/* sequin8.c * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information (NCBI) * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government do not place any restriction on its use or reproduction. * We would, however, appreciate having the NCBI and the author cited in * any work or product based on this material * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * =========================================================================== * * File Name: sequin8.c * * Author: Jonathan Kans * * Version Creation Date: 2/3/98 * * $Revision: 6.147 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include "sequin.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include typedef struct evidenceformdata { FEATURE_FORM_BLOCK LisT objlist; TexT findthis; Uint2 itemtype; Uint2 subtype; PopuP evdence; Uint2 exp_ev; ObjMgrPtr omp; ObjMgrTypePtr omtp; ValNodePtr head; Boolean stringfound; Char findStr [128]; } EvidenceFormData, PNTR EvidenceFormPtr; static void LIBCALLBACK AsnWriteEvidenceCallBack (AsnExpOptStructPtr pAEOS) { EvidenceFormPtr efp; CharPtr pchFind; CharPtr pchSource; efp = (EvidenceFormPtr) pAEOS->data; if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) { pchSource = (CharPtr) pAEOS->dvp->ptrvalue; pchFind = efp->findStr; if (StringSearch (pchSource, pchFind) != NULL) { efp->stringfound = TRUE; } } } static Boolean EvidenceHasSubstring (ObjMgrTypePtr omtp, AsnIoPtr aip, Pointer ptr, EvidenceFormPtr efp) { efp->stringfound = FALSE; (omtp->asnwrite) (ptr, aip, NULL); return efp->stringfound; } static void EvidenceCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { AsnExpOptPtr aeop; AsnIoPtr aip; BioseqPtr bsp; BioseqSetPtr bssp; EvidenceFormPtr efp; Boolean notext; ObjMgrTypePtr omtp; SeqAnnotPtr sap; SeqFeatPtr sfp; Uint2 subtype; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; efp = (EvidenceFormPtr) mydata; if (efp == NULL) return; omtp = efp->omtp; if (omtp == NULL || omtp->subtypefunc == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; } else return; GetTitle (efp->findthis, efp->findStr, sizeof (efp->findStr) - 1); notext = StringHasNoText (efp->findStr); aip = AsnIoNullOpen (); aeop = AsnExpOptNew (aip, NULL, NULL, AsnWriteEvidenceCallBack); if (aeop != NULL) { aeop->user_data = (Pointer) efp; } while (sap != NULL) { if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { subtype = (*(omtp->subtypefunc)) ((Pointer) sfp); if (efp->subtype == 0 || subtype == efp->subtype || (efp->subtype == FEATDEF_IMP && subtype >= FEATDEF_allele && subtype <= FEATDEF_site_ref)) { if (notext || EvidenceHasSubstring (omtp, aip, (Pointer) sfp, efp)) { sfp->exp_ev = (Uint1) efp->exp_ev; } } sfp = sfp->next; } } sap = sap->next; } AsnIoClose (aip); } static void DoEvidence (ButtoN b) { EvidenceFormPtr efp; SeqEntryPtr sep; Uint2 subtype; Int2 val; ValNodePtr vnp; efp = GetObjectExtra (b); if (efp == NULL) return; sep = GetTopSeqEntryForEntityID (efp->input_entityID); if (sep == NULL) return; Hide (efp->form); WatchCursor (); Update (); efp->itemtype = OBJ_SEQFEAT; subtype = 0; vnp = NULL; val = GetValue (efp->objlist); if (val > 0) { vnp = efp->head; while (vnp != NULL && val > 1) { val--; vnp = vnp->next; } } if (vnp != NULL) { subtype = vnp->choice; } efp->omp = ObjMgrGet (); efp->omtp = NULL; if (efp->omp != NULL) { efp->omtp = ObjMgrTypeFind (efp->omp, efp->itemtype, NULL, NULL); } efp->subtype = subtype; efp->exp_ev = GetValue (efp->evdence) - 1; if (efp->itemtype != 0 && efp->omtp != NULL) { SeqEntryExplore (sep, (Pointer) efp, EvidenceCallback); } ArrowCursor (); Update (); ObjMgrSetDirtyFlag (efp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, efp->input_entityID, 0, 0); Remove (efp->form); } static void EvidenceMessageProc (ForM f, Int2 mssg) { EvidenceFormPtr efp; efp = (EvidenceFormPtr) GetObjectExtra (f); if (efp != NULL) { if (efp->appmessage != NULL) { efp->appmessage (f, mssg); } } } static void CleanupEvidencePage (GraphiC g, VoidPtr data) { EvidenceFormPtr efp; efp = (EvidenceFormPtr) data; if (efp != NULL) { ValNodeFreeData (efp->head); } StdCleanupFormProc (g, data); } extern void EditEvidenceFlag (IteM i) { BaseFormPtr bfp; ButtoN b; GrouP c; FeatDefPtr curr; EvidenceFormPtr efp; GrouP g; GrouP h; ValNodePtr head; GrouP k; Uint1 key; CharPtr label = NULL; Int2 listHeight; GrouP q; SeqEntryPtr sep; StdEditorProcsPtr sepp; Uint2 subtype; ValNodePtr vnp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; efp = (EvidenceFormPtr) MemNew (sizeof (EvidenceFormData)); if (efp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Feature Evidence", StdCloseWindowProc); SetObjectExtra (w, efp, CleanupEvidencePage); efp->form = (ForM) w; efp->formmessage = EvidenceMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); efp->appmessage = sepp->handleMessages; } efp->input_entityID = bfp->input_entityID; efp->input_itemID = bfp->input_itemID; efp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 0, 2, NULL); StaticPrompt (g, "Feature", 0, 0, programFont, 'c'); if (indexerVersion) { listHeight = 16; } else { listHeight = 8; } efp->objlist = SingleList (g, 16, listHeight, NULL); head = ValNodeNew (NULL); if (head != NULL) { head->choice = 0; head->data.ptrvalue = StringSave ("[ALL FEATURES]"); } curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE); while (curr != NULL) { if (key != FEATDEF_BAD) { subtype = curr->featdef_key; if (subtype != FEATDEF_misc_RNA && subtype != FEATDEF_precursor_RNA && subtype != FEATDEF_mat_peptide && subtype != FEATDEF_sig_peptide && subtype != FEATDEF_transit_peptide) { vnp = ValNodeNew (head); /* if (head == NULL) { head = vnp; } */ if (vnp != NULL) { vnp->choice = subtype; vnp->data.ptrvalue = StringSave (curr->typelabel); } } } curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE); } if (head != NULL) { head = SortValNode (head, SortByVnpChoice); for (vnp = head; vnp != NULL; vnp = vnp->next) { ListItem (efp->objlist, (CharPtr) vnp->data.ptrvalue); } } efp->head = head; q = HiddenGroup (h, 2, 0, NULL); StaticPrompt (q, "Evidence", 0, popupMenuHeight, programFont, 'c'); efp->evdence = PopupList (q, TRUE, NULL); PopupItem (efp->evdence, " "); PopupItem (efp->evdence, "Experimental"); PopupItem (efp->evdence, "Non-Experimental"); SetValue (efp->evdence, 1); k = HiddenGroup (h, 0, 2, NULL); StaticPrompt (k, "Optional string constraint", 0, dialogTextHeight, programFont, 'c'); efp->findthis = DialogText (k, "", 14, NULL); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoEvidence); SetObjectExtra (b, efp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) q, (HANDLE) k, (HANDLE) c, NULL); RealizeWindow (w); Show (w); Update (); } typedef struct exceptionformdata { FEATURE_FORM_BLOCK LisT objlist; TexT findthis; Uint2 itemtype; Uint2 subtype; GrouP xception; TexT xceptText; ButtoN rescueExpl; Boolean excpt; CharPtr except_text; Boolean rescue; ObjMgrPtr omp; ObjMgrTypePtr omtp; ValNodePtr head; Boolean stringfound; Char findStr [128]; } ExceptionFormData, PNTR ExceptionFormPtr; static void LIBCALLBACK AsnWriteExceptionCallBack (AsnExpOptStructPtr pAEOS) { ExceptionFormPtr efp; CharPtr pchFind; CharPtr pchSource; efp = (ExceptionFormPtr) pAEOS->data; if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) { pchSource = (CharPtr) pAEOS->dvp->ptrvalue; pchFind = efp->findStr; if (StringSearch (pchSource, pchFind) != NULL) { efp->stringfound = TRUE; } } } static Boolean ExceptionHasSubstring (ObjMgrTypePtr omtp, AsnIoPtr aip, Pointer ptr, ExceptionFormPtr efp) { efp->stringfound = FALSE; (omtp->asnwrite) (ptr, aip, NULL); return efp->stringfound; } static void ExceptionCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { AsnExpOptPtr aeop; AsnIoPtr aip; BioseqPtr bsp; BioseqSetPtr bssp; ExceptionFormPtr efp; Boolean notext; ObjMgrTypePtr omtp; SeqAnnotPtr sap; SeqFeatPtr sfp; CharPtr str; Uint2 subtype; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; efp = (ExceptionFormPtr) mydata; if (efp == NULL) return; omtp = efp->omtp; if (omtp == NULL || omtp->subtypefunc == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; } else return; GetTitle (efp->findthis, efp->findStr, sizeof (efp->findStr) - 1); notext = StringHasNoText (efp->findStr); aip = AsnIoNullOpen (); aeop = AsnExpOptNew (aip, NULL, NULL, AsnWriteExceptionCallBack); if (aeop != NULL) { aeop->user_data = (Pointer) efp; } while (sap != NULL) { if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { subtype = (*(omtp->subtypefunc)) ((Pointer) sfp); if (efp->subtype == 0 || subtype == efp->subtype || (efp->subtype == FEATDEF_IMP && subtype >= FEATDEF_allele && subtype <= FEATDEF_site_ref)) { if (notext || ExceptionHasSubstring (omtp, aip, (Pointer) sfp, efp)) { sfp->excpt = efp->excpt; if (sfp->excpt) { if (! StringHasNoText (efp->except_text)) { sfp->except_text = MemFree (sfp->except_text); sfp->except_text = StringSave (efp->except_text); } } else { if (efp->rescue) { if (sfp->comment == NULL) { sfp->comment = sfp->except_text; } else { str = MemNew (StringLen (sfp->comment) + StringLen (sfp->except_text) + 5); if (str != NULL) { StringCpy (str, sfp->comment); StringCat (str, "; "); StringCat (str, sfp->except_text); sfp->comment = MemFree (sfp->comment); sfp->comment = str; } } sfp->except_text = NULL; } else { sfp->except_text = MemFree (sfp->except_text); } } } } sfp = sfp->next; } } sap = sap->next; } AsnIoClose (aip); } static void DoException (ButtoN b) { ExceptionFormPtr efp; SeqEntryPtr sep; Uint2 subtype; Int2 val; ValNodePtr vnp; efp = GetObjectExtra (b); if (efp == NULL) return; sep = GetTopSeqEntryForEntityID (efp->input_entityID); if (sep == NULL) return; Hide (efp->form); WatchCursor (); Update (); efp->itemtype = OBJ_SEQFEAT; subtype = 0; vnp = NULL; val = GetValue (efp->objlist); if (val > 0) { vnp = efp->head; while (vnp != NULL && val > 1) { val--; vnp = vnp->next; } } if (vnp != NULL) { subtype = vnp->choice; } efp->omp = ObjMgrGet (); efp->omtp = NULL; if (efp->omp != NULL) { efp->omtp = ObjMgrTypeFind (efp->omp, efp->itemtype, NULL, NULL); } efp->subtype = subtype; efp->excpt = (Boolean) (GetValue (efp->xception) == 2); if (efp->excpt) { efp->except_text = SaveStringFromText (efp->xceptText); } else { efp->except_text = NULL; } efp->rescue = GetStatus (efp->rescueExpl); if (efp->itemtype != 0 && efp->omtp != NULL) { SeqEntryExplore (sep, (Pointer) efp, ExceptionCallback); } MemFree (efp->except_text); ArrowCursor (); Update (); ObjMgrSetDirtyFlag (efp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, efp->input_entityID, 0, 0); Remove (efp->form); } static void ExceptionMessageProc (ForM f, Int2 mssg) { ExceptionFormPtr efp; efp = (ExceptionFormPtr) GetObjectExtra (f); if (efp != NULL) { if (efp->appmessage != NULL) { efp->appmessage (f, mssg); } } } static void CleanupExceptionPage (GraphiC g, VoidPtr data) { ExceptionFormPtr efp; efp = (ExceptionFormPtr) data; if (efp != NULL) { ValNodeFreeData (efp->head); } StdCleanupFormProc (g, data); } extern void EditExceptionFlag (IteM i) { BaseFormPtr bfp; ButtoN b; GrouP c; FeatDefPtr curr; ExceptionFormPtr efp; GrouP g; GrouP h; ValNodePtr head; GrouP k; Uint1 key; CharPtr label = NULL; Int2 listHeight; PrompT ppt; GrouP q; SeqEntryPtr sep; StdEditorProcsPtr sepp; Uint2 subtype; ValNodePtr vnp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; efp = (ExceptionFormPtr) MemNew (sizeof (ExceptionFormData)); if (efp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Feature Exception", StdCloseWindowProc); SetObjectExtra (w, efp, CleanupExceptionPage); efp->form = (ForM) w; efp->formmessage = ExceptionMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); efp->appmessage = sepp->handleMessages; } efp->input_entityID = bfp->input_entityID; efp->input_itemID = bfp->input_itemID; efp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 0, 2, NULL); StaticPrompt (g, "Feature", 0, 0, programFont, 'c'); if (indexerVersion) { listHeight = 16; } else { listHeight = 8; } efp->objlist = SingleList (g, 16, listHeight, NULL); head = ValNodeNew (NULL); if (head != NULL) { head->choice = 0; head->data.ptrvalue = StringSave ("[ALL FEATURES]"); } curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE); while (curr != NULL) { if (key != FEATDEF_BAD) { subtype = curr->featdef_key; if (subtype != FEATDEF_misc_RNA && subtype != FEATDEF_precursor_RNA && subtype != FEATDEF_mat_peptide && subtype != FEATDEF_sig_peptide && subtype != FEATDEF_transit_peptide) { vnp = ValNodeNew (head); /* if (head == NULL) { head = vnp; } */ if (vnp != NULL) { vnp->choice = subtype; vnp->data.ptrvalue = StringSave (curr->typelabel); } } } curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE); } if (head != NULL) { head = SortValNode (head, SortByVnpChoice); for (vnp = head; vnp != NULL; vnp = vnp->next) { ListItem (efp->objlist, (CharPtr) vnp->data.ptrvalue); } } efp->head = head; q = HiddenGroup (h, -2, 0, NULL); ppt = StaticPrompt (q, "Exception ", 0, stdLineHeight, programFont, 'l'); efp->xception = HiddenGroup (q, -2, 0, NULL); SetObjectExtra (efp->xception, efp, NULL); RadioButton (efp->xception, "Clear"); RadioButton (efp->xception, "Set"); SetValue (efp->xception, 1); StaticPrompt (q, "Explanation", 0, dialogTextHeight, programFont, 'l'); efp->xceptText = DialogText (q, "", 12, NULL); AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt, (HANDLE) efp->xception, NULL); efp->rescueExpl = CheckBox (q, "Move explanation to comment", NULL); k = HiddenGroup (h, 0, 2, NULL); StaticPrompt (k, "Optional string constraint", 0, dialogTextHeight, programFont, 'c'); efp->findthis = DialogText (k, "", 14, NULL); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoException); SetObjectExtra (b, efp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) q, (HANDLE) k, (HANDLE) c, NULL); RealizeWindow (w); Show (w); Update (); } static void BreakIntoAGroup (BioseqSetPtr parent, Uint1 _class, SeqEntryPtr list) { BioseqSetPtr bssp; Int2 count; SeqEntryPtr sep; SeqEntryPtr tmp; while (list != NULL) { bssp = BioseqSetNew (); if (bssp == NULL) return; bssp->_class = _class; sep = SeqEntryNew (); if (sep == NULL) return; sep->choice = 2; sep->data.ptrvalue = (Pointer) bssp; if (parent->seq_set != NULL) { tmp = parent->seq_set; while (tmp->next != NULL) { tmp = tmp->next; } tmp->next = sep; } else { parent->seq_set = sep; } bssp->seq_set = list; for (tmp = list, count = 0; tmp != NULL && count < 99; tmp = tmp->next, count++) continue; if (tmp != NULL) { list = tmp->next; tmp->next = NULL; } else { list = NULL; } } } extern void MakeGroupsOf200 (IteM i) { AsnIoPtr aip; BaseFormPtr bfp; BioseqSetPtr bssp; Uint1 _class; Int2 count; Char file [FILENAME_MAX]; SeqEntryPtr list; SeqEntryPtr next; ObjMgrDataPtr omdptop; ObjMgrData omdata; Char output [PATH_MAX]; Uint2 parenttype; Pointer parentptr; Char path [PATH_MAX]; CharPtr ptr; SeqEntryPtr sep; SeqSubmitPtr ssp; Char str [FILENAME_MAX]; SeqEntryPtr tmp; #ifdef WIN_MAC FILE *f; #endif #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; if (! IS_Bioseq_set (sep)) return; bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; _class = bssp->_class; if (_class != 7 && _class != 13 && _class != 14 && _class != 15) return; SaveSeqEntryObjMgrData (sep, &omdptop, &omdata); GetSeqEntryParent (sep, &parentptr, &parenttype); list = bssp->seq_set; bssp->seq_set = NULL; bssp->_class = 7; BreakIntoAGroup (bssp, _class, list); SeqMgrLinkSeqEntry (sep, parenttype, parentptr); RestoreSeqEntryObjMgrData (sep, omdptop, &omdata); PropagateFromGenBankBioseqSet (sep, TRUE); if (parenttype == OBJ_SEQSUB) { if (GetOutputFileName (path, sizeof (path), "")) { ssp = (SeqSubmitPtr) parentptr; if (ssp != NULL && ssp->datatype == 1) { sep = (SeqEntryPtr) ssp->data; ptr = StringRChr (path, DIRDELIMCHR); if (ptr != NULL) { ptr++; StringNCpy_0 (file, ptr, sizeof (file)); *ptr = '\0'; tmp = bssp->seq_set; count = 0; while (tmp != NULL) { next = tmp->next; tmp->next = NULL; ssp->data = (Pointer) tmp; StringCpy (output, path); count++; if (count < 10) { sprintf (str, "%s0%1d", file, (int) count); } else { sprintf (str, "%s%2d", file, (int) count); } FileBuildPath (output, NULL, str); #ifdef WIN_MAC f = FileOpen (output, "r"); if (f != NULL) { FileClose (f); } else { FileCreate (output, "TEXT", "ttxt"); } #endif aip = AsnIoOpen (output, "w"); if (aip != NULL) { SeqSubmitAsnWrite (ssp, aip, NULL); } AsnIoClose (aip); tmp->next = next; tmp = next; } ssp->data = (Pointer) sep; } } } } ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); Update (); } extern void ParseInNucUpdates (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; Message (MSG_OK, "Not yet implemented"); } #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif NLM_EXTERN void CdTransCheck(ValidStructPtr vsp, SeqFeatPtr sfp); static Boolean CdsTranslatesProperly (SeqFeatPtr sfp, GatherContextPtr gcp) { Int2 errors; Int2 j; ErrSev oldErrSev; ValidStructPtr vsp; if (sfp == NULL) return TRUE; vsp = ValidStructNew (); if (vsp == NULL) return TRUE; vsp->gcp = gcp; oldErrSev = ErrSetMessageLevel (SEV_MAX); CdTransCheck (vsp, sfp); ErrSetMessageLevel (oldErrSev); ErrClear (); ErrShow (); errors = 0; for (j = 0; j < 6; j++) { errors += vsp->errors [j]; } ValidStructFree (vsp); return (Boolean) (errors == 0); } typedef struct recompdata { Int4 count; MonitorPtr mon; BioseqPtr batchbsp; Boolean include_stop; } RecompData, PNTR RecompDataPtr; static Int2 GeneticCodeFromCrp (CdRegionPtr crp) { Int2 code; GeneticCodePtr gcp; Char name [256]; ValNodePtr tmp; code = 0; name [0] = '\0'; gcp = crp->genetic_code; if (gcp != NULL) { tmp = (ValNodePtr) gcp->data.ptrvalue; for (tmp = (ValNodePtr) gcp->data.ptrvalue; tmp != NULL; tmp = tmp->next) { switch (tmp->choice) { case 1 : if (name [0] == '\0') { StringNCpy_0 (name, (CharPtr) tmp->data.ptrvalue, sizeof (name)); } break; case 2 : code = tmp->data.intvalue; break; default : break; } } if (code == 0) { gcp = GeneticCodeFind (code, name); if (gcp != NULL) { for (tmp = (ValNodePtr) gcp->data.ptrvalue; tmp != NULL; tmp = tmp->next) { switch (tmp->choice) { case 2 : code = tmp->data.intvalue; break; default : break; } } } } } return code; } static Boolean RecomputeSuggCallback (GatherContextPtr gcp) { Int2 code; CdRegionPtr crp; BioseqPtr nucbsp; BioseqPtr protbsp; RecompDataPtr rdp; SeqFeatPtr sfp; SeqIdPtr sip; SeqLocPtr slp; Char str [256]; Char tmp [256]; if (gcp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; rdp = (RecompDataPtr) gcp->userdata; if (rdp == NULL) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return TRUE; crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp == NULL) return TRUE; /* if (CdsTranslatesProperly (sfp, gcp)) return TRUE; */ code = GeneticCodeFromCrp (crp); nucbsp = GetBioseqGivenSeqLoc (sfp->location, gcp->entityID); if (nucbsp != NULL && rdp->batchbsp != NULL && nucbsp != rdp->batchbsp) { ClearBatchSuggestNucleotide (); rdp->batchbsp = NULL; Message (MSG_POSTERR, "Recompute Suggest is reverting to slower processing"); } sip = SeqLocId (sfp->product); if (sip != NULL) { protbsp = BioseqFind (sip); if (nucbsp != NULL && protbsp != NULL && ISA_na (nucbsp->mol) && ISA_aa (protbsp->mol) && nucbsp->length > 0 && protbsp->length > 0) { str [0] = '\0'; tmp [0] = '\0'; sip = SeqIdFindWorst (protbsp->id); SeqIdWrite (sip, tmp, PRINTID_REPORT, sizeof (tmp)); (rdp->count)++; sprintf (str, "Processing sequence %d [%s]", (int) rdp->count, tmp); if (rdp->mon != NULL) { MonitorStrValue (rdp->mon, str); Update (); } slp = PredictCodingRegion (nucbsp, protbsp, code); if (slp == NULL) return TRUE; sfp->location = SeqLocFree (sfp->location); sfp->location = slp; sfp->partial = LocationHasNullsBetween (sfp->location); } } return TRUE; } extern void RecomputeSuggest (IteM i) { BaseFormPtr bfp; Int2 code; GatherScope gs; SeqEntryPtr nucsep; RecompData rd; 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; WatchCursor (); Update (); rd.count = 0; rd.mon = MonitorStrNewEx ("Correcting Coding Regions", 20, FALSE); rd.batchbsp = NULL; nucsep = FindNucSeqEntry (sep); if (nucsep != NULL && IS_Bioseq (nucsep)) { rd.batchbsp = (BioseqPtr) nucsep->data.ptrvalue; } if (rd.batchbsp != NULL) { code = SeqEntryToGeneticCode (sep, NULL, NULL, 0); SetBatchSuggestNucleotide (rd.batchbsp, code); } MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = FALSE; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; GatherEntity (bfp->input_entityID, (Pointer) (&rd), RecomputeSuggCallback, &gs); MonitorFree (rd.mon); if (rd.batchbsp != NULL) { ClearBatchSuggestNucleotide (); } ArrowCursor (); Update (); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); } static Boolean RetranslateOneCDS (SeqFeatPtr sfp, Uint2 entityID, Boolean include_stop) { SeqFeatPtr bestprot; ByteStorePtr bs; BioseqPtr bsp; Char ch; SeqEntryPtr master; MolInfoPtr mip; SeqEntryPtr old; Boolean partial5; Boolean partial3; CharPtr prot; CharPtr ptr; SeqEntryPtr sep; SeqIdPtr sip; SeqLocPtr slp; ValNodePtr vnp; if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return TRUE; slp = SeqLocFindNext (sfp->location, NULL); if (slp == NULL) return TRUE; CheckSeqLocForPartial (slp, &partial5, &partial3); /* if (CdsTranslatesProperly (sfp, gcp)) return TRUE; */ if (sfp->product == NULL) { master = NULL; old = NULL; bsp = GetBioseqGivenSeqLoc (sfp->location, entityID); if (bsp != NULL) { master = GetBestTopParentForData (entityID, bsp); } bsp = BioseqNew (); if (bsp != NULL) { bsp->mol = Seq_mol_aa; bsp->repr = Seq_repr_raw; bsp->seq_data_type = Seq_code_ncbieaa; bsp->length = 0; bsp->seq_data = BSNew (0); if (master != NULL) { old = SeqEntrySetScope (master); } bsp->id = MakeNewProteinSeqId (sfp->location, NULL); SeqMgrAddToBioseqIndex (bsp); if (master != NULL) { SeqEntrySetScope (old); } sep = SeqEntryNew (); if (sep != NULL) { sep->choice = 1; sep->data.ptrvalue = (Pointer) bsp; SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep); } SetSeqFeatProduct (sfp, bsp); if (master != NULL && sep != NULL) { AddSeqEntryToSeqEntry (master, sep, TRUE); } } } sip = SeqLocId (sfp->product); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL && ISA_aa (bsp->mol) && bsp->repr == Seq_repr_raw) { bestprot = FindBestProtein (entityID, sfp->product); bs = ProteinFromCdRegionEx (sfp, include_stop, FALSE); if (bs == NULL) return TRUE; prot = BSMerge (bs, NULL); bs = BSFree (bs); if (prot == NULL) return TRUE; ptr = prot; ch = *ptr; while (ch != '\0') { *ptr = TO_UPPER (ch); ptr++; ch = *ptr; } bs = BSNew (1000); if (bs != NULL) { ptr = prot; /* if (prot [0] == '-') { ptr++; } */ BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr)); } bsp->repr = Seq_repr_raw; bsp->mol = Seq_mol_aa; bsp->seq_data_type = Seq_code_ncbieaa; bsp->seq_data = BSFree (bsp->seq_data); bsp->seq_data = bs; bsp->length = BSLen (bs); sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return TRUE; if (bestprot != NULL) { bestprot->location = SeqLocFree (bestprot->location); bestprot->location = CreateWholeInterval (sep); SetSeqLocPartial (bestprot->location, partial5, partial3); bestprot->partial = (partial5 || partial3); } vnp = SeqEntryGetSeqDescr (sep, Seq_descr_molinfo, NULL); if (vnp == NULL) { vnp = CreateNewDescriptor (sep, Seq_descr_molinfo); if (vnp != NULL) { mip = MolInfoNew (); vnp->data.ptrvalue = (Pointer) mip; if (mip != NULL) { mip->biomol = 8; mip->tech = 13; } } } if (vnp != NULL) { mip = (MolInfoPtr) vnp->data.ptrvalue; if (mip != NULL) { if (partial5 && partial3) { mip->completeness = 5; } else if (partial5) { mip->completeness = 3; } else if (partial3) { mip->completeness = 4; /* } else if (partial) { mip->completeness = 2; */ } else { mip->completeness = 0; } } } } } return TRUE; } static Boolean RetranslateCDSCallback (GatherContextPtr gcp) { RecompDataPtr rdp; SeqFeatPtr sfp; if (gcp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; rdp = (RecompDataPtr) gcp->userdata; if (rdp == NULL) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; return RetranslateOneCDS (sfp, gcp->entityID, rdp->include_stop); } static void RetranslateCdRegions (IteM i, Boolean include_stop) { BaseFormPtr bfp; GatherScope gs; RecompData rd; 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; WatchCursor (); Update (); rd.count = 0; rd.mon = MonitorStrNewEx ("Correcting Coding Regions", 20, FALSE); rd.include_stop = include_stop; MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = FALSE; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; GatherEntity (bfp->input_entityID, (Pointer) (&rd), RetranslateCDSCallback, &gs); MonitorFree (rd.mon); ArrowCursor (); Update (); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); } extern void RetranslateCdRegionsNoStop (IteM i) { RetranslateCdRegions (i, FALSE); } extern void RetranslateCdRegionsDoStop (IteM i) { RetranslateCdRegions (i, TRUE); } static Boolean CorrectGenCodeCallback (GatherContextPtr gcp) { CdRegionPtr crp; GeneticCodePtr gc; Int2 genCode; SeqEntryPtr sep; SeqFeatPtr sfp; ValNodePtr vnp; if (gcp == NULL) return TRUE; sep = (SeqEntryPtr) gcp->userdata; if (sep == NULL ) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return TRUE; crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp == NULL) return TRUE; genCode = SeqEntryToGeneticCode (sep, NULL, NULL, 0); gc = GeneticCodeNew (); if (gc == NULL) return TRUE; crp->genetic_code = GeneticCodeFree (crp->genetic_code); vnp = ValNodeNew (NULL); gc->data.ptrvalue = vnp; if (vnp != NULL) { vnp->choice = 2; vnp->data.intvalue = (Int4) genCode; } crp->genetic_code = gc; return TRUE; } extern void CorrectGenCodes (SeqEntryPtr sep, Uint2 entityID) { BioseqSetPtr bssp; GatherScope gs; if (sep == NULL) return; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && (bssp->_class == 7 || (bssp->_class >= 13 && bssp->_class <= 16))) { for (sep = bssp->seq_set; sep != NULL; sep = sep->next) { CorrectGenCodes (sep, entityID); } return; } } MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = FALSE; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.scope = sep; GatherEntity (entityID, (Pointer) sep, CorrectGenCodeCallback, &gs); } extern void CorrectCDSGenCodes (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; CorrectGenCodes (sep, bfp->input_entityID); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); } static BioseqPtr SqnGetBioseqGivenSeqLoc (SeqLocPtr slp, Uint2 entityID) { BioseqPtr bsp; SeqEntryPtr sep; SeqIdPtr sip; SeqLocPtr tmp; if (slp == NULL) return NULL; bsp = NULL; sip = SeqLocId (slp); if (sip != NULL) { bsp = BioseqFind (sip); } else { tmp = SeqLocFindNext (slp, NULL); if (tmp != NULL) { sip = SeqLocId (tmp); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); bsp = GetBioseqGivenSeqLoc (slp, entityID); } } } } return bsp; } static BioseqPtr GetBioseqReferencedByAnnot (SeqAnnotPtr sap, Uint2 entityID) { SeqAlignPtr align; BioseqPtr bsp; DenseDiagPtr ddp; DenseSegPtr dsp; SeqFeatPtr feat; SeqGraphPtr graph; SeqIdPtr sip; SeqLocPtr slp; StdSegPtr ssp; SeqLocPtr tloc; if (sap == NULL) return NULL; switch (sap->type) { case 1 : feat = (SeqFeatPtr) sap->data; while (feat != NULL) { slp = feat->location; if (slp != NULL) { bsp = SqnGetBioseqGivenSeqLoc (slp, entityID); if (bsp != NULL) return bsp; } feat = feat->next; } break; case 2 : align = (SeqAlignPtr) sap->data; while (align != NULL) { if (align->segtype == 1) { ddp = (DenseDiagPtr) align->segs; if (ddp != NULL) { for (sip = ddp->id; sip != NULL; sip = sip->next) { bsp = BioseqFind (sip); if (bsp != NULL) return bsp; } } } else if (align->segtype == 2) { dsp = (DenseSegPtr) align->segs; if (dsp != NULL) { for (sip = dsp->ids; sip != NULL; sip = sip->next) { bsp = BioseqFind (sip); if (bsp != NULL) return bsp; } } } else if (align->segtype == 3) { ssp = (StdSegPtr) align->segs; if (ssp != NULL && ssp->loc != NULL) { for (tloc = ssp->loc; tloc != NULL; tloc = tloc->next) { bsp = BioseqFind (SeqLocId (tloc)); if (bsp != NULL) return bsp; } } } align = align->next; } break; case 3 : graph = (SeqGraphPtr) sap->data; while (graph != NULL) { slp = graph->loc; if (slp != NULL) { bsp = SqnGetBioseqGivenSeqLoc (slp, entityID); if (bsp != NULL) return bsp; } graph = graph->next; } break; default : break; } return NULL; } static Int4 GetScore (ScorePtr score) { ObjectIdPtr id; while (score != NULL) { id = score->id; if (id != NULL) { if (StringICmp (id->str, "score") == 0) { if (score->choice == 1) { return (score->value.intvalue); } } } score = score->next; } return 0; } static Int4 FindScore (SeqAlignPtr align) { if (align == NULL) return 0; if (align->score != NULL) { return GetScore (align->score); } return 0; } static int LIBCALLBACK SortByScoreCallback (VoidPtr ptr1, VoidPtr ptr2) { SeqAlignPtr sap1; SeqAlignPtr sap2; Int4 score1; Int4 score2; if (ptr1 != NULL && ptr2 != NULL) { sap1 = *((SeqAlignPtr PNTR) ptr1); sap2 = *((SeqAlignPtr PNTR) ptr2); if (sap1 != NULL && sap2 != NULL) { score1 = FindScore (sap1); score2 = FindScore (sap2); if (score1 < score2) { return 1; } else if (score1 > score2) { return -1; } else { return 0; } } else { return 0; } } else { return 0; } } static SeqAlignPtr SortBySeqAlignScore (SeqAlignPtr list) { SeqAlignPtr align; Int4 count, i; SeqAlignPtr PNTR head; if (list == NULL) return 0; count = 0; for (align = list; align != NULL; align = align->next) { count++; } head = MemNew (sizeof (SeqAlignPtr) * (size_t) (count + 1)); if (head == NULL) return 0; for (align = list, i = 0; align != NULL && i < count; i++) { head [i] = align; align = align->next; } HeapSort (head, (size_t) count, sizeof (SeqAlignPtr), SortByScoreCallback); for (i = 0; i < count; i++) { align = head [i]; align->next = head [i + 1]; } list = head [0]; MemFree (head); return list; } static void TakeTop10Alignments (SeqAnnotPtr sap) { SeqAlignPtr align; MsgAnswer ans; Int2 count; SeqAlignPtr next; if (sap == NULL || sap->type != 2 || sap->data == NULL) return; count = 0; for (align = (SeqAlignPtr) sap->data; align != NULL; align = align->next) { count++; } if (count <= 10) return; ans = Message (MSG_YN, "Do you want to take only the top 10 (out of %d) alignments?", (int) count); if (ans == ANS_NO) return; sap->data = SortBySeqAlignScore ((SeqAlignPtr) sap->data); for (align = (SeqAlignPtr) sap->data, count = 0; align != NULL && count < 10; align = align->next) { count++; } next = align->next; align->next = NULL; align = next; while (align != NULL) { next = align->next; align->next = NULL; SeqAlignFree (align); align = next; } } static void DoOnePub (PubdescPtr pdp) { ValNodePtr citartptr = NULL; Int4 muid = 0; Int4 pmid = 0; ValNodePtr tmp = NULL; ValNodePtr vnp; if (pdp != NULL) { for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { if (vnp->choice == PUB_Muid) { muid = vnp->data.intvalue; } else if (vnp->choice == PUB_PMid) { pmid = vnp->data.intvalue; } else if (vnp->choice == PUB_Article) { citartptr = vnp; } } if (pmid != 0) { tmp = MedArchGetPubPmId (pmid); muid = MedArchPm2Mu (pmid); } else if (muid != 0) { tmp = MedArchGetPub (muid); pmid = MedArchMu2Pm (muid); } else if (citartptr != NULL) { muid = MedArchCitMatch (citartptr); if (muid != 0) { tmp = MedArchGetPub (muid); pmid = MedArchMu2Pm (muid); } } if (tmp != NULL) { MedlineToISO (tmp); if (pmid != 0) { ValNodeAddInt (&tmp, PUB_PMid, pmid); } if (muid != 0) { ValNodeAddInt (&tmp, PUB_Muid, muid); } pdp->pub = PubEquivFree (pdp->pub); pdp->pub = tmp; } } } static void DoLookupPub (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; PubdescPtr pdp; SeqAnnotPtr sap; ValNodePtr sdp; SeqFeatPtr sfp; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; sdp = bsp->descr; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; sdp = bssp->descr; } else return; while (sap != NULL) { if (sap->type == 1) { for (sfp = (SeqFeatPtr) sap->data; sfp != NULL; sfp = sfp->next) { if (sfp->data.choice == SEQFEAT_PUB) { pdp = (PubdescPtr) sfp->data.value.ptrvalue; DoOnePub (pdp); } } } sap = sap->next; } while (sdp != NULL) { if (sdp->choice == Seq_descr_pub) { pdp = (PubdescPtr) sdp->data.ptrvalue; DoOnePub (pdp); } sdp = sdp->next; } } extern void LookupAllPubs (IteM i); extern void LookupAllPubs (IteM i) { BaseFormPtr bfp; MonitorPtr mon = NULL; SeqEntryPtr sep; ErrSev sev; if (! useMedarch) return; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; sev = ErrSetMessageLevel (SEV_FATAL); WatchCursor (); mon = MonitorStrNewEx ("Processing Publications", 40, FALSE); MonitorStrValue (mon, "Connecting to MedArch"); Update (); if (! MedArchInit ()) { MonitorFree (mon); ArrowCursor (); Update (); Message (MSG_POST, "Unable to connect to MedArch"); return; } SeqEntryExplore (sep, NULL, DoLookupPub); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); MonitorStrValue (mon, "Closing MedArch"); Update (); MedArchFini (); MonitorFree (mon); ArrowCursor (); Update (); ErrSetMessageLevel (sev); ErrClear (); ErrShow (); } static void LookupPublications (SeqAnnotPtr sap) { MonitorPtr mon = NULL; PubdescPtr pdp; SeqFeatPtr sfp; ValNodePtr tmp; Int4 uid; Boolean usingMedarch = FALSE; ValNodePtr vnp; if (! useMedarch) return; if (sap == NULL || sap->type != 1) return; for (sfp = (SeqFeatPtr) sap->data; sfp != NULL; sfp = sfp->next) { if (sfp->data.choice == SEQFEAT_PUB) { pdp = (PubdescPtr) sfp->data.value.ptrvalue; if (pdp != NULL) { vnp = pdp->pub; if (vnp != NULL && vnp->next == NULL) { if (vnp->choice == PUB_Muid || vnp->choice == PUB_PMid) { if (! usingMedarch) { WatchCursor (); mon = MonitorStrNewEx ("Processing Publications", 40, FALSE); MonitorStrValue (mon, "Connecting to MedArch"); Update (); if (MedArchInit ()) { usingMedarch = TRUE; } else { MonitorFree (mon); ArrowCursor (); Update (); Message (MSG_POST, "Unable to connect to MedArch"); return; } } } tmp = NULL; if (vnp->choice == PUB_Muid) { uid = vnp->data.intvalue; tmp = MedArchGetPub (uid); } else if (vnp->choice == PUB_PMid) { uid = vnp->data.intvalue; tmp = MedArchGetPubPmId (uid); } if (tmp != NULL) { MedlineToISO (tmp); tmp->next = vnp; pdp->pub = tmp; } } } } } if (usingMedarch) { MonitorStrValue (mon, "Closing MedArch"); Update (); MedArchFini (); MonitorFree (mon); ArrowCursor (); Update (); } } static void PromotePubs (SeqFeatPtr first, BioseqPtr bsp, Uint2 entityID) { MsgAnswer ans; Boolean asked = FALSE; PubdescPtr pdp; SeqDescrPtr sdp; SeqEntryPtr sep; SeqFeatPtr sfp; ValNode vn; MemSet ((Pointer) &vn, 0, sizeof (ValNode)); vn.choice = SEQLOC_WHOLE; vn.data.ptrvalue = (Pointer) SeqIdFindBest (bsp->id, 0); vn.next = NULL; for (sfp = first; sfp != NULL; sfp = sfp->next) { if (sfp->data.choice == SEQFEAT_PUB) { if (SeqLocCompare (sfp->location, &vn) == SLC_A_EQ_B) { if (! asked) { ans = Message (MSG_YN, "Do you wish to convert full-length publication features to descriptors?"); if (ans == ANS_NO) return; asked = TRUE; } } } } sep = GetBestTopParentForData (entityID, bsp); for (sfp = first; sfp != NULL; sfp = sfp->next) { if (sfp->data.choice == SEQFEAT_PUB) { if (SeqLocCompare (sfp->location, &vn) == SLC_A_EQ_B) { sfp->idx.deleteme = TRUE; sfp->data.choice = SEQFEAT_COMMENT; pdp = (PubdescPtr) sfp->data.value.ptrvalue; sfp->data.value.ptrvalue = NULL; sdp = CreateNewDescriptor (sep, Seq_descr_pub); if (sdp != NULL) { sdp->data.ptrvalue = (Pointer) pdp; } } } } DeleteMarkedObjects (entityID, 0, NULL); } extern Uint2 SmartAttachSeqAnnotToSeqEntry (Uint2 entityID, SeqAnnotPtr sap) { BioseqPtr bsp; Int2 genCode; SeqEntryPtr oldscope; OMProcControl ompc; SeqEntryPtr sep; SeqFeatPtr sfp = NULL; if (sap == NULL) return entityID; bsp = GetBioseqReferencedByAnnot (sap, entityID); if (bsp == NULL) { oldscope = SeqEntrySetScope (NULL); if (oldscope != NULL) { bsp = GetBioseqReferencedByAnnot (sap, entityID); SeqEntrySetScope (oldscope); } } if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; sep = GetBestTopParentForData (entityID, bsp); genCode = SeqEntryToGeneticCode (sep, NULL, NULL, 0); SetEmptyGeneticCodes (sap, genCode); LookupPublications (sap); } else if (sap->type == 2) { TakeTop10Alignments (sap); } MemSet ((Pointer) &ompc, 0, sizeof (OMProcControl)); ompc.input_entityID = entityID; ompc.input_itemID = GetItemIDGivenPointer (entityID, OBJ_BIOSEQ, (Pointer) bsp); ompc.input_itemtype = OBJ_BIOSEQ; ompc.output_itemtype = OBJ_SEQANNOT; ompc.output_data = (Pointer) sap; if (! AttachDataForProc (&ompc, FALSE)) { Message (MSG_ERROR, "SmartAttachSeqAnnotToSeqEntry failed"); } else if (sfp != NULL) { PromoteXrefs (sfp, bsp, entityID); PromotePubs (sfp, bsp, entityID); } } else { Message (MSG_ERROR, "Feature table identifiers do not match record"); } return entityID; } typedef struct removeformdata { FEATURE_FORM_BLOCK Boolean is_feature; LisT objlist; TexT findthis; Uint2 itemtype; Uint2 subtype; ObjMgrPtr omp; ObjMgrTypePtr omtp; ValNodePtr head; Boolean stringfound; Char findStr [128]; ValNodePtr bsplist; ValNodePtr bssplist; } RemoveFormData, PNTR RemoveFormPtr; static void LIBCALLBACK AsnWriteRemoveForDCallBack (AsnExpOptStructPtr pAEOS) { CharPtr pchFind; CharPtr pchSource; RemoveFormPtr rfp; rfp = (RemoveFormPtr) pAEOS->data; if (ISA_STRINGTYPE (AsnFindBaseIsa (pAEOS->atp))) { pchSource = (CharPtr) pAEOS->dvp->ptrvalue; pchFind = rfp->findStr; if (StringSearch (pchSource, pchFind) != NULL) { rfp->stringfound = TRUE; } } } static Boolean ObjectHasSubstring (ObjMgrTypePtr omtp, AsnIoPtr aip, Pointer ptr, RemoveFormPtr rfp) { rfp->stringfound = FALSE; (omtp->asnwrite) (ptr, aip, NULL); return rfp->stringfound; } static void RemoveFeatureCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { AsnExpOptPtr aeop; AsnIoPtr aip; BioseqPtr bsp; BioseqSetPtr bssp; SeqAnnotPtr nextsap; SeqFeatPtr nextsfp; Boolean notext; ObjMgrTypePtr omtp; Pointer PNTR prevsap; Pointer PNTR prevsfp; BioseqPtr productbsp; BioseqPtr productcdna; BioseqSetPtr productnps; RemoveFormPtr rfp; SeqAnnotPtr sap; SeqFeatPtr sfp; SeqIdPtr sip; Uint2 subtype; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; rfp = (RemoveFormPtr) mydata; if (rfp == NULL) return; omtp = rfp->omtp; if (omtp == NULL || omtp->subtypefunc == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; prevsap = (Pointer PNTR) &(bsp->annot); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; prevsap = (Pointer PNTR) &(bssp->annot); } else return; GetTitle (rfp->findthis, rfp->findStr, sizeof (rfp->findStr) - 1); notext = StringHasNoText (rfp->findStr); aip = AsnIoNullOpen (); aeop = AsnExpOptNew (aip, NULL, NULL, AsnWriteRemoveForDCallBack); if (aeop != NULL) { aeop->user_data = (Pointer) rfp; } while (sap != NULL) { nextsap = sap->next; if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; prevsfp = (Pointer PNTR) &(sap->data); while (sfp != NULL) { nextsfp = sfp->next; subtype = (*(omtp->subtypefunc)) ((Pointer) sfp); if (subtype == rfp->subtype || (rfp->subtype == FEATDEF_IMP && subtype >= FEATDEF_allele && subtype <= FEATDEF_site_ref)) { if (notext || ObjectHasSubstring (omtp, aip, (Pointer) sfp, rfp)) { if (sfp->data.choice == SEQFEAT_CDREGION) { if (sfp->product != NULL) { sip = SeqLocId (sfp->product); if (sip != NULL) { productbsp = BioseqFind (sip); if (productbsp != NULL) { ValNodeAddPointer (&(rfp->bsplist), 0, (Pointer) productbsp); } } } } else if (sfp->data.choice == SEQFEAT_RNA) { if (sfp->product != NULL) { sip = SeqLocId (sfp->product); if (sip != NULL) { productcdna = BioseqFind (sip); if (productcdna != NULL && productcdna->idx.parenttype == OBJ_BIOSEQSET) { productnps = (BioseqSetPtr) productcdna->idx.parentptr; if (productnps != NULL && productnps->_class == BioseqseqSet_class_nuc_prot) { ValNodeAddPointer (&(rfp->bssplist), 0, (Pointer) productnps); } } } } } *(prevsfp) = sfp->next; sfp->next = NULL; SeqFeatFree (sfp); } else { prevsfp = (Pointer PNTR) &(sfp->next); } } else { prevsfp = (Pointer PNTR) &(sfp->next); } sfp = nextsfp; } } if (sap->data == NULL) { *(prevsap) = sap->next; sap->next = NULL; SeqAnnotFree (sap); } else { prevsap = (Pointer PNTR) &(sap->next); } sap = nextsap; } AsnIoClose (aip); } static void RemoveDescriptorCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { AsnExpOptPtr aeop; AsnIoPtr aip; BioseqPtr bsp; BioseqSetPtr bssp; ValNodePtr nextsdp; Boolean notext; ObjMgrTypePtr omtp; Pointer PNTR prevsdp; RemoveFormPtr rfp; ValNodePtr sdp; Uint2 subtype; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; rfp = (RemoveFormPtr) mydata; if (rfp == NULL) return; omtp = rfp->omtp; if (omtp == NULL || omtp->subtypefunc == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sdp = bsp->descr; prevsdp = (Pointer PNTR) &(bsp->descr); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sdp = bssp->descr; prevsdp = (Pointer PNTR) &(bssp->descr); } else return; GetTitle (rfp->findthis, rfp->findStr, sizeof (rfp->findStr) - 1); notext = StringHasNoText (rfp->findStr); aip = AsnIoNullOpen (); aeop = AsnExpOptNew (aip, NULL, NULL, AsnWriteRemoveForDCallBack); if (aeop != NULL) { aeop->user_data = (Pointer) rfp; } while (sdp != NULL) { nextsdp = sdp->next; subtype = (*(omtp->subtypefunc)) ((Pointer) sdp); if (subtype == rfp->subtype) { if (notext || ObjectHasSubstring (omtp, aip, (Pointer) sdp, rfp)) { *(prevsdp) = sdp->next; sdp->next = NULL; SeqDescFree (sdp); } else { prevsdp = (Pointer PNTR) &(sdp->next); } } else { prevsdp = (Pointer PNTR) &(sdp->next); } sdp = nextsdp; } AsnIoClose (aip); } static void DoRemoveAsnObject (ButtoN b) { MsgAnswer ans; BioseqPtr bsp; BioseqSetPtr bssp; Uint2 itemID; OMProcControl ompc; RemoveFormPtr rfp; SeqEntryPtr sep; ValNodePtr tmp; Int2 val; ValNodePtr vnp; rfp = GetObjectExtra (b); if (rfp == NULL) return; sep = GetTopSeqEntryForEntityID (rfp->input_entityID); if (sep == NULL) return; Hide (rfp->form); WatchCursor (); Update (); if (rfp->is_feature) { rfp->itemtype = OBJ_SEQFEAT; } else { rfp->itemtype = OBJ_SEQDESC; } vnp = NULL; val = GetValue (rfp->objlist); if (val > 0) { vnp = rfp->head; while (vnp != NULL && val > 1) { val--; vnp = vnp->next; } } if (vnp != NULL) { rfp->omp = ObjMgrGet (); rfp->omtp = NULL; if (rfp->omp != NULL) { rfp->omtp = ObjMgrTypeFind (rfp->omp, rfp->itemtype, NULL, NULL); } rfp->subtype = vnp->choice; if (rfp->itemtype != 0 && rfp->subtype != 0 && rfp->omtp != NULL) { if (rfp->is_feature) { SeqEntryExplore (sep, (Pointer) rfp, RemoveFeatureCallback); if (rfp->bsplist != NULL) { ans = Message (MSG_YN, "Remove protein products?"); if (ans == ANS_YES) { for (tmp = rfp->bsplist; tmp != NULL; tmp = tmp->next) { bsp = (BioseqPtr) tmp->data.ptrvalue; itemID = GetItemIDGivenPointer (rfp->input_entityID, OBJ_BIOSEQ, (Pointer) bsp); if (itemID > 0) { MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl)); ompc.do_not_reload_from_cache = TRUE; ompc.input_entityID = rfp->input_entityID; ompc.input_itemID = itemID; ompc.input_itemtype = OBJ_BIOSEQ; if (! DetachDataForProc (&ompc, FALSE)) { Message (MSG_POSTERR, "DetachDataForProc failed"); } } } } } if (rfp->bssplist != NULL) { ans = Message (MSG_YN, "Remove cDNA nuc-prot products?"); if (ans == ANS_YES) { for (tmp = rfp->bssplist; tmp != NULL; tmp = tmp->next) { bssp = (BioseqSetPtr) tmp->data.ptrvalue; itemID = GetItemIDGivenPointer (rfp->input_entityID, OBJ_BIOSEQSET, (Pointer) bssp); if (itemID > 0) { MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl)); ompc.do_not_reload_from_cache = TRUE; ompc.input_entityID = rfp->input_entityID; ompc.input_itemID = itemID; ompc.input_itemtype = OBJ_BIOSEQSET; if (! DetachDataForProc (&ompc, FALSE)) { Message (MSG_POSTERR, "DetachDataForProc failed"); } } } } } } else { SeqEntryExplore (sep, (Pointer) rfp, RemoveDescriptorCallback); } } } ArrowCursor (); Update (); ObjMgrSetDirtyFlag (rfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, rfp->input_entityID, 0, 0); ObjMgrDeSelect (0, 0, 0, 0, NULL); Remove (rfp->form); } int LIBCALLBACK SortByVnpChoice (VoidPtr ptr1, VoidPtr ptr2) { ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { if (vnp1->choice > vnp2->choice) { return 1; } else if (vnp1->choice < vnp2->choice) { return -1; } else { return 0; } } else { return 0; } } else { return 0; } } static void RemoveMessageProc (ForM f, Int2 mssg) { RemoveFormPtr rfp; rfp = (RemoveFormPtr) GetObjectExtra (f); if (rfp != NULL) { if (rfp->appmessage != NULL) { rfp->appmessage (f, mssg); } } } static void CleanupRemovePage (GraphiC g, VoidPtr data) { RemoveFormPtr rfp; rfp = (RemoveFormPtr) data; if (rfp != NULL) { ValNodeFreeData (rfp->head); ValNodeFree (rfp->bsplist); ValNodeFree (rfp->bssplist); } StdCleanupFormProc (g, data); } static CharPtr descNames [] = { " ", "MolType", "Modif", "Method", "Name", "Title", "Organism", "Comment", "Numbering", "MapLoc", "PIR", "GenBank", "Publication", "Region", "User", "SWISS-PROT", "dbXREF", "EMBL", "Create Date", "Update Date", "PRF", "PDB", "Heterogen", "BioSource", "MolInfo", NULL }; /* #ifdef INTERNAL_NCBI_SEQUIN #define LISTHEIGHT 16 #else #define LISTHEIGHT 8 #endif */ static void RemoveAsnObject (IteM i, Boolean feature) { BaseFormPtr bfp; ButtoN b; GrouP c; FeatDefPtr curr; GrouP g; GrouP h; ValNodePtr head; Int2 j; GrouP k; Uint1 key; CharPtr label = NULL; Int2 listHeight; RemoveFormPtr rfp; SeqEntryPtr sep; StdEditorProcsPtr sepp; Char str [256]; Uint2 subtype; CharPtr title; ValNodePtr vnp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; rfp = (RemoveFormPtr) MemNew (sizeof (RemoveFormData)); if (rfp == NULL) return; if (feature) { title = "Feature Removal"; } else { title = "Descriptor Removal"; } w = FixedWindow (-50, -33, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, rfp, CleanupRemovePage); rfp->form = (ForM) w; rfp->formmessage = RemoveMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); rfp->appmessage = sepp->handleMessages; } rfp->input_entityID = bfp->input_entityID; rfp->input_itemID = bfp->input_itemID; rfp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 0, 2, NULL); rfp->is_feature = feature; if (feature) { StaticPrompt (g, "Feature", 0, 0, programFont, 'c'); } else { StaticPrompt (g, "Descriptor", 0, 0, programFont, 'c'); } if (indexerVersion) { listHeight = 16; } else { listHeight = 8; } rfp->objlist = SingleList (g, 16, listHeight, NULL); head = NULL; if (feature) { curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE); while (curr != NULL) { if (key != FEATDEF_BAD) { subtype = curr->featdef_key; vnp = ValNodeNew (head); if (head == NULL) { head = vnp; } if (vnp != NULL) { vnp->choice = subtype; if (subtype != FEATDEF_misc_RNA && subtype != FEATDEF_precursor_RNA && subtype != FEATDEF_mat_peptide && subtype != FEATDEF_sig_peptide && subtype != FEATDEF_transit_peptide) { vnp->data.ptrvalue = StringSave (curr->typelabel); } else { StringNCpy_0 (str, curr->typelabel, sizeof (str) - 10); StringCat (str, "_imp"); vnp->data.ptrvalue = StringSave (str); } } } curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE); } } else { for (j = 1; descNames [j] != NULL; j++) { vnp = ValNodeNew (head); if (head == NULL) { head = vnp; } if (vnp != NULL) { vnp->choice = j; vnp->data.ptrvalue = StringSave (descNames [j]); } } } if (head != NULL) { head = SortValNode (head, SortByVnpChoice); for (vnp = head; vnp != NULL; vnp = vnp->next) { ListItem (rfp->objlist, (CharPtr) vnp->data.ptrvalue); } } rfp->head = head; rfp->bsplist = NULL; rfp->bssplist = NULL; k = HiddenGroup (h, 0, 2, NULL); StaticPrompt (k, "Optional string constraint", 0, dialogTextHeight, programFont, 'c'); rfp->findthis = DialogText (k, "", 14, NULL); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoRemoveAsnObject); SetObjectExtra (b, rfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) c, NULL); RealizeWindow (w); Show (w); Update (); } extern void RemoveFeature (IteM i) { RemoveAsnObject (i, TRUE); } extern void RemoveDescriptor (IteM i) { RemoveAsnObject (i, FALSE); } #define SLCT_FEAT 1 #define SLCT_DESC 2 #define SLCT_BIOSEQ 3 typedef struct selectformdata { FEATURE_FORM_BLOCK Int2 type; LisT objlist; TexT findthis; Uint2 itemtype; Uint2 subtype; ObjMgrPtr omp; ObjMgrTypePtr omtp; ValNodePtr head; Boolean stringfound; Char findStr [128]; } SelectFormData, PNTR SelectFormPtr; static Boolean SelectObjCallback (GatherContextPtr gcp) { ObjMgrTypePtr omtp; SelectFormPtr selfp; Uint2 subtype; if (gcp == NULL) return TRUE; selfp = (SelectFormPtr) gcp->userdata; if (selfp == NULL) return TRUE; if (gcp->thistype != selfp->itemtype) return TRUE; omtp = selfp->omtp; if (omtp == NULL) return TRUE; subtype = (*(omtp->subtypefunc)) ((Pointer) gcp->thisitem); if (subtype != selfp->subtype) return TRUE; ObjMgrAlsoSelect (gcp->entityID, gcp->itemID, gcp->thistype, 0, NULL); return TRUE; } static void DoSelectAsnObject (ButtoN b) { GatherScope gs; SelectFormPtr selfp; SeqEntryPtr sep; Int2 val; ValNodePtr vnp; selfp = GetObjectExtra (b); if (selfp == NULL) return; sep = GetTopSeqEntryForEntityID (selfp->input_entityID); if (sep == NULL) return; Hide (selfp->form); switch (selfp->type) { case SLCT_FEAT : selfp->itemtype = OBJ_SEQFEAT; break; case SLCT_DESC : selfp->itemtype = OBJ_SEQDESC; break; case SLCT_BIOSEQ : selfp->itemtype = OBJ_BIOSEQ; break; default : Remove (selfp->form); Update (); return; } WatchCursor (); Update (); vnp = NULL; val = GetValue (selfp->objlist); if (val > 0) { vnp = selfp->head; while (vnp != NULL && val > 1) { val--; vnp = vnp->next; } } if (selfp->type == SLCT_BIOSEQ || vnp != NULL) { selfp->omp = ObjMgrGet (); selfp->omtp = NULL; if (selfp->omp != NULL) { selfp->omtp = ObjMgrTypeFind (selfp->omp, selfp->itemtype, NULL, NULL); } if (selfp->type == SLCT_BIOSEQ) { selfp->subtype = Seq_repr_raw; } else { selfp->subtype = vnp->choice; } if (selfp->itemtype != 0 && selfp->subtype != 0 && selfp->omtp != NULL) { MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQDESC] = FALSE; GatherEntity (selfp->input_entityID, (Pointer) selfp, SelectObjCallback, &gs); } } ArrowCursor (); Update (); /* ObjMgrSendMsg (OM_MSG_UPDATE, selfp->input_entityID, 0, 0); */ Remove (selfp->form); } static void SelectMessageProc (ForM f, Int2 mssg) { SelectFormPtr selfp; selfp = (SelectFormPtr) GetObjectExtra (f); if (selfp != NULL) { if (selfp->appmessage != NULL) { selfp->appmessage (f, mssg); } } } static void CleanupSelectPage (GraphiC g, VoidPtr data) { SelectFormPtr selfp; selfp = (SelectFormPtr) data; if (selfp != NULL) { ValNodeFreeData (selfp->head); } StdCleanupFormProc (g, data); } static void SelectAsnObject (IteM i, Int2 type) { BaseFormPtr bfp; ButtoN b; GrouP c; FeatDefPtr curr; GrouP g; GrouP h; ValNodePtr head; Int2 j; Uint1 key; CharPtr label = NULL; Int2 listHeight; SelectFormPtr selfp; SeqEntryPtr sep; StdEditorProcsPtr sepp; Uint2 subtype; CharPtr title; ValNodePtr vnp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; selfp = (SelectFormPtr) MemNew (sizeof (SelectFormData)); if (selfp == NULL) return; switch (type) { case SLCT_FEAT : title = "Feature Selection"; break; case SLCT_DESC : title = "Descriptor Selection"; break; case SLCT_BIOSEQ : title = "Sequence Selection"; break; default : title = "? Selection"; break; } w = FixedWindow (-50, -33, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, selfp, CleanupSelectPage); selfp->form = (ForM) w; selfp->formmessage = SelectMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); selfp->appmessage = sepp->handleMessages; } selfp->input_entityID = bfp->input_entityID; selfp->input_itemID = bfp->input_itemID; selfp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 0, 2, NULL); selfp->type = type; switch (type) { case SLCT_FEAT : StaticPrompt (g, "Feature", 0, 0, programFont, 'c'); break; case SLCT_DESC : StaticPrompt (g, "Descriptor", 0, 0, programFont, 'c'); break; case SLCT_BIOSEQ : StaticPrompt (g, "Sequence", 0, 0, programFont, 'c'); break; default : break; } if (indexerVersion) { listHeight = 16; } else { listHeight = 8; } selfp->objlist = SingleList (g, 16, listHeight, NULL); head = NULL; if (type == SLCT_FEAT) { curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE); while (curr != NULL) { if (key != FEATDEF_BAD) { subtype = curr->featdef_key; vnp = ValNodeNew (head); if (head == NULL) { head = vnp; } if (vnp != NULL) { vnp->choice = subtype; vnp->data.ptrvalue = StringSave (curr->typelabel); } } curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE); } } else if (type == SLCT_DESC) { for (j = 1; descNames [j] != NULL; j++) { vnp = ValNodeNew (head); if (head == NULL) { head = vnp; } if (vnp != NULL) { vnp->choice = j; vnp->data.ptrvalue = StringSave (descNames [j]); } } } if (head != NULL) { head = SortValNode (head, SortByVnpChoice); for (vnp = head; vnp != NULL; vnp = vnp->next) { ListItem (selfp->objlist, (CharPtr) vnp->data.ptrvalue); } } selfp->head = head; c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoSelectAsnObject); SetObjectExtra (b, selfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); if (type == SLCT_BIOSEQ) { DoSelectAsnObject (b); Update (); return; } Show (w); Update (); } extern void SelectFeature (IteM i) { SelectAsnObject (i, SLCT_FEAT); } extern void SelectDescriptor (IteM i) { SelectAsnObject (i, SLCT_DESC); } extern void SelectBioseq (IteM i) { SelectAsnObject (i, SLCT_BIOSEQ); } typedef struct fuseformdata { FEATURE_FORM_BLOCK LisT objlist; Uint2 subtype; ObjMgrPtr omp; ObjMgrTypePtr omtp; ValNodePtr head; } FuseFormData, PNTR FuseFormPtr; static void FuseFeatureCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; FuseFormPtr ffp; SeqFeatPtr first; SeqFeatPtr nextsfp; ObjMgrTypePtr omtp; Pointer PNTR prevsfp; SeqAnnotPtr sap; SeqFeatPtr sfp; SeqLocPtr slp; Uint2 subtype; BioseqPtr target; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; ffp = (FuseFormPtr) mydata; if (ffp == NULL) return; omtp = ffp->omtp; if (omtp == NULL || omtp->subtypefunc == NULL) return; if (! IS_Bioseq (sep)) return; bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; first = NULL; while (sap != NULL) { if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; prevsfp = (Pointer PNTR) &(sap->data); while (sfp != NULL) { nextsfp = sfp->next; subtype = (*(omtp->subtypefunc)) ((Pointer) sfp); if (subtype == ffp->subtype || (ffp->subtype == FEATDEF_IMP && subtype >= FEATDEF_allele && subtype <= FEATDEF_site_ref)) { if (first != NULL) { target = GetBioseqGivenSeqLoc (sfp->location, ffp->input_entityID); if (target != NULL) { slp = SeqLocMerge (target, sfp->location, first->location, FALSE, TRUE, FALSE); first->location = SeqLocFree (first->location); first->location = slp; first->partial = CheckSeqLocForPartial (slp, NULL, NULL); } *(prevsfp) = sfp->next; sfp->next = NULL; SeqFeatFree (sfp); } else { first = sfp; prevsfp = (Pointer PNTR) &(sfp->next); } } sfp = nextsfp; } } sap = sap->next; } } static void DoFuseFeature (ButtoN b) { FuseFormPtr ffp; SeqEntryPtr sep; Int2 val; ValNodePtr vnp; ffp = (FuseFormPtr) GetObjectExtra (b); if (ffp == NULL) return; sep = GetTopSeqEntryForEntityID (ffp->input_entityID); if (sep == NULL) return; Hide (ffp->form); WatchCursor (); Update (); vnp = NULL; val = GetValue (ffp->objlist); if (val > 0) { vnp = ffp->head; while (vnp != NULL && val > 1) { val--; vnp = vnp->next; } } if (vnp != NULL) { ffp->omp = ObjMgrGet (); ffp->omtp = NULL; if (ffp->omp != NULL) { ffp->omtp = ObjMgrTypeFind (ffp->omp, OBJ_SEQFEAT, NULL, NULL); } ffp->subtype = vnp->choice; if (ffp->subtype != 0 && ffp->omtp != NULL) { SeqEntryExplore (sep, (Pointer) ffp, FuseFeatureCallback); } } ArrowCursor (); Update (); ObjMgrSetDirtyFlag (ffp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, ffp->input_entityID, 0, 0); ObjMgrDeSelect (0, 0, 0, 0, NULL); Remove (ffp->form); } static void FuseMessageProc (ForM f, Int2 mssg) { FuseFormPtr ffp; ffp = (FuseFormPtr) GetObjectExtra (f); if (ffp != NULL) { if (ffp->appmessage != NULL) { ffp->appmessage (f, mssg); } } } static void CleanupFusePage (GraphiC g, VoidPtr data) { FuseFormPtr ffp; ffp = (FuseFormPtr) data; if (ffp != NULL) { ValNodeFreeData (ffp->head); } StdCleanupFormProc (g, data); } extern void FuseFeature (IteM i) { BaseFormPtr bfp; ButtoN b; GrouP c; FeatDefPtr curr; FuseFormPtr ffp; GrouP g; GrouP h; ValNodePtr head; Uint1 key; CharPtr label = NULL; Int2 listHeight; SeqEntryPtr sep; StdEditorProcsPtr sepp; Uint2 subtype; ValNodePtr vnp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; ffp = (FuseFormPtr) MemNew (sizeof (FuseFormData)); if (ffp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Fuse Feature", StdCloseWindowProc); SetObjectExtra (w, ffp, CleanupFusePage); ffp->form = (ForM) w; ffp->formmessage = FuseMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); ffp->appmessage = sepp->handleMessages; } ffp->input_entityID = bfp->input_entityID; ffp->input_itemID = bfp->input_itemID; ffp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 0, 2, NULL); StaticPrompt (g, "Feature", 0, 0, programFont, 'c'); if (indexerVersion) { listHeight = 16; } else { listHeight = 8; } ffp->objlist = SingleList (g, 16, listHeight, NULL); head = NULL; curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE); while (curr != NULL) { if (key != FEATDEF_BAD) { subtype = curr->featdef_key; if (subtype != FEATDEF_misc_RNA && subtype != FEATDEF_precursor_RNA && subtype != FEATDEF_mat_peptide && subtype != FEATDEF_sig_peptide && subtype != FEATDEF_transit_peptide) { vnp = ValNodeNew (head); if (head == NULL) { head = vnp; } if (vnp != NULL) { vnp->choice = subtype; vnp->data.ptrvalue = StringSave (curr->typelabel); } } } curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE); } if (head != NULL) { head = SortValNode (head, SortByVnpChoice); for (vnp = head; vnp != NULL; vnp = vnp->next) { ListItem (ffp->objlist, (CharPtr) vnp->data.ptrvalue); } } ffp->head = head; c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoFuseFeature); SetObjectExtra (b, ffp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); Show (w); Update (); } extern Int2 LIBCALLBACK RefGeneUserGenFunc (Pointer data); #define REFGENE_ASSEMBLY 1 #define REFGENE_RELATED 2 #define REFGENE_SPLICEVAR 3 #define REFGENE_RELDREK 4 #define REFGENE_REJECT 5 #define REFGENE_UNKNOWN 6 typedef struct refgeneuserdialog { DIALOG_MESSAGE_BLOCK GrouP status; TexT curator; DialoG fields; } RefgeneUserDialog, PNTR RefgeneUserDialogPtr; typedef struct refgeneuserform { FEATURE_FORM_BLOCK SeqEntryPtr sep; } RefgeneUserForm, PNTR RefgeneUserFormPtr; static ENUM_ALIST(changeflags_alist) {" ", 0}, {"Sequence", 1}, {"Annotation", 2}, {"Both", 3}, END_ENUM_ALIST static ENUM_ALIST(refgene_alist) {" ", 0}, {"Assembly", REFGENE_ASSEMBLY}, {"Related", REFGENE_RELATED}, {"SpliceVar", REFGENE_SPLICEVAR}, {"RelatedDrek", REFGENE_RELDREK}, {"Reject", REFGENE_REJECT}, {"Unknown", REFGENE_UNKNOWN}, END_ENUM_ALIST static Uint2 refgene_types [] = { TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_TEXT, TAGLIST_POPUP, TAGLIST_POPUP }; static Uint2 refgene_widths [] = { 9, 7, 15, 0, 0 }; static EnumFieldAssocPtr refgene_popups [] = { NULL, NULL, NULL, changeflags_alist, refgene_alist }; static CharPtr refgene_labels [] = { "", "Assembly", "Related", "SpliceVar", "RelatedDrek", "Reject", "Unknown", NULL }; static CharPtr refgene_fields [] = { "Accession", "GI", "Comment", "Change", "Type", NULL }; static void AccessionUserFieldPtrToVisStringDialog (DialoG d, Pointer data) { CharPtr accession; Boolean annotChange; CharPtr comment; UserFieldPtr curr; UserFieldPtr entry; Int2 field; Int2 flags; Int4 from; Int4 gi; ValNodePtr head; Int2 i; Int2 j; ObjectIdPtr oip; Boolean seqChange; CharPtr str; TagListPtr tlp; Int4 to; UserFieldPtr ufp; ValNodePtr vnp; tlp = (TagListPtr) GetObjectExtra (d); if (tlp == NULL) return; str = MemNew (sizeof (Char) * 1024); head = NULL; curr = (UserFieldPtr) data; while (curr != NULL) { oip = curr->label; if (oip != NULL) { field = 0; for (i = REFGENE_ASSEMBLY; i <= REFGENE_UNKNOWN; i++) { if (StringICmp (oip->str, refgene_labels [i]) == 0 && curr->choice == 11) { field = i; } } if (field > 0) { entry = (UserFieldPtr) curr->data.ptrvalue; while (entry != NULL && entry->choice == 11) { accession = NULL; comment = NULL; gi = 0; from = 0; to = 0; annotChange = FALSE; seqChange = FALSE; ufp = (UserFieldPtr) entry->data.ptrvalue; while (ufp != NULL) { oip = ufp->label; if (oip != NULL && oip->str != NULL) { if (StringICmp (oip->str, "accession") == 0 && ufp->choice == 1) { accession = (CharPtr) ufp->data.ptrvalue; } else if (StringICmp (oip->str, "gi") == 0 && ufp->choice == 2) { gi = ufp->data.intvalue; } else if (StringICmp (oip->str, "from") == 0 && ufp->choice == 2) { from = ufp->data.intvalue; } else if (StringICmp (oip->str, "to") == 0 && ufp->choice == 2) { to = ufp->data.intvalue; } else if (StringICmp (oip->str, "sequenceChange") == 0 && ufp->choice == 4) { seqChange = ufp->data.boolvalue; } else if (StringICmp (oip->str, "annotationChange") == 0 && ufp->choice == 4) { annotChange = ufp->data.boolvalue; } else if (StringICmp (oip->str, "comment") == 0 && ufp->choice == 1) { comment = (CharPtr) ufp->data.ptrvalue; } } ufp = ufp->next; } if (accession != NULL) { if (comment == NULL) { comment = ""; } flags = 0; if (seqChange) { flags++; } if (annotChange) { flags += 2; } if (gi != 0) { sprintf (str, "%s\t%ld\t%s\t%d\t%d\n", accession, (long) gi, comment, (int) flags, (int) field); } else { sprintf (str, "%s\t\t%s\t%d\t%d\n", accession, comment, (int) flags, (int) field); } vnp = ValNodeNew (head); if (head == NULL) { head = vnp; } if (vnp != NULL) { vnp->data.ptrvalue = StringSave (str); } } entry = entry->next; } } } curr = curr->next; } MemFree (str); SendMessageToDialog (tlp->dialog, VIB_MSG_RESET); tlp->vnp = head; SendMessageToDialog (tlp->dialog, VIB_MSG_REDRAW); for (j = 0, vnp = tlp->vnp; vnp != NULL; j++, vnp = vnp->next) { } tlp->max = MAX ((Int2) 0, (Int2) (j - tlp->rows + 1)); CorrectBarMax (tlp->bar, tlp->max); CorrectBarPage (tlp->bar, tlp->rows - 1, tlp->rows - 1); } static Pointer VisStringDialogToUserFieldPtr (DialoG d) { return NULL; } static void UserObjectPtrToRefGeneDialog (DialoG d, Pointer data) { UserFieldPtr curr; ObjectIdPtr oip; RefgeneUserDialogPtr rdp; Int2 status = 0; CharPtr str; UserObjectPtr uop; rdp = (RefgeneUserDialogPtr) GetObjectExtra (d); if (rdp == NULL) return; uop = (UserObjectPtr) data; if (uop == NULL || uop->type == NULL || StringICmp (uop->type->str, "RefGeneTracking") != 0) { SetValue (rdp->status, 0); PointerToDialog (rdp->fields, NULL); return; } PointerToDialog (rdp->fields, uop->data); for (curr = uop->data; curr != NULL; curr = curr->next) { oip = curr->label; if (oip != NULL && StringICmp (oip->str, "Status") == 0) { break; } } if (curr != NULL && curr->choice == 1) { str = (CharPtr) curr->data.ptrvalue; if (StringICmp (str, "Predicted") == 0) { status = 1; } else if (StringICmp (str, "Provisional") == 0) { status = 2; } else if (StringICmp (str, "Validated") == 0) { status = 3; } else if (StringICmp (str, "Reviewed") == 0) { status = 4; } } for (curr = uop->data; curr != NULL; curr = curr->next) { oip = curr->label; if (oip != NULL && StringICmp (oip->str, "Collaborator") == 0) { break; } } if (curr != NULL && curr->choice == 1) { str = (CharPtr) curr->data.ptrvalue; SetTitle (rdp->curator, str); } SetValue (rdp->status, status); } static Pointer RefGeneDialogToUserObjectPtr (DialoG d) { Boolean annotChange; Char ch; Char curator [256]; Int2 i; Int2 j; size_t len; Int4 num [5]; Boolean okay; CharPtr organism = NULL; RefgeneUserDialogPtr rdp; Boolean seqChange; Int2 status; CharPtr str; TagListPtr tlp; CharPtr txt [5]; UserObjectPtr uop; long int val; ValNodePtr vnp; rdp = (RefgeneUserDialogPtr) GetObjectExtra (d); if (rdp == NULL) return NULL; uop = CreateRefGeneTrackUserObject (); if (uop == NULL) return NULL; status = GetValue (rdp->status); if (status == 1) { AddStatusToRefGeneTrackUserObject (uop, "Predicted"); } else if (status == 2) { AddStatusToRefGeneTrackUserObject (uop, "Provisional"); } else if (status == 3) { AddStatusToRefGeneTrackUserObject (uop, "Validated"); } else if (status == 4) { AddStatusToRefGeneTrackUserObject (uop, "Reviewed"); } GetTitle (rdp->curator, curator, sizeof (curator)); if (! StringHasNoText (curator)) { AddCuratorToRefGeneTrackUserObject (uop, curator); } tlp = (TagListPtr) GetObjectExtra (rdp->fields); if (tlp != NULL && tlp->vnp != NULL) { for (vnp = tlp->vnp; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; okay = FALSE; len = StringLen (str); for (j = 0; j < len; j++) { ch = str [j]; if (ch != ' ' && ch != '\t' && ch != '\n') { okay = TRUE; } } if (okay) { for (j = 0; j < 5; j++) { txt [j] = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, j); num [j] = 0; } for (j = 1; j < 5; j++) { if (j != 2) { num [j] = 0; if (txt [j] != NULL && sscanf (txt [j], "%ld", &val) == 1) { num [j] = val; } } } annotChange = FALSE; seqChange = FALSE; if (num [3] >= 2) { annotChange = TRUE; (num [3]) -= 2; } if (num [3] > 0) { seqChange = TRUE; } i = num [4]; if (i >= REFGENE_ASSEMBLY && i <= REFGENE_UNKNOWN) { if (! StringHasNoText (txt [0])) { AddAccessionToRefGeneTrackUserObject (uop, refgene_labels [i], txt [0], num [1], seqChange, annotChange, txt [2]); } for (j = 0; j < 5; j++) { txt [j] = MemFree (txt [j]); } } } } } return uop; } static DialoG CreateRefGeneDialog (GrouP g) { Int2 i; PrompT lastppt; GrouP p; PrompT ppt; GrouP q; RefgeneUserDialogPtr rdp; TagListPtr tlp; GrouP x; GrouP y; p = HiddenGroup (g, -1, 0, NULL); SetGroupSpacing (p, 10, 10); rdp = (RefgeneUserDialogPtr) MemNew (sizeof (RefgeneUserDialog)); if (rdp == NULL) return NULL; SetObjectExtra (p, rdp, NULL); rdp->dialog = (DialoG) p; rdp->todialog = UserObjectPtrToRefGeneDialog; rdp->fromdialog = RefGeneDialogToUserObjectPtr; x = HiddenGroup (p, 4, 0, NULL); /* StaticPrompt (x, "Status", 0, stdLineHeight, programFont, 'l'); */ rdp->status = HiddenGroup (x, 4, 0, NULL); SetObjectExtra (rdp->status, rdp, NULL); RadioButton (rdp->status, "Predicted"); RadioButton (rdp->status, "Provisional"); RadioButton (rdp->status, "Validated"); RadioButton (rdp->status, "Reviewed"); y = HiddenGroup (p, 2, 0, NULL); StaticPrompt (y, "Curator", 0, dialogTextHeight, programFont, 'l'); rdp->curator = DialogText (y, "", 14, NULL); q = HiddenGroup (p, -6, 0, NULL); lastppt = NULL; ppt = NULL; for (i = 0; i < 5; i++) { lastppt = ppt; ppt = StaticPrompt (q, refgene_fields [i], refgene_widths [i] * stdCharWidth, 0, systemFont, 'c'); } rdp->fields = CreateTagListDialog (p, 6, 5, STD_TAG_SPACING, refgene_types, refgene_widths, refgene_popups, AccessionUserFieldPtrToVisStringDialog, VisStringDialogToUserFieldPtr); tlp = (TagListPtr) GetObjectExtra (rdp->fields); if (tlp != NULL) { AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [3], (HANDLE) lastppt, NULL); AlignObjects (ALIGN_JUSTIFY, (HANDLE) tlp->control [4], (HANDLE) ppt, NULL); } AlignObjects (ALIGN_CENTER, (HANDLE) x, (HANDLE) y, (HANDLE) q, (HANDLE) rdp->fields, NULL); return (DialoG) p; } static void RefgeneUserFormMessage (ForM f, Int2 mssg) { RefgeneUserFormPtr rfp; rfp = (RefgeneUserFormPtr) GetObjectExtra (f); if (rfp != NULL) { switch (mssg) { case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : StdDeleteTextProc (NULL); break; default : if (rfp->appmessage != NULL) { rfp->appmessage (f, mssg); } break; } } } static ForM CreateRefGeneDescForm (Int2 left, Int2 top, Int2 width, Int2 height, CharPtr title, ValNodePtr sdp, SeqEntryPtr sep, FormActnFunc actproc) { ButtoN b; GrouP c; GrouP g; RefgeneUserFormPtr rfp; StdEditorProcsPtr sepp; WindoW w; w = NULL; rfp = (RefgeneUserFormPtr) MemNew (sizeof (RefgeneUserForm)); if (rfp != NULL) { w = FixedWindow (left, top, width, height, title, StdCloseWindowProc); SetObjectExtra (w, rfp, StdDescFormCleanupProc); rfp->form = (ForM) w; rfp->actproc = actproc; rfp->formmessage = RefgeneUserFormMessage; rfp->sep = sep; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); rfp->appmessage = sepp->handleMessages; } g = HiddenGroup (w, -1, 0, NULL); rfp->data = CreateRefGeneDialog (g); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdAcceptFormButtonProc); SetObjectExtra (b, rfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); } return (ForM) w; } extern Int2 LIBCALLBACK RefGeneUserGenFunc (Pointer data) { ObjectIdPtr oip; OMProcControlPtr ompcp; OMUserDataPtr omudp; ObjMgrProcPtr proc; RefgeneUserFormPtr rfp; ValNodePtr sdp; SeqEntryPtr sep; UserObjectPtr uop; WindoW w; ompcp = (OMProcControlPtr) data; w = NULL; sdp = NULL; sep = NULL; uop = NULL; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; proc = ompcp->proc; switch (ompcp->input_itemtype) { case OBJ_SEQDESC : sdp = (ValNodePtr) ompcp->input_data; if (sdp != NULL && sdp->choice != Seq_descr_user) { return OM_MSG_RET_ERROR; } uop = (UserObjectPtr) sdp->data.ptrvalue; break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { if (StringCmp (proc->procname, "Edit RefGene UserTrack Desc") == 0) { rfp = (RefgeneUserFormPtr) omudp->userdata.ptrvalue; if (rfp != NULL) { Select (rfp->form); } return OM_MSG_RET_DONE; } else { return OM_MSG_RET_OK; /* not this type, check next registered user object editor */ } } if (uop != NULL) { oip = uop->type; if (oip == NULL || oip->str == NULL) return OM_MSG_RET_OK; if (StringCmp (oip->str, "RefGeneTracking") != 0) return OM_MSG_RET_OK; } sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); w = (WindoW) CreateRefGeneDescForm (-50, -33, -10, -10, "Reference Gene Tracking", sdp, sep, StdDescFormActnProc); rfp = (RefgeneUserFormPtr) GetObjectExtra (w); if (rfp != NULL) { rfp->input_entityID = ompcp->input_entityID; rfp->input_itemID = ompcp->input_itemID; rfp->input_itemtype = ompcp->input_itemtype; rfp->this_itemtype = OBJ_SEQDESC; rfp->this_subtype = Seq_descr_user; rfp->procid = ompcp->proc->procid; rfp->proctype = ompcp->proc->proctype; rfp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, rfp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) rfp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToForm (rfp->form, VIB_MSG_INIT); if (sdp != NULL) { PointerToDialog (rfp->data, (Pointer) sdp->data.ptrvalue); SetClosestParentIfDuplicating ((BaseFormPtr) rfp); } } Show (w); Select (w); return OM_MSG_RET_DONE; } /* static void TestGeneRefStuff (void) { UserObjectPtr uop; ValNodePtr sdp; uop = CreateRefGeneTrackUserObject (); AddAccessionToRefGeneTrackUserObject (uop, "Assembly", "U12345", 57, 29, 1995); AddAccessionToRefGeneTrackUserObject (uop, "Assembly", "L97531", 142, 66, 963); AddAccessionToRefGeneTrackUserObject (uop, "Assembly", "M66778", 823, 7677, 343); AddAccessionToRefGeneTrackUserObject (uop, "Related", "P34345", 445, 0, 0); AddAccessionToRefGeneTrackUserObject (uop, "Reject", "S19635", 1765, 0, 0); AddAccessionToRefGeneTrackUserObject (uop, "Related", "Q14884", 664, 35, 97); sdp = ValNodeNew (NULL); sdp->choice = Seq_descr_user; sdp->data.ptrvalue = (Pointer) uop; if (! ObjMgrRegister (OBJ_SEQDESC, (Pointer) sdp)) { ErrPostEx (SEV_ERROR, 0, 0, "ObjMgrRegister failed."); } } */ typedef struct cka_acc { CharPtr accession; SeqIdPtr sip_whole; SeqAlignPtr sap; Int4 start_acc; Int4 stop_acc; Int4 start_seq; Int4 stop_seq; Uint1 strand; Int4 num; struct cka_acc PNTR next; } CKA_Acc, PNTR CKA_AccPtr; static SeqAlignPtr CKA_MakeAlign(BioseqPtr bsp, CKA_AccPtr acc_head); static void CKA_FindAllTpaDescr(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent) { CKA_AccPtr acc; CKA_AccPtr PNTR acc_head; CKA_AccPtr acc_prev; BioseqPtr bsp; SeqMgrDescContext context; UserFieldPtr curr; ObjectIdPtr oip; SeqDescrPtr sdp; UserFieldPtr ufp; UserObjectPtr uop; acc_head = (CKA_AccPtr PNTR)data; acc_prev = *acc_head; while (acc_prev != NULL && acc_prev->next != NULL) { acc_prev = acc_prev->next; } sdp = NULL; if (IS_Bioseq(sep)) { bsp = (BioseqPtr)sep->data.ptrvalue; if (ISA_na(bsp->mol)) { while ((sdp = SeqMgrGetNextDescriptor(bsp, sdp, Seq_descr_user, &context)) != NULL) { uop = (UserObjectPtr)sdp->data.ptrvalue; if (!StringICmp(uop->type->str, "TpaAssembly")) { for (curr = uop->data; curr != NULL; curr = curr->next) { if (curr->choice != 11) continue; for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) { if (ufp->choice != 1) continue; oip = ufp->label; if (oip == NULL || StringICmp (oip->str, "accession") != 0) continue; acc = (CKA_AccPtr)MemNew(sizeof(CKA_Acc)); acc->accession = StringSave((CharPtr)ufp->data.ptrvalue); acc->sip_whole = SeqIdDup(bsp->id); if (acc_prev == NULL) *acc_head = acc_prev = acc; else { acc_prev->next = acc; acc_prev = acc; } } } } } } } } static int LIBCALLBACK CKA_SortAccs(VoidPtr ptr1, VoidPtr ptr2) { CKA_AccPtr acc1; CKA_AccPtr acc2; acc1 = *((CKA_AccPtr PNTR)ptr1); acc2 = *((CKA_AccPtr PNTR)ptr2); if (acc1->num < acc2->num) return -1; else if (acc1->num > acc2->num) return 1; else return 0; /* no alignment */ } static Boolean CKA_ValidateSeqAlign(SeqAlignPtr sap, CKA_AccPtr acc_head, Int4 bioseqlen) { CKA_AccPtr acc; CKA_AccPtr PNTR accarray; AMAlignIndex2Ptr amaip; Int4 first; Boolean found; Int4 i; Int4 j; Int4 last; Int4 prev; if (sap == NULL || sap->saip == NULL || sap->saip->indextype != INDEX_PARENT) return FALSE; amaip = (AMAlignIndex2Ptr)(sap->saip); for (i=0; inumsaps; i++) { acc = acc_head; found = FALSE; while (acc != NULL && !found) { if (amaip->saps[i] == acc->sap) found = TRUE; else acc = acc->next; } if (!found) /* big error */ { Message(MSG_ERROR, "Serious error. Please contact sequindev."); return FALSE; } acc->num = i+1; AlnMgr2GetNthSeqRangeInSA(amaip->saps[i], 1, &acc->start_seq, &acc->stop_seq); AlnMgr2GetNthSeqRangeInSA(amaip->saps[i], 2, &acc->start_acc, &acc->stop_acc); acc->strand = AlnMgr2GetNthStrand(amaip->saps[i], 2); } acc = acc_head; i = 0; while (acc != NULL) { if (acc->num == 0) acc->num = amaip->numsaps; /* sort these guys all to the end */ i++; acc = acc->next; } accarray = (CKA_AccPtr PNTR)MemNew(i*sizeof(CKA_AccPtr)); i = 0; acc = acc_head; while (acc != NULL) { accarray[i] = acc; i++; acc = acc->next; } HeapSort(accarray, i, sizeof(CKA_AccPtr), CKA_SortAccs); first = last = -1; prev = -1; for (j=0; jsap != NULL) { if (first == -1) first = acc->start_seq; last = MAX(last, acc->stop_seq); } else Message (MSG_OKC, "Accession %s does not align to the bioseq.", acc->accession); if (prev != -1) { if (acc->start_seq > prev) { Message (MSG_ERROR, "The annotated accessions do not completely cover the bioseq:\n %s aligns to %d-%d but next aln is %s to %d-%d", accarray[j-1]->accession, accarray[j-1]->start_seq, accarray[j-1]->stop_seq, acc->accession, acc->start_seq, acc->stop_seq); MemFree(accarray); return FALSE; } } prev = acc->stop_seq+1; } if (first != 0 || last != bioseqlen-1) { if (first != 0) Message (MSG_ERROR, "The annotated accessions do not completely cover the bioseq:\n %s (the first aln) starts at position %d", accarray[0]->accession, accarray[0]->start_seq); if (accarray[i-1]->stop_seq != bioseqlen-1) Message (MSG_ERROR, "The annotated accessions do not completely cover the bioseq:\n %s (the last aln) goes to %d, bioseq length is %d", accarray[i-1]->accession, accarray[i-1]->stop_seq, bioseqlen-1); MemFree(accarray); return FALSE; } MemFree(accarray); return TRUE; } static void CKA_RunChecker(SeqEntryPtr sep) { CKA_AccPtr acc_head; CKA_AccPtr acc_head_next; CKA_AccPtr acc_head_prev; CKA_AccPtr acc_head_tmp; BioseqPtr bsp; Boolean found; SeqIdPtr lastid; SeqAlignPtr sap; SeqHistPtr shp; if (sep == NULL) { Message(MSG_ERROR, "Null SeqEntry passed to CKA_RunChecker"); return; } acc_head = NULL; SeqMgrIndexFeatures(0, (Pointer)(sep)); SeqEntryExplore(sep, &acc_head, CKA_FindAllTpaDescr); lastid = NULL; if (acc_head == NULL) { Message(MSG_ERROR, "No Tpa features found in SeqEntry."); return; } acc_head_tmp = acc_head; acc_head_prev = NULL; while (acc_head != NULL) { lastid = acc_head->sip_whole; acc_head_prev = acc_head; acc_head_tmp = acc_head->next; found = FALSE; while (!found && acc_head_tmp != NULL) { if (SeqIdComp(lastid, acc_head_tmp->sip_whole) != SIC_YES) found = TRUE; else { acc_head_prev = acc_head_tmp; acc_head_tmp = acc_head_tmp->next; } } acc_head_next = acc_head_prev->next; acc_head_prev->next = NULL; bsp = BioseqLockById(acc_head->sip_whole); if (ISA_na(bsp->mol)) { sap = CKA_MakeAlign(bsp, acc_head); if (CKA_ValidateSeqAlign(sap, acc_head, bsp->length)) { /* make seq-hist and add it to record */ if (bsp->hist != NULL) { shp = bsp->hist; if (shp->assembly != NULL) SeqAlignSetFree(shp->assembly); shp->assembly = sap; } else { shp = SeqHistNew(); shp->assembly = sap; bsp->hist = shp; } } else SeqAlignSetFree(sap); } else Message(MSG_ERROR, "%s is annotated on a non-nucleotide bioseq.", acc_head->accession); while (acc_head != NULL) { acc_head_tmp = acc_head->next; acc_head->next = NULL; MemFree(acc_head->accession); SeqIdFree(acc_head->sip_whole); MemFree(acc_head); acc_head = acc_head_tmp; } acc_head = acc_head_next; } } static void CKA_FindNuc(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqPtr PNTR bspptr; bspptr = (BioseqPtr PNTR)data; if (IS_Bioseq(sep)) { bsp = (BioseqPtr)sep->data.ptrvalue; if (ISA_na(bsp->mol)) { *bspptr = bsp; } } } static int LIBCALLBACK CKA_CompareAlns(VoidPtr ptr1, VoidPtr ptr2) { Int4 len1; Int4 len2; SeqAlignPtr sap1; SeqAlignPtr sap2; sap1 = *((SeqAlignPtr PNTR) ptr1); sap2 = *((SeqAlignPtr PNTR) ptr2); if (sap1 == NULL || sap2 == NULL) return 0; len1 = AlnMgr2GetAlnLength(sap1, FALSE); len2 = AlnMgr2GetAlnLength(sap2, FALSE); if (len1 < len2) return 1; if (len1 > len2) return -1; return 0; } static SeqAlignPtr CKA_MakeAlign(BioseqPtr bsp, CKA_AccPtr acc_head) { CKA_AccPtr acc; SeqAlignPtr allsap; SeqAlignPtr allsap_prev; AMAlignIndex2Ptr amaip; BioseqPtr bsp_tmp; Int4 i; BLAST_OptionsBlkPtr options; SeqAlignPtr salp; SeqAlignPtr sap_new; SeqIdPtr sip; Uint1 strand; if (bsp == NULL || acc_head == NULL) return NULL; acc = acc_head; allsap = NULL; allsap_prev = NULL; while (acc != NULL) { options = BLASTOptionNew("blastn", TRUE); options->wordsize = 32; options->gap_open = 0; options->gap_extend = 0; /* faster with no filtering */ options->is_megablast_search = TRUE; sip = SeqIdFromAccessionDotVersion(acc->accession); bsp_tmp = BioseqLockById(sip); if (!ISA_na(bsp_tmp->mol)) { BioseqUnlock(bsp_tmp); Message(MSG_ERROR, "%s is not a nucleotide bioseq.", acc->accession); break; } acc->sap = BlastTwoSequences(bsp_tmp, bsp, "blastn", options); if (acc->sap != NULL) SPI_flip_sa_list(acc->sap); if (acc->sap != NULL && acc->sap->next != NULL) { AlnMgr2IndexLite(acc->sap); amaip = (AMAlignIndex2Ptr)(acc->sap->saip); HeapSort(amaip->saps, amaip->numsaps, sizeof(SeqAlignPtr), CKA_CompareAlns); salp = (amaip->saps[0]); sap_new = SeqAlignDup(salp); SeqAlignSetFree(acc->sap); acc->sap = sap_new; } if (acc->sap != NULL) { AlnMgr2IndexSingleChildSeqAlign(acc->sap); strand = AlnMgr2GetNthStrand(acc->sap, 1); if (strand == Seq_strand_minus) { SeqAlignListReverseStrand(acc->sap); SAIndex2Free2(acc->sap->saip); acc->sap->saip = NULL; } if (allsap != NULL && acc->sap != NULL) { allsap_prev->next = acc->sap; allsap_prev = allsap_prev->next;; } else if (acc->sap != NULL) allsap_prev = allsap = (acc->sap); } BioseqUnlock(bsp_tmp); acc = acc->next; BLASTOptionDelete(options); } if (allsap == NULL) return NULL; sap_new = SeqAlignNew(); sap_new->segtype = SAS_DISC; sap_new->segs = (Pointer)(allsap); allsap = sap_new; AlnMgr2IndexLite(allsap); AlnMgr2SortAlnSetByNthRowPos(allsap, 1); amaip = (AMAlignIndex2Ptr)(allsap->saip); for (i=0; inumsaps-1; i++) { amaip->saps[i]->next = amaip->saps[i+1]; } amaip->saps[amaip->numsaps-1]->next = NULL; allsap->segs = (Pointer)(amaip->saps[0]); return allsap; } extern void CreateSeqHistTPA (IteM i); extern void CreateSeqHistTPA (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; CKA_RunChecker(sep); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); } extern Int2 LIBCALLBACK AssemblyUserGenFunc (Pointer data); typedef struct assemblyuserdialog { DIALOG_MESSAGE_BLOCK DialoG accns; } AssemblyUserDialog, PNTR AssemblyUserDialogPtr; typedef struct assemblyuserform { FEATURE_FORM_BLOCK SeqEntryPtr sep; } AssemblyUserForm, PNTR AssemblyUserFormPtr; static void UserObjectPtrToAssemblyDialog (DialoG d, Pointer data) { AssemblyUserDialogPtr adp; UserFieldPtr curr; ValNodePtr head = NULL; ObjectIdPtr oip; CharPtr str; UserFieldPtr ufp; UserObjectPtr uop; adp = (AssemblyUserDialogPtr) GetObjectExtra (d); if (adp == NULL) return; uop = (UserObjectPtr) data; if (uop == NULL || uop->type == NULL || StringICmp (uop->type->str, "TpaAssembly") != 0) { PointerToDialog (adp->accns, NULL); return; } for (curr = uop->data; curr != NULL; curr = curr->next) { if (curr->choice != 11) continue; for (ufp = curr->data.ptrvalue; ufp != NULL; ufp = ufp->next) { if (ufp->choice != 1) continue; oip = ufp->label; if (oip == NULL || StringICmp (oip->str, "accession") != 0) continue; str = (CharPtr) ufp->data.ptrvalue; if (StringHasNoText (str)) continue; ValNodeCopyStr (&head, 0, (Pointer) str); } } PointerToDialog (adp->accns, (Pointer) head); ValNodeFreeData (head); } static Pointer AssemblyDialogToUserObjectPtr (DialoG d) { AssemblyUserDialogPtr adp; Char ch; ValNodePtr head; CharPtr last; UserObjectPtr uop; CharPtr ptr; CharPtr str; CharPtr tmp; ValNodePtr vnp; adp = (AssemblyUserDialogPtr) GetObjectExtra (d); if (adp == NULL) return NULL; uop = CreateTpaAssemblyUserObject (); if (uop == NULL) return NULL; head = (ValNodePtr) DialogToPointer (adp->accns); if (head == NULL) return NULL; for (vnp = head; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; tmp = StringSave (str); last = tmp; ptr = last; ch = *ptr; while (ch != '\0') { if (ch == ',') { *ptr = '\0'; TrimSpacesAroundString (last); AddAccessionToTpaAssemblyUserObject (uop, last); ptr++; last = ptr; ch = *ptr; } else { ptr++; ch = *ptr; } } if (! StringHasNoText (last)) { TrimSpacesAroundString (last); AddAccessionToTpaAssemblyUserObject (uop, last); } /* AddAccessionToTpaAssemblyUserObject (uop, str); */ MemFree (tmp); } ValNodeFreeData (head); return uop; } static DialoG CreateAssemblyDialog (GrouP g) { AssemblyUserDialogPtr adp; GrouP p; GrouP x; p = HiddenGroup (g, -1, 0, NULL); SetGroupSpacing (p, 10, 10); adp = (AssemblyUserDialogPtr) MemNew (sizeof (AssemblyUserDialog)); if (adp == NULL) return NULL; SetObjectExtra (p, adp, NULL); adp->dialog = (DialoG) p; adp->todialog = UserObjectPtrToAssemblyDialog; adp->fromdialog = AssemblyDialogToUserObjectPtr; x = HiddenGroup (p, 0, 2, NULL); StaticPrompt (x, "Accessions", 0, 0, programFont, 'c'); adp->accns = CreateVisibleStringDialog (x, 3, -1, 15); return (DialoG) p; } static void AssemblyUserFormMessage (ForM f, Int2 mssg) { AssemblyUserFormPtr afp; afp = (AssemblyUserFormPtr) GetObjectExtra (f); if (afp != NULL) { switch (mssg) { case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : StdDeleteTextProc (NULL); break; default : if (afp->appmessage != NULL) { afp->appmessage (f, mssg); } break; } } } static ForM CreateAssemblyDescForm (Int2 left, Int2 top, Int2 width, Int2 height, CharPtr title, ValNodePtr sdp, SeqEntryPtr sep, FormActnFunc actproc) { AssemblyUserFormPtr afp; ButtoN b; GrouP c; GrouP g; StdEditorProcsPtr sepp; WindoW w; w = NULL; afp = (AssemblyUserFormPtr) MemNew (sizeof (AssemblyUserForm)); if (afp != NULL) { w = FixedWindow (left, top, width, height, title, StdCloseWindowProc); SetObjectExtra (w, afp, StdDescFormCleanupProc); afp->form = (ForM) w; afp->actproc = actproc; afp->formmessage = AssemblyUserFormMessage; afp->sep = sep; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); afp->appmessage = sepp->handleMessages; } g = HiddenGroup (w, -1, 0, NULL); afp->data = CreateAssemblyDialog (g); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdAcceptFormButtonProc); SetObjectExtra (b, afp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); } return (ForM) w; } extern Int2 LIBCALLBACK AssemblyUserGenFunc (Pointer data) { AssemblyUserFormPtr afp; ObjectIdPtr oip; OMProcControlPtr ompcp; OMUserDataPtr omudp; ObjMgrProcPtr proc; ValNodePtr sdp; SeqEntryPtr sep; UserObjectPtr uop; WindoW w; ompcp = (OMProcControlPtr) data; w = NULL; sdp = NULL; sep = NULL; uop = NULL; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; proc = ompcp->proc; switch (ompcp->input_itemtype) { case OBJ_SEQDESC : sdp = (ValNodePtr) ompcp->input_data; if (sdp != NULL && sdp->choice != Seq_descr_user) { return OM_MSG_RET_ERROR; } uop = (UserObjectPtr) sdp->data.ptrvalue; break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { if (StringCmp (proc->procname, "Edit Assembly User Desc") == 0) { afp = (AssemblyUserFormPtr) omudp->userdata.ptrvalue; if (afp != NULL) { Select (afp->form); } return OM_MSG_RET_DONE; } else { return OM_MSG_RET_OK; /* not this type, check next registered user object editor */ } } if (uop != NULL) { oip = uop->type; if (oip == NULL || oip->str == NULL) return OM_MSG_RET_OK; if (StringCmp (oip->str, "TpaAssembly") != 0) return OM_MSG_RET_OK; } sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); w = (WindoW) CreateAssemblyDescForm (-50, -33, -10, -10, "Assembly Tracking", sdp, sep, StdDescFormActnProc); afp = (AssemblyUserFormPtr) GetObjectExtra (w); if (afp != NULL) { afp->input_entityID = ompcp->input_entityID; afp->input_itemID = ompcp->input_itemID; afp->input_itemtype = ompcp->input_itemtype; afp->this_itemtype = OBJ_SEQDESC; afp->this_subtype = Seq_descr_user; afp->procid = ompcp->proc->procid; afp->proctype = ompcp->proc->proctype; afp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, afp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) afp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToForm (afp->form, VIB_MSG_INIT); if (sdp != NULL) { PointerToDialog (afp->data, (Pointer) sdp->data.ptrvalue); SetClosestParentIfDuplicating ((BaseFormPtr) afp); } } Show (w); Select (w); return OM_MSG_RET_DONE; } typedef struct historyformdata { FEATURE_FORM_BLOCK BioseqPtr bsp; DialoG replace_date; DialoG replace_ids; ButtoN secondary_on_part; DialoG replaced_by_date; DialoG replaced_by_ids; ButtoN deleted; DialoG deleted_date; } HistoryFormData, PNTR HistoryFormPtr; static SeqIdPtr VisStrDialogToSeqIdSet (DialoG d) { long gi; SeqIdPtr head = NULL; ValNodePtr list; CharPtr str; TextSeqIdPtr tsip; ValNodePtr vnp; if (d == NULL) return NULL; list = DialogToPointer (d); for (vnp = list; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (str != NULL) { if (sscanf (str, "%ld", &gi)) { /* ValNodeAddInt (&head, SEQID_GI, (Int4) gi); */ } else { tsip = TextSeqIdNew (); if (tsip != NULL) { tsip->accession = StringSaveNoNull (str); ValNodeAddPointer (&head, SEQID_GENBANK, (Pointer) tsip); } } } } ValNodeFreeData (list); return head; } static int LIBCALLBACK SortByName (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 != NULL && str2 != NULL) { return StringICmp (str1, str2); } else { return 0; } } else { return 0; } } else { return 0; } } static ValNodePtr GetStringsForSeqIDs (SeqIdPtr sip) { Char buf [40]; ValNodePtr head = NULL; TextSeqIdPtr tsip; if (sip == NULL) return NULL; while (sip != NULL) { buf [0] = '\0'; switch (sip->choice) { case SEQID_GENBANK : case SEQID_EMBL : case SEQID_DDBJ : tsip = (TextSeqIdPtr) sip->data.ptrvalue; if (tsip != NULL && (! StringHasNoText (tsip->accession))) { StringNCpy_0 (buf, tsip->accession, sizeof (buf)); } break; case SEQID_GI : /* gi = sip->data.intvalue; if (gi > 0) { sprintf (buf, "%ld", (long) gi); } */ break; default : break; } if (! StringHasNoText (buf)) { ValNodeCopyStr (&head, 0, buf); } sip = sip->next; } return head; } static void AddGenBankBlockToBioseq (BioseqPtr bsp, ValNodePtr head1, ValNodePtr head2) { GBBlockPtr gbp = NULL; CharPtr last = NULL; ValNodePtr next; ValNodePtr PNTR prev; ValNodePtr sdp; SeqEntryPtr sep; CharPtr str1, str2; ValNodePtr vnp, vnp1, vnp2; sdp = BioseqGetSeqDescr (bsp, Seq_descr_genbank, NULL); if (sdp != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL) { for (vnp1 = head1; vnp1 != NULL; vnp1 = vnp1->next) { str1 = (CharPtr) vnp1->data.ptrvalue; if (str1 != NULL) { for (vnp2 = gbp->extra_accessions; vnp2 != NULL; vnp2 = vnp2->next) { str2 = (CharPtr) vnp2->data.ptrvalue; if (StringICmp (str1, str2) == 0) { vnp2->data.ptrvalue = MemFree (vnp2->data.ptrvalue); } } } } } } if (sdp == NULL) { sep = SeqMgrGetSeqEntryForData (bsp); sdp = CreateNewDescriptor (sep, Seq_descr_genbank); if (sdp != NULL) { sdp->data.ptrvalue = GBBlockNew (); } } if (sdp != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (gbp != NULL) { while (head2 != NULL) { ValNodeCopyStr (&(gbp->extra_accessions), 0, (CharPtr) head2->data.ptrvalue); head2 = head2->next; } /* ValNodeLink (&(gbp->extra_accessions), head2); head2 = NULL; */ gbp->extra_accessions = SortValNode (gbp->extra_accessions, SortByName); prev = &(gbp->extra_accessions); vnp = gbp->extra_accessions; last = NULL; while (vnp != NULL) { next = vnp->next; str2 = (CharPtr) vnp->data.ptrvalue; if (str2 == NULL || StringHasNoText (str2) || StringICmp (last, str2) == 0) { *prev = next; vnp->next = NULL; MemFree (vnp); vnp = next; } else { last = str2; prev = &(vnp->next); vnp = next; } } } } } static void DoChangeHistory (ButtoN b) { MsgAnswer ans; BioseqPtr bsp; ValNodePtr head1 = NULL, head2 = NULL; HistoryFormPtr hfp; SeqHistPtr hist; BioseqPtr pbsp; SeqEntryPtr sep; SeqLocPtr slp; CharPtr str1, str2; ValNodePtr vnp1, vnp2; hfp = (HistoryFormPtr) GetObjectExtra (b); if (hfp == NULL) return; ans = Message (MSG_OKC, "Are you sure you want to edit the history?"); if (ans == ANS_CANCEL) { return; } Hide (hfp->form); Update (); bsp = hfp->bsp; hist = bsp->hist; if (hist == NULL) { hist = SeqHistNew (); bsp->hist = hist; } if (hist != NULL) { hist->replace_date = DateFree (hist->replace_date); hist->replace_date = DialogToPointer (hfp->replace_date); head1 = GetStringsForSeqIDs (hist->replace_ids); hist->replace_ids = SeqIdSetFree (hist->replace_ids); hist->replace_ids = VisStrDialogToSeqIdSet (hfp->replace_ids); head2 = GetStringsForSeqIDs (hist->replace_ids); hist->replaced_by_date = DateFree (hist->replaced_by_date); hist->replaced_by_date = DialogToPointer (hfp->replaced_by_date); hist->replaced_by_ids = SeqIdSetFree (hist->replaced_by_ids); hist->replaced_by_ids = VisStrDialogToSeqIdSet (hfp->replaced_by_ids); hist->deleted = GetStatus (hfp->deleted); hist->deleted_date = DateFree (hist->deleted_date); hist->deleted_date = DialogToPointer (hfp->deleted_date); } if (hist->assembly == NULL && hist->replace_date == NULL && hist->replace_ids == NULL && hist->replaced_by_date == NULL && hist->replaced_by_ids == NULL && (! hist->deleted) && hist->deleted_date == NULL) { bsp->hist = SeqHistFree (bsp->hist); } head1 = SortValNode (head1, SortByName); head2 = SortValNode (head2, SortByName); for (vnp1 = head1; vnp1 != NULL; vnp1 = vnp1->next) { str1 = (CharPtr) vnp1->data.ptrvalue; for (vnp2 = head2; vnp2 != NULL; vnp2 = vnp2->next) { str2 = (CharPtr) vnp2->data.ptrvalue; if (StringICmp (str1, str2) == 0) { vnp1->data.ptrvalue = MemFree (vnp1->data.ptrvalue); } } } AddGenBankBlockToBioseq (bsp, head1, head2); if (GetStatus (hfp->secondary_on_part)) { if (bsp->repr == Seq_repr_seg) { for (slp = (SeqLocPtr) bsp->seq_ext; slp != NULL; slp = slp->next) { pbsp = BioseqFind (SeqLocId (slp)); if (pbsp != NULL) { AddGenBankBlockToBioseq (pbsp, head1, head2); } } } } ValNodeFreeData (head1); ValNodeFreeData (head2); sep = GetTopSeqEntryForEntityID (hfp->input_entityID); EntryCheckGBBlock (sep); Update (); ObjMgrSetDirtyFlag (hfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, hfp->input_entityID, 0, 0); ObjMgrDeSelect (0, 0, 0, 0, NULL); Remove (hfp->form); } static void SeqIdSetToVisStrDialog (DialoG d, SeqIdPtr sip) { ValNodePtr head = NULL; if (d == NULL || sip == NULL) return; head = GetStringsForSeqIDs (sip); PointerToDialog (d, head); ValNodeFreeData (head); } static void HistoryMessageProc (ForM f, Int2 mssg) { HistoryFormPtr hfp; hfp = (HistoryFormPtr) GetObjectExtra (f); if (hfp != NULL) { if (hfp->appmessage != NULL) { hfp->appmessage (f, mssg); } } } static void CleanupHistoryPage (GraphiC g, VoidPtr data) { HistoryFormPtr hfp; hfp = (HistoryFormPtr) data; if (hfp != NULL) { } StdCleanupFormProc (g, data); } extern void EditSequenceHistory (IteM i) { ButtoN b; BaseFormPtr bfp; BioseqPtr bsp; GrouP c; GrouP g; GrouP h; HistoryFormPtr hfp; SeqHistPtr hist; GrouP j; GrouP k; PrompT ppt1, ppt2, ppt3; SeqEntryPtr sep; StdEditorProcsPtr sepp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; bsp = GetBioseqGivenIDs (bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype); if (bsp == NULL) return; hist = bsp->hist; hfp = (HistoryFormPtr) MemNew (sizeof (HistoryFormData)); if (hfp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Sequence History", StdCloseWindowProc); SetObjectExtra (w, hfp, CleanupHistoryPage); hfp->form = (ForM) w; hfp->formmessage = HistoryMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); hfp->appmessage = sepp->handleMessages; } hfp->input_entityID = bfp->input_entityID; hfp->input_itemID = bfp->input_itemID; hfp->input_itemtype = bfp->input_itemtype; hfp->bsp = bsp; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); ppt1 = StaticPrompt (h, "Replaces", 0, 0, systemFont, 'c'); g = HiddenGroup (h, -1, 0, NULL); hfp->replace_ids = CreateVisibleStringDialog (g, 4, -1, 10); hfp->secondary_on_part = CheckBox (g, "Secondary on Parts", NULL); hfp->replace_date = CreateDateDialog (g, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) hfp->replace_ids, (HANDLE) hfp->secondary_on_part, (HANDLE) hfp->replace_date, NULL); ppt2 = StaticPrompt (h, "Replaced By", 0, 0, systemFont, 'c'); j = HiddenGroup (h, -1, 0, NULL); hfp->replaced_by_ids = CreateVisibleStringDialog (j, 4, -1, 10); hfp->replaced_by_date = CreateDateDialog (j, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) hfp->replaced_by_ids, (HANDLE) hfp->replaced_by_date, NULL); ppt3 = StaticPrompt (h, "Status", 0, 0, systemFont, 'c'); k = HiddenGroup (h, -1, 0, NULL); hfp->deleted = CheckBox (k, "Deleted", NULL); hfp->deleted_date = CreateDateDialog (k, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) hfp->deleted, (HANDLE) hfp->deleted_date, NULL); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoChangeHistory); SetObjectExtra (b, hfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) j, (HANDLE) k, (HANDLE) c, (HANDLE) ppt1, (HANDLE) ppt2, (HANDLE) ppt3, NULL); RealizeWindow (w); if (bsp->repr != Seq_repr_seg) { Disable (hfp->secondary_on_part); } else { SetStatus (hfp->secondary_on_part, TRUE); } if (hist != NULL) { PointerToDialog (hfp->replace_date, hist->replace_date); SeqIdSetToVisStrDialog (hfp->replace_ids, hist->replace_ids); PointerToDialog (hfp->replaced_by_date, hist->replaced_by_date); SeqIdSetToVisStrDialog (hfp->replaced_by_ids, hist->replaced_by_ids); PointerToDialog (hfp->deleted_date, hist->deleted_date); SetStatus (hfp->deleted, hist->deleted); } Show (w); Update (); } /* automatic defline generator */ typedef struct deffeats { SeqFeatPtr sfp; SeqFeatPtr gene; SeqFeatPtr prot; CharPtr genename; CharPtr allelename; CharPtr protname; Boolean alreadyTrimmed; Uint2 entityID; Uint2 itemID; Uint2 subtype; Boolean lastInString; Boolean lastInGroup; Boolean lastInType; Boolean lastInPenultimate; Boolean pseudo; Boolean ignore; Boolean suppressprefix; Int2 altSplices; Int2 numUnknown; } DefFeatsData, PNTR DefFeatsPtr; static Boolean GetMolBioFeatsGatherFunc (GatherContextPtr gcp, Boolean getGene, Boolean getMrna) { DefFeatsPtr dfp; RnaRefPtr rrp; SeqFeatPtr sfp; CharPtr str; Uint1 type; ValNodePtr PNTR vnpp; if (gcp == NULL || gcp->thisitem == NULL || gcp->userdata == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; vnpp = (ValNodePtr PNTR) gcp->userdata; sfp = (SeqFeatPtr) gcp->thisitem; switch (sfp->data.choice) { case SEQFEAT_GENE : if (getGene) { dfp = MemNew (sizeof (DefFeatsData)); if (dfp == NULL) return TRUE; dfp->entityID = gcp->entityID; dfp->itemID = gcp->itemID; dfp->sfp = sfp; dfp->subtype = FEATDEF_GENE; ValNodeAddPointer (vnpp, 0, (Pointer) dfp); } break; case SEQFEAT_CDREGION : dfp = MemNew (sizeof (DefFeatsData)); if (dfp == NULL) return TRUE; dfp->entityID = gcp->entityID; dfp->itemID = gcp->itemID; dfp->sfp = sfp; dfp->subtype = FEATDEF_CDS; dfp->altSplices = 1; ValNodeAddPointer (vnpp, 0, (Pointer) dfp); break; case SEQFEAT_RNA : rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp == NULL) return TRUE; switch (rrp->type) { case 2 : if (getMrna) { dfp = MemNew (sizeof (DefFeatsData)); if (dfp == NULL) return TRUE; dfp->entityID = gcp->entityID; dfp->itemID = gcp->itemID; dfp->sfp = sfp; dfp->subtype = FEATDEF_mRNA; ValNodeAddPointer (vnpp, 0, (Pointer) dfp); } break; case 3 : dfp = MemNew (sizeof (DefFeatsData)); if (dfp == NULL) return TRUE; dfp->entityID = gcp->entityID; dfp->itemID = gcp->itemID; dfp->sfp = sfp; dfp->subtype = FEATDEF_tRNA; ValNodeAddPointer (vnpp, 0, (Pointer) dfp); break; case 4 : dfp = MemNew (sizeof (DefFeatsData)); if (dfp == NULL) return TRUE; dfp->entityID = gcp->entityID; dfp->itemID = gcp->itemID; dfp->sfp = sfp; dfp->subtype = FEATDEF_rRNA; ValNodeAddPointer (vnpp, 0, (Pointer) dfp); break; case 255 : if (rrp->ext.choice == 1) { str = (CharPtr) rrp->ext.value.ptrvalue; if (StringICmp (str, "internal transcribed spacer 1") == 0 || StringICmp (str, "internal transcribed spacer 2") == 0 || StringICmp (str, "internal transcribed spacer 3") == 0 || StringICmp (str, "internal transcribed spacer ITS1") == 0 || StringICmp (str, "internal transcribed spacer ITS2") == 0 || StringICmp (str, "internal transcribed spacer ITS3") == 0 || StringICmp (str, "ITS1") == 0 || StringICmp (str, "ITS2") == 0 || StringICmp (str, "ITS3") == 0) { dfp = MemNew (sizeof (DefFeatsData)); if (dfp == NULL) return TRUE; dfp->entityID = gcp->entityID; dfp->itemID = gcp->itemID; dfp->sfp = sfp; dfp->subtype = FEATDEF_otherRNA; ValNodeAddPointer (vnpp, 0, (Pointer) dfp); } } break; default : break; } break; case SEQFEAT_IMP : type = FindFeatDefType (sfp); if (type == FEATDEF_LTR || type == FEATDEF_exon) { dfp = MemNew (sizeof (DefFeatsData)); if (dfp == NULL) return TRUE; dfp->entityID = gcp->entityID; dfp->itemID = gcp->itemID; dfp->sfp = sfp; dfp->subtype = type; ValNodeAddPointer (vnpp, 0, (Pointer) dfp); } break; default : break; } return TRUE; } static Boolean GetCDStRNArRNAGatherFunc (GatherContextPtr gcp) { return GetMolBioFeatsGatherFunc (gcp, FALSE, FALSE); } static Boolean GetGeneCDStRNArRNAGatherFunc (GatherContextPtr gcp) { return GetMolBioFeatsGatherFunc (gcp, TRUE, FALSE); } static Boolean GetGeneCDStRNArRNAmRNAGatherFunc (GatherContextPtr gcp) { return GetMolBioFeatsGatherFunc (gcp, TRUE, TRUE); } static void LabelAModifier (CharPtr str, CharPtr text, Boolean labelMods) { Char ch; CharPtr ptr; if (str == NULL || text == NULL) return; if (StringHasNoText (text)) { str [0] = '\0'; text [0] = '\0'; } else { if (labelMods) { ptr = str; while (*ptr != '\0') { ch = *ptr; *ptr = TO_LOWER (ch); ptr++; } StringCat (str, " "); } else { str [0] = '\0'; } StringCat (str, text); } } static int LIBCALLBACK SortCDStRNArRNAByLocation (VoidPtr ptr1, VoidPtr ptr2) { BioseqPtr bsp1; BioseqPtr bsp2; DefFeatsPtr dfp1; DefFeatsPtr dfp2; Int4 leftend1; Int4 leftend2; Int4 rightend1; Int4 rightend2; SeqFeatPtr sfp1; SeqFeatPtr sfp2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { dfp1 = (DefFeatsPtr) vnp1->data.ptrvalue; dfp2 = (DefFeatsPtr) vnp2->data.ptrvalue; if (dfp1 != NULL && dfp2 != NULL) { sfp1 = dfp1->sfp; sfp2 = dfp2->sfp; if (sfp1 != NULL && sfp2 != NULL) { bsp1 = GetBioseqGivenSeqLoc (sfp1->location, dfp1->entityID); bsp2 = GetBioseqGivenSeqLoc (sfp2->location, dfp2->entityID); if (bsp1 != NULL && bsp2 != NULL) { leftend1 = GetOffsetInBioseq (sfp1->location, bsp1, SEQLOC_LEFT_END); leftend2 = GetOffsetInBioseq (sfp2->location, bsp2, SEQLOC_LEFT_END); rightend1 = GetOffsetInBioseq (sfp1->location, bsp1, SEQLOC_RIGHT_END); rightend2 = GetOffsetInBioseq (sfp2->location, bsp2, SEQLOC_RIGHT_END); if (leftend1 > leftend2) { return 1; } else if (leftend1 < leftend2) { return -1; } else if (sfp2->data.choice == SEQFEAT_GENE) { return 1; } else if (sfp1->data.choice == SEQFEAT_GENE) { return -1; } else if (rightend1 > rightend2) { return 1; } else if (rightend1 < rightend2) { return -1; } else { return 0; } } } } } } return 0; } static int LIBCALLBACK SortCDSAfterExons (VoidPtr ptr1, VoidPtr ptr2) { DefFeatsPtr dfp1; DefFeatsPtr dfp2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { dfp1 = (DefFeatsPtr) vnp1->data.ptrvalue; dfp2 = (DefFeatsPtr) vnp2->data.ptrvalue; if (dfp1 != NULL && dfp2 != NULL) { if (dfp1->subtype == FEATDEF_CDS && dfp2->subtype == FEATDEF_exon) { return 1; } else if (dfp1->subtype == FEATDEF_exon && dfp2->subtype == FEATDEF_CDS) { return -1; } else { /* return 0; */ return SortCDStRNArRNAByLocation (ptr1, ptr2); } } } } return 0; } extern EnumFieldAssoc orgmod_subtype_alist []; extern EnumFieldAssoc subsource_subtype_alist []; static Int2 orgmod_rank [32]; static Int2 subsource_rank [26]; static Boolean StrainAlreadyInParentheses (CharPtr taxname, CharPtr strain) { size_t len; CharPtr ptr; ptr = StringChr (taxname, '('); if (ptr == NULL) return FALSE; ptr++; len = StringLen (strain); if (StringNCmp (taxname, strain, len) != 0) return FALSE; ptr += len; if (*ptr != ')') return FALSE; return TRUE; } static void AddOrgModsToDef (ValNodePtr PNTR stringsPtr, BioSourcePtr biop, Boolean labelMods) { EnumFieldAssocPtr ap; OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; CharPtr ptr; SubSourcePtr ssp; Char str [128]; Char text [64]; if (stringsPtr != NULL && biop != NULL) { orp = biop->org; if (orp != NULL) { onp = orp->orgname; if (onp != NULL) { mod = onp->mod; while (mod != NULL) { if (mod->subtype < 32 && orgmod_rank [mod->subtype] > 0) { if (mod->subtype == 2 && StrainAlreadyInParentheses (orp->taxname, mod->subname)) { /* do not add strain if already parenthetical in organism name */ } else { text [0] = '\0'; str [0] = '\0'; StringNCpy_0 (text, mod->subname, sizeof (text)); for (ap = orgmod_subtype_alist; ap->name != NULL; ap++) { if (ap->value == mod->subtype) { StringNCpy_0 (str, ap->name, sizeof (str)); } } LabelAModifier (str, text, labelMods); if (! StringHasNoText (str)) { ValNodeCopyStr (stringsPtr, orgmod_rank [mod->subtype], str); } } } mod = mod->next; } } } ssp = biop->subtype; while (ssp != NULL) { if (ssp->subtype < 26 && subsource_rank [ssp->subtype] > 0) { text [0] = '\0'; str [0] = '\0'; StringNCpy_0 (text, ssp->name, sizeof (text)); for (ap = subsource_subtype_alist; ap->name != NULL; ap++) { if (ap->value == ssp->subtype) { StringNCpy_0 (str, ap->name, sizeof (str)); ptr = StringStr (str, "-name"); if (ptr != NULL) { *ptr = '\0'; } if (ssp->subtype == 23) { /* country */ ptr = StringStr (text, ":"); if (ptr != NULL) { *ptr = '\0'; } } } } if (ssp->subtype == 23 /* && (! labelMods) */) { StringCpy (str, "from"); } LabelAModifier (str, text, labelMods || (ssp->subtype == 23)); if (! StringHasNoText (str)) { ValNodeCopyStr (stringsPtr, subsource_rank [ssp->subtype], str); } } ssp = ssp->next; } } } static CharPtr GetExonNumber (GBQualPtr gbq) { while (gbq != NULL) { if (StringICmp (gbq->qual, "number") == 0) { return gbq->val; } gbq = gbq->next; } return NULL; } static Boolean NextIsExon (ValNodePtr vnp) { DefFeatsPtr nextdfp; ValNodePtr nextvnp; if (vnp == NULL) return FALSE; nextvnp = vnp->next; if (nextvnp == NULL) return FALSE; nextdfp = (DefFeatsPtr) nextvnp->data.ptrvalue; if (nextdfp != NULL && nextdfp->subtype == FEATDEF_exon) return TRUE; return FALSE; } static CharPtr organelleByGenome [] = { NULL, NULL, "chloroplast", "chromoplast", "kinetoplast", "mitochondrial", "plastid", "", "", "", "", "", "cyanelle", "", "", "", "apicoplast", "leucoplast", "proplastid", NULL }; static CharPtr organelleByPopup [] = { NULL, "mitochondrial", "chloroplast", "kinetoplast", "plastid", "chromoplast", "cyanelle", "apicoplast", "leucoplast", "proplastid", NULL }; static void FinishAutoDefProc (Uint2 entityID, SeqEntryPtr sep, ValNodePtr head, BioseqPtr target, SeqEntryPtr nsep, MolInfoPtr mip, ValNodePtr strings, BioSourcePtr biop, Int2 mitochloroflag) { Int2 count; Boolean ddbjstyle = FALSE; DefFeatsPtr dfp; CharPtr exonnumber; Int2 mitocount; DefFeatsPtr nextdfp; CharPtr ptr; RnaRefPtr rrp; SeqFeatPtr sfp; Char str [380]; tRNAPtr trna; ValNodePtr ttl; Char text [64]; Char orgnelle [80]; ValNodePtr vnp; if (GetAppParam ("SEQUIN", "PREFERENCES", "DATABASE", NULL, str, sizeof (str))) { if (StringICmp (str, "DDBJ") == 0) { ddbjstyle = TRUE; } } vnp = head; count = 0; mitocount = 0; while (vnp != NULL) { str [0] = '\0'; dfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp != NULL) { sfp = dfp->sfp; if (sfp != NULL || dfp->numUnknown > 0) { count++; mitocount++; /* FindGeneAndProtForCDS (entityID, sfp, &(dfp->gene), &(dfp->prot)); */ /* StringCpy (str, "unknown"); */ text [0] = '\0'; if (dfp->subtype == FEATDEF_CDS && dfp->prot != NULL) { if (dfp->suppressprefix) { str [0] = '\0'; if (dfp->sfp->partial) { StringCat (str, "partial cds"); } else { StringCat (str, "complete cds"); } if (dfp->altSplices > 1) { StringCat (str, ", alternatively spliced"); } } else if (dfp->protname != NULL) { if (StringICmp (dfp->protname, "unknown") == 0 && (! StringHasNoText (dfp->genename))) { StringNCpy_0 (text, dfp->genename, sizeof (text)); /* StringCat (str, "("); */ StringCat (str, text); /* StringCat (str, ")"); */ } else { StringNCpy_0 (str, dfp->protname, sizeof (str) - 100); if (dfp->genename != NULL) { StringNCpy_0 (text, dfp->genename, sizeof (text)); if (! StringHasNoText (text)) { StringCat (str, " ("); StringCat (str, text); StringCat (str, ")"); } } } if (dfp->lastInGroup || dfp->lastInType) { if (mip != NULL) { ptr = StringISearch (str, "precursor"); if (ptr != NULL && StringICmp (ptr, "precursor") == 0) { StringCat (str, ","); } if (mip->biomol == MOLECULE_TYPE_MRNA) { StringCat (str, " mRNA"); } else if (mip->biomol == MOLECULE_TYPE_PRE_MRNA) { StringCat (str, " precursor RNA"); } else { StringCat (str, " gene"); } } if (count > 1) { StringCat (str, "s"); } if (count < 2 && /* dfp->altSplices < 2 && */ (! StringHasNoText (dfp->allelename))) { StringNCpy_0 (text, dfp->allelename, sizeof (text)); StringCat (str, ", "); StringCat (str, text); StringCat (str, " allele"); } if (dfp->sfp->partial) { StringCat (str, ", partial cds"); } else { StringCat (str, ", complete cds"); } if (dfp->altSplices > 1) { StringCat (str, ", alternatively spliced"); } } } } else if (dfp->subtype == FEATDEF_CDS && dfp->pseudo) { if (dfp->genename != NULL) { StringNCpy_0 (str, dfp->genename, sizeof (str) - 50); } if (dfp->lastInGroup || dfp->lastInType) { StringCat (str, " pseudogene"); if (count > 1) { StringCat (str, "s"); } if (count < 2 && (! StringHasNoText (dfp->allelename))) { StringNCpy_0 (text, dfp->allelename, sizeof (text)); StringCat (str, ", "); StringCat (str, text); StringCat (str, " allele"); } if (dfp->sfp->partial) { StringCat (str, ", partial sequence"); } else { StringCat (str, ", complete sequence"); } } } else if (dfp->subtype == FEATDEF_CDS && dfp->prot == NULL && dfp->genename != NULL) { StringNCpy_0 (str, dfp->genename, sizeof (str) - 50); if (dfp->lastInGroup || dfp->lastInType) { if (mip != NULL) { ptr = StringISearch (str, "precursor"); if (ptr != NULL && StringICmp (ptr, "precursor") == 0) { StringCat (str, ","); } if (mip->biomol == MOLECULE_TYPE_MRNA) { StringCat (str, " mRNA"); } else if (mip->biomol == MOLECULE_TYPE_PRE_MRNA) { StringCat (str, " precursor RNA"); } else { StringCat (str, " gene"); } } if (count > 1) { StringCat (str, "s"); } if (count < 2 && (! StringHasNoText (dfp->allelename))) { StringNCpy_0 (text, dfp->allelename, sizeof (text)); StringCat (str, ", "); StringCat (str, text); StringCat (str, " allele"); } if (dfp->sfp->partial) { StringCat (str, ", partial cds"); } else { StringCat (str, ", complete cds"); } } } else if (dfp->subtype == FEATDEF_GENE) { if (dfp->genename != NULL) { StringNCpy_0 (str, dfp->genename, sizeof (str) - 50); } if (dfp->lastInGroup || dfp->lastInType) { if (mip != NULL) { if (mip->biomol == MOLECULE_TYPE_MRNA) { StringCat (str, " mRNA"); } else if (mip->biomol == MOLECULE_TYPE_PRE_MRNA) { StringCat (str, " precursor RNA"); } else { StringCat (str, " gene"); } } else { StringCat (str, " gene"); } if (count > 1) { StringCat (str, "s"); } if (count < 2 && (! StringHasNoText (dfp->allelename))) { StringNCpy_0 (text, dfp->allelename, sizeof (text)); StringCat (str, ", "); StringCat (str, text); StringCat (str, " allele"); } if (dfp->sfp->partial) { StringCat (str, ", partial sequence"); } else { StringCat (str, ", complete sequence"); } } } else if (dfp->subtype == FEATDEF_rRNA || dfp->subtype == FEATDEF_otherRNA) { rrp = (RnaRefPtr) dfp->sfp->data.value.ptrvalue; if (rrp != NULL) { if (rrp->ext.choice == 1) { StringNCpy_0 (str, (CharPtr) rrp->ext.value.ptrvalue, sizeof (str) - 50); if (dfp->subtype == FEATDEF_rRNA) { ptr = StringISearch (str, " rRNA"); if (ptr != NULL) { *ptr = '\0'; } ptr = StringISearch (str, " ribosomal RNA"); if (ptr != NULL) { *ptr = '\0'; } if (! StringHasNoText (str)) { StringCat (str, " ribosomal RNA"); } } else if (dfp->subtype == FEATDEF_otherRNA) { } if (dfp->genename != NULL) { StringNCpy_0 (text, dfp->genename, sizeof (text)); if (! StringHasNoText (text)) { StringCat (str, " ("); StringCat (str, text); StringCat (str, ")"); } } if (dfp->lastInString || dfp->lastInGroup || dfp->lastInType) { if (dfp->subtype == FEATDEF_rRNA && mip->biomol == MOLECULE_TYPE_GENOMIC) { StringCat (str, " gene"); if (count > 1) { StringCat (str, "s"); } } } if (dfp->lastInGroup || dfp->lastInType) { if (dfp->sfp->partial) { StringCat (str, ", partial sequence"); } else { StringCat (str, ", complete sequence"); } } } } } else if (dfp->subtype == FEATDEF_tRNA) { rrp = (RnaRefPtr) dfp->sfp->data.value.ptrvalue; if (rrp != NULL) { if (rrp->ext.choice == 2) { trna = rrp->ext.value.ptrvalue; if (trna != NULL) { if (FeatDefLabel (dfp->sfp, str, sizeof (str) - 2, OM_LABEL_CONTENT) > 0) { if (dfp->genename != NULL) { StringNCpy_0 (text, dfp->genename, sizeof (text)); if (! StringHasNoText (text)) { StringCat (str, " ("); StringCat (str, text); StringCat (str, ")"); } } if (dfp->lastInGroup || dfp->lastInType) { StringCat (str, " gene"); if (count > 1) { StringCat (str, "s"); } if (dfp->sfp->partial) { StringCat (str, ", partial sequence"); } else { StringCat (str, ", complete sequence"); } } } } } } } else if (dfp->subtype == FEATDEF_LTR) { if (! StringHasNoText (sfp->comment)) { StringNCpy_0 (str, sfp->comment, sizeof (str)); ptr = StringISearch (str, " long terminal repeat"); if (ptr != NULL) { *ptr = '\0'; } ptr = StringISearch (str, " long terminal repeat"); if (ptr != NULL) { *ptr = '\0'; } if (! StringHasNoText (str)) { StringCat (str, " long terminal repeat"); } } else { /* StringCpy (str, "uncharacterized"); */ StringCpy (str, "long terminal repeat"); } if (dfp->lastInGroup || dfp->lastInType) { if (dfp->sfp->partial) { StringCat (str, ", partial sequence"); } else { StringCat (str, ", complete sequence"); } } } else if (dfp->subtype == FEATDEF_exon && target != NULL) { if (dfp->protname != NULL) { str [0] = '\0'; if (! dfp->suppressprefix) { StringNCpy_0 (str, dfp->protname, sizeof (str) - 100); if (dfp->genename != NULL) { StringNCpy_0 (text, dfp->genename, sizeof (text)); if (! StringHasNoText (text)) { StringCat (str, " ("); StringCat (str, text); StringCat (str, ") gene,"); if (/* count < 2 && */ /* dfp->altSplices < 2 && */ (! StringHasNoText (dfp->allelename))) { StringNCpy_0 (text, dfp->allelename, sizeof (text)); StringCat (str, " "); StringCat (str, text); StringCat (str, " allele,"); } } } } if ((! StringHasNoText (str)) || dfp->suppressprefix) { exonnumber = GetExonNumber (sfp->qual); if (! dfp->suppressprefix) { if (exonnumber == NULL) { if (StringStr (sfp->comment, "exon") != NULL && (! NextIsExon (vnp))) { } else { StringCat (str, " exon"); if (NextIsExon (vnp)) { StringCat (str, "s"); } } } else { StringCat (str, " exon"); if (NextIsExon (vnp)) { StringCat (str, "s"); } } } if (exonnumber != NULL) { if (! dfp->suppressprefix) { StringCat (str, " "); } StringCat (str, exonnumber); } else { if (! StringHasNoText (sfp->comment)) { if (! dfp->suppressprefix) { StringCat (str, " "); } StringCat (str, sfp->comment); } } } } else if (dfp->genename != NULL) { str [0] = '\0'; if (! dfp->suppressprefix) { StringNCpy_0 (str, dfp->genename, sizeof (str)); StringCat (str, " gene,"); } if ((! StringHasNoText (str)) || dfp->suppressprefix) { exonnumber = GetExonNumber (sfp->qual); if (! dfp->suppressprefix) { if (exonnumber == NULL) { if (StringStr (sfp->comment, "exon") != NULL && (! NextIsExon (vnp))) { } else { StringCat (str, " exon"); if (NextIsExon (vnp)) { StringCat (str, "s"); } } } else { StringCat (str, " exon"); if (NextIsExon (vnp)) { StringCat (str, "s"); } } } if (exonnumber != NULL) { if (! dfp->suppressprefix) { StringCat (str, " "); } StringCat (str, exonnumber); } else { if (! StringHasNoText (sfp->comment)) { if (! dfp->suppressprefix) { StringCat (str, " "); } StringCat (str, sfp->comment); } } } } else { StringCpy (str, "uncharacterized exon"); } /* if (dfp->lastInGroup || dfp->lastInType) { if (dfp->sfp->partial) { StringCat (str, ", partial sequence"); } else { StringCat (str, ", complete sequence"); } } */ } else if (dfp->numUnknown > 0) { if (mip != NULL && mip->biomol == MOLECULE_TYPE_MRNA) { StringCat (str, "unknown mRNA"); } else if (mip->biomol == MOLECULE_TYPE_PRE_MRNA) { StringCat (str, " unknown precursor RNA"); } else { StringCat (str, "unknown gene"); } if (dfp->numUnknown > 1) { StringCat (str, "s"); } } } } vnp = vnp->next; if (! StringHasNoText (str)) { if (vnp == NULL) { if (biop != NULL) { orgnelle [0] = '\0'; switch (biop->genome) { case GENOME_chloroplast : case GENOME_chromoplast : case GENOME_kinetoplast : case GENOME_mitochondrion : case GENOME_plastid : case GENOME_cyanelle : case GENOME_apicoplast : case GENOME_leucoplast : case GENOME_proplastid : if (mitocount > 1) { sprintf (orgnelle, "; %s genes for %s products", organelleByGenome [biop->genome], organelleByGenome [biop->genome]); } else { sprintf (orgnelle, "; %s gene for %s product", organelleByGenome [biop->genome], organelleByGenome [biop->genome]); } StringCat (str, orgnelle); break; default : if (mitochloroflag > 0) { if (mitochloroflag > 10) { /* beyond list */ } else if (mitochloroflag == 10) { StringCat (str, "; alternatively spliced"); } else { if (mitocount > 1) { sprintf (orgnelle, "; nuclear genes for %s products", organelleByPopup [mitochloroflag]); } else { sprintf (orgnelle, "; nuclear gene for %s product", organelleByPopup [mitochloroflag]); } StringCat (str, orgnelle); } } break; } /* if (biop->genome == GENOME_mitochondrion) { if (mitocount > 1) { StringCat (str, "; mitochondrial genes for mitochondrial products"); } else { StringCat (str, "; mitochondrial gene for mitochondrial product"); } } else if (biop->genome == GENOME_chloroplast) { if (mitocount > 1) { StringCat (str, "; chloroplast genes for chloroplast products"); } else { StringCat (str, "; chloroplast gene for chloroplast product"); } } else if (mitochloroflag > 0) { switch (mitochloroflag) { case 1 : if (mitocount > 1) { StringCat (str, "; nuclear genes for mitochondrial products"); } else { StringCat (str, "; nuclear gene for mitochondrial product"); } break; case 2 : if (mitocount > 1) { StringCat (str, "; nuclear genes for chloroplast products"); } else { StringCat (str, "; nuclear gene for chloroplast product"); } break; case 3 : if (mitocount > 1) { StringCat (str, "; mitochondrial genes for mitochondrial products"); } else { StringCat (str, "; mitochondrial gene for mitochondrial product"); } break; case 4 : if (mitocount > 1) { StringCat (str, "; chloroplast genes for chloroplast products"); } else { StringCat (str, "; chloroplast gene for chloroplast product"); } break; default : break; } } */ } StringCat (str, "."); } else if (vnp->next == NULL) { nextdfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp->lastInPenultimate) { if ((dfp->subtype == FEATDEF_rRNA && nextdfp->subtype == FEATDEF_otherRNA && dfp->sfp->partial == nextdfp->sfp->partial) || (dfp->subtype == FEATDEF_otherRNA && nextdfp->subtype == FEATDEF_rRNA && dfp->sfp->partial == nextdfp->sfp->partial)) { StringCat (str, ", and"); } else if (dfp->subtype == FEATDEF_exon && nextdfp->subtype == FEATDEF_exon /* && dfp->sfp->partial == nextdfp->sfp->partial */) { StringCat (str, " and"); } else { StringCat (str, "; and"); } } else if (dfp->lastInType || dfp->lastInGroup) { if (count > 1) { StringCat (str, ", and"); } else { StringCat (str, " and"); } } else if (nextdfp->lastInType || nextdfp->lastInGroup) { if (count > 1) { StringCat (str, ", and"); } else { StringCat (str, " and"); } } else { if (count > 1) { StringCat (str, ", and"); } else { StringCat (str, " and"); } } } else { nextdfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp->lastInPenultimate) { if ((dfp->subtype == FEATDEF_rRNA && nextdfp->subtype == FEATDEF_otherRNA && dfp->sfp->partial == nextdfp->sfp->partial) || (dfp->subtype == FEATDEF_otherRNA && nextdfp->subtype == FEATDEF_rRNA && dfp->sfp->partial == nextdfp->sfp->partial)) { StringCat (str, ", and"); } else if (dfp->subtype == FEATDEF_exon && nextdfp->subtype == FEATDEF_exon /* && dfp->sfp->partial == nextdfp->sfp->partial */) { StringCat (str, ","); } else { StringCat (str, "; and"); } } else if (dfp->lastInType || dfp->lastInGroup) { StringCat (str, ";"); } else if (nextdfp->lastInType || nextdfp->lastInGroup) { if (count > 1) { StringCat (str, ", and"); } else { StringCat (str, " and"); } } else { StringCat (str, ","); } } ValNodeCopyStr (&strings, 0, str); } if (dfp->lastInString || dfp->lastInGroup || dfp->lastInType) { count = 0; } } ptr = MergeValNodeStrings (strings, FALSE); if (nsep != NULL) { ttl = SeqEntryGetSeqDescr (nsep, Seq_descr_title, NULL); if (ttl == NULL) { ttl = SeqEntryGetSeqDescr (sep, Seq_descr_title, NULL); } if (ttl == NULL) { ttl = CreateNewDescriptor (nsep, Seq_descr_title); } if (ttl != NULL) { MemFree (ttl->data.ptrvalue); ttl->data.ptrvalue = ptr; ptr = NULL; } } MemFree (ptr); ValNodeFreeData (strings); ValNodeFreeData (head); } static void CombineProteinNames (DefFeatsPtr dfp1, DefFeatsPtr dfp2) { Int2 i, j, lastspace, lastdash, lastcomma; size_t len1, len2; CharPtr str1 = NULL, str2 = NULL; if (dfp1 == NULL || dfp2 == NULL) return; if (dfp1->protname == NULL && dfp2->protname == NULL) return; len1 = StringLen (dfp1->protname); len2 = StringLen (dfp2->protname); if (len1 < 1 || len2 < 1) return; i = 0; j = 0; lastspace = 0; lastdash = 0; lastcomma = 0; while (i < len1 && j < len2 && dfp1->protname [i] == dfp2->protname [j]) { if (dfp1->protname [i] == ' ') { lastspace = i; } if (dfp1->protname [i] == '-') { lastdash = i; } if (dfp1->protname [i] == ',') { lastcomma = i; } i++; j++; } str1 = StringSave (dfp1->protname); if (str1 != NULL) { str1 [i] = '\0'; if (! dfp1->alreadyTrimmed) { if (lastcomma > 0) { str1 [lastcomma] = '\0'; dfp1->alreadyTrimmed = TRUE; } else if (lastdash > 0) { str1 [lastdash] = '\0'; dfp1->alreadyTrimmed = TRUE; } else if (lastspace > 0) { str1 [lastspace] = '\0'; dfp1->alreadyTrimmed = TRUE; } } } i = len1; j = len2; while (i > 0 && j > 0 && dfp1->protname [i - 1] == dfp2->protname [j - 1]) { i--; j--; } str2 = StringSave (dfp1->protname + i); TrimSpacesAroundString (str1); TrimSpacesAroundString (str2); len1 = StringLen (str1); len2 = StringLen (str2); if (len1 > len2) { dfp1->protname = str1; MemFree (str2); } else { dfp1->protname = str2; MemFree (str1); } } static Boolean AreAltSpliceGenes (DefFeatsPtr dfp1, DefFeatsPtr dfp2) { Int2 comp; SeqFeatPtr sfp1, sfp2; Uint1 strand1, strand2; if (dfp1 == NULL || dfp2 == NULL) return FALSE; if (dfp1->prot == NULL || dfp2->prot == NULL) return FALSE; if (dfp1->pseudo || dfp2->pseudo) return FALSE; sfp1 = dfp1->sfp; sfp2 = dfp2->sfp; if (sfp1 == NULL || sfp2 == NULL) return FALSE; if (sfp1->partial != sfp2->partial) return FALSE; strand1 = SeqLocStrand (sfp1->location); strand2 = SeqLocStrand (sfp2->location); if (strand1 != strand2) return FALSE; comp = SeqLocCompare (sfp1->location, sfp2->location); if (comp == SLC_NO_MATCH) return FALSE; if (dfp1->genename == NULL || dfp2->genename == NULL) return FALSE; if (StringICmp (dfp1->genename, dfp2->genename) != 0) return FALSE; CombineProteinNames (dfp1, dfp2); return TRUE; } static void MergeAltSpliceCDSs (ValNodePtr head) { DefFeatsPtr dfp1, dfp2; ValNodePtr nextvnp; ValNodePtr PNTR prevvnp; ValNodePtr vnp1, vnp2; vnp1 = head; while (vnp1 != NULL) { dfp1 = (DefFeatsPtr) vnp1->data.ptrvalue; if (dfp1 != NULL && dfp1->subtype == FEATDEF_CDS) { vnp2 = vnp1->next; prevvnp = &(vnp1->next); while (vnp2 != NULL) { nextvnp = vnp2->next; dfp2 = (DefFeatsPtr) vnp2->data.ptrvalue; if (dfp2 != NULL && dfp2->subtype == FEATDEF_CDS) { if (AreAltSpliceGenes (dfp1, dfp2)) { (dfp1->altSplices)++; *prevvnp = vnp2->next; vnp2->next = NULL; ValNodeFreeData (vnp2); } else { prevvnp = (ValNodePtr PNTR) &(vnp2->next); } } else { prevvnp = (ValNodePtr PNTR) &(vnp2->next); } vnp2 = nextvnp; } } vnp1 = vnp1->next; } } static void AutoDefProc (Uint2 entityID, SeqEntryPtr sep, Boolean addMods, Boolean labelMods, Int2 maxMods, Boolean leaveInParen, BioseqPtr target, BioseqPtr seg, ValNodePtr nonUniqueOrgs, Int2 mitochloroflag, Boolean suppressAltSplice, BioseqPtr parent) { Char allele [256]; BioseqContextPtr bcp; BioSourcePtr biop; BioseqPtr bsp; BioseqSetPtr bssp; SeqFeatPtr cds; Boolean change; CdRegionPtr crp; DefFeatsData df; DefFeatsPtr dfp; DefFeatsPtr dfpx; SeqMgrFeatContext fcontext; GBQualPtr gbq; SeqFeatPtr gene; Int2 group; GeneRefPtr grp; GatherScope gs; ValNodePtr head; SeqLocPtr lastslp; Int4 left; size_t lenallele; size_t lenlocus; MolInfoPtr mip; DefFeatsPtr nextdfp; SeqLocPtr nextslp; ValNodePtr nextvnp; SeqEntryPtr nsep; Int2 numUnknown; BioseqPtr part; DefFeatsPtr penult; ValNodePtr PNTR prevvnp; ProtRefPtr prp; CharPtr ptr; Int4 right; ValNodePtr sdp; SeqFeatPtr sfp; SeqIdPtr sip; SeqLocPtr slp; Char str [128]; ValNodePtr ttl; ValNodePtr strings; ValNode vn; ValNodePtr vnp; ValNodePtr vnpx; SeqFeatXrefPtr xref; if (sep == NULL) return; if (target == NULL && seg == NULL) { if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; if (bssp->_class == 7 || (bssp->_class >= 13 && bssp->_class <= 16)) { for (sep = bssp->seq_set; sep != NULL; sep = sep->next) { AutoDefProc (entityID, sep, addMods, labelMods, maxMods, leaveInParen, NULL, NULL, nonUniqueOrgs, mitochloroflag, suppressAltSplice, NULL); } return; } } nsep = FindNucSeqEntry (sep); if (nsep != NULL) { bsp = (BioseqPtr) nsep->data.ptrvalue; if (bsp != NULL && bsp->repr == Seq_repr_seg && bsp->seq_ext != NULL && bsp->seq_ext_type == 1) { vn.choice = SEQLOC_MIX; vn.next = NULL; vn.data.ptrvalue = bsp->seq_ext; slp = SeqLocFindNext (&vn, NULL); while (slp != NULL) { nextslp = SeqLocFindNext (&vn, slp); sip = SeqLocId (slp); if (sip != NULL) { part = BioseqFind (sip); if (part != NULL) { AutoDefProc (entityID, sep, addMods, labelMods, maxMods, leaveInParen, part, NULL, nonUniqueOrgs, mitochloroflag, suppressAltSplice, bsp); } } slp = nextslp; } AutoDefProc (entityID, sep, addMods, labelMods, maxMods, leaveInParen, NULL, bsp, nonUniqueOrgs, mitochloroflag, suppressAltSplice, bsp); return; } } } else if (target != NULL) { nsep = SeqMgrGetSeqEntryForData (target); } else { nsep = SeqMgrGetSeqEntryForData (seg); } biop = NULL; strings = NULL; str [0] = '\0'; SeqEntryToBioSource (sep, NULL, str, sizeof (str) - 1, &biop); if (! leaveInParen) { ptr = StringStr (str, "("); if (ptr != NULL) { *ptr = '\0'; } } TrimSpacesAroundString (str); if (StringICmp (str, "Human immunodeficiency virus type 1") == 0) { StringCpy (str, "HIV-1"); } else if (StringICmp (str, "Human immunodeficiency virus type 2") == 0) { StringCpy (str, "HIV-2"); } str [0] = TO_UPPER (str [0]); ValNodeCopyStr (&strings, 0, str); mip = NULL; if (nsep != NULL) { bsp = (BioseqPtr) nsep->data.ptrvalue; bcp = BioseqContextNew (bsp); sdp = BioseqContextGetSeqDescr (bcp, Seq_descr_molinfo, NULL, NULL); BioseqContextFree (bcp); if (sdp != NULL) { mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL) { if (mip->tech == MI_TECH_htgs_0 || mip->tech == MI_TECH_htgs_1 || mip->tech == MI_TECH_htgs_2 || mip->tech == MI_TECH_est || mip->tech == MI_TECH_sts || mip->tech == MI_TECH_survey) { ttl = ValNodeExtract (&(bsp->descr), Seq_descr_title); if (ttl != NULL) { ttl = ValNodeFreeData (ttl); } return; } } } } /* nsep = FindNucSeqEntry (sep); if (nsep != NULL) { sdp = SeqEntryGetSeqDescr (nsep, Seq_descr_molinfo, NULL); if (sdp == NULL) { sdp = SeqEntryGetSeqDescr (sep, Seq_descr_molinfo, NULL); } if (sdp != NULL) { mip = (MolInfoPtr) sdp->data.ptrvalue; } } */ if (nonUniqueOrgs != NULL) { for (vnp = nonUniqueOrgs; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, str) == 0) { if (vnp->choice == 1) { addMods = FALSE; /* if only one organism in record, already unique defline */ } } } } if (addMods) { AddOrgModsToDef (&strings, biop, labelMods); strings = SortValNode (strings, SortByVnpChoice); vnp = strings; while (vnp != NULL && maxMods > 0) { maxMods--; vnp = vnp->next; } if (vnp != NULL) { vnp->next = ValNodeFreeData (vnp->next); } } MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = TRUE; MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.scope = sep; gs.target = NULL; if (target != NULL) { slp = ValNodeNew (NULL); slp->choice = SEQLOC_WHOLE; sip = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (target->id, 0))); slp->data.ptrvalue = sip; gs.target = slp; } head = NULL; GatherEntity (entityID, (Pointer) (&head), GetGeneCDStRNArRNAGatherFunc, &gs); gs.target = SeqLocFree (gs.target); head = SortValNode (head, SortCDStRNArRNAByLocation); if (head == NULL && mip != NULL && mip->tech == MI_TECH_survey) { ValNodeCopyStr (&strings, 0, ", genome survey sequence."); } numUnknown = 0; vnp = head; while (vnp != NULL) { dfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp != NULL) { sfp = dfp->sfp; if (sfp != NULL) { FindGeneAndProtForCDS (entityID, sfp, &(dfp->gene), &(dfp->prot)); grp = SeqMgrGetGeneXref (sfp); if (SeqMgrGeneIsSuppressed (grp)) { dfp->gene = NULL; } dfp->pseudo = FALSE; dfp->genename = NULL; dfp->allelename = NULL; grp = NULL; if (dfp->gene != NULL) { grp = (GeneRefPtr) dfp->gene->data.value.ptrvalue; if (grp != NULL && grp->pseudo) { dfp->pseudo = TRUE; } } xref = sfp->xref; while (xref != NULL && xref->data.choice != SEQFEAT_GENE) { xref = xref->next; } if (xref != NULL) { grp = (GeneRefPtr) xref->data.value.ptrvalue; } if (grp != NULL) { dfp->genename = (CharPtr) grp->locus; if ((! StringHasNoText (grp->locus)) && (! StringHasNoText (grp->allele))) { lenallele = StringLen (grp->allele); lenlocus = StringLen (grp->locus); if (lenallele > lenlocus && StringNICmp (grp->locus, grp->allele, lenlocus) == 0) { sprintf (allele, "%s", grp->allele); } else if (StringNCmp (grp->allele, "-", 1) == 0) { sprintf (allele, "%s%s", grp->locus, grp->allele); } else { sprintf (allele, "%s-%s", grp->locus, grp->allele); } dfp->allelename = StringSave (allele); } if (grp->pseudo) { dfp->pseudo = TRUE; } } if (dfp->subtype == FEATDEF_CDS) { if (target != NULL) { lastslp = NULL; slp = SeqLocFindNext (sfp->location, NULL); while (slp != NULL) { lastslp = slp; slp = SeqLocFindNext (sfp->location, slp); } if (lastslp != NULL && nsep != NULL) { bsp = (BioseqPtr) nsep->data.ptrvalue; if (GetBioseqGivenSeqLoc (lastslp, entityID) != bsp) { dfp->ignore = TRUE; } } } crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { if (crp->orf) { dfp->ignore = TRUE; } } gbq = sfp->qual; while (gbq != NULL) { if (StringICmp (gbq->qual, "pseudo") == 0) { dfp->pseudo = TRUE; } gbq = gbq->next; } if (dfp->pseudo) { } else if (dfp->prot == NULL) { if (dfp->gene == NULL) { dfp->ignore = TRUE; } } else { prp = (ProtRefPtr) dfp->prot->data.value.ptrvalue; if (prp != NULL) { if (prp->name == NULL || StringHasNoText ((CharPtr) prp->name->data.ptrvalue)) { if (prp->desc == NULL || StringHasNoText (prp->desc)) { dfp->ignore = TRUE; } else { dfp->protname = prp->desc; } } else { dfp->protname = (CharPtr) prp->name->data.ptrvalue; } if (! dfp->ignore) { if (StringICmp (dfp->protname, "unknown") == 0) { if (StringHasNoText (dfp->genename)) { numUnknown++; dfp->ignore = TRUE; } } } } } } else if (dfp->subtype == FEATDEF_exon && target == NULL) { dfp->ignore = TRUE; } } } vnp = vnp->next; } for (vnp = head; vnp != NULL; vnp = vnp->next) { dfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp != NULL) { sfp = dfp->sfp; if (sfp != NULL) { if (sfp->data.choice == SEQFEAT_GENE) { for (vnpx = vnp->next; vnpx != NULL; vnpx = vnpx->next) { dfpx = (DefFeatsPtr) vnpx->data.ptrvalue; if (dfpx != NULL) { if (sfp == dfpx->gene) { dfp->ignore = TRUE; } } } } } } } vnp = head; prevvnp = &head; while (vnp != NULL) { nextvnp = vnp->next; dfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp->ignore) { *prevvnp = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } else { prevvnp = (ValNodePtr PNTR) &(vnp->next); } vnp = nextvnp; } if (! suppressAltSplice) { MergeAltSpliceCDSs (head); } if (target != NULL) { head = SortValNode (head, SortCDSAfterExons); } if (numUnknown > 0) { dfp = (DefFeatsPtr) MemNew (sizeof (DefFeatsData)); if (dfp != NULL) { dfp->entityID = entityID; dfp->subtype = 0; dfp->numUnknown = numUnknown; ValNodeAddPointer (&head, 0, (Pointer) dfp); } } if (target != NULL) { for (vnp = head; vnp != NULL; vnp = vnp->next) { dfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp != NULL && dfp->subtype == FEATDEF_exon && dfp->gene != NULL) { gene = SeqMgrGetDesiredFeature (entityID, NULL, 0, 0, dfp->gene, &fcontext); if (gene == dfp->gene && (! gene->pseudo)) { left = fcontext.left; right = fcontext.right; cds = SeqMgrGetNextFeature (parent, NULL, SEQFEAT_CDREGION, 0, &fcontext); while (cds != NULL) { if (fcontext.left >= left && fcontext.right <= right && (! cds->pseudo)) { if (dfp->protname == NULL) { dfp->protname = fcontext.label; /* points to stable string */ } else { df.protname = fcontext.label; CombineProteinNames (dfp, &df); } } cds = SeqMgrGetNextFeature (parent, cds, SEQFEAT_CDREGION, 0, &fcontext); } } } } vnp = head; while (vnp != NULL) { dfp = (DefFeatsPtr) vnp->data.ptrvalue; vnp = vnp->next; if (dfp != NULL && dfp->subtype == FEATDEF_exon && vnp != NULL) { nextdfp = (DefFeatsPtr) vnp->data.ptrvalue; if (nextdfp != NULL && (nextdfp->subtype == FEATDEF_exon || nextdfp->subtype == FEATDEF_CDS)) { if (StringCmp (dfp->genename, nextdfp->genename) == 0 && StringCmp (dfp->protname, nextdfp->protname) == 0) { nextdfp->suppressprefix = TRUE; } } } } } vnp = head; group = 0; penult = NULL; while (vnp != NULL) { dfp = (DefFeatsPtr) vnp->data.ptrvalue; vnp->choice = (Uint1) group; vnp = vnp->next; if (vnp != NULL) { change = FALSE; nextdfp = (DefFeatsPtr) vnp->data.ptrvalue; if ((dfp->subtype == FEATDEF_rRNA && nextdfp->subtype == FEATDEF_otherRNA) || (dfp->subtype == FEATDEF_otherRNA && nextdfp->subtype == FEATDEF_rRNA)) { dfp->lastInString = TRUE; if (dfp->sfp->partial != nextdfp->sfp->partial) { dfp->lastInGroup = TRUE; } change = TRUE; } else if (dfp->subtype != nextdfp->subtype) { if (dfp->subtype == FEATDEF_exon && nextdfp->subtype == FEATDEF_CDS && nextdfp->suppressprefix) { /* no separator between exons and appropriate cds */ } else { dfp->lastInType = TRUE; change = TRUE; } } else if (dfp->sfp->partial != nextdfp->sfp->partial) { dfp->lastInGroup = TRUE; change = TRUE; } else if (dfp->pseudo != nextdfp->pseudo) { dfp->lastInGroup = TRUE; change = TRUE; } else if (dfp->allelename != NULL || nextdfp->allelename != NULL) { dfp->lastInGroup = TRUE; change = TRUE; } else if (dfp->altSplices > 1 || nextdfp->altSplices > 1) { dfp->lastInGroup = TRUE; change = TRUE; } if (change) { group++; penult = dfp; } } else { dfp->lastInString = TRUE; dfp->lastInGroup = TRUE; dfp->lastInType = TRUE; group++; } } if (penult != NULL) { penult->lastInPenultimate = TRUE; } FinishAutoDefProc (entityID, sep, head, target, nsep, mip, strings, biop, mitochloroflag); } static CharPtr sourceModRankList [] = { "Strain", "Isolate", "Clone", "Type", "Cultivar", "Haplotype", "Substrain", "Subclone", "Subtype", "Serotype", "Serogroup", "Serovar", "Variety", "Pathovar", "Chemovar", "Biovar", "Biotype", "Group", "Subgroup", "Cell-line", "Cell-type", "Tissue-type", "Clone-lib", "Tissue-lib", "Dev-stage", "Lab-host", "Pop-variant", "Frequency", "Germline", "Rearranged", "Transgenic", "Environmental-sample", "Chromosome", "Segment", "Map", "Genotype", "Sex", "Plasmid-name", "Transposon-name", "Ins-seq-name", "Endogenous-virus-name", "Plastid-name", "Country", "Old Name", "Common", "Acronym", "Dosage", "Natural-host", "Sub-species", "Specimen-voucher", "Isolation-source", "Authority", "Forma", "Forma-specialis", "Ecotype", "Synonym", "Anamorph", "Teleomorph", "Breed", NULL }; typedef struct { CharPtr value; Int2 rank; } AlphaInfo, PNTR AlphaInfoPtr; static AlphaInfoPtr sourceModAlphaList = NULL; typedef struct deflineform { FORM_MESSAGE_BLOCK SeqEntryPtr sep; ButtoN addLabels; GrouP customGrp; GrouP sourceListGrp; ButtoN PNTR sourceBoxList; PopuP modLimit; ButtoN onlyModifyTargeted; BioseqPtr target; ButtoN leaveInParentheses; /* GrouP nucformitoorchloro; */ PopuP nucformitoorchloro; Boolean smartMods; ButtoN suppressAltSplice; } DeflineForm, PNTR DeflineFormPtr; static Boolean GatherOrgnamesFunc (GatherContextPtr gcp) { BioSourcePtr biop; OrgRefPtr orp; ValNodePtr sdp; SeqFeatPtr sfp; CharPtr str; ValNodePtr PNTR vnpp; if (gcp == NULL || gcp->thisitem == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT && gcp->thistype != OBJ_SEQDESC) return TRUE; vnpp = (ValNodePtr PNTR) gcp->userdata; if (vnpp == NULL) return TRUE; orp = NULL; biop = NULL; switch (gcp->thistype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; switch (sfp->data.choice) { case SEQFEAT_ORG : orp = (OrgRefPtr) sfp->data.value.ptrvalue; break; case SEQFEAT_BIOSRC : biop = (BioSourcePtr) sfp->data.value.ptrvalue; break; default : break; } break; case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; switch (sdp->choice) { case Seq_descr_org : orp = (OrgRefPtr) sdp->data.ptrvalue; break; case Seq_descr_source : biop = (BioSourcePtr) sdp->data.ptrvalue; break; default : break; } break; default : break; } if (orp == NULL && biop != NULL) { orp = biop->org; } if (orp != NULL) { str = StringSave (orp->taxname); if (str == NULL) return TRUE; TrimSpacesAroundString (str); if (StringICmp (str, "Human immunodeficiency virus type 1") == 0) { StringCpy (str, "HIV-1"); } else if (StringICmp (str, "Human immunodeficiency virus type 2") == 0) { StringCpy (str, "HIV-2"); } str [0] = TO_UPPER (str [0]); ValNodeAddStr (vnpp, 1, str); } return TRUE; } static void DefLineModFormAcceptProc (ButtoN b) { EnumFieldAssocPtr ap; Int2 count; DeflineFormPtr dfp; GatherScope gs; Boolean labelMods; Boolean leaveInParen; Int2 maxMods; Int2 mitochloroflag; ValNodePtr nextvnp; ValNodePtr nonUniqueOrgs; Boolean suppressAltSplice; Int2 val; ValNodePtr vnp; dfp = (DeflineFormPtr) GetObjectExtra (b); if (dfp == NULL) return; WatchCursor (); Hide (dfp->form); Update (); labelMods = GetStatus (dfp->addLabels); if (dfp->sourceBoxList != NULL && GetValue (dfp->customGrp) == 2) { count = 0; while ((sourceModAlphaList [count].value != NULL) && (dfp->sourceBoxList [count] != NULL)) { if (! GetStatus (dfp->sourceBoxList [count])) { for (ap = orgmod_subtype_alist; ap->name != NULL; ap++) { if (StringICmp (ap->name, sourceModAlphaList [count].value) == 0 && ap->value > 0 && ap->value < 32) { orgmod_rank [ap->value] = 0; } } for (ap = subsource_subtype_alist; ap->name != NULL; ap++) { if (StringICmp (ap->name, sourceModAlphaList [count].value) == 0 && ap->value > 0 && ap->value < 25) { subsource_rank [ap->value] = 0; } } } count++; } } maxMods = INT2_MAX; val = GetValue (dfp->modLimit); if (val > 1) { maxMods = val - 1; } if (dfp->onlyModifyTargeted != NULL && GetStatus (dfp->onlyModifyTargeted)) { dfp->sep = GetBestTopParentForData (dfp->input_entityID, dfp->target); } leaveInParen = FALSE; if (dfp->leaveInParentheses != NULL && GetStatus (dfp->leaveInParentheses)) { leaveInParen = TRUE; } nonUniqueOrgs = NULL; if (dfp->smartMods) { MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQDESC] = FALSE; GatherEntity (dfp->input_entityID, (Pointer) (&nonUniqueOrgs), GatherOrgnamesFunc, &gs); nonUniqueOrgs = SortValNode (nonUniqueOrgs, SortByName); vnp = nonUniqueOrgs; while (vnp != NULL) { nextvnp = vnp->next; if (nextvnp != NULL && StringICmp ((CharPtr) vnp->data.ptrvalue, (CharPtr) nextvnp->data.ptrvalue) == 0) { vnp->next = nextvnp->next; nextvnp->next = NULL; ValNodeFreeData (nextvnp); nextvnp = vnp; (vnp->choice)++; } vnp = nextvnp; } } mitochloroflag = GetValue (dfp->nucformitoorchloro) - 1; suppressAltSplice = GetStatus (dfp->suppressAltSplice); AutoDefProc (dfp->input_entityID, dfp->sep, TRUE, labelMods, maxMods, leaveInParen, NULL, NULL, nonUniqueOrgs, mitochloroflag, suppressAltSplice, NULL); ValNodeFreeData (nonUniqueOrgs); ClearProteinTitlesInNucProts (dfp->input_entityID, NULL); InstantiateProteinTitles (dfp->input_entityID, NULL); ArrowCursor (); Remove (dfp->form); Update (); ObjMgrSetDirtyFlag (dfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, dfp->input_entityID, 0, 0); } static void ChangeCustomGrp (GrouP g) { DeflineFormPtr dfp; dfp = (DeflineFormPtr) GetObjectExtra (g); if (dfp == NULL) return; if (GetValue (g) == 1) { SafeDisable (dfp->sourceListGrp); } else { SafeEnable (dfp->sourceListGrp); } } static void CleanupDeflineForm (GraphiC g, VoidPtr data) { DeflineFormPtr dfp; dfp = (DeflineFormPtr) data; if (dfp != NULL) { MemFree (dfp->sourceBoxList); } StdCleanupFormProc (g, data); } static void DeflineMessageProc (ForM f, Int2 mssg) { StdEditorProcsPtr sepp; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { if (sepp->handleMessages != NULL) { sepp->handleMessages (f, mssg); } } } /*---------------------------------------------------------------------*/ /* */ /* SourceModCompare () -- Compare callback for qsort function used in */ /* AlphabetizeSourceMods (). */ /* */ /*---------------------------------------------------------------------*/ static int SourceModCompare (const void *p1, const void *p2) { AlphaInfoPtr sourceMod1; AlphaInfoPtr sourceMod2; sourceMod1 = (AlphaInfoPtr) p1; sourceMod2 = (AlphaInfoPtr) p2; if (StringCmp (sourceMod1->value, sourceMod2->value) < 0) return -1; else if (StringCmp (sourceMod1->value, sourceMod2->value) > 0) return 1; else return 0; } /*---------------------------------------------------------------------*/ /* */ /* AlphabetizeSourceMods () -- Create an alphabetized copy of the list */ /* of source mods in sourceModRankList. */ /* */ /*---------------------------------------------------------------------*/ static void AlphabetizeSourceMods () { Int2 i; Int2 count; /* If already alphabetized, don't re-do */ if (sourceModAlphaList != NULL) return; /* Size the new list based on the existing one */ /* and initialize it to all zeros. */ count = 0; while (sourceModRankList [count] != NULL) count++; sourceModAlphaList = (AlphaInfoPtr) MemNew ((count+1) * sizeof (AlphaInfo)); MemSet (sourceModAlphaList, (count+1) * sizeof (AlphaInfo), 0); /* Point each item in the new list to the old */ for (i = 0; i < count; i++) { sourceModAlphaList[i].value = sourceModRankList[i]; sourceModAlphaList[i].rank = i; } /* Sort the new list */ qsort ((void *) sourceModAlphaList, count, sizeof (AlphaInfo), SourceModCompare); } static ForM CreateDefLineModForm (Uint2 entityID, SeqEntryPtr sep, BioseqPtr target, Boolean smartMods, Int2 maxCount) { ButtoN b; GrouP c; Int2 count; DeflineFormPtr dfp; GrouP h; Int2 i; GrouP p; GrouP q; Char str [16]; WindoW w; w = NULL; dfp = MemNew (sizeof (DeflineForm)); if (dfp != NULL) { w = FixedWindow (-50, -33, -10, -10, "Defline Modifier Customization", StdCloseWindowProc); SetObjectExtra (w, dfp, CleanupDeflineForm); dfp->form = (ForM) w; dfp->formmessage = DeflineMessageProc; dfp->input_entityID = entityID; dfp->sep = sep; dfp->target = target; dfp->smartMods = smartMods; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); dfp->addLabels = CheckBox (h, "Use Labels (e.g., 'strain BALB/c')", NULL); if (smartMods) { SetStatus (dfp->addLabels, TRUE); } p = NormalGroup (h, -1, 0, "Modifier Classes", programFont, ChangeCustomGrp); SetGroupSpacing (p, 10, 10); dfp->customGrp = HiddenGroup (p, 2, 0, ChangeCustomGrp); SetObjectExtra (dfp->customGrp, dfp, NULL); RadioButton (dfp->customGrp, "All"); RadioButton (dfp->customGrp, "Custom"); SetValue (dfp->customGrp, 1); dfp->sourceListGrp = HiddenGroup (p, 3, 0, NULL); count = 0; while (sourceModRankList [count] != NULL) { count++; } /* Create an alphabetically sorted list for */ /* display purposes. */ AlphabetizeSourceMods (); dfp->sourceBoxList = MemNew (sizeof (ButtoN) * (count + 3)); if (count > maxCount) count = maxCount; if (dfp->sourceBoxList != NULL) { for (i = 0; i < count; i++) dfp->sourceBoxList [i] = CheckBox (dfp->sourceListGrp, sourceModAlphaList [i].value, NULL); } Disable (dfp->sourceListGrp); q = HiddenGroup (h, 4, 0, NULL); StaticPrompt (q, "Maximum modifiers per line", 0, popupMenuHeight, programFont, 'l'); dfp->modLimit = PopupList (q, TRUE, NULL); PopupItem (dfp->modLimit, "no limit"); for (i = 1; i <= count; i++) { sprintf (str, "%d", (int) i); PopupItem (dfp->modLimit, str); } if (smartMods) { SetValue (dfp->modLimit, 2); } else { SetValue (dfp->modLimit, 1); } /* dfp->nucformitoorchloro = HiddenGroup (h, -1, 0, NULL); RadioButton (dfp->nucformitoorchloro, "No mitochondrial or chloroplast suffix"); RadioButton (dfp->nucformitoorchloro, "Nuclear gene(s) for mitochondrial product(s)"); RadioButton (dfp->nucformitoorchloro, "Nuclear gene(s) for chloroplast product(s)"); RadioButton (dfp->nucformitoorchloro, "Mitochondrial gene(s) for mitochondrial product(s)"); RadioButton (dfp->nucformitoorchloro, "Chloroplast gene(s) for chloroplast product(s)"); */ dfp->nucformitoorchloro = PopupList (h, FALSE, NULL); PopupItem (dfp->nucformitoorchloro, "No mitochondrial or chloroplast suffix"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for mitochondrial product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for chloroplast product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for kinetoplast product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for plastid product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for chromoplast product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for cyanelle product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for apicoplast product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for leucoplast product(s)"); PopupItem (dfp->nucformitoorchloro, "Nuclear gene(s) for proplastid product(s)"); PopupItem (dfp->nucformitoorchloro, "Alternatively Spliced"); SetValue (dfp->nucformitoorchloro, 1); dfp->leaveInParentheses = CheckBox (w, "Leave in parenthetical organism info", NULL); SetStatus (dfp->leaveInParentheses, TRUE); dfp->suppressAltSplice = CheckBox (w, "Suppress alternative splice phrase", NULL); dfp->onlyModifyTargeted = NULL; if (target != NULL) { dfp->onlyModifyTargeted = CheckBox (w, "Only modify targeted record", NULL); } c = HiddenGroup (w, 4, 0, NULL); b = PushButton (c, "Accept", DefLineModFormAcceptProc); SetObjectExtra (b, dfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) dfp->addLabels, (HANDLE) dfp->customGrp, (HANDLE) dfp->sourceListGrp, (HANDLE) q, (HANDLE) dfp->leaveInParentheses, (HANDLE) dfp->suppressAltSplice, (HANDLE) dfp->nucformitoorchloro, (HANDLE) c, (HANDLE) dfp->onlyModifyTargeted, NULL); RealizeWindow (w); } if (smartMods) { DefLineModFormAcceptProc (b); return NULL; } return (ForM) w; } extern void GenerateAutomaticDefLinesCommon (IteM i, Boolean addMods, Boolean smartMods, ButtoN b) { EnumFieldAssocPtr ap; BaseFormPtr bfp; BioseqSetPtr bssp; Int2 count; ForM f; Int2 maxCount; SeqEntryPtr sep; BioseqPtr target; if (b != NULL) { bfp = GetObjectExtra (b); } else { #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif } if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; MemSet ((Pointer) (orgmod_rank), (int)(0), sizeof(orgmod_rank)); MemSet ((Pointer) (subsource_rank), (int)(0), sizeof(subsource_rank)); AlphabetizeSourceMods (); count = 0; while (sourceModAlphaList [count].value != NULL) { for (ap = orgmod_subtype_alist; ap->name != NULL; ap++) { if (StringICmp (ap->name, sourceModAlphaList [count].value) == 0 && ap->value > 0 && ap->value < 32) { orgmod_rank [ap->value] = sourceModAlphaList[count].rank + 1; } } for (ap = subsource_subtype_alist; ap->name != NULL; ap++) { if (StringICmp (ap->name, sourceModAlphaList [count].value) == 0 && ap->value > 0 && ap->value < 25) { subsource_rank [ap->value] = sourceModAlphaList[count].rank + 1; } } count++; } if (smartMods) { if (CountSeqEntryComponents (sep) == 1) { smartMods = FALSE; } else if (IS_Bioseq_set (sep) && b != NULL /* from toolbar */ ) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == BioseqseqSet_class_genbank) { smartMods = FALSE; } } } if (addMods || smartMods) { target = GetBioseqGivenIDs (bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype); if (addMods) { maxCount = INT2_MAX; } else { maxCount = 6; } f = CreateDefLineModForm (bfp->input_entityID, sep, target, smartMods, maxCount); if (addMods && f != NULL) { Show (f); Select (f); } else if (bfp->activate != NULL) { bfp->activate ((WindoW) bfp->form); } return; } WatchCursor (); Update (); AutoDefProc (bfp->input_entityID, sep, FALSE, FALSE, INT2_MAX, TRUE, NULL, NULL, NULL, 0, FALSE, NULL); ClearProteinTitlesInNucProts (bfp->input_entityID, NULL); InstantiateProteinTitles (bfp->input_entityID, NULL); ArrowCursor (); Update (); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); } void GenerateAutoDefLinesNoMods (IteM i) { GenerateAutomaticDefLinesCommon (i, FALSE, FALSE, NULL); } void GenerateAutoDefLinesWithMods (IteM i) { GenerateAutomaticDefLinesCommon (i, TRUE, FALSE, NULL); } void GenerateAutoDefLinesSmartMods (IteM i) { GenerateAutomaticDefLinesCommon (i, FALSE, TRUE, NULL); } static void StringToLower (CharPtr str) { Char ch; if (str == NULL) return; ch = *str; while (ch != '\0') { *str = TO_LOWER (ch); str++; ch = *str; } } static void MakeNucleotideTitlesInSequinStyle (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { EnumFieldAssocPtr ap; BioseqContextPtr bcp; BioSourcePtr biop; BioseqPtr bsp; OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; SeqDescrPtr sdp; SubSourcePtr ssp; CharPtr str; Char text [256]; ValNodePtr ttl; ValNodePtr vnp; if (sep == NULL) return; if (! IS_Bioseq (sep)) return; bsp = sep->data.ptrvalue; if (bsp == NULL) return; if (! ISA_na (bsp->mol)) return; bcp = BioseqContextNew (bsp); sdp = BioseqContextGetSeqDescr (bcp, Seq_descr_source, NULL, NULL); BioseqContextFree (bcp); if (sdp == NULL) return; biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop == NULL) return; if (bsp->descr != NULL) { vnp = ValNodeExtract (&(bsp->descr), Seq_descr_title); vnp = ValNodeFreeData (vnp); } str = MemNew (2000); orp = biop->org; if (orp != NULL) { StringCpy (text, "[organism="); StringCat (text, orp->taxname); StringCat (text, "] "); StringCat (str, text); } ssp = biop->subtype; while (ssp != NULL) { for (ap = subsource_subtype_alist; ap->name != NULL; ap++) { if (ssp->subtype == ap->value) { StringCpy (text, "["); if (ap->value != 255) { StringCat (text, ap->name); } else { StringCat (text, "subsource"); } StringToLower (text); StringCat (text, "="); StringCat (text, ssp->name); StringCat (text, "] "); StringCat (str, text); } } ssp = ssp->next; } orp = biop->org; if (orp != NULL) { onp = orp->orgname; if (onp != NULL) { mod = onp->mod; while (mod != NULL) { for (ap = orgmod_subtype_alist; ap->name != NULL; ap++) { if (mod->subtype == ap->value) { StringCpy (text, "["); if (ap->value != 255) { StringCat (text, ap->name); } else { StringCat (text, "note"); } StringToLower (text); StringCat (text, "="); StringCat (text, mod->subname); StringCat (text, "] "); StringCat (str, text); } } mod = mod->next; } } } TrimSpacesAroundString (str); if (! StringHasNoText (str)) { ttl = CreateNewDescriptor (sep, Seq_descr_title); if (ttl != NULL) { ttl->data.ptrvalue = StringSave (str); } } MemFree (str); } extern Int2 LIBCALLBACK MakeSequinProteinTitles (Pointer data); extern Int2 LIBCALLBACK MakeSequinNucleotideTitles (Pointer data); extern Int2 LIBCALLBACK MakeSequinFeatureTable (Pointer data); extern Int2 LIBCALLBACK MakeContigBuildTable (Pointer data); extern Int2 LIBCALLBACK MakeSequinNucleotideTitles (Pointer data) { OMProcControlPtr ompcp; SeqEntryPtr sep; ompcp = (OMProcControlPtr) data; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; switch (ompcp->input_itemtype) { case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : return OM_MSG_RET_ERROR; default : return OM_MSG_RET_ERROR; } if (ompcp->input_data == NULL) return OM_MSG_RET_ERROR; sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); if (sep == NULL) return OM_MSG_RET_ERROR; SeqEntryExplore (sep, NULL, MakeNucleotideTitlesInSequinStyle); ObjMgrSetDirtyFlag (ompcp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, ompcp->input_entityID, 0, 0); return OM_MSG_RET_DONE; } static void MakeProteinTitlesInSequinStyle (Uint2 entityID, SeqEntryPtr sep) { BioseqPtr bsp; BioseqSetPtr bssp; DefFeatsPtr dfp; GeneRefPtr grp; GatherScope gs; ValNodePtr head; SeqEntryPtr nsep; ProtRefPtr prp; SeqEntryPtr psep; Char str [256]; Char text [256]; ValNodePtr ttl; ValNodePtr vnp; if (sep == NULL) return; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; if (bssp->_class == 7 || (bssp->_class >= 13 && bssp->_class <= 16)) { for (sep = bssp->seq_set; sep != NULL; sep = sep->next) { MakeProteinTitlesInSequinStyle (entityID, sep); } return; } } nsep = FindNucSeqEntry (sep); if (nsep == NULL) return; MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = TRUE; MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.scope = sep; gs.target = NULL; head = NULL; GatherEntity (entityID, (Pointer) (&head), GetCDStRNArRNAGatherFunc, &gs); /* head = SortValNode (head, SortCDStRNArRNAByLocation); */ if (head == NULL) return; vnp = head; while (vnp != NULL) { dfp = (DefFeatsPtr) vnp->data.ptrvalue; if (dfp != NULL && dfp->sfp != NULL && dfp->subtype == FEATDEF_CDS) { FindGeneAndProtForCDS (entityID, dfp->sfp, &(dfp->gene), &(dfp->prot)); bsp = GetBioseqGivenSeqLoc (dfp->sfp->product, entityID); if (bsp != NULL) { str [0] = '\0'; if (dfp->gene != NULL) { grp = (GeneRefPtr) dfp->gene->data.value.ptrvalue; if (grp != NULL) { StringNCpy_0 (text, (CharPtr) grp->locus, sizeof (text)); if (! StringHasNoText (text)) { StringCat (str, "[gene="); StringCat (str, text); StringCat (str, "]"); } } } if (dfp->prot != NULL) { prp = (ProtRefPtr) dfp->prot->data.value.ptrvalue; if (prp != NULL && prp->name != NULL) { StringNCpy_0 (text, (CharPtr) prp->name->data.ptrvalue, sizeof (text)); if (! StringHasNoText (text)) { if (str [0] != '\0') { StringCat (str, " "); } StringCat (str, "[protein="); StringCat (str, text); StringCat (str, "]"); } } } if (! StringHasNoText (str)) { psep = SeqMgrGetSeqEntryForData (bsp); if (psep != NULL) { ttl = CreateNewDescriptor (psep, Seq_descr_title); if (ttl != NULL) { ttl->data.ptrvalue = StringSave (str); } } } } } vnp = vnp->next; } ValNodeFreeData (head); } extern Int2 LIBCALLBACK MakeSequinProteinTitles (Pointer data) { OMProcControlPtr ompcp; SeqEntryPtr sep; ompcp = (OMProcControlPtr) data; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; switch (ompcp->input_itemtype) { case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : return OM_MSG_RET_ERROR; default : return OM_MSG_RET_ERROR; } if (ompcp->input_data == NULL) return OM_MSG_RET_ERROR; sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); if (sep == NULL) return OM_MSG_RET_ERROR; MakeProteinTitlesInSequinStyle (ompcp->input_entityID, sep); ObjMgrSetDirtyFlag (ompcp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, ompcp->input_entityID, 0, 0); return OM_MSG_RET_DONE; } static Boolean LIBCALLBACK SequinFTableBioseq (BioseqPtr bsp, SeqMgrBioseqContextPtr context) { FILE *fp; if (bsp == NULL) return TRUE; fp = (FILE *) context->userdata; BioseqToGnbk (bsp, NULL, FTABLE_FMT, DUMP_MODE, NORMAL_STYLE, 0, fp); return TRUE; } extern Int2 LIBCALLBACK MakeSequinFeatureTable (Pointer data) { FILE *fp; OMProcControlPtr ompcp; Char path [PATH_MAX]; SeqEntryPtr sep; ompcp = (OMProcControlPtr) data; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; switch (ompcp->input_itemtype) { case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : return OM_MSG_RET_ERROR; default : return OM_MSG_RET_ERROR; } if (ompcp->input_data == NULL) return OM_MSG_RET_ERROR; sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); if (sep == NULL) return OM_MSG_RET_ERROR; TmpNam (path); fp = FileOpen (path, "w"); if (fp == NULL) return OM_MSG_RET_ERROR; SeqMgrExploreBioseqs (ompcp->input_entityID, NULL, (Pointer) fp, SequinFTableBioseq, TRUE, FALSE, FALSE); FileClose (fp); LaunchGeneralTextViewer (path, "Gene - CDS Feature Table"); FileRemove (path); return OM_MSG_RET_DONE; } /* the following two functions are modified from PrintGenome in wprint.c */ static void SqLitPrintGenome(SeqLitPtr slp, FILE *fp) { static Char val[166]; if (slp->seq_data != NULL) /* not a gap */ { if (slp->length == 0) /* unknown length */ { fprintf(fp, "gap\t0\t0\t0\n"); } else { /* don't know what to do here */ } } else { /* gap length was set */ fprintf(fp, "gap\t0\t0\t%ld\n", (long) slp->length); } } static void SqLocPrintGenome(SeqLocPtr slp_head, FILE *fp) { SeqLocPtr slp; static Char buf[11]; SeqIdPtr sid, newid; Int4 start, stop; for (slp = slp_head; slp; slp = slp->next) { sid = SeqLocId(slp); if (slp->choice == SEQLOC_INT || slp->choice == SEQLOC_WHOLE) { start = SeqLocStart(slp); stop = SeqLocStop(slp); } else if (slp->choice == SEQLOC_NULL){ fprintf(fp, "gap\t0\t0\t0\n"); continue; } else { continue; } if (sid->choice == SEQID_GI) { newid = GetSeqIdForGI(sid->data.intvalue); } else if (sid->choice == SEQID_GENERAL) { newid = sid; } else { newid = sid; } SeqIdWrite(newid, buf, PRINTID_TEXTID_ACCESSION, 10); fprintf(fp, "%s\t%ld\t%ld\n", buf, (long) start+1, (long) stop+1); } } static Boolean DeltaLitOnly (BioseqPtr bsp) { ValNodePtr vnp; if (bsp == NULL || bsp->repr != Seq_repr_delta) return FALSE; for (vnp = (ValNodePtr)(bsp->seq_ext); vnp != NULL; vnp = vnp->next) { if (vnp->choice == 1) return FALSE; } return TRUE; } extern Int2 LIBCALLBACK MakeContigBuildTable (Pointer data) { BioseqPtr bsp; DeltaSeqPtr dsp; FILE *fp; SeqLitPtr litp; OMProcControlPtr ompcp; Char path [PATH_MAX]; SeqEntryPtr sep; ompcp = (OMProcControlPtr) data; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; bsp = NULL; switch (ompcp->input_itemtype) { case OBJ_BIOSEQ : bsp = (BioseqPtr) ompcp->input_data; break; default : return OM_MSG_RET_ERROR; } if (bsp == NULL) return OM_MSG_RET_ERROR; sep = GetBestTopParentForData (ompcp->input_entityID, bsp); if (sep == NULL) return OM_MSG_RET_ERROR; if (IsAGenomeRecord (sep) || IsSegmentedBioseqWithoutParts (sep)) { } else if (IsADeltaBioseq (sep) && (! DeltaLitOnly (bsp))) { } else return OM_MSG_RET_ERROR; TmpNam (path); fp = FileOpen (path, "w"); if (fp == NULL) return OM_MSG_RET_ERROR; /* the following code is modified from PrintGenome in wprint.c */ if (bsp->seq_ext_type == 1) { SqLocPrintGenome((SeqLocPtr) bsp->seq_ext, fp); } else if (bsp->seq_ext_type == 4) { for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp; dsp=dsp->next) { if (dsp->choice == 1) { /* SeqLoc */ SqLocPrintGenome((SeqLocPtr)(dsp->data.ptrvalue), fp); } else { litp = (SeqLitPtr)(dsp->data.ptrvalue); if (litp == NULL) continue; SqLitPrintGenome(litp, fp); } } } FileClose (fp); LaunchGeneralTextViewer (path, "Contig Build Table"); FileRemove (path); return OM_MSG_RET_DONE; }