = alnlabels + (row - 1) * (label_len + 1) * sizeof (Char);
MemCpy (printed_line, label_pos, StringLen (label_pos));
- AlignmentIntervalToString (salp, row, start, stop, 1, FALSE,
+ AlignmentIntervalToString (salp, row, start, stop, 1, TRUE,
seqbuf, alnbuf, &alnbuf_len);
MemCpy (printed_line + label_len + 1, alnbuf, alnbuf_len);
fprintf (fp, printed_line);
@@ -9028,8 +9062,95 @@ WriteAlignmentInterleaveToFile
}
}
+static void WriteAlignmentContiguousToFile
+(SeqAlignPtr salp,
+ FILE *fp)
+{
+ Int4 num_segments;
+ SeqAlignPtr tmp_salp;
+ Int4 idx;
+ CharPtr PNTR alnlabels = NULL;
+ Int4Ptr label_len = NULL;
+ Int4Ptr aln_len = NULL;
+ Uint1Ptr alnbuf = NULL;
+ Uint1Ptr seqbuf = NULL;
+ CharPtr printed_line = NULL;
+ Int4 alnbuf_len;
+ Int4 printed_line_len;
+ CharPtr label_pos;
+ Int4 row, start, stop;
+ Int4 seq_chars_per_row = 80;
+
+ if (salp == NULL || fp == NULL) return;
+
+ num_segments = 0;
+ for (tmp_salp = salp; tmp_salp != NULL; tmp_salp = tmp_salp->next)
+ {
+ num_segments++;
+ }
+
+
+ /* get labels and lengths for all segments */
+ alnlabels = (CharPtr PNTR) MemNew (sizeof (CharPtr) * num_segments);
+ label_len = (Int4Ptr) MemNew (sizeof (Int4) * num_segments);
+ aln_len = (Int4Ptr) MemNew (sizeof (Int4) * num_segments);
+ if (alnlabels != NULL && label_len != NULL && aln_len != NULL)
+ {
+ for (tmp_salp = salp, idx = 0; tmp_salp != NULL, idx < num_segments; tmp_salp = tmp_salp->next, idx++)
+ {
+ alnlabels [idx] = GetSeqAlignLabels (tmp_salp, &label_len[idx]);
+ aln_len [idx]= AlnMgr2GetAlnLength(tmp_salp, FALSE);
+
+ }
+
+ /* get buffers */
+ alnbuf = (Uint1Ptr) MemNew (seq_chars_per_row * sizeof (Uint1));
+ seqbuf = (Uint1Ptr) MemNew (seq_chars_per_row * sizeof (Uint1));
+ printed_line_len = seq_chars_per_row + 3;
+ printed_line = (CharPtr) MemNew (printed_line_len * sizeof (Char));
+ if (alnbuf != NULL && seqbuf != NULL && printed_line != NULL) {
+ printed_line [ printed_line_len - 1] = 0;
+ printed_line [ printed_line_len - 2] = '\n';
+
+ for (row = 1; row <= salp->dim; row++) {
+ if (salp->next != NULL)
+ {
+ fprintf (fp, "[\n");
+ }
+ for (tmp_salp = salp, idx = 0; tmp_salp != NULL, idx < num_segments; tmp_salp = tmp_salp->next, idx++)
+ {
+ label_pos = alnlabels [idx] + (row - 1) * (label_len[idx] + 1) * sizeof (Char);
+ fprintf (fp, ">%s\n", label_pos);
+ start = 0;
+ stop = seq_chars_per_row - 1;
+ while (start < aln_len [idx]) {
+ MemSet (printed_line, ' ', printed_line_len - 2);
+ AlignmentIntervalToString (tmp_salp, row, start, stop, 1, TRUE,
+ seqbuf, alnbuf, &alnbuf_len);
+ MemCpy (printed_line, alnbuf, alnbuf_len);
+ fprintf (fp, printed_line);
+ start = stop + 1;
+ stop += seq_chars_per_row;
+ }
+ fprintf (fp, "\n");
+ }
+ if (salp->next != NULL)
+ {
+ fprintf (fp, "]\n");
+ }
+ }
+ }
+ MemFree (alnbuf);
+ MemFree (seqbuf);
+ MemFree (printed_line);
+ }
+ MemFree (label_len);
+ MemFree (alnlabels);
+ MemFree (aln_len);
+}
+
static void
-WriteAlignmentContiguousToFile
+OldWriteAlignmentContiguousToFile
(SeqAlignPtr salp,
FILE *fp)
{
@@ -9085,26 +9206,83 @@ WriteAlignmentContiguousToFile
}
}
+static SetAlignmentDim (SeqAlignPtr salp)
+{
+ AMAlignIndex2Ptr amaip;
+ DenseSegPtr dsp;
+
+ if (salp == NULL || salp->dim > 0 || salp->saip == NULL) return;
+
+ if (salp->saip->indextype == INDEX_PARENT)
+ {
+ amaip = (AMAlignIndex2Ptr)(salp->saip);
+ salp->dim = amaip->sharedaln->dim;
+ }
+ else if (salp->saip->indextype == INDEX_CHILD)
+ {
+ dsp = (DenseSegPtr)(salp->segs);
+ salp->dim = dsp->dim;
+ }
+}
+
+static void IndexAlignmentSet (SeqAlignPtr salp)
+{
+ SeqAlignPtr tmp_salp, next_salp;
+
+ if (salp == NULL || salp->saip != NULL) return;
+
+ if (salp->next != NULL && salp->dim > 2)
+ {
+ for (tmp_salp = salp; tmp_salp != NULL; tmp_salp = tmp_salp->next)
+ {
+ next_salp = tmp_salp->next;
+ tmp_salp->next = NULL;
+ if (tmp_salp->segtype == SAS_DENSEG && tmp_salp->next == NULL) {
+ AlnMgr2IndexSingleChildSeqAlign(tmp_salp);
+ } else {
+ AlnMgr2IndexSeqAlign(tmp_salp);
+ }
+ SetAlignmentDim (tmp_salp);
+ tmp_salp->next = next_salp;
+ }
+ }
+ else
+ {
+ if (salp->segtype == SAS_DENSEG && salp->next == NULL) {
+ AlnMgr2IndexSingleChildSeqAlign(salp);
+ } else {
+ AlnMgr2IndexSeqAlign(salp);
+ }
+ SetAlignmentDim (salp);
+ }
+}
+
static void WriteSeqEntryAlignmentToFile (SeqEntryPtr sep, FILE *fp, Boolean Interleave)
{
BioseqSetPtr bssp;
SeqAnnotPtr sap;
- SeqAlignPtr salp;
+ SeqAlignPtr salp = NULL;
if (sep == NULL || ! IS_Bioseq_set (sep)) return;
bssp = (BioseqSetPtr) sep->data.ptrvalue;
if (bssp == NULL) return;
for (sap = bssp->annot; sap != NULL; sap = sap->next) {
if (sap->type == 2) {
- salp = (SeqAlignPtr) sap->data;
- if (salp->saip == NULL) {
- AlnMgr2IndexSingleChildSeqAlign (salp);
- }
+ salp = SeqAlignListDup((SeqAlignPtr) sap->data);
+ IndexAlignmentSet (salp);
+
if (Interleave) {
+ if (salp->next != NULL)
+ {
+ Message (MSG_ERROR, "Unable to write segmented alignments as interleave");
+ return;
+ }
WriteAlignmentInterleaveToFile (salp, fp);
} else {
WriteAlignmentContiguousToFile (salp, fp);
}
+ SeqAlignFree (salp);
+ salp = NULL;
}
}
diff --git a/sequin/sequin8.c b/sequin/sequin8.c
index 4030fd05..fd9ede6d 100644
--- a/sequin/sequin8.c
+++ b/sequin/sequin8.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 2/3/98
*
-* $Revision: 6.255 $
+* $Revision: 6.256 $
*
* File Description:
*
@@ -3343,6 +3343,27 @@ static int LIBCALLBACK SortMostUsedDescriptorsFirst (VoidPtr ptr1, VoidPtr ptr2)
}
}
+extern ValNodePtr BuildDescriptorValNodeList (void)
+{
+ Int4 j;
+ ValNodePtr vnp;
+ ValNodePtr head = NULL;
+
+ for (j = 1; descNames [j] != NULL; j++) {
+ if (StringHasNoText (descNames [j])) continue;
+ vnp = ValNodeNew (head);
+ if (head == NULL) {
+ head = vnp;
+ }
+ if (vnp != NULL) {
+ vnp->choice = j;
+ vnp->data.ptrvalue = StringSave (descNames [j]);
+ }
+ }
+ head = SortValNode (head, SortMostUsedDescriptorsFirst);
+ return head;
+}
+
static void RemoveAsnObject (IteM i, Boolean feature)
{
@@ -3413,18 +3434,7 @@ static void RemoveAsnObject (IteM i, Boolean feature)
if (feature) {
head = BuildFeatureValNodeList (TRUE, "All", ALL_FEATURES, TRUE, FALSE);
} else {
- for (j = 1; descNames [j] != NULL; j++) {
- if (StringHasNoText (descNames [j])) continue;
- vnp = ValNodeNew (head);
- if (head == NULL) {
- head = vnp;
- }
- if (vnp != NULL) {
- vnp->choice = j;
- vnp->data.ptrvalue = StringSave (descNames [j]);
- }
- }
- head = SortValNode (head, SortMostUsedDescriptorsFirst);
+ head = BuildDescriptorValNodeList();
}
if (head != NULL) {
diff --git a/sequin/sequin9.c b/sequin/sequin9.c
index 0f8a4845..802fb0c2 100644
--- a/sequin/sequin9.c
+++ b/sequin/sequin9.c
@@ -29,7 +29,7 @@
*
* Version Creation Date: 4/20/99
*
-* $Revision: 6.254 $
+* $Revision: 6.260 $
*
* File Description:
*
@@ -4445,7 +4445,8 @@ static TransTablePtr GetTranslationTable (CdRegionPtr crp, Boolean PNTR table_is
static CharPtr ExtendProtein5
(SeqFeatPtr sfp,
- Uint2 input_entityID)
+ Uint2 input_entityID,
+ Boolean force_partial)
{
CdRegionPtr crp;
TransTablePtr tbl = NULL;
@@ -4486,8 +4487,14 @@ static CharPtr ExtendProtein5
strand = SeqLocStrand (sfp->location);
sip = SeqLocId (sfp->location);
offset = -1;
+
+ start = GetOffsetInBioseq (test_slp, nucBsp, SEQLOC_START);
+ if (start == 0)
+ {
+ stop_looking = TRUE;
+ }
- while (! found_start && ! found_stop && ! stop_looking) {
+ while (((! found_start && ! found_stop) || force_partial) && ! stop_looking) {
start = GetOffsetInBioseq (test_slp, nucBsp, SEQLOC_START);
stop = GetOffsetInBioseq (test_slp, nucBsp, SEQLOC_STOP);
if (strand == Seq_strand_minus) {
@@ -4537,7 +4544,7 @@ static CharPtr ExtendProtein5
MemFree (bases);
}
}
-
+
SeqLocFree (test_slp);
if (! found_stop) {
start = GetOffsetInBioseq (sfp->location, nucBsp, SEQLOC_START);
@@ -4552,12 +4559,16 @@ static CharPtr ExtendProtein5
CheckSeqLocForPartial (sfp->location, &partial5, &partial3);
SetSeqLocPartial (sfp->location, TRUE, partial3);
sfp->partial = TRUE;
+ if (crp->frame == 0)
+ {
+ crp->frame = 1;
+ }
if (strand == Seq_strand_minus) {
sfp->location = ExpandSeqLoc (stop, nucBsp->length - 1, strand, nucBsp, sfp->location);
- crp->frame = (nucBsp->length - 1 - start) % 3 + 1;
+ crp->frame = (nucBsp->length - 1 - start + crp->frame - 1) % 3 + 1;
} else {
sfp->location = ExpandSeqLoc (0, stop, strand, nucBsp, sfp->location);
- crp->frame = start % 3 + 1;
+ crp->frame = (start + crp->frame - 1) % 3 + 1;
}
}
}
@@ -4573,7 +4584,8 @@ static CharPtr ExtendProtein5
static CharPtr ExtendProtein3
(SeqFeatPtr sfp,
- Uint2 input_entityID)
+ Uint2 input_entityID,
+ Boolean force_partial)
{
BioseqPtr nucBsp;
Int4 max_stop, min_start, start, stop;
@@ -4609,7 +4621,14 @@ static CharPtr ExtendProtein3
contains_stop = FALSE;
contains_start = FALSE;
newprot = NULL;
- while (! contains_stop &&
+ /* need to initialize newprot in case we're already at the edge */
+ if ((strand != Seq_strand_minus && stop == max_stop)
+ || (strand == Seq_strand_minus && stop == min_start))
+ {
+ newprot = FixProteinString (sfp, strand, FALSE, &truncated,
+ &contains_start, &contains_stop);
+ }
+ while ((! contains_stop || force_partial) &&
( (strand == Seq_strand_minus && stop > min_start)
|| (strand != Seq_strand_minus && stop < max_stop)))
{
@@ -4634,7 +4653,7 @@ static CharPtr ExtendProtein3
&contains_start, &contains_stop);
}
- if (! contains_stop) {
+ if (! contains_stop || force_partial) {
start = GetOffsetInBioseq (sfp->location, nucBsp, SEQLOC_START);
stop = GetOffsetInBioseq (sfp->location, nucBsp, SEQLOC_STOP);
if (strand == Seq_strand_minus) {
@@ -4673,6 +4692,8 @@ PrepareUpdatePtrForProtein
Uint1 strand;
SeqLocPtr newloc;
BioseqPtr nucBsp;
+ Boolean partial5, partial3;
+
if (sfp == NULL
|| sfp->idx.subtype != FEATDEF_CDS
@@ -4683,7 +4704,9 @@ PrepareUpdatePtrForProtein
{
return NULL;
}
-
+
+ CheckSeqLocForPartial (sfp->location, &partial3, &partial5);
+
nucBsp = GetBioseqGivenSeqLoc (sfp->location, input_entityID);
if (nucBsp == NULL) return NULL;
newloc = SeqLocMerge (nucBsp, sfp->location, NULL, FALSE, FALSE, FALSE);
@@ -4701,17 +4724,18 @@ PrepareUpdatePtrForProtein
&contains_start, &contains_stop);
/* Must do 3' end first, otherwise may truncate at stops introduced by expanding 5' end for partiality */
- if (! contains_stop && extend_proteins3 && transl_except_len == 0) {
+ if ((! contains_stop && extend_proteins3 && transl_except_len == 0)
+ || ((extend_proteins3 || partial3) && !truncate_proteins)) {
MemFree (newprot);
- newprot = ExtendProtein3 (sfp, input_entityID);
+ newprot = ExtendProtein3 (sfp, input_entityID, partial3 && !truncate_proteins);
if (newprot == NULL) return NULL;
*extended3 = TRUE;
} else {
*extended3 = FALSE;
}
- if (! contains_start && extend_proteins5) {
+ if (! contains_start && (extend_proteins5 || partial5)) {
MemFree (newprot);
- newprot = ExtendProtein5 (sfp, input_entityID);
+ newprot = ExtendProtein5 (sfp, input_entityID, partial5);
if (newprot == NULL) return NULL;
*extended5 = TRUE;
} else {
@@ -6818,7 +6842,7 @@ static void DetermineButtonState (UpsDataPtr udp,
/* Replace */
- else if (udp->new5 >= udp->old5 && udp->new3 >= udp->old3) {
+ else {
SetValue (udp->rmc, 1);
Disable (*extend5ButtonPtr);
Disable (*extend3ButtonPtr);
@@ -6827,7 +6851,7 @@ static void DetermineButtonState (UpsDataPtr udp,
}
/* Patch */
-
+/* This section removed - do not set patch as a default
else if (udp->new5 <= udp->old5 && udp->new3 <= udp->old3) {
SetValue (udp->rmc, 4);
Disable (*extend5ButtonPtr);
@@ -6836,14 +6860,13 @@ static void DetermineButtonState (UpsDataPtr udp,
udp->recomb2 = udp->aln_length;
/* If patch sequence matches, must be feature propagation only */
-
- if (StringNICmp (udp->seq1 + udp->old5 - udp->new5,
+/* if (StringNICmp (udp->seq1 + udp->old5 - udp->new5,
udp->seq2,
StringLen (udp->seq2)) == 0) {
SetValue (udp->sfb, 2);
Disable (udp->sfb);
}
- }
+ } */
/* If no features, must be sequence update only */
@@ -7561,7 +7584,7 @@ static Int2 UpdateNextBioseqInFastaSet (UpsDataPtr udp)
/* */
/*=====================================================================*/
-extern void UpdateFastaSetEx (IteM i, Boolean use_new_blast)
+static void UpdateFastaSetEx (IteM i, Boolean use_new_blast)
{
BaseFormPtr bfp;
FILE *fp;
@@ -7788,13 +7811,13 @@ extern void NewExtendSequence (IteM i)
NewUpdateOrExtendSequence (i, FALSE, FALSE);
}
-extern void NewExtendSequenceNewBlast (IteM i)
+static void NewExtendSequenceNewBlast (IteM i)
{
NewUpdateOrExtendSequence (i, FALSE, TRUE);
}
-extern void UpdateSeqAfterDownloadEx
+static void UpdateSeqAfterDownloadEx
(BaseFormPtr bfp,
BioseqPtr oldbsp,
BioseqPtr newbsp,
@@ -7870,7 +7893,7 @@ extern void UpdateSeqAfterDownload
UpdateSeqAfterDownloadEx (bfp, oldbsp, newbsp, FALSE);
}
-extern void ExtendSeqAfterDownloadEx
+static void ExtendSeqAfterDownloadEx
(BaseFormPtr bfp,
BioseqPtr oldbsp,
BioseqPtr newbsp,
@@ -9018,6 +9041,7 @@ static ForM FeaturePropagateForm (
fdp->transPast = CheckBox (g, "Translate CDS after partial 3' boundary", NULL);
fdp->fixCDS = CheckBox (g, "Cleanup CDS partials after propagation", NULL);
+ SetStatus (fdp->fixCDS, TRUE);
fdp->fuseJoints = CheckBox (g, "Fuse adjacent propagated intervals", NULL);
SetStatus (fdp->fuseJoints, TRUE);
@@ -10106,11 +10130,6 @@ NLM_EXTERN SeqAlignPtr Sqn_LocalAlign2SeqEx (BioseqPtr bsp1, BioseqPtr bsp2, Boo
return sap_final;
}
-NLM_EXTERN SeqAlignPtr Sqn_LocalAlign2Seq (BioseqPtr bsp1, BioseqPtr bsp2, BoolPtr revcomp)
-{
- return Sqn_LocalAlign2SeqEx (bsp1, bsp2, revcomp, FALSE);
-}
-
/* End of implementation of the new BLAST library .
*/
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-03 10:24:41 +0000