diff options
Diffstat (limited to 'sequin/sequin.h')
| -rw-r--r-- | sequin/sequin.h | 176 |
1 files changed, 135 insertions, 41 deletions
diff --git a/sequin/sequin.h b/sequin/sequin.h index b27516a2..aa5bff85 100644 --- a/sequin/sequin.h +++ b/sequin/sequin.h @@ -29,7 +29,7 @@ * * Version Creation Date: 1/22/95 * -* $Revision: 6.477 $ +* $Revision: 6.513 $ * * File Description: * @@ -167,7 +167,6 @@ extern void ExtendFastaSet (IteM i); extern void ExtendAllSequencesInSet (IteM i); extern void SeqLocAdjustByOffset (SeqLocPtr slp, Int4 offset); extern void SplitSegmentedFeatsMenuItem (IteM i); -extern SeqLocPtr SeqLocWholeNew (BioseqPtr bsp); extern SeqFeatPtr SeqFeatCopy (SeqFeatPtr sfp); extern SeqLocPtr SeqLocReplaceLocalID (SeqLocPtr slp, SeqIdPtr new_sip); @@ -248,6 +247,7 @@ extern void EditPubsEx (BaseFormPtr bfp); extern void RemovePubConsortiums (IteM i); extern void ExtendPartialFeatures (IteM i); +extern void ExtendPartialFeaturesWithConstraint (IteM i); extern void TrimOrganismName (IteM i); extern void SUCSubmitterProc (IteM i); @@ -348,7 +348,6 @@ extern Uint2 PackageFormResults (SequinBlockPtr sbp, SeqEntryPtr sep, extern void EnableFeaturesPerTarget (BaseFormPtr bfp); extern void EnableAnalysisItems (BaseFormPtr bfp, Boolean isDocSum); -extern Int4 ExtendSeqLocToEnd (SeqLocPtr slp, BioseqPtr bsp, Boolean end5); extern void ExtendSeqLocToPosition (SeqLocPtr slp, Boolean end5, Int4 pos); #define REGISTER_BIOSEQ_SEG_EDIT ObjMgrProcLoad(OMPROC_EDIT,"Edit Bioseq Seg","BioseqSegEditor",OBJ_BIOSEQ_SEG,0,OBJ_BIOSEQ_SEG,0,NULL,BioseqSegEditFunc,PROC_PRIORITY_DEFAULT) @@ -435,7 +434,6 @@ extern void CombineMultipleCDS (IteM i); extern void NewDescriptorMenuFunc (ObjMgrProcPtr ompp, BaseFormPtr bfp, Uint2 descsubtype); extern Boolean PropagateFromGenBankBioseqSet (SeqEntryPtr sep, Boolean ask); -extern CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn); extern int LIBCALLBACK SortByVnpChoice (VoidPtr ptr1, VoidPtr ptr2); extern void PrepareToConvertToCDS (SeqEntryPtr sep, Uint2 entityID, Uint2 subtype, CharPtr findthis); @@ -449,23 +447,21 @@ extern void ChangeGenBankNameToLocal (IteM i); extern void RemoveGBIDsFromBioseqs (IteM i); extern void RemoveGBIDsFromProteins (IteM i); extern void RemoveGIsFromBioseqs (IteM i); -extern CharPtr MergeValNodeStrings (ValNodePtr list, Boolean useReturn); extern void CommonApplyToAllProc (BaseFormPtr bfp, Int2 type); extern void ApplyTitle (IteM i); extern void ApplyCDS (IteM i); extern void ApplyRRNA (IteM i); extern void ApplyImpFeat (IteM i); -extern void AdjustCDSLocationsForUnknownGapsCallback (SeqFeatPtr sfp, Pointer userdata); extern void AdjustCDSLocationsForKnownAndUnknownGapsCallback (SeqFeatPtr sfp, Pointer userdata); extern void AdjustFeaturesForGaps (IteM i); extern void LoadTPAAccessionNumbersFromFile (IteM i); extern void LoadSecondaryAccessionNumbersFromFile (IteM i); extern void LoadHistoryAccessionNumbersFromFile (IteM i); extern void LoadOrganismModifierTable (IteM i); +extern void LoadTaxConsult (IteM i); extern void ExportOrganismTable (IteM i); extern void LoadFeatureQualifierTable (IteM i); -extern CharPtr GetModifierPopupPositionName (Int2 val); extern void AddCodonListTotRNA (tRNAPtr trna, ValNodePtr codons); @@ -807,13 +803,6 @@ extern void LogCDSAmbiguousFrame (LogInfoPtr lip, SeqFeatPtr sfp); extern void LoadGenomeProjectIDsFromFile (IteM i); extern void RemoveEmptyGenomeProjectIDs (IteM i); -typedef struct sourcequaldesc -{ - CharPtr name; - Boolean isOrgMod; - Uint1 subtype; -} SourceQualDescData, PNTR SourceQualDescPtr; - extern CharPtr SourceQualValNodeName (ValNodePtr vnp); extern ValNodePtr SourceQualValNodeDataCopy (ValNodePtr vnp); extern Boolean SourceQualValNodeMatch (ValNodePtr vnp1, ValNodePtr vnp2); @@ -888,7 +877,7 @@ extern void ExportLastLineage (IteM i); #define LOCATION_CONSTRAINT_NUC_SEQ 2 #define LOCATION_CONSTRAINT_PROT_SEQ 3 -typedef struct locationconstraint +typedef struct LocationConstraintX { Int4 left; Int4 right; @@ -896,7 +885,7 @@ typedef struct locationconstraint Int4 match_choice; Int4 strand; Int4 sequence_type; -} LocationConstraintData, PNTR LocationConstraintPtr; +} LocationConstraintXData, PNTR LocationConstraintXPtr; typedef enum { @@ -914,9 +903,9 @@ typedef struct stringconstraint Boolean insensitive; Boolean whole_word; Boolean not_present; -} StringConstraintData, PNTR StringConstraintPtr; +} StringConstraintData, PNTR StringConstraintXPtr; -extern StringConstraintPtr StringConstraintFree (StringConstraintPtr scp); +extern StringConstraintXPtr StringConstraintXFree (StringConstraintXPtr scp); typedef struct pseudoconstraint { @@ -935,7 +924,7 @@ typedef struct choiceconstraint Int4 constraint_type; ValNodePtr qual_choice; ValNodePtr qual_choice_match; - StringConstraintPtr string_constraint; + StringConstraintXPtr string_constraint; PseudoConstraintPtr pseudo_constraint; FreeValNodeProc free_vn_proc; CopyValNodeDataProc copy_vn_proc; @@ -943,20 +932,38 @@ typedef struct choiceconstraint extern ChoiceConstraintPtr ChoiceConstraintFree (ChoiceConstraintPtr scp); +typedef struct sequenceconstraint +{ + Boolean nucs_ok; + Boolean prots_ok; + + Int4 other_constraint_type; + StringConstraintXPtr string_constraint; + ChoiceConstraintPtr source_constraint; + ValNodePtr feature_list; + +} SequenceConstraintXData, PNTR SequenceConstraintXPtr; + +extern SequenceConstraintXPtr SequenceConstraintXFree (SequenceConstraintXPtr scp); +extern DialoG SequenceConstraintXDialog (GrouP g); +extern Boolean DoesSequenceMatchSequenceConstraintX (BioseqPtr bsp, SequenceConstraintXPtr scp); + + + typedef struct filterset { - StringConstraintPtr scp; + StringConstraintXPtr scp; ChoiceConstraintPtr ccp; - LocationConstraintPtr lcp; + LocationConstraintXPtr lcp; ChoiceConstraintPtr cgp; - StringConstraintPtr id_list; + StringConstraintXPtr id_list; } FilterSetData, PNTR FilterSetPtr; extern void FilterSetClearText (FilterSetPtr fsp); extern FilterSetPtr FilterSetNew (void); extern FilterSetPtr FilterSetFree (FilterSetPtr fsp); -extern Boolean DoesStringMatchConstraint (CharPtr pchSource, StringConstraintPtr scp); +extern Boolean DoesStringMatchConstraintX (CharPtr pchSource, StringConstraintXPtr scp); typedef CharPtr (*GetFeatureFieldString) PROTO ((SeqFeatPtr, ValNodePtr, FilterSetPtr)); typedef void (*SetFeatureFieldString) PROTO ((SeqFeatPtr, Pointer, FilterSetPtr)); @@ -999,18 +1006,18 @@ typedef struct textportion CharPtr end_text; Boolean insensitive; Boolean whole_word; -} TextPortionData, PNTR TextPortionPtr; +} TextPortionXData, PNTR TextPortionXPtr; -extern TextPortionPtr TextPortionFree (TextPortionPtr tp); +extern TextPortionXPtr TextPortionXFree (TextPortionXPtr tp); extern void -FindTextPortionInString +FindTextPortionXInString (CharPtr str, - TextPortionPtr tp, + TextPortionXPtr tp, CharPtr PNTR ploc, Int4Ptr plen); -extern DialoG TextPortionDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata); -extern DialoG TextPortionDialog (GrouP h); +extern DialoG TextPortionXDialogEx (GrouP h, Boolean inside, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata); +extern DialoG TextPortionXDialog (GrouP h); #define CONVERT_TYPE_MOVE 0 #define CONVERT_TYPE_COPY 1 @@ -1031,13 +1038,13 @@ typedef struct convertfield RemoveDescriptorFieldString remove_d_str_func; NameFromValNodeProc name_field_func; FilterSetPtr fsp; - TextPortionPtr text_portion; + TextPortionXPtr text_portion; Boolean strip_name_from_text; Boolean remove_parsed; } ConvertFieldData, PNTR ConvertFieldPtr; -extern DialoG StringConstraintDialog (GrouP h, CharPtr label, Boolean clear_btn); -extern DialoG LocationConstraintDialog (GrouP h, Boolean show_interval_controls, Boolean clear_btn); +extern DialoG StringConstraintDialogX (GrouP h, CharPtr label, Boolean clear_btn); +extern DialoG LocationConstraintXDialog (GrouP h, Boolean show_interval_controls, Boolean clear_btn); enum pub_field_nums { @@ -1235,7 +1242,7 @@ ConstraintChoiceDialog CharPtr text_name, Boolean clear_btn, Boolean use_pseudo); -extern DialoG SourceConstraintDialog (GrouP h, Boolean clear_btn); +extern DialoG SourceConstraintDialogX (GrouP h, Boolean clear_btn); extern Boolean DoesOneSourceMatchConstraint (BioSourcePtr biop, ChoiceConstraintPtr scp); extern DialoG CDSGeneProtConstraintDialog (GrouP h, Boolean clear_btn); extern DialoG @@ -1259,6 +1266,12 @@ typedef struct parsefield extern ParseFieldPtr ParseFieldFree (ParseFieldPtr pfp); +extern DialoG ParseFieldDestDialogEx +(GrouP h, + Nlm_ChangeNotifyProc change_notify, + Pointer change_userdata, + Boolean is_search_field, + Boolean include_dbxref); extern DialoG ParseFieldDestDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, @@ -1452,7 +1465,7 @@ extern void ConvertCodingRegionsWithInternalKnownGapToMiscFeat (IteM i); extern void FixOneAlignmentOverGaps (SeqAlignPtr salp, Uint2 entityID); extern void ConsolidateSegmentsOverKnownLengthGaps (SeqAlignPtr salp); -extern void CreateDiscrepancyReportWindow (); +extern void CreateDiscrepancyReportWindow (void); extern void ScrollToDiscrepancyItem (ValNodePtr vnp, Pointer userdata); extern void EditDiscrepancyItem (ValNodePtr vnp, Pointer userdata); extern void WriteClickableListReport (FILE *fp, ValNodePtr discrepancy_list, Boolean show_all, Boolean use_feature_table_fmt); @@ -1462,9 +1475,8 @@ extern void ChangeKnownGapLength (IteM i); extern void AddFlankingNsToKnownLengthGaps (IteM i); extern Int2 GetSequinAppParam (CharPtr section, CharPtr type, CharPtr dflt, CharPtr buf, Int2 buflen); -extern Boolean DoBioseqFeaturesMatchSequenceConstraint (BioseqPtr bsp, ValNodePtr feat_list, StringConstraintPtr scp); -extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintPtr string_constraint); -extern void ResetCapitalization (Boolean first_is_upper, CharPtr pString); +extern Boolean DoBioseqFeaturesMatchSequenceConstraintX (BioseqPtr bsp, ValNodePtr feat_list, StringConstraintXPtr scp); +extern Boolean DoesIDListMeetStringConstraint (SeqIdPtr sip, StringConstraintXPtr string_constraint); extern Int2 LIBCALLBACK ReorderSetByAccession (Pointer data); extern Int2 LIBCALLBACK CopyDescriptorToList (Pointer data); @@ -1516,7 +1528,7 @@ extern void MakeGeneralIDsFromLocusTags (IteM i); extern void ShowClickableItemList (ValNodePtr clickable_list, BaseFormPtr bfp, CharPtr win_title, CharPtr label1, CharPtr label2); extern Int4 CountChosenDiscrepancies (ValNodePtr discrepancy_list, Boolean count_all); -extern void AddTranslExcept (SeqFeatPtr sfp, CharPtr cds_comment, Boolean use_strict); +extern void AddTranslExcept (SeqFeatPtr sfp, CharPtr cds_comment, Boolean use_strict, Boolean extend); enum table_data_errors { @@ -1603,17 +1615,20 @@ ConvertOneCDSToMiscFeat extern void SuppressGenesOnFeaturesInsideMobileElements (IteM i); -extern Int4 GetDeltaSeqLen (DeltaSeqPtr dsp); extern BaseFormPtr GetBaseFormForEntityID (Uint2 entityID); extern ValNodePtr ParseAccessionNumberListFromString (CharPtr list_str, SeqEntryPtr sep); -extern SeqIdPtr CreateSeqIdFromText (CharPtr id_str, SeqEntryPtr sep); extern SubSourcePtr FindBadLatLon (BioSourcePtr biop); extern DialoG LatLonTestResultsDisplay (GrouP h); extern void LatLonTool (IteM i); extern DialoG SpecificHostResultsDisplay (GrouP h); extern void FixSpecificHostValues (IteM i); +extern DialoG LatLonCountryResultsDisplay (GrouP h); +extern Pointer GetLatLonCountryCorrection (Uint1 data_choice, Pointer data, Pointer metadata); +extern void LatLonCountryTool (IteM i); +extern DialoG CountryTestResultsDisplay (GrouP h, Pointer metadata); +extern void CountryFixupTool (IteM i); extern void SetTransgenicOnSourceDescWhenSourceFeatPresent (IteM i); extern void SetFocusOnSourceDescWhenSourceFeatPresent (IteM i); @@ -1624,7 +1639,7 @@ extern const char *nucleotide_alphabet; extern const char *protein_alphabet; extern DialoG AlnSettingsDlg (GrouP h, Boolean allow_sequence_type); -extern TSequenceInfoPtr GetDefaultSequenceInfo (); +extern TSequenceInfoPtr GetDefaultSequenceInfo (void); extern TSequenceInfoPtr GetAlignmentOptions (Uint1Ptr moltype, TSequenceInfoPtr sequence_info); @@ -1634,6 +1649,85 @@ extern SeqFeatPtr GetGeneForFeature (SeqFeatPtr sfp); extern void LoadFeatureFieldTable (IteM i); +/* structure used for taxname options for loading values froma table or the Apply/Edit/Convert/Remove dialogs */ +typedef struct taxnameoptions { + Boolean remove_taxref; + Boolean remove_old_name; + Boolean remove_common; +} TaxnameOptionsData, PNTR TaxnameOptionsPtr; + +extern void ApplyTaxnameOptionsToBioSource (BioSourcePtr biop, TaxnameOptionsPtr top); +extern DialoG TaxnameOptionsDialog (GrouP h, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata); + +extern void CleanTableLine (CharPtr line); + +extern void ApplyTagToCodingRegionsInSourceFeatures (IteM i); +extern Boolean EntityIDAlreadyInList (Uint2 entityID, ValNodePtr entityIDList); + +extern void ResolveFeatureOverlaps (IteM i); +extern void ConvertGeneralIdToLocalID (IteM i); + +extern void UpdateFeatures (IteM i); + +extern void AbbreviateCitSubAffilStates (IteM i); +extern void RemoveQualityScores (BioseqPtr bsp, FILE *log_fp, BoolPtr data_in_log); +extern void NewLoadFeatureQualifierTable (IteM i); +extern void ListAllSequences (BioseqPtr bsp, Pointer userdata); +extern void ChooseCategories (ValNodePtr value_list, Boolean do_choose); +extern void ChooseCategoriesByStringConstraint (ValNodePtr value_list, StringConstraintXPtr scp, Boolean do_choose); +extern void CapitalizeFirstLetterOfEveryWord (CharPtr pString); + +typedef void (*BulkSetFieldFunc) PROTO ((Pointer, Pointer)); +typedef Pointer (*BulkSetFieldStringFunc) PROTO ((Pointer, ApplyValuePtr)); +typedef Pointer (*BulkGetFieldFunc) PROTO ((Uint1, Pointer, Pointer)); +typedef CharPtr (*BulkDisplayFieldFunc) PROTO ((Pointer)); +typedef void (*BulkFreeFieldFunc) PROTO ((Pointer)); +typedef DialoG (*BulkCreateDlgFunc) PROTO ((GrouP, CharPtr, SeqEntryPtr)); +typedef Int4 (*BulkFormatColumnFunc) PROTO ((ColPtr, CharPtr)); +typedef void (*BulkDrawColumnFunc) PROTO ((Pointer, RectPtr)); +typedef Pointer (*BulkReleaseCellFunc) PROTO ((Pointer)); +typedef Pointer (*BulkCopyFieldFunc) PROTO ((Pointer)); + +typedef struct bulkedfield { + CharPtr name; + BulkSetFieldFunc set_func; + BulkSetFieldStringFunc set_str_func; + BulkGetFieldFunc get_func; + BulkDisplayFieldFunc display_func; + BulkFreeFieldFunc free_func; + BulkCreateDlgFunc create_dlg_func; + BulkFormatColumnFunc format_col_func; + BulkDrawColumnFunc draw_col_func; + BulkReleaseCellFunc release_cell_func; + BulkCopyFieldFunc copy_func; +} BulkEdFieldData, PNTR BulkEdFieldPtr; + +NLM_EXTERN Pointer BulkSetSimpleTextString (Pointer curr_val, ApplyValuePtr avp); +NLM_EXTERN CharPtr BulkDisplaySimpleText (Pointer data); +NLM_EXTERN void BulkFreeSimpleText (Pointer data); +NLM_EXTERN Int4 BulkFormatSimpleText (ColPtr col, CharPtr name); +NLM_EXTERN Pointer BulkSimpleTextCopy (Pointer data); +NLM_EXTERN DialoG BulkSimpleTextDialog (GrouP g, CharPtr name, SeqEntryPtr sep); + +NLM_EXTERN void BulkEditorObjectList (Uint2 entityID, CharPtr title, ValNodePtr feat_list, BulkEdFieldPtr field_list); +NLM_EXTERN DialoG +CreateBulkEditorDialog +(GrouP h, + BulkEdFieldPtr field_list, + ValNodePtr feat_list, + SeqEntryPtr sep, + Boolean collapse_by_default, + ClickableCallback single_click_func, + ClickableCallback double_click_func); + +NLM_EXTERN void RevCompOneFeatForBioseq (SeqFeatPtr sfp, BioseqPtr bsp); +NLM_EXTERN void FlipSequenceIntervals (IteM i); + +#ifdef OS_MSWIN +NLM_EXTERN Int4 RunSilent(const char *cmdline); +#endif + + #ifdef __cplusplus } #endif |