/* sequin7.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: sequin7.c * * Author: Jonathan Kans * * Version Creation Date: 1/3/98 * * $Revision: 6.89 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #ifndef CODECENTER static char *date_of_compilation = __DATE__; static char *time_of_compilation = __TIME__; #else static char *date_of_compilation = "today"; static char *time_of_compilation = "now"; #endif #include "sequin.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include NLM_EXTERN SeqEntryPtr FastaToSeqEntryInternal ( VoidPtr input, /* input pointer (file or memory) */ Int4 type, /* type of inquiry FASTA_MEM_IO or FASTA_FILE_IO */ CharPtr PNTR last_char, /* returned pointer to next FASTA sequence */ Boolean is_na, /* type of sequence */ CharPtr PNTR errormsg, /* error messge for debugging */ Boolean parseSeqId, /* Parse SeqID from def line */ CharPtr special_symbol /* Returns special symbol if no SeqEntry */ ); NLM_EXTERN SeqEntryPtr SequinFastaToSeqEntryEx ( FILE *fp, /* file to get sequence from */ Boolean is_na, /* type of sequence */ CharPtr PNTR errormsg, /* error message for debugginq */ Boolean parseSeqId, /* Parse SeqID from def line */ CharPtr special_symbol /* Returns special symbol if no SeqEntry */ ) { return FastaToSeqEntryInternal((void *)fp, 2, NULL,is_na, errormsg, parseSeqId, special_symbol); } static FonT titleFont = NULL; #ifndef WIN_MAC void CreateSqnInitialFormMenus (WindoW w) { BaseFormPtr bfp; MenU m; bfp = (BaseFormPtr) GetObjectExtra (w); if (bfp != NULL) { m = PulldownMenu (w, "File"); AddAboutAndHelpMenuItems (m); if (bfp->importform != NULL || bfp->exportform != NULL) { if (bfp->importform != NULL) { FormCommandItem (m, "Import...", bfp, VIB_MSG_IMPORT); } if (bfp->exportform != NULL) { FormCommandItem (m, "Export...", bfp, VIB_MSG_EXPORT); } SeparatorItem (m); } FormCommandItem (m, "Quit", bfp, VIB_MSG_QUIT); m = PulldownMenu (w, "Edit"); FormCommandItem (m, CUT_MENU_ITEM, bfp, VIB_MSG_CUT); FormCommandItem (m, COPY_MENU_ITEM, bfp, VIB_MSG_COPY); FormCommandItem (m, PASTE_MENU_ITEM, bfp, VIB_MSG_PASTE); FormCommandItem (m, CLEAR_MENU_ITEM, bfp, VIB_MSG_DELETE); } } #endif static void DefaultMessageProc (ForM f, Int2 mssg) { StdEditorProcsPtr sepp; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { if (sepp->handleMessages != NULL) { sepp->handleMessages (f, mssg); } } } typedef struct startupform { FORM_MESSAGE_BLOCK } StartupForm, PNTR StartupFormPtr; static void ChangeDestination (GrouP g) { Char str [64]; Int2 val; val = GetValue (g); switch (val) { case 1 : RemoveAppProperty ("SequinUseEMBLStyle"); RemoveAppProperty ("SequinUseDDBJStyle"); if (GetAppParam ("SEQUIN", "PREFERENCES", "DATABASE", NULL, str, sizeof (str))) { if (! StringHasNoText (str)) { if (StringICmp (str, "GenBank") != 0) { SetAppParam ("SEQUIN", "PREFERENCES", "DATABASE", "GenBank"); } } } break; case 2 : SetAppProperty ("SequinUseEMBLStyle", (void *) 1024); RemoveAppProperty ("SequinUseDDBJStyle"); SetAppParam ("SEQUIN", "PREFERENCES", "DATABASE", "EMBL"); break; case 3 : RemoveAppProperty ("SequinUseEMBLStyle"); SetAppProperty ("SequinUseDDBJStyle", (void *) 1024); SetAppParam ("SEQUIN", "PREFERENCES", "DATABASE", "DDBJ"); break; default : break; } SetupBioseqPageList (); } static void CenterString (RectPtr rptr, CharPtr text, FonT fnt, Int2 inc) { if (fnt != NULL) { SelectFont (fnt); } rptr->bottom = rptr->top + LineHeight (); DrawString (rptr, text, 'c', FALSE); rptr->top = rptr->bottom + inc; } extern void DrawAbout (PaneL p) { RecT r; if (titleFont == NULL) { #ifdef WIN_MAC titleFont = GetFont ("Geneva", 18, TRUE, TRUE, FALSE, ""); #endif #ifdef WIN_MSWIN titleFont = GetFont ("Arial", 24, TRUE, TRUE, FALSE, ""); #endif #ifdef WIN_MOTIF titleFont = GetFont ("Courier", 24, TRUE, TRUE, FALSE, ""); #endif } ObjectRect (p, &r); InsetRect (&r, 4, 4); r.top += 5; Blue (); CenterString (&r, "Sequin", titleFont, 5); CenterString (&r, SEQUIN_VERSION, programFont, 5); CenterString (&r, SEQUIN_SERVICES, programFont, 10); CenterString (&r, "National Center for Biotechnology Information", systemFont, 5); CenterString (&r, "National Library of Medicine", systemFont, 5); CenterString (&r, "National Institutes of Health", systemFont, 10); CenterString (&r, "(301) 496-2475", systemFont, 5); CenterString (&r, "info@ncbi.nlm.nih.gov", systemFont, 0); } extern Int2 AboutBoxWidth (void) { Int2 max; CharPtr ptr; Char sequinServices [60]; Char sequinVersion [60]; Int2 wid; if (titleFont == NULL) { #ifdef WIN_MAC titleFont = GetFont ("Geneva", 18, TRUE, TRUE, FALSE, ""); #endif #ifdef WIN_MSWIN titleFont = GetFont ("Arial", 24, TRUE, TRUE, FALSE, ""); #endif #ifdef WIN_MOTIF titleFont = GetFont ("Courier", 24, TRUE, TRUE, FALSE, ""); #endif } sprintf (sequinVersion, "Sequin Application Version %s", SEQUIN_APPLICATION); ptr = "Standard Release"; /*#ifdef USE_ENTREZ*/ if (useEntrez || useBlast) { ptr = "Network Aware"; } /*#endif*/ /*#ifdef INTERNAL_NCBI_SEQUIN*/ if (indexerVersion) { ptr = "Indexer Services"; } /*#endif*/ if (genomeCenter != NULL) { ptr = "Genome Center"; } sprintf (sequinServices, "%s [%s]", ptr, date_of_compilation); SelectFont (titleFont); max = StringWidth ("Sequin"); SelectFont (programFont); wid = StringWidth (sequinVersion); if (wid > max) { max = wid; } wid = StringWidth (sequinServices); if (wid > max) { max = wid; } SelectFont (systemFont); wid = StringWidth ("National Center for Biotechnology Information"); if (wid > max) { max = wid; } max += 2 * stdCharWidth + 2; return max; } extern Int2 AboutBoxHeight (void) { Int2 hgt; if (titleFont == NULL) { #ifdef WIN_MAC titleFont = GetFont ("Geneva", 18, TRUE, TRUE, FALSE, ""); #endif #ifdef WIN_MSWIN titleFont = GetFont ("Arial", 24, TRUE, TRUE, FALSE, ""); #endif #ifdef WIN_MOTIF titleFont = GetFont ("Courier", 24, TRUE, TRUE, FALSE, ""); #endif } SelectFont (titleFont); hgt = LineHeight () + 5; SelectFont (programFont); hgt += 2 * LineHeight () + 15; SelectFont (systemFont); hgt += 5 * LineHeight () + 25; hgt += 18; return hgt; } extern ForM CreateStartupForm (Int2 left, Int2 top, CharPtr title, BtnActnProc startFa2htgs, BtnActnProc startPhrap, BtnActnProc buildContig, BtnActnProc startNew, BtnActnProc readExisting, BtnActnProc fetchFromNet, BtnActnProc showHelp, BtnActnProc quitProgram, WndActnProc activateForm) { ButtoN b; GrouP c; GrouP d; GrouP k; PaneL p; StartupFormPtr sfp; Char str [32]; WindoW w; #ifndef WIN_MAC MenU m; #endif w = NULL; sfp = MemNew (sizeof (StartupForm)); if (sfp != NULL) { w = FixedWindow (left, top, -10, -10, title, NULL); SetObjectExtra (w, sfp, StdCleanupFormProc); sfp->form = (ForM) w; sfp->formmessage = DefaultMessageProc; #ifndef WIN_MAC m = PulldownMenu (w, "Misc"); CommandItem (m, "Net Configure...", NetConfigureProc); if (useEntrez) { SeparatorItem (m); CommandItem (m, "Entrez Query...", EntrezQueryProc); if (extraServices) { SeparatorItem (m); CommandItem (m, "Process FASTA Nucleotide Updates", ParseInNucUpdates); } } if (useDesktop) { SeparatorItem (m); VSMAddToMenu (m, VSM_DESKTOP); } #endif p = SimplePanel (w, AboutBoxWidth (), AboutBoxHeight (), DrawAbout); k = HiddenGroup (w, 4, 0, NULL); SetGroupSpacing (k, 3, 10); StaticPrompt (k, "Database for submission", 0, stdLineHeight, programFont, 'l'); d = HiddenGroup (k, 4, 0, ChangeDestination); RadioButton (d, "GenBank"); RadioButton (d, "EMBL"); RadioButton (d, "DDBJ"); if (GetAppParam ("SEQUIN", "PREFERENCES", "DATABASE", NULL, str, sizeof (str))) { if (StringICmp (str, "GenBank") == 0) { SetValue (d, 1); } else if (StringICmp (str, "EMBL") == 0) { SetValue (d, 2); } else if (StringICmp (str, "DDBJ") == 0) { SetValue (d, 3); } else { SetValue (d, 1); } } else { SetValue (d, 1); } ChangeDestination (d); c = HiddenGroup (w, 1, 0, NULL); SetGroupSpacing (c, 10, 5); if (startFa2htgs != NULL) { b = PushButton (c, "New FA2HTGS Submission", startFa2htgs); SetObjectExtra (b, sfp, NULL); } if (startPhrap != NULL) { b = PushButton (c, "New PHRAP Submission", startPhrap); SetObjectExtra (b, sfp, NULL); } if (buildContig != NULL) { b = PushButton (c, "Read CONTIG Instructions", buildContig); SetObjectExtra (b, sfp, NULL); } b = PushButton (c, "Start New Submission", startNew); SetObjectExtra (b, sfp, NULL); b = PushButton (c, "Read Existing Record", readExisting); SetObjectExtra (b, sfp, NULL); if (fetchFromNet != NULL) { b = PushButton (c, "Download From Entrez", fetchFromNet); SetObjectExtra (b, sfp, NULL); } b = PushButton (c, "Show Help", showHelp); SetObjectExtra (b, sfp, NULL); b = PushButton (c, "Quit Program", quitProgram); SetObjectExtra (b, sfp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) k, NULL); RealizeWindow (w); if (activateForm != NULL) { SetActivate (w, activateForm); } } return (ForM) w; } typedef struct formatform { FORM_MESSAGE_BLOCK GrouP package; GrouP format; ButtoN nexusButton; ButtoN paupButton; TexT numseqs; Int2 restoreFormatTo; } FormatForm, PNTR FormatFormPtr; static Boolean allowGenomicPlusCDNA = FALSE; static void FormatBlockPtrToFormatForm (ForM f, Pointer data) { FormatBlockPtr fbp; FormatFormPtr ffp; Char str [32]; ffp = (FormatFormPtr) GetObjectExtra (f); fbp = (FormatBlockPtr) data; if (ffp == NULL) return; if (fbp != NULL) { if (fbp->seqPackage > 0 && fbp->seqPackage <= NUM_SEQ_PKG) { if ((! allowGenomicPlusCDNA) && fbp->seqPackage >= SEQ_PKG_GENOMICCDNA) { SafeSetValue (ffp->package, fbp->seqPackage - 1); } else { SafeSetValue (ffp->package, fbp->seqPackage); } if (fbp->seqPackage <= SEQ_PKG_GENOMICCDNA || fbp->seqPackage == SEQ_PKG_GENBANK) { SafeDisable (ffp->nexusButton); SafeDisable (ffp->paupButton); } else { SafeEnable (ffp->nexusButton); SafeEnable (ffp->paupButton); } } else { SafeSetValue (ffp->package, SEQ_PKG_SINGLE); SafeDisable (ffp->nexusButton); SafeDisable (ffp->paupButton); } if (fbp->seqFormat > 0 && fbp->seqFormat <= NUM_SEQ_FMT) { SafeSetValue (ffp->format, fbp->seqFormat); } else { SafeSetValue (ffp->format, SEQ_FMT_FASTA); } if (fbp->numSeqs > 0) { IntToStr (fbp->numSeqs, str, 0, sizeof (str)); SafeSetTitle (ffp->numseqs, str); } else { SafeSetTitle (ffp->numseqs, ""); } } else { SafeSetValue (ffp->package, SEQ_PKG_SINGLE); SafeDisable (ffp->nexusButton); SafeDisable (ffp->paupButton); SafeSetValue (ffp->format, SEQ_FMT_FASTA); SafeSetTitle (ffp->numseqs, ""); ffp->restoreFormatTo = SEQ_FMT_FASTA; } } static Pointer FormatFormToFormatBlockPtr (ForM f) { FormatBlockPtr fbp; FormatFormPtr ffp; Char str [32]; Int2 val; fbp = NULL; ffp = (FormatFormPtr) GetObjectExtra (f); if (ffp == NULL) return NULL; fbp = (FormatBlockPtr) MemNew (sizeof (FormatBlock)); if (fbp == NULL) return NULL; fbp->seqPackage = GetValue (ffp->package); if ((! allowGenomicPlusCDNA) && fbp->seqPackage >= SEQ_PKG_GENOMICCDNA) { (fbp->seqPackage)++; } fbp->seqFormat = GetValue (ffp->format); GetTitle (ffp->numseqs, str, sizeof (str)); if (StrToInt (str, &val) && val > 0) { fbp->numSeqs = val; } else { fbp->numSeqs = 0; } return (Pointer) fbp; } static void EnableOrDisableFormats (GrouP g) { FormatFormPtr ffp; Int2 val; ffp = (FormatFormPtr) GetObjectExtra (g); if (ffp == NULL) return; val = GetValue (g); if ((! allowGenomicPlusCDNA) && val >= SEQ_PKG_GENOMICCDNA) { val++; } if (val <= SEQ_PKG_GENOMICCDNA || val == SEQ_PKG_GENBANK) { if (Enabled (ffp->nexusButton)) { ffp->restoreFormatTo = GetValue (ffp->format); } SafeSetValue (ffp->format, SEQ_FMT_FASTA); SafeDisable (ffp->nexusButton); SafeDisable (ffp->paupButton); } else { if (! Enabled (ffp->nexusButton)) { SafeSetValue (ffp->format, ffp->restoreFormatTo); } SafeEnable (ffp->nexusButton); SafeEnable (ffp->paupButton); } } extern ForM CreateFormatForm (Int2 left, Int2 top, CharPtr title, BtnActnProc goToNext, BtnActnProc goBack, WndActnProc activateForm) { ButtoN b; GrouP c; FormatFormPtr ffp; GrouP g1, g2; GrouP h; PrompT ppt; Char str [32]; WindoW w; w = NULL; ffp = MemNew (sizeof (FormatForm)); if (ffp != NULL) { w = FixedWindow (left, top, -10, -10, title, NULL); SetObjectExtra (w, ffp, StdCleanupFormProc); ffp->form = (ForM) w; ffp->toform = FormatBlockPtrToFormatForm; ffp->fromform = FormatFormToFormatBlockPtr; ffp->formmessage = DefaultMessageProc; SetGroupSpacing (w, 10, 10); h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 3, 10); g1 = HiddenGroup (h, 2, 0, NULL); allowGenomicPlusCDNA = FALSE; if (GetAppParam ("SEQUIN", "SETTINGS", "GENOMICPLUSTRANSCRIPTS", NULL, str, sizeof (str))) { if (StringICmp (str, "TRUE") == 0) { allowGenomicPlusCDNA = TRUE; } } ppt = StaticPrompt (g1, "Submission type", 0, 0, programFont, 'l'); ffp->package = HiddenGroup (g1, 2, 0, EnableOrDisableFormats); SetObjectExtra (ffp->package, ffp, NULL); RadioButton (ffp->package, "Single sequence"); RadioButton (ffp->package, "Segmented sequence"); if (allowGenomicPlusCDNA) { RadioButton (ffp->package, "Genomic + Transcripts"); } RadioButton (ffp->package, "Population study"); RadioButton (ffp->package, "Phylogenetic study"); RadioButton (ffp->package, "Mutation study"); RadioButton (ffp->package, "Environmental samples"); RadioButton (ffp->package, "Batch submission"); SetValue (ffp->package, SEQ_PKG_SINGLE); AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt, (HANDLE) ffp->package, NULL); g2 = HiddenGroup (h, 2, 0, NULL); ppt = StaticPrompt (g2, "Sequence data format", 0, 0, programFont, 'l'); ffp->format = HiddenGroup (g2, -1, 0, NULL); SetObjectExtra (ffp->format, ffp, NULL); RadioButton (ffp->format, "FASTA"); ffp->paupButton = RadioButton (ffp->format, "Contiguous (FASTA+GAP, NEXUS, MACAW)"); ffp->nexusButton = RadioButton (ffp->format, "Interleaved (PHYLIP, NEXUS)"); Disable (ffp->nexusButton); Disable (ffp->paupButton); SetValue (ffp->format, SEQ_FMT_FASTA); ffp->restoreFormatTo = SEQ_FMT_FASTA; AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt, (HANDLE) ffp->format, NULL); c = HiddenGroup (w, 4, 0, NULL); SetGroupSpacing (c, 10, 2); b = PushButton (c, " << Prev Form ", goBack); SetObjectExtra (b, ffp, NULL); b = PushButton (c, " Next Form >> ", goToNext); SetObjectExtra (b, ffp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) g1, (HANDLE) g2, (HANDLE) c, NULL); RealizeWindow (w); if (activateForm != NULL) { SetActivate (w, activateForm); } } return (ForM) w; } extern SequinBlockPtr SequinBlockFree (SequinBlockPtr sbp) { if (sbp != NULL) { AuthorFree (sbp->contactperson); AuthListFree (sbp->citsubauthors); AffilFree (sbp->citsubaffil); MemFree (sbp->citsubtitle); DateFree (sbp->releasedate); } return NULL; } extern void ExciseString (CharPtr str, CharPtr from, CharPtr to) { Char ch; CharPtr ptrf; CharPtr ptrt; if (str == NULL || from == NULL || to == NULL) return; ptrf = StringISearch (str, from); if (ptrf == NULL) return; ptrt = StringISearch (ptrf, to); if (ptrt == NULL) return; ptrt += StringLen (to); ch = *ptrt; while (ch != '\0') { *ptrf = ch; ptrf++; ptrt++; ch = *ptrt; } *ptrf = '\0'; } typedef struct geneextendlist { GeneRefPtr grp; SeqLocPtr slp; ObjMgrPtr omp; Boolean rsult; Char label [41]; } GeneExtendList, PNTR GeneExtendPtr; static Boolean GeneExtendFunc (GatherContextPtr gcp) { BioseqPtr bsp; GeneExtendPtr gep; GeneRefPtr grp; Boolean hasNulls; ObjMgrTypePtr omtp; SeqFeatPtr sfp; SeqLocPtr slp; Char thislabel [41]; if (gcp == NULL) return TRUE; gep = (GeneExtendPtr) gcp->userdata; if (gep == NULL ) return TRUE; thislabel [0] = '\0'; if (gcp->thistype == OBJ_SEQFEAT) { sfp = (SeqFeatPtr) gcp->thisitem; if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE && sfp->data.value.ptrvalue != NULL) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; omtp = ObjMgrTypeFind (gep->omp, gcp->thistype, NULL, NULL); if (omtp == NULL) { return TRUE; } if (omtp->labelfunc != NULL) { (*(omtp->labelfunc)) (gcp->thisitem, thislabel, 40, OM_LABEL_CONTENT); } if (thislabel [0] != '\0') { if (StringICmp (thislabel, gep->label) == 0) { if (SeqLocCompare (gep->slp, sfp->location) != SLC_NO_MATCH) { bsp = GetBioseqGivenSeqLoc (sfp->location, gcp->entityID); if (bsp != NULL) { slp = SeqLocMerge (bsp, sfp->location, gep->slp, TRUE, FALSE, FALSE); if (slp != NULL) { sfp->location = SeqLocFree (sfp->location); sfp->location = slp; if (bsp->repr == Seq_repr_seg) { slp = SegLocToPartsEx (bsp, sfp->location, TRUE); sfp->location = SeqLocFree (sfp->location); sfp->location = slp; hasNulls = LocationHasNullsBetween (sfp->location); sfp->partial = (sfp->partial || hasNulls); } FreeAllFuzz (slp); gep->rsult = TRUE; } } } return FALSE; } } } } return TRUE; } extern Boolean ExtendGene (GeneRefPtr grp, SeqEntryPtr nsep, SeqLocPtr slp) { GeneExtendList gel; GatherScope gs; ObjMgrTypePtr omtp; SeqFeatPtr sfp; if (grp == NULL || nsep == NULL || slp == NULL) return FALSE; gel.grp = grp; gel.slp = slp; gel.omp = ObjMgrGet (); gel.label [0] = '\0'; gel.rsult = FALSE; omtp = ObjMgrTypeFind (gel.omp, OBJ_SEQFEAT, NULL, NULL); if (omtp != NULL && omtp->labelfunc != NULL) { sfp = SeqFeatNew (); if (sfp != NULL) { sfp->data.choice = SEQFEAT_GENE; sfp->data.value.ptrvalue = (Pointer) grp; (*(omtp->labelfunc)) ((Pointer) sfp, gel.label, 40, OM_LABEL_CONTENT); sfp->data.value.ptrvalue = NULL; SeqFeatFree (sfp); } } 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_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; GatherSeqEntry (nsep, (Pointer) &gel, GeneExtendFunc, &gs); return gel.rsult; } /*=====================================================================*/ /* */ /* CreateGeneAndProtFeats() - */ /* */ /*=====================================================================*/ static void CreateGeneAndProtFeats (SeqEntryPtr nsep, SeqEntryPtr psep, SeqLocPtr slp, CdRegionPtr crp, CharPtr title, CharPtr best, size_t maxsize, CharPtr PNTR ttl) { Char activity [256]; CharPtr allele = NULL; BioseqPtr bsp; Char ec [32]; GeneRefPtr grp = NULL; SeqLocPtr gslp; Boolean hasNulls; BioseqPtr nbsp; BioseqPtr pbsp; ProtRefPtr prp; CharPtr ptr; SeqFeatPtr sfp; SeqIdPtr sip; Char str [256]; Char str2 [256]; Char geneSynStr[256]; if (nsep != NULL && psep != NULL && slp != NULL && crp != NULL && title != NULL) { if (best != NULL) { best [0] = '\0'; } if (IS_Bioseq (nsep) && IS_Bioseq (psep)) { nbsp = (BioseqPtr) nsep->data.ptrvalue; pbsp = (BioseqPtr) psep->data.ptrvalue; if (nbsp != NULL && pbsp != NULL) { /*---------------------------------*/ /* Parse the gene and gene-related */ /* fields from the title. */ /*---------------------------------*/ ptr = StringISearch (title, "[gene="); if (ptr != NULL) { StringNCpy_0 (str, ptr + 6, sizeof (str)); ptr = StringChr (str, ']'); if (ptr != NULL) { *ptr = '\0'; ptr = StringChr (str, ';'); if (ptr != NULL) { *ptr = '\0'; ptr++; allele = StringChr (ptr, ';'); if (allele != NULL) { *allele = '\0'; allele++; } } StringNCpy_0 (best, str, maxsize); if (StringHasNoText (best)) { StringNCpy_0 (best, ptr, maxsize); } /*--------------------------------------*/ /* Create a Gene Reference pointer with */ /* the gene, gene description, allele, */ /* and gene_syn information. */ /*--------------------------------------*/ grp = CreateNewGeneRef (str, allele, ptr, FALSE); } } /*-----------------------------------------*/ /* Parse the gene_syn field from the title */ /*-----------------------------------------*/ ptr = StringISearch (title, "[gene_syn="); if (ptr != NULL) { StringNCpy_0 (geneSynStr, ptr + 10, sizeof (str)); ptr = StringChr (geneSynStr, ']'); if (ptr != NULL) { *ptr = '\0'; } if (grp == NULL) { grp = GeneRefNew (); } ValNodeCopyStr(&(grp->syn),0,geneSynStr); } if (grp != NULL) { if (ExtendGene (grp, nsep, slp)) { grp = GeneRefFree (grp); } else { sfp = CreateNewFeature (nsep, NULL, SEQFEAT_GENE, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) grp; sfp->location = SeqLocFree (sfp->location); sfp->location = AsnIoMemCopy ((Pointer) slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); sip = SeqLocId (sfp->location); if (sip != NULL) { bsp = BioseqFind (sip); } else { bsp = nbsp; } if (bsp != NULL) { gslp = SeqLocMerge (bsp, sfp->location, NULL, TRUE, FALSE, FALSE); if (gslp != NULL) { sfp->location = SeqLocFree (sfp->location); sfp->location = gslp; if (bsp->repr == Seq_repr_seg) { gslp = SegLocToPartsEx (bsp, sfp->location, TRUE); sfp->location = SeqLocFree (sfp->location); sfp->location = gslp; hasNulls = LocationHasNullsBetween (sfp->location); sfp->partial = (sfp->partial || hasNulls); } FreeAllFuzz (gslp); } } } } } /*-----------------------------------------*/ /* Parse the function field from the title */ /*-----------------------------------------*/ activity [0] = '\0'; ec [0] = '\0'; ptr = StringISearch (title, "[function="); if (ptr != NULL) { StringNCpy_0 (activity, ptr + 10, sizeof (str)); ptr = StringChr (activity, ']'); if (ptr != NULL) { *ptr = '\0'; } } /*------------------------------------------*/ /* Parse the EC_number field from the title */ /*------------------------------------------*/ ptr = StringISearch (title, "[EC_number="); if (ptr != NULL) { StringNCpy_0 (ec, ptr + 11, sizeof (str)); ptr = StringChr (ec, ']'); if (ptr != NULL) { *ptr = '\0'; } } /*---------------------------------*/ /* Parse the protein and prot_desc */ /* fields from the title. */ /*---------------------------------*/ ptr = StringISearch (title, "[prot="); if (ptr != NULL) { StringNCpy_0 (str, ptr + 6, sizeof (str)); ptr = StringChr (str, ']'); } else { ptr = StringISearch (title, "[protein="); if (ptr != NULL) { StringNCpy_0 (str, ptr + 9, sizeof (str)); ptr = StringChr (str, ']'); } } /*---------------------------------*/ /* If we found a protein value ... */ /*---------------------------------*/ if (ptr != NULL) { /*------------------------------------*/ /* ... trim off extraneous characters */ /*------------------------------------*/ *ptr = '\0'; /*----------------------------------------------*/ /* ... search for a protein description, either */ /* in the prot field (seperated by a ';') */ /* or in its own 'prot_desc' field. */ /*----------------------------------------------*/ ptr = StringChr (str, ';'); if (ptr != NULL) { *ptr = '\0'; ptr++; } else { ptr = StringISearch (title, "[prot_desc="); if (ptr != NULL) { StringNCpy_0 (str2, ptr + 11, sizeof (str2)); ptr = StringChr (str2, ']'); if (ptr != NULL) { *ptr = '\0'; ptr = str2; } } } /*-----------*/ /* ... ??? */ /*-----------*/ StringNCpy_0 (best, str, maxsize); if (StringHasNoText (best)) StringNCpy_0 (best, ptr, maxsize); /*--------------------------------*/ /* ... add the prot and prot_desc */ /* to the Seq Features. */ /*--------------------------------*/ prp = CreateNewProtRef (str, ptr, ec, activity); if (prp != NULL) { sfp = CreateNewFeature (psep, NULL, SEQFEAT_PROT, NULL); if (sfp != NULL) sfp->data.value.ptrvalue = (Pointer) prp; } } /*---------------------*/ /* Parse the ORF field */ /*---------------------*/ ptr = StringISearch (title, "[orf]"); if (ptr != NULL) { crp->orf = TRUE; } /*-------------------------*/ /* Parse the comment field */ /*-------------------------*/ ptr = StringISearch (title, "[comment="); if (ptr != NULL) { StringNCpy_0 (str, ptr + 9, sizeof (str)); ptr = StringChr (str, ']'); if (ptr != NULL) { *ptr = '\0'; if (ttl != NULL) { *ttl = StringSave (str); } } } /*----------------------*/ /* Parse the note field */ /*----------------------*/ ptr = StringISearch (title, "[note="); if (ptr != NULL) { StringNCpy_0 (str, ptr + 6, sizeof (str)); ptr = StringChr (str, ']'); if (ptr != NULL) { *ptr = '\0'; if (ttl != NULL && *ttl == NULL) { *ttl = StringSave (str); } } } } } } } static Boolean intBoxUp; static Boolean intBoxRsult; static void AcceptAskProc (ButtoN b) { intBoxRsult = TRUE; intBoxUp = FALSE; } static void CancelAskProc (ButtoN b) { intBoxRsult = FALSE; intBoxUp = FALSE; } static SeqLocPtr AskForInterval (SeqEntryPtr sep, BioseqPtr nuc, BioseqPtr prot) { GrouP c; DialoG d; GrouP g; GrouP m; SeqIdPtr sip; SeqLocPtr slp; Char str [128]; ValNodePtr vnp; WindoW w; slp = NULL; if (sep == NULL || nuc == NULL || prot == NULL) return NULL; if (GetAppParam ("SEQUIN", "PREFERENCES", "ASKIFSUGGESTFAILED", NULL, str, sizeof (str))) { if (StringICmp (str, "FALSE") == 0) { sip = SeqIdFindWorst (prot->id); SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str)); Message (MSG_POSTERR, "Suggest failure for %s", str); return NULL; } } w = MovableModalWindow (-50, -33, -10, -10, "Enter coding region interval", NULL); g = HiddenGroup (w, -1, 0, NULL); m = NULL; SetGroupSpacing (g, 3, 10); if (prot->descr != NULL) { vnp = ValNodeFindNext (prot->descr, NULL, Seq_descr_title); if (vnp != NULL && vnp->data.ptrvalue != NULL) { m = MultiLinePrompt (g, (CharPtr) vnp->data.ptrvalue, stdCharWidth * 28, programFont); } } d = CreateIntervalEditorDialog (g, NULL, 4, 2, sep, TRUE, FALSE); c = HiddenGroup (g, 2, 0, NULL); SetGroupSpacing (c, 10, 2); PushButton (c, "Accept", AcceptAskProc); PushButton (c, "Cancel", CancelAskProc); AlignObjects (ALIGN_CENTER, (HANDLE) d, (HANDLE) c, (HANDLE) m, NULL); Show (w); Select (w); intBoxUp = TRUE; intBoxRsult = FALSE; while (intBoxUp) { ProcessEventOrIdle (); } ProcessAnEvent (); if (intBoxRsult) { slp = (SeqLocPtr) DialogToPointer (d); } Remove (w); return slp; } extern Boolean AutomaticProteinProcess (SeqEntryPtr esep, SeqEntryPtr psep, Int2 code, Boolean makeMRNA, BioseqPtr forceTarget) { SeqFeatPtr cds; CdRegionPtr crp; Char mRnaName [128]; BioseqPtr nbsp; SeqEntryPtr nsep; BioseqPtr pbsp; SeqFeatPtr rna; RnaRefPtr rrp; SeqEntryPtr sep; SeqLocPtr slp; CharPtr ttl; ValNodePtr vnp; CharPtr vnpstr; if (esep == NULL || psep == NULL) return FALSE; nsep = FindNucSeqEntry (esep); if (nsep == NULL || (! IS_Bioseq (nsep)) || (! IS_Bioseq (psep))) return FALSE; nbsp = (BioseqPtr) nsep->data.ptrvalue; pbsp = (BioseqPtr) psep->data.ptrvalue; if (nbsp == NULL || pbsp == NULL) return FALSE; cds = NULL; WatchCursor (); Update (); if (forceTarget == NULL) { slp = PredictCodingRegion (nbsp, pbsp, code); if (slp == NULL) { ArrowCursor (); Update (); slp = AskForInterval (nsep, nbsp, pbsp); } } else { sep = SeqMgrGetSeqEntryForData (forceTarget); slp = CreateWholeInterval (sep); } if (slp == NULL) return FALSE; mRnaName [0] = '\0'; ttl = NULL; crp = CreateNewCdRgn (0, FALSE, code); if (crp != NULL) { if (pbsp->descr != NULL) { vnp = ValNodeFindNext (pbsp->descr, NULL, Seq_descr_title); if (vnp != NULL && vnp->data.ptrvalue != NULL) { vnpstr = (CharPtr) vnp->data.ptrvalue; CreateGeneAndProtFeats (nsep, psep, slp, crp, vnpstr, mRnaName, sizeof (mRnaName), &ttl); ExciseString (vnpstr, "[gene=", "]"); ExciseString (vnpstr, "[prot=", "]"); ExciseString (vnpstr, "[protein=", "]"); ExciseString (vnpstr, "[function=", "]"); ExciseString (vnpstr, "[EC_number=", "]"); ExciseString (vnpstr, "[orf", "]"); ExciseString (vnpstr, "[comment", "]"); ExciseString (vnpstr, "[note", "]"); TrimSpacesAroundString (vnpstr); if (StringHasNoText (vnpstr)) { ValNodeExtract (&(pbsp->descr), Seq_descr_title); } } } if (makeMRNA) { rrp = RnaRefNew (); if (rrp != NULL) { rrp->type = 2; if (! StringHasNoText (mRnaName)) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = StringSave (mRnaName); } rna = CreateNewFeature (nsep, NULL, SEQFEAT_RNA, NULL); if (rna != NULL) { rna->data.value.ptrvalue = (Pointer) rrp; rna->location = SeqLocFree (rna->location); rna->location = AsnIoMemCopy ((Pointer) slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); } } } cds = CreateNewFeature (nsep, NULL, SEQFEAT_CDREGION, NULL); if (cds != NULL) { cds->data.value.ptrvalue = (Pointer) crp; cds->location = SeqLocFree (cds->location); cds->location = slp; slp = NULL; SetSeqFeatProduct (cds, pbsp); if (! StringHasNoText (ttl)) { cds->comment = ttl; } } } SeqLocFree (slp); return TRUE; } typedef struct fa2htgsform { FORM_MESSAGE_BLOCK SeqSubmitPtr ssp; SeqEntryPtr sep; GrouP templateblock; GrouP fastablock; GrouP orderblock; GrouP controlblock; GrouP contigtype; DialoG contigorder; EnumFieldAssocPtr alists [1]; GrouP htgsphase; ButtoN draft; ButtoN fulltop; ButtoN activefin; TexT orgname; TexT seqname; ButtoN update; TexT accession; TexT knownlength; TexT gaplength; TexT remark; TexT clone; TexT strain; TexT chromosome; TexT title; DialoG secondaries; SeqEntryPtr seplist; ButtoN okBtn; BtnActnProc finish; BtnActnProc cancel; Boolean readPhrap; Boolean buildContig; } Fa2htgsForm, PNTR Fa2htgsFormPtr; /*------------- MakeAc2GBSeqId() -----------------------*/ /*************************************************************** * MakeAc2GBSeqId: * -- return NULL if acnum == null * Hsiu-Chuan 4-18-97 ****************************************************************/ static SeqIdPtr SqnMakeAc2GBSeqId(CharPtr accession) { TextSeqIdPtr tsip; SeqIdPtr sip; if (accession == NULL || *accession == '\0') return NULL; sip = ValNodeNew(NULL); sip->choice = SEQID_GENBANK; tsip = TextSeqIdNew(); sip->data.ptrvalue = tsip; tsip->accession = StringSave(accession); return sip; } /* MakeAc2GBSeqId */ /*----------- AddExtraAc2Entry() ----------------------------*/ /*************************************************************** * AddExtraAc2Entry: * Hsiu-Chuan 4-11-97, modified by JK ****************************************************************/ static void SqnAddDraft2Entry (SeqEntryPtr entry, CharPtr keyword) { BioseqPtr bsp; ValNodePtr vnp; GBBlockPtr gbp; if (entry == NULL) return; bsp = (BioseqPtr)(entry->data.ptrvalue); for (gbp= NULL, vnp = bsp->descr; vnp != NULL; vnp = vnp->next) { if (vnp->choice == Seq_descr_genbank) { gbp = vnp->data.ptrvalue; break; } } if (gbp == NULL) { vnp = (ValNodePtr) NewDescrOnSeqEntry (entry, Seq_descr_genbank); gbp = GBBlockNew(); vnp->data.ptrvalue = (Pointer)gbp; } if (gbp != NULL) { ValNodeCopyStr (&gbp->keywords, 0, keyword); } } static Boolean SqnAddExtraAc2Entry (SeqEntryPtr entry , ValNodePtr extra_accs ) { BioseqPtr bsp; ValNodePtr vnp; GBBlockPtr gbp; Char acnum[17]; CharPtr p; Int4 i, j; SeqHistPtr shp; SeqIdPtr sip; ValNodePtr tmp; if ((entry == NULL) || (extra_accs == NULL)) return FALSE; bsp = (BioseqPtr)(entry->data.ptrvalue); for (gbp= NULL, vnp = bsp->descr; vnp != NULL; vnp = vnp->next) { if (vnp->choice == Seq_descr_genbank) { gbp = vnp->data.ptrvalue; break; } } shp = bsp->hist; if (gbp == NULL) { vnp = (ValNodePtr) NewDescrOnSeqEntry (entry, Seq_descr_genbank); gbp = GBBlockNew(); vnp->data.ptrvalue = (Pointer)gbp; } for (tmp = extra_accs; tmp != NULL; tmp = tmp->next) { p = (CharPtr) tmp->data.ptrvalue; if (p == NULL) continue; for (i = 0; isalnum(*p) && *p != '\0'; ++p, ++i) acnum[i] = *p; acnum[i] = '\0'; /* check one_letter+5digits or two_letter+6digits */ if (i == 6 || i == 8) { if (!isalpha(acnum[0]) || (!(isdigit(acnum[1]) && i == 6) && !(isalpha(acnum[1]) && i == 8))) { ErrPostEx(SEV_ERROR,0,0, "Invalid accession (one_letter+5digits or two_letter+6digits): %s", acnum); return FALSE; } for (j = 2; j < i; ++j) { if (!(isdigit(acnum[j]))) { ErrPostEx(SEV_ERROR,0,0, "Invalid accession (one_letter+5digits or two_letter+6digits): %s", acnum); return FALSE; } } ValNodeCopyStr(&gbp->extra_accessions, 0, acnum); sip = SqnMakeAc2GBSeqId (acnum); if (shp == NULL) { shp = SeqHistNew(); bsp->hist = shp; } ValNodeLink(&shp->replace_ids, sip); } else { ErrPostEx(SEV_ERROR,0,0, "Invalid accession (one_letter+5digits or two_letter+6digits): %s", acnum); return FALSE; } while (!isalnum(*p) && *p != '\0') ++p; } return TRUE; } /* AddExtraAc2Entry */ static void RescueSeqGraphs (BioseqPtr bsp, Int2 index, ValNodePtr PNTR vnpp) { SeqAnnotPtr nextsap; SeqGraphPtr nextsgp; Pointer PNTR prevsap; Pointer PNTR prevsgp; SeqAnnotPtr sap; SeqGraphPtr sgp; if (bsp == NULL || vnpp == NULL) return; sap = bsp->annot; prevsap = (Pointer PNTR) &(bsp->annot); while (sap != NULL) { nextsap = sap->next; if (sap->type == 3) { sgp = (SeqGraphPtr) sap->data; prevsgp = (Pointer PNTR) &(sap->data); while (sgp != NULL) { nextsgp = sgp->next; *(prevsgp) = sgp->next; sgp->next = NULL; ValNodeAddPointer (vnpp, index, (Pointer) sgp); sgp = nextsgp; } } if (sap->data == NULL) { *(prevsap) = sap->next; sap->next = NULL; SeqAnnotFree (sap); } else { prevsap = (Pointer PNTR) &(sap->next); } sap = nextsap; } } static SeqAnnotPtr NewSeqAnnotType3 (CharPtr name, SeqGraphPtr sgp) { SeqAnnotPtr sap = NULL; if (sgp == NULL) return NULL; sap = SeqAnnotNew (); if (sap == NULL) return NULL; if (! StringHasNoText (name)) { ValNodeAddPointer (&(sap->desc), Annot_descr_name, StringSave (name)); } sap->type = 3; sap->data = (Pointer) sgp; return sap; } static void OffsetAndLinkSeqGraph (BioseqPtr bsp, SeqGraphPtr sgp, Int2 index) { DeltaSeqPtr dsp; SeqGraphPtr lastsgp; Int4 len; SeqLitPtr litp; SeqAnnotPtr sap; SeqIntPtr sintp; SeqLocPtr slp; if (bsp == NULL || sgp == NULL || index < 1) return; len = 0; if (bsp->repr == Seq_repr_delta && bsp->seq_ext_type == 4) { for (dsp = (DeltaSeqPtr) (bsp->seq_ext); dsp != NULL && index > 1; dsp = dsp->next, index--) { if (dsp->choice == 1) { len += SeqLocLen ((SeqLocPtr) dsp->data.ptrvalue); } else if (dsp->choice == 2) { litp = (SeqLitPtr) dsp->data.ptrvalue; if (litp != NULL) { len += litp->length; } } } } slp = sgp->loc; if (slp != NULL && slp->choice == SEQLOC_INT) { sintp = (SeqIntPtr) slp->data.ptrvalue; if (sintp != NULL) { sintp->from += len; sintp->to += len; sintp->id = SeqIdFree (sintp->id); sintp->id = SeqIdDup (bsp->id); } } for (sap = bsp->annot; sap != NULL; sap = sap->next) { if (sap->type == 3) { for (lastsgp = sap->data; lastsgp->next != NULL; lastsgp = lastsgp->next) { continue; } lastsgp->next = sgp; break; } } if (sap == NULL) { if (bsp->annot != NULL) { for (sap = bsp->annot; sap->next != NULL; sap = sap->next) { continue; } sap->next = NewSeqAnnotType3 ("Graphs", sgp); } else { bsp->annot = NewSeqAnnotType3 ("Graphs", sgp); } } } static CharPtr phrapBoilerPlate = "Sequence Quality Assessment:~ \ This entry has been annotated with sequence quality~ \ estimates computed by the Phrap assembly program.~ \ All manually edited bases have been reduced to quality zero.~ \ Quality levels above 40 are expected to have less than ~ \ 1 error in 10,000 bp.~ \ Base-by-base quality values are not generally visible from the~ \ GenBank flat file format but are available as part~ \ of this entry's ASN.1 file.~----------------------~"; static void ProcessFa2htgs (Fa2htgsFormPtr ffp, SeqSubmitPtr ssp) { SeqEntryPtr sep, oldsep, the_entry, nextsep; NCBISubPtr nsp; Int2 htgs_phase = -1; Uint1 tech; CharPtr seqname = NULL, accession = NULL, orgname = NULL; CharPtr clone = NULL, strain = NULL, chromosome = NULL; CharPtr remark = NULL, title = NULL, seqbuf = NULL; Int4 length = 0, cumlength = 0, gaplen; BioseqPtr bsp; BioseqSetPtr bssp; SeqLitPtr slp; ValNodePtr vnp, PNTR prevpnt, next, extra_accs; Boolean lastwasraw, draft, fulltop, activefin, usedelta = FALSE; Char str [64]; long int val; Int2 index = 0; ValNodePtr rescuedsgps = NULL; ValNodePtr seqlitlist = NULL; IntFuzzPtr ifp; ObjectIdPtr oip; UserFieldPtr ufp; UserObjectPtr uop; DatePtr dp; if (ffp == NULL || ssp == NULL) return; htgs_phase = GetValue (ffp->htgsphase) - 1; orgname = SaveStringFromText (ffp->orgname); seqname = SaveStringFromText (ffp->seqname); if (GetStatus (ffp->update)) { accession = SaveStringFromText (ffp->accession); } clone = SaveStringFromText (ffp->clone); strain = SaveStringFromText (ffp->strain); chromosome = SaveStringFromText (ffp->chromosome); remark = SaveStringFromText (ffp->remark); title = SaveStringFromText (ffp->title); extra_accs = DialogToPointer (ffp->secondaries); draft = GetStatus (ffp->draft); fulltop = GetStatus (ffp->fulltop); activefin = GetStatus (ffp->activefin); length = 0; /* may need to really calculate length */ GetTitle (ffp->knownlength, str, sizeof (str)); if (! StringHasNoText (str)) { if (sscanf (str, "%ld", &val) == 1 && val > 0) { length = (Int4) val; } } gaplen = 0; /* now usually filling in with gaps of 100 bases */ GetTitle (ffp->gaplength, str, sizeof (str)); if (! StringHasNoText (str)) { if (sscanf (str, "%ld", &val) == 1 && val > 0) { gaplen = (Int4) val; } } /* modified from fa2htgs */ oldsep = (SeqEntryPtr)(ssp->data); /* clear out template */ ssp->data = NULL; MemFree(ssp->sub->tool); sprintf (str, "Sequin %s", SEQUIN_APPLICATION); ssp->sub->tool = StringSave (str); nsp = MemNew(sizeof(NCBISub)); nsp->ssp = ssp; nsp->submittor_key = StringSave (genomeCenter); /* MemFree(ssp->sub->cit->descr); ssp->sub->cit->descr = remark; */ cumlength = 0; index = 0; sep = ffp->seplist; if (sep != NULL && sep->next != NULL) { usedelta = TRUE; } if (ffp->buildContig) { ssp->data = (Pointer) ffp->seplist; the_entry = ffp->seplist; sep = the_entry; oip = ObjectIdNew (); oip->str = StringSave ("info"); uop = UserObjectNew (); uop->type = oip; uop->_class = StringSave ("Genomes"); oip = ObjectIdNew (); oip->id = 0; ufp = UserFieldNew (); ufp->choice = 2; ufp->data.intvalue = 0; ufp->label = oip; uop->data = ufp; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; vnp = SeqDescrNew (NULL); vnp->choice = Seq_descr_user; vnp->data.ptrvalue = (Pointer) uop; vnp->next = bsp->descr; bsp->descr = vnp; cumlength = bsp->length; } } else if (htgs_phase < 3 || usedelta) { the_entry = AddDeltaSeqOnlyToSubmission ( nsp, seqname, NULL, accession, 0, MOLECULE_CLASS_DNA, MOLECULE_TYPE_GENOMIC, length, TOPOLOGY_LINEAR, STRANDEDNESS_DOUBLE); sep = ffp->seplist; lastwasraw = FALSE; while (sep != NULL) { nextsep = sep->next; sep->next = NULL; bsp = (BioseqPtr)(sep->data.ptrvalue); if (bsp->repr == Seq_repr_raw) { if (lastwasraw) { slp = AddFakeGapToDeltaSeq(nsp, the_entry, gaplen); ValNodeAddPointer (&seqlitlist, 0, (Pointer) slp); index++; cumlength += gaplen; } BioseqRawConvert(bsp, Seq_code_iupacna); seqbuf = BSMerge((ByteStorePtr)(bsp->seq_data), NULL); slp = AddLiteralToDeltaSeq(nsp, the_entry, bsp->length); AddBasesToLiteral(nsp, slp, seqbuf); MemFree(seqbuf); lastwasraw = TRUE; index++; } else { if (bsp->length < 0) bsp->length = 0; /* -1 may be set */ AddGapToDeltaSeq(nsp, the_entry, bsp->length); lastwasraw = FALSE; index++; } cumlength += bsp->length; RescueSeqGraphs (bsp, index, &rescuedsgps); SeqEntryFree(sep); sep = nextsep; } } else { the_entry = AddSeqOnlyToSubmission ( nsp, seqname, NULL, accession, 0, MOLECULE_CLASS_DNA, MOLECULE_TYPE_GENOMIC, length, TOPOLOGY_LINEAR, STRANDEDNESS_DOUBLE); sep = ffp->seplist; nextsep = sep->next; sep->next = NULL; bsp = (BioseqPtr)(sep->data.ptrvalue); if (bsp->repr == Seq_repr_raw) { BioseqRawConvert(bsp, Seq_code_iupacna); seqbuf = BSMerge((ByteStorePtr)(bsp->seq_data), NULL); AddBasesToBioseq(nsp, the_entry, seqbuf); MemFree(seqbuf); index++; } cumlength += bsp->length; RescueSeqGraphs (bsp, index, &rescuedsgps); SeqEntryFree(sep); if (nextsep != NULL) { ErrPostEx (SEV_ERROR ,0, 0, "Only the first contig was used for HTGS 3"); } if (length > 0 && length != cumlength) { ErrPostEx (SEV_ERROR ,0, 0, "Length is exactly %ld, not %ld", (long) cumlength, (long) length); length = cumlength; } } /* get data from template: pub, organism, and comment */ if (IS_Bioseq(oldsep)) { bsp = (BioseqPtr)(oldsep->data.ptrvalue); prevpnt = &(bsp->descr); } else { bssp = (BioseqSetPtr)(oldsep->data.ptrvalue); prevpnt = &(bssp->descr); } bsp = (BioseqPtr)(the_entry->data.ptrvalue); if (bsp != NULL) { bsp->length = MAX (cumlength, length); } for (vnp = *prevpnt; vnp != NULL; vnp = next) { next = vnp->next; if (vnp->choice == Seq_descr_pub) { *prevpnt = next; vnp->next = NULL; ValNodeLink(&(bsp->descr), vnp); } else prevpnt = &(vnp->next); } if (remark != NULL) { vnp = SeqDescrNew (NULL); if (vnp != NULL) { vnp->choice = Seq_descr_comment; vnp->data.ptrvalue = remark; ValNodeLink(&(bsp->descr), vnp); } } SeqEntryFree(oldsep); AddOrganismToEntryNew(nsp, the_entry, orgname, NULL, NULL, NULL, NULL, NULL, NULL, NULL); AddGenomeToEntry(nsp, the_entry, 1); if (clone != NULL) AddSubSourceToEntry(nsp, the_entry, 3, clone); if (chromosome != NULL) AddSubSourceToEntry(nsp, the_entry, 1, chromosome); if (clone != NULL) AddOrgModToEntry(nsp, the_entry, 2, strain); if (title != NULL) AddTitleToEntry(nsp, the_entry, title); if (ffp->readPhrap) { AddCommentToEntry(nsp, the_entry, phrapBoilerPlate); } if (extra_accs != NULL) { SqnAddExtraAc2Entry(the_entry, extra_accs); } if (draft) { SqnAddDraft2Entry(the_entry, "HTGS_DRAFT"); } if (fulltop) { SqnAddDraft2Entry(the_entry, "HTGS_FULLTOP"); } if (activefin) { SqnAddDraft2Entry(the_entry, "HTGS_ACTIVEFIN"); } AddBiomolToEntry(nsp, the_entry, 1); if (ffp->buildContig) { } else { switch (htgs_phase) { case 0 : tech = MI_TECH_htgs_0; break; case 1 : tech = MI_TECH_htgs_1; break; case 2 : tech = MI_TECH_htgs_2; break; case 3 : tech = MI_TECH_htgs_3; break; default : tech = MI_TECH_htgs_3; break; } AddTechToEntry(nsp, the_entry, tech); } vnp = NewDescrOnSeqEntry (the_entry, Seq_descr_create_date); if (vnp != NULL) { dp = DateCurr (); vnp->data.ptrvalue = (Pointer) dp; } if (bsp != NULL) { for (vnp = rescuedsgps; vnp != NULL; vnp = vnp->next) { OffsetAndLinkSeqGraph (bsp, (SeqGraphPtr) vnp->data.ptrvalue, (Int2) vnp->choice); vnp->data.ptrvalue = NULL; } } rescuedsgps = ValNodeFreeData (rescuedsgps); for (vnp = seqlitlist; vnp != NULL; vnp = vnp->next) { slp = (SeqLitPtr) vnp->data.ptrvalue; if (slp != NULL) { ifp = IntFuzzNew(); ifp->choice = 4; /* lim - unk*/ slp->fuzz = ifp; } } seqlitlist = ValNodeFree (seqlitlist); MemFree (nsp); } static Pointer Fa2htgsToSeqSubmitPtr (ForM f) { Fa2htgsFormPtr ffp; SeqSubmitPtr ssp; ffp = (Fa2htgsFormPtr) GetObjectExtra (f); if (ffp == NULL) return NULL; ProcessFa2htgs (ffp, ffp->ssp); ssp = ffp->ssp; ffp->ssp = NULL; ffp->sep = NULL; ffp->seplist = NULL; return (Pointer) ssp; } static void Fa2htgsFormMessage (ForM f, Int2 mssg) { Fa2htgsFormPtr ffp; ffp = (Fa2htgsFormPtr) GetObjectExtra (f); if (ffp) { switch (mssg) { 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 (ffp->appmessage != NULL) { ffp->appmessage (f, mssg); } break; } } } #ifndef WIN_MAC void CreateFa2htgsFormMenus (WindoW w) { BaseFormPtr bfp; MenU m; bfp = (BaseFormPtr) GetObjectExtra (w); if (bfp != NULL) { m = PulldownMenu (w, "File"); AddAboutAndHelpMenuItems (m); FormCommandItem (m, "Quit", bfp, VIB_MSG_QUIT); m = PulldownMenu (w, "Edit"); FormCommandItem (m, CUT_MENU_ITEM, bfp, VIB_MSG_CUT); FormCommandItem (m, COPY_MENU_ITEM, bfp, VIB_MSG_COPY); FormCommandItem (m, PASTE_MENU_ITEM, bfp, VIB_MSG_PASTE); FormCommandItem (m, CLEAR_MENU_ITEM, bfp, VIB_MSG_DELETE); } } #endif static void FillInFa2htgsFields (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; Fa2htgsFormPtr ffp; ValNodePtr sdp = NULL; if (sep == NULL || sep->data.ptrvalue == NULL) return; ffp = (Fa2htgsFormPtr) mydata; if (ffp == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sdp = bsp->descr; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sdp = bssp->descr; } else return; while (sdp != NULL) { if (sdp->choice == Seq_descr_comment) { SetTitle (ffp->remark, (CharPtr) sdp->data.ptrvalue); } sdp = sdp->next; } } static void ReadTemplate (ButtoN b) { AsnIoPtr aip; Fa2htgsFormPtr ffp; Char path [PATH_MAX]; SeqEntryPtr sep; SeqSubmitPtr ssp; Char str [128]; ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; if (GetInputFileName (path, sizeof (path), "", "TEXT")) { ffp->ssp = SeqSubmitFree (ffp->ssp); aip = AsnIoOpen (path, "r"); if (aip != NULL) { ffp->ssp = SeqSubmitAsnRead (aip, NULL); } AsnIoClose (aip); } if (ffp->ssp != NULL) { SafeShow (ffp->fastablock); SafeDisable (b); ssp = ffp->ssp; if (ssp->datatype == 1) { sep = (SeqEntryPtr) ssp->data; if (sep != NULL) { SeqEntryToGeneticCode (sep, NULL, str, sizeof (str)); SetTitle (ffp->orgname, str); SeqEntryExplore (sep, (Pointer) ffp, FillInFa2htgsFields); } } } } static Boolean Fa2htgsFormOkay (Fa2htgsFormPtr ffp) { if (ffp == NULL) return FALSE; if (ffp->ssp == NULL) return FALSE; if (ffp->seplist == NULL) return FALSE; if (GetValue (ffp->htgsphase) == 0 && (! ffp->buildContig)) return FALSE; if (TextHasNoText (ffp->orgname)) return FALSE; if (TextHasNoText (ffp->seqname)) return FALSE; return TRUE; } static void ReadFastaHtgsFile (ButtoN b) { Fa2htgsFormPtr ffp; FILE *fp; SeqEntryPtr head; Char path [PATH_MAX]; SeqEntryPtr sep; CharPtr ttl; ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; if (! GetInputFileName (path, sizeof (path), "", "TEXT")) return; if (! StringHasNoText (path)) { fp = FileOpen (path, "r"); if (fp != NULL) { head = NULL; sep = FastaToSeqEntry (fp, TRUE); while (sep != NULL) { ValNodeLink (&head, sep); sep = FastaToSeqEntry (fp, TRUE); } if (head != NULL) { ttl = SeqEntryGetTitle (head); SetTitle (ffp->title, ttl); } ffp->seplist = head; } FileClose (fp); if (ffp->seplist != NULL) { SafeShow (ffp->controlblock); SafeDisable (b); if (TextHasNoText (ffp->orgname)) { Select (ffp->orgname); } else { Select (ffp->seqname); } if (Fa2htgsFormOkay (ffp)) { SafeEnable (ffp->okBtn); } else { SafeDisable (ffp->okBtn); } } } } static EnumFieldAssocPtr MakePhrapAlists (SeqEntryPtr head) { EnumFieldAssocPtr alist = NULL; BioseqPtr bsp; Int2 count; Int2 j; SeqEntryPtr sep; SeqIdPtr sip; Char str [128]; if (head == NULL) return NULL; count = ValNodeLen (head); alist = MemNew (sizeof (EnumFieldAssoc) * (size_t) (count + 4)); if (alist == NULL) return NULL; j = 0; alist [j].name = StringSave (" "); alist [j].value = (UIEnum) 0; for (j = 1, sep = head; j <= count && sep != NULL; j++, sep = sep->next) { if (sep != NULL && sep->choice == 1 && sep->data.ptrvalue != NULL) { bsp = (BioseqPtr) sep->data.ptrvalue; sip = SeqIdFindWorst (bsp->id); SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str)); str [30] = '\0'; alist [j].name = StringSave (str); alist [j].value = (UIEnum) j; } } j = count + 1; alist [j].name = NULL; alist [j].value = (UIEnum) 0; return alist; } static void ReadAPhrapFile (ButtoN b) { PopuP control; Int2 count; Fa2htgsFormPtr ffp; FILE *fp; SeqEntryPtr head; Int2 i; Char path [PATH_MAX]; RecT r; TagListPtr tlp; ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; if (! GetInputFileName (path, sizeof (path), "", "TEXT")) return; if (! StringHasNoText (path)) { WatchCursor (); fp = FileOpen (path, "r"); if (fp != NULL) { head = ReadPhrapFile (fp); ffp->seplist = head; } FileClose (fp); tlp = (TagListPtr) GetObjectExtra (ffp->contigorder); if (tlp != NULL) { ffp->alists [0] = MakePhrapAlists (ffp->seplist); tlp->alists = ffp->alists; for (i = 0; i < tlp->rows; i++) { control = (PopuP) tlp->control [i * MAX_TAGLIST_COLS + 0]; if (control != NULL) { GetPosition (control, &r); Reset (control); InitEnumPopup (control, ffp->alists [0], NULL); SetEnumPopup (control, ffp->alists [0], 0); SetPosition (control, &r); } } count = ValNodeLen (ffp->seplist); for (i = 0; i < count; i++) { ValNodeCopyStr (&(tlp->vnp), 0, "0"); } tlp->max = MAX ((Int2) 0, (Int2) (count - tlp->rows)); CorrectBarMax (tlp->bar, tlp->max); CorrectBarPage (tlp->bar, tlp->rows - 1, tlp->rows - 1); } SafeShow (ffp->orderblock); SafeDisable (b); ArrowCursor (); } } static void PhrapOrderChosen (ButtoN b) { SeqEntryPtr PNTR collision; Int2 count; Fa2htgsFormPtr ffp; Int2 i; Int2 j; SeqEntryPtr lastsep; SeqEntryPtr nextsep; Boolean okay; SeqEntryPtr PNTR order; SeqEntryPtr sep; CharPtr str; TagListPtr tlp; int val; ValNodePtr vnp; /* Char contigs [256]; Char tmp [256]; BioseqPtr bsp; SeqIdPtr sip; Boolean notfirst; */ ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; tlp = (TagListPtr) GetObjectExtra (ffp->contigorder); if (tlp == NULL) return; count = ValNodeLen (tlp->vnp); order = MemNew (sizeof (SeqEntryPtr) * (count + 1)); if (order == NULL) return; collision = MemNew (sizeof (SeqEntryPtr) * (count + 1)); if (collision == NULL) return; okay = TRUE; for (i = 0, vnp = tlp->vnp; i < count && vnp != NULL; i++, vnp = vnp->next) { str = ExtractTagListColumn ((CharPtr) vnp->data.ptrvalue, 0); if (str != NULL && sscanf (str, "%d", &val) == 1 && val > 0) { val--; for (j = 0, sep = ffp->seplist; j < (Int2) val && sep != NULL; j++, sep = sep->next) continue; if (sep != NULL) { if (collision [j] != NULL) { okay = FALSE; } collision [j] = sep; order [i] = sep; } } MemFree (str); } if (! okay) { Message (MSG_ERROR, "You must not select a contig more than once"); MemFree (order); MemFree (collision); return; } okay = FALSE; for (i = 0; i < count; i++) { if (order [i] != NULL) { okay = TRUE; } } /* if no contigs selected, use all in order */ if (! okay) { for (j = 0, sep = ffp->seplist; j < count && sep != NULL; j++, sep = sep->next) { order [j] = sep; } okay = TRUE; } /* if (! okay) { Message (MSG_ERROR, "You must select at least one contig"); MemFree (order); MemFree (collision); return; } */ /* use spreadsheet to reorder ffp->seplist, delete unwanted items */ /* contigs [0] = '\0'; notfirst = FALSE; for (i = 0; i < count; i++) { if (order [i] != NULL) { sep = order [i]; bsp = (BioseqPtr) sep->data.ptrvalue; sip = SeqIdFindWorst (bsp->id); SeqIdWrite (sip, tmp, PRINTID_REPORT, sizeof (tmp)); if (notfirst) { StringCat (contigs, " "); } StringCat (contigs, tmp); notfirst = TRUE; } } ffp->seplist = SetPhrapContigOrder (ffp->seplist, contigs); */ for (i = 0; i < count; i++) { if (order [i] != NULL) { sep = ffp->seplist; lastsep = NULL; while (sep != NULL && sep != order [i]) { lastsep = sep; sep = sep->next; } if (sep != NULL) { if (lastsep != NULL) { lastsep->next = sep->next; sep->next = NULL; } else { ffp->seplist = sep->next; sep->next = NULL; } } } } sep = ffp->seplist; while (sep != NULL) { nextsep = sep->next; sep->next = NULL; SeqEntryFree (sep); sep = nextsep; } ffp->seplist = NULL; for (i = 0; i < count; i++) { if (order [i] != NULL) { ValNodeLink (&(ffp->seplist), order [i]); } } MemFree (order); MemFree (collision); SafeDisable (b); SafeHide (ffp->orderblock); SafeShow (ffp->controlblock); if (TextHasNoText (ffp->orgname)) { Select (ffp->orgname); } else { Select (ffp->seqname); } if (Fa2htgsFormOkay (ffp)) { SafeEnable (ffp->okBtn); } else { SafeDisable (ffp->okBtn); } } static void ReadContigFile (ButtoN b) { BioseqPtr bsp; Fa2htgsFormPtr ffp; FILE *fp; Boolean onMaster; Char path [PATH_MAX]; SeqEntryPtr sep = NULL; ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; if (! GetInputFileName (path, sizeof (path), "", "TEXT")) return; if (! StringHasNoText (path)) { WatchCursor (); fp = FileOpen (path, "r"); if (fp != NULL) { onMaster = (Boolean) (GetValue (ffp->contigtype) == 2); sep = ReadContigList (fp, onMaster); if (sep != NULL && sep->choice == 1) { ffp->seplist = sep; bsp = (BioseqPtr) sep->data.ptrvalue; SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, sep); } } FileClose (fp); ArrowCursor (); if (ffp->seplist != NULL) { SafeShow (ffp->controlblock); SafeDisable (b); SafeDisable (ffp->contigtype); if (TextHasNoText (ffp->orgname)) { Select (ffp->orgname); } else { Select (ffp->seqname); } if (Fa2htgsFormOkay (ffp)) { SafeEnable (ffp->okBtn); } else { SafeDisable (ffp->okBtn); } } } } static void AcceptFa2htgs (ButtoN b) { Fa2htgsFormPtr ffp; ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; Hide (ffp->form); Update (); if (ffp->finish != NULL) { ffp->finish (b); } SeqSubmitFree (ffp->ssp); SeqEntryFree (ffp->sep); Remove (ffp->form); } static void CancelFa2htgs (ButtoN b) { Fa2htgsFormPtr ffp; ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; Hide (ffp->form); Update (); if (ffp->cancel != NULL) { ffp->cancel (b); } SeqSubmitFree (ffp->ssp); SeqEntryFree (ffp->sep); Remove (ffp->form); } static void SetFa2htgsAcceptBtn (Handle control) { Fa2htgsFormPtr ffp; ffp = (Fa2htgsFormPtr) GetObjectExtra (control); if (ffp == NULL) return; if (Fa2htgsFormOkay (ffp)) { SafeEnable (ffp->okBtn); } else { SafeDisable (ffp->okBtn); } } static void SetFa2htgsUpdate (ButtoN b) { Fa2htgsFormPtr ffp; ffp = (Fa2htgsFormPtr) GetObjectExtra (b); if (ffp == NULL) return; if (GetStatus (b)) { SafeEnable (ffp->accession); } else { SafeDisable (ffp->accession); } SetFa2htgsAcceptBtn ((Handle) b); } static void CleanupGenomeCenterForm (GraphiC g, VoidPtr data) { Fa2htgsFormPtr ffp; SeqEntryPtr next; SeqEntryPtr sep; ffp = (Fa2htgsFormPtr) data; if (ffp != NULL) { sep = ffp->seplist; while (sep != NULL) { next = sep->next; sep->next = NULL; SeqEntryFree (sep); sep = next; } if (ffp->alists [0] != NULL) { FreeEnumFieldAlist (ffp->alists [0]); } } StdCleanupFormProc (g, data); } static CharPtr secaccstrings [] = {"Secondary", "Accessions", NULL}; static Uint2 contigorder_types [] = { TAGLIST_POPUP }; static ENUM_ALIST(contigdefault_alist) {" ", 0}, END_ENUM_ALIST static EnumFieldAssocPtr contigdefault_alists [] = { contigdefault_alist }; extern DialoG CreateTagListDialogEx (GrouP h, Uint2 rows, Uint2 cols, Int2 spacing, Uint2Ptr types, Uint2Ptr textWidths, EnumFieldAssocPtr PNTR alists, Boolean useBar, Boolean noExtend, ToDialogFunc tofunc, FromDialogFunc fromfunc); extern ForM CreateGenomeCenterForm (Int2 left, Int2 top, CharPtr title, BtnActnProc finish, BtnActnProc cancel, Boolean readPhrap, Boolean buildContig, WndActnProc activateForm) { ButtoN b; GrouP c; Fa2htgsFormPtr ffp; GrouP g; GrouP h; PrompT ppt; GrouP q; GrouP sa; StdEditorProcsPtr sepp; WindoW w; Int2 wid; GrouP x; GrouP y; ffp = (Fa2htgsFormPtr) MemNew (sizeof (Fa2htgsForm)); if (ffp == NULL) return NULL; ffp->finish = finish; ffp->cancel = cancel; ffp->readPhrap = readPhrap; ffp->buildContig = buildContig; w = FixedWindow (left, top, -10, -10, title, NULL); if (w == NULL) return NULL; SetObjectExtra (w, ffp, CleanupGenomeCenterForm); ffp->form = (ForM) w; ffp->toform = NULL; ffp->fromform = Fa2htgsToSeqSubmitPtr; ffp->formmessage = Fa2htgsFormMessage; ffp->ssp = NULL; ffp->sep = NULL; ffp->seplist = NULL; ffp->alists [0] = NULL; #ifndef WIN_MAC CreateFa2htgsFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { ffp->appmessage = sepp->handleMessages; } SetGroupSpacing (w, 10, 10); h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); ffp->templateblock = HiddenGroup (h, -1, 0, NULL); b = PushButton (ffp->templateblock, "Read Seq-submit Template", ReadTemplate); SetObjectExtra (b, ffp, NULL); ffp->fastablock = HiddenGroup (h, -1, 0, NULL); if (readPhrap) { b = PushButton (ffp->fastablock, "Read PHRAP File", ReadAPhrapFile); } else if (buildContig) { SetGroupSpacing (ffp->fastablock, 10, 10); y = HiddenGroup (ffp->fastablock, 1, 0, NULL); StaticPrompt (y, "Coordinates are on", 0, stdLineHeight, programFont, 'c'); ffp->contigtype = HiddenGroup (y, 3, 0, NULL); RadioButton (ffp->contigtype, "Individual Accessions"); RadioButton (ffp->contigtype, "Master Sequence"); SetValue (ffp->contigtype, 1); b = PushButton (ffp->fastablock, "Read CONTIG Instructions", ReadContigFile); AlignObjects (ALIGN_CENTER, (HANDLE) y, (HANDLE) b, NULL); } else { b = PushButton (ffp->fastablock, "Read FASTA File", ReadFastaHtgsFile); } SetObjectExtra (b, ffp, NULL); Hide (ffp->fastablock); x = HiddenGroup (h, 0, 0, NULL); ffp->orderblock = HiddenGroup (x, -1, 0, NULL); SetGroupSpacing (ffp->orderblock, 5, 5); ppt = StaticPrompt (ffp->orderblock, "Enter contigs in desired order", 0, 0, programFont, 'c'); ffp->contigorder = CreateTagListDialogEx (ffp->orderblock, 8, 1, 2, contigorder_types, NULL, contigdefault_alists, TRUE, TRUE, NULL, NULL); b = PushButton (ffp->orderblock, "Proceed", PhrapOrderChosen); SetObjectExtra (b, ffp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) ppt, (HANDLE) ffp->contigorder, (HANDLE) b, NULL); Hide (ffp->orderblock); ffp->controlblock = HiddenGroup (x, -1, 0, NULL); g = HiddenGroup (ffp->controlblock, 2, 0, NULL); ffp->htgsphase = NULL; if (! buildContig) { StaticPrompt (g, "Phase", 0, stdLineHeight, programFont, 'l'); ffp->htgsphase = HiddenGroup (g, 4, 0, (GrpActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->htgsphase, ffp, NULL); RadioButton (ffp->htgsphase, "HTGS-0"); RadioButton (ffp->htgsphase, "HTGS-1"); RadioButton (ffp->htgsphase, "HTGS-2"); RadioButton (ffp->htgsphase, "HTGS-3"); StaticPrompt (g, "HTGS_", 0, stdLineHeight, programFont, 'l'); q = HiddenGroup (g, 3, 0, NULL); ffp->draft = CheckBox (q, "Draft", NULL); ffp->fulltop = CheckBox (q, "Fulltop", NULL); ffp->activefin = CheckBox (q, "Activefin", NULL); } StaticPrompt (g, "Organism", 0, dialogTextHeight, programFont, 'l'); ffp->orgname = DialogText (g, "", 10, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->orgname, ffp, NULL); StaticPrompt (g, "Sequence name", 0, dialogTextHeight, programFont, 'l'); ffp->seqname = DialogText (g, "", 10, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->seqname, ffp, NULL); StaticPrompt (g, "Length", 0, dialogTextHeight, programFont, 'l'); ffp->knownlength = DialogText (g, "", 10, NULL); SetObjectExtra (ffp->knownlength, ffp, NULL); StaticPrompt (g, "Gap Length", 0, dialogTextHeight, programFont, 'l'); ffp->gaplength = DialogText (g, "100", 10, NULL); SetObjectExtra (ffp->gaplength, ffp, NULL); ffp->update = CheckBox (g, "Update", SetFa2htgsUpdate); SetObjectExtra (ffp->update, ffp, NULL); ffp->accession = DialogText (g, "", 10, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->accession, ffp, NULL); Disable (ffp->accession); StaticPrompt (g, "Chromosome", 0, dialogTextHeight, programFont, 'l'); ffp->chromosome = DialogText (g, "", 10, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->chromosome, ffp, NULL); StaticPrompt (g, "Clone", 0, dialogTextHeight, programFont, 'l'); ffp->clone = DialogText (g, "", 10, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->clone, ffp, NULL); StaticPrompt (g, "Strain", 0, dialogTextHeight, programFont, 'l'); ffp->strain = DialogText (g, "", 10, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->strain, ffp, NULL); wid = MaxStringWidths (secaccstrings) + 2; sa = MultiLinePrompt (g, "Secondary Accessions", wid, programFont); ffp->secondaries = CreateVisibleStringDialog (g, 3, -1, 15); AlignObjects (ALIGN_MIDDLE, (HANDLE) sa, (HANDLE) ffp->secondaries, NULL); q = HiddenGroup (ffp->controlblock, 1, 0, NULL); StaticPrompt (q, "Title", 0, 0, programFont, 'c'); ffp->title = ScrollText (q, 20, 4, programFont, TRUE, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->title, ffp, NULL); StaticPrompt (q, "Remark", 0, 0, programFont, 'c'); ffp->remark = ScrollText (q, 20, 4, programFont, TRUE, (TxtActnProc) SetFa2htgsAcceptBtn); SetObjectExtra (ffp->remark, ffp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) q, NULL); Hide (ffp->controlblock); c = HiddenGroup (h, 2, 0, NULL); ffp->okBtn = PushButton (c, "Accept", AcceptFa2htgs); SetObjectExtra (ffp->okBtn, ffp, NULL); Disable (ffp->okBtn); b = PushButton (c, "Cancel", CancelFa2htgs); SetObjectExtra (b, ffp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) ffp->templateblock, (HANDLE) ffp->fastablock, (HANDLE) ffp->orderblock, (HANDLE) ffp->controlblock, (HANDLE) c, NULL); RealizeWindow (w); if (activateForm != NULL) { SetActivate (w, activateForm); } Show (w); Select (w); Select (ffp->orgname); return (ForM) w; } typedef struct convcdsdata { FEATURE_FORM_BLOCK SeqEntryPtr sep; TexT geneName; TexT protName; TexT featcomment; ButtoN retain; Uint2 subtype; Int2 errcount; Char findThis [128]; SeqLocPtr slp; SeqEntryPtr nsep; ObjMgrPtr omp; ObjMgrTypePtr omtp; } ConvCdsData, PNTR ConvCdsPtr; static Boolean CollectCDSAncestorGatherFunc (GatherContextPtr gcp) { BioseqPtr bsp; ConvCdsPtr ccp; Boolean noLeft; Boolean noRight; ObjMgrTypePtr omtp; SeqEntryPtr sep; SeqFeatPtr sfp; SeqLocPtr slp; Uint2 subtype; if (gcp == NULL) return TRUE; ccp = (ConvCdsPtr) gcp->userdata; if (ccp == NULL ) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; omtp = ccp->omtp; if (omtp == NULL || omtp->subtypefunc == NULL) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; subtype = (*(omtp->subtypefunc)) ((Pointer) sfp); if (subtype != ccp->subtype) return TRUE; bsp = GetBioseqGivenSeqLoc (sfp->location, gcp->entityID); if (bsp == NULL) return TRUE; if (ISA_aa (bsp->mol)) return TRUE; if (bsp->repr != Seq_repr_seg) { sep = ccp->nsep; if (sep == NULL || sep->choice != 1) return TRUE; bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return TRUE; } CheckSeqLocForPartial (sfp->location, &noLeft, &noRight); slp = SeqLocMerge (bsp, sfp->location, ccp->slp, FALSE, TRUE, FALSE); if (slp == NULL) return TRUE; SetSeqLocPartial (slp, noLeft, noRight); ccp->slp = SeqLocFree (ccp->slp); ccp->slp = slp; return TRUE; } static void FinishConvertingToCDS (SeqEntryPtr sep, Uint2 entityID, ConvCdsPtr ccp) { ByteStorePtr bs; BioseqPtr bsp; Char ch; CdRegionPtr crp; ValNodePtr descr; Uint1 frame; Int2 genCode; Int2 i; Int4 len; Int4 lens [4]; Int4 max; Boolean noLeft; Boolean noRight; MolInfoPtr mip; SeqEntryPtr nsep; SeqEntryPtr old; CharPtr prot; ProtRefPtr prp; SeqEntryPtr psep; CharPtr ptr; SeqFeatPtr sfp; Char str [128]; ValNodePtr vnp; if (sep == NULL || ccp == NULL) return; genCode = SeqEntryToGeneticCode (sep, NULL, NULL, 0); crp = CreateNewCdRgn (1, FALSE, genCode); if (crp == NULL) return; sfp = CreateNewFeature (ccp->nsep, NULL, SEQFEAT_CDREGION, NULL); if (sfp == NULL) { CdRegionFree (crp); return; } sfp->data.value.ptrvalue = (Pointer) crp; sfp->location = SeqLocFree (sfp->location); sfp->location = AsnIoMemCopy ((Pointer) ccp->slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); CheckSeqLocForPartial (sfp->location, &noLeft, &noRight); sfp->partial = (sfp->partial || noLeft || noRight); if (! TextHasNoText (ccp->featcomment)) { sfp->comment = SaveStringFromTextAndStripNewlines (ccp->featcomment); } max = 0; frame = 0; for (i = 1; i <= 3; i++) { crp->frame = (Uint1) i; bs = ProteinFromCdRegionEx (sfp, FALSE, FALSE); len = BSLen (bs); BSFree (bs); lens [i] = len; if (len > max) { max = len; frame = (Uint1) i; } } for (i = 1; i <= 3; i++) { if (lens [i] == max && i != frame) { (ccp->errcount)++; } } crp->frame = frame; bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE); if (bs == NULL) return; prot = BSMerge (bs, NULL); bs = BSFree (bs); if (prot == NULL) return; ptr = prot; ch = *ptr; while (ch != '\0') { *ptr = TO_UPPER (ch); ptr++; ch = *ptr; } i = (Int2) StringLen (prot); if (i > 0 && prot [i - 1] == '*') { prot [i - 1] = '\0'; } bs = BSNew (1000); if (bs != NULL) { ptr = prot; /* if (prot [0] == '-') { ptr++; } */ BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr)); } MemFree (prot); if (bs == NULL) return; bsp = BioseqNew (); if (bsp == NULL) return; bsp->repr = Seq_repr_raw; bsp->mol = Seq_mol_aa; bsp->seq_data_type = Seq_code_ncbieaa; bsp->seq_data = bs; bsp->length = BSLen (bs); bs = NULL; old = SeqEntrySetScope (sep); bsp->id = MakeNewProteinSeqId (sfp->location, NULL); SeqMgrAddToBioseqIndex (bsp); SeqEntrySetScope (old); psep = SeqEntryNew (); if (psep != NULL) { psep->choice = 1; psep->data.ptrvalue = (Pointer) bsp; SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) bsp, psep); mip = MolInfoNew (); if (mip != NULL) { mip->biomol = 8; mip->tech = 8; if (noLeft && noRight) { mip->completeness = 5; } else if (noLeft) { mip->completeness = 3; } else if (noRight) { mip->completeness = 4; } vnp = CreateNewDescriptor (psep, Seq_descr_molinfo); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) mip; } } descr = ExtractBioSourceAndPubs (sep); /* AddSeqEntryToSeqEntry (sep, psep, FALSE); */ AddSeqEntryToSeqEntry (sep, psep, TRUE); nsep = FindNucSeqEntry (sep); ReplaceBioSourceAndPubs (sep, descr); SetSeqFeatProduct (sfp, bsp); GetTitle (ccp->protName, str, sizeof (str)); if (! StringHasNoText (str)) { prp = CreateNewProtRef (str, NULL, NULL, NULL); if (prp != NULL) { sfp = CreateNewFeature (psep, NULL, SEQFEAT_PROT, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) prp; SetSeqLocPartial (sfp->location, noLeft, noRight); sfp->partial = (sfp->partial || noLeft || noRight); } } } } } static void RemoveCDSAncestorCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; ConvCdsPtr ccp; SeqAnnotPtr nextsap; SeqFeatPtr nextsfp; ObjMgrTypePtr omtp; Pointer PNTR prevsap; Pointer PNTR prevsfp; SeqAnnotPtr sap; SeqFeatPtr sfp; Uint2 subtype; if (sep == NULL || sep->data.ptrvalue == NULL) return; ccp = (ConvCdsPtr) mydata; if (ccp == NULL) return; omtp = ccp->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; 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 == ccp->subtype) { *(prevsfp) = sfp->next; sfp->next = NULL; SeqFeatFree (sfp); } 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; } } static void ConvertToCDSCallback (SeqEntryPtr sep, Uint2 entityID, ConvCdsPtr ccp) { BioseqPtr bsp; BioseqSetPtr bssp; GeneRefPtr grp; GatherScope gs; SeqLocPtr gslp; Boolean hasNulls; Boolean noLeft; Boolean noRight; SeqEntryPtr nsep; SeqFeatPtr sfp; SeqIdPtr sip; SeqLocPtr slp; Char str [128]; if (sep == NULL || ccp == 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) { ConvertToCDSCallback (sep, entityID, ccp); } return; } } ccp->nsep = FindNucSeqEntry (sep); if (ccp->nsep == NULL) 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; ccp->slp = NULL; GatherEntity (entityID, (Pointer) ccp, CollectCDSAncestorGatherFunc, &gs); if (ccp->slp != NULL) { CheckSeqLocForPartial (ccp->slp, &noLeft, &noRight); sip = SeqLocId (ccp->slp); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL && ISA_na (bsp->mol)) { slp = SegLocToParts (bsp, ccp->slp); if (slp != NULL) { ccp->slp = SeqLocFree (ccp->slp); ccp->slp = slp; FreeAllFuzz (ccp->slp); SetSeqLocPartial (ccp->slp, noLeft, noRight); } } } FinishConvertingToCDS (sep, entityID, ccp); nsep = FindNucSeqEntry (sep); GetTitle (ccp->geneName, str, sizeof (str)); if (! StringHasNoText (str)) { grp = CreateNewGeneRef (str, NULL, NULL, FALSE); if (grp != NULL) { if (ExtendGene (grp, nsep, ccp->slp)) { grp = GeneRefFree (grp); } else { sfp = CreateNewFeature (nsep, NULL, SEQFEAT_GENE, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) grp; sfp->location = SeqLocFree (sfp->location); sfp->location = AsnIoMemCopy ((Pointer) ccp->slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); sip = SeqLocId (sfp->location); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL) { gslp = SeqLocMerge (bsp, sfp->location, NULL, TRUE, FALSE, FALSE); if (gslp != NULL) { sfp->location = SeqLocFree (sfp->location); sfp->location = gslp; if (bsp->repr == Seq_repr_seg) { gslp = SegLocToPartsEx (bsp, sfp->location, TRUE); sfp->location = SeqLocFree (sfp->location); sfp->location = gslp; hasNulls = LocationHasNullsBetween (sfp->location); sfp->partial = (sfp->partial || hasNulls); } FreeAllFuzz (gslp); SetSeqLocPartial (sfp->location, noLeft, noRight); sfp->partial = (sfp->partial || noLeft || noRight); } } } } } } } } ccp->slp = SeqLocFree (ccp->slp); } static void DoConvertToCDS (ButtoN b) { ConvCdsPtr ccp; CharPtr plural; Char str [128]; ccp = GetObjectExtra (b); if (ccp == NULL) { Remove (ParentWindow (b)); return; } GetTitle (ccp->protName, str, sizeof (str)); if (StringHasNoText (str)) { Message (MSG_OK, "Protein name is required"); return; } Hide (ccp->form); WatchCursor (); ccp->omp = ObjMgrGet (); if (ccp->omp != NULL) { ccp->omtp = ObjMgrTypeFind (ccp->omp, OBJ_SEQFEAT, NULL, NULL); if (ccp->omtp != NULL && ccp->omtp->subtypefunc != NULL) { ConvertToCDSCallback (ccp->sep, ccp->input_entityID, ccp); if (! GetStatus (ccp->retain)) { SeqEntryExplore (ccp->sep, (Pointer) ccp, RemoveCDSAncestorCallback); } } } ArrowCursor (); Update (); if (ccp->errcount > 0) { if (ccp->errcount > 1) { plural = "records"; } else { plural = "record"; } Message (MSG_ERROR, "Possible ambiguous frames detected in %d %s", (int) ccp->errcount, plural); } ObjMgrSetDirtyFlag (ccp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, ccp->input_entityID, 0, 0); Remove (ccp->form); Update (); } extern void PrepareToConvertToCDS (SeqEntryPtr sep, Uint2 entityID, Uint2 subtype, CharPtr findthis) { ButtoN b; GrouP c; ConvCdsPtr ccp; GrouP g; GrouP h; StdEditorProcsPtr sepp; WindoW w; if (sep == NULL || entityID == 0 || subtype == 0) return; ccp = (ConvCdsPtr) MemNew (sizeof (ConvCdsData)); if (ccp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Convert to CDS", StdCloseWindowProc); SetObjectExtra (w, ccp, StdCleanupFormProc); ccp->form = (ForM) w; ccp->formmessage = DefaultMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); ccp->appmessage = sepp->handleMessages; } ccp->input_entityID = entityID; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); ccp->sep = sep; ccp->subtype = subtype; StringNCpy_0 (ccp->findThis, findthis, sizeof (ccp->findThis)); ccp->errcount = 0; g = HiddenGroup (h, 2, 0, NULL); StaticPrompt (g, "Gene Symbol", 0, dialogTextHeight, programFont, 'l'); ccp->geneName = DialogText (g, "", 20, NULL); StaticPrompt (g, "Protein Name", 0, dialogTextHeight, programFont, 'l'); ccp->protName = DialogText (g, "", 20, NULL); StaticPrompt (g, "Comment", 0, 4 * Nlm_stdLineHeight, programFont, 'l'); ccp->featcomment = ScrollText (g, 20, 4, programFont, TRUE, NULL); ccp->retain = CheckBox (h, "Retain original features", NULL); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoConvertToCDS); SetObjectExtra (b, ccp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, (HANDLE) ccp->retain, NULL); RealizeWindow (w); Show (w); Select (ccp->geneName); Update (); } typedef struct alignform { FORM_MESSAGE_BLOCK DoC doc; } AlignForm, PNTR AlignFormPtr; static ParData bioseqParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData bioseqColFmt [] = { {0, 5, 0, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE} }; static ParData annotParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData annotColFmt [] = { {0, 10, 0, 0, NULL, 'l', FALSE, FALSE, FALSE, FALSE, TRUE} }; static ParData alignParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData alignColFmt [] = { {0, 15, 0, 0, NULL, 'l', FALSE, FALSE, FALSE, FALSE, FALSE}, {0, 5, 0, 0, NULL, 'l', FALSE, FALSE, FALSE, FALSE, FALSE}, {0, 0, 0, 0, NULL, 'l', FALSE, FALSE, FALSE, FALSE, TRUE} }; static Boolean AlignFormPopulateProc (GatherContextPtr gcp) { AlignFormPtr afp; SeqAlignPtr align; Char annotDB [32]; Uint1 annot_type; BioseqContextPtr bcp; BioseqPtr bsp; DenseDiagPtr ddp; DenseSegPtr dsp; ProtRefPtr prp; CharPtr ptr; SeqAnnotPtr sap; SeqEntryPtr sep; SeqFeatPtr sfp; SeqIdPtr sip; StdSegPtr ssp; Char str [256]; Char tmp [128]; if (gcp == NULL) return TRUE; afp = (AlignFormPtr) gcp->userdata; if (afp == NULL ) return TRUE; switch (gcp->thistype) { case OBJ_BIOSEQ : bsp = (BioseqPtr) gcp->thisitem; if (bsp != NULL) { SeqIdWrite (bsp->id, str, PRINTID_REPORT, sizeof (str)); bcp = BioseqContextNew (bsp); sfp = BioseqContextGetSeqFeat (bcp, SEQFEAT_PROT, NULL, NULL, 0); BioseqContextFree (bcp); if (sfp != NULL) { prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp != NULL) { if (prp->name != NULL && (! StringHasNoText (prp->name->data.ptrvalue))) { StringCat (str, " ("); StringCat (str, (CharPtr) prp->name->data.ptrvalue); StringCat (str, ")"); } else if (! StringHasNoText (prp->desc)) { StringCat (str, " ("); StringCat (str, (CharPtr) prp->desc); StringCat (str, ")"); } } } StringCat (str, ":\n"); AppendText (afp->doc, str, &bioseqParFmt, bioseqColFmt, programFont); } break; case OBJ_SEQANNOT : sap = (SeqAnnotPtr) gcp->thisitem; if (sap != NULL && sap->type == 2) { get_align_annot_qual (sap, annotDB, sizeof (annotDB), &annot_type); if (annot_type == ANNOT_BLAST) { StringCpy (str, annotDB); StringCat (str, ":\n"); AppendText (afp->doc, str, &annotParFmt, annotColFmt, programFont); } } break; case OBJ_SEQALIGN : case OBJ_SEQHIST_ALIGN : align = (SeqAlignPtr) gcp->thisitem; sip = NULL; if (align->segtype == 1) { ddp = (DenseDiagPtr) align->segs; if (ddp != NULL) { for (sip = ddp->id; sip != NULL && sip->next != NULL; sip = sip->next) { } } } else if (align->segtype == 2) { dsp = (DenseSegPtr) align->segs; if (dsp != NULL) { for (sip = dsp->ids; sip != NULL && sip->next != NULL; sip = sip->next) { } } } else if (align->segtype == 3) { ssp = (StdSegPtr) align->segs; if (ssp != NULL) { for (sip = ssp->ids; sip != NULL && sip->next != NULL; sip = sip->next) { } } } if (sip != NULL) { bsp = BioseqLockById (sip); if (bsp != NULL) { /* SeqIdWrite (bsp->id, str, PRINTID_FASTA_LONG, sizeof (str)); */ SeqIdWrite (bsp->id, str, PRINTID_REPORT, sizeof (str)); StringNCpy_0 (tmp, BioseqGetTitle (bsp), sizeof (tmp)); StringCat (str, "\t"); if (! StringHasNoText (tmp)) { StringCat (str, tmp); } tmp [0] = '\0'; sep = SeqMgrGetSeqEntryForData (bsp); if (sep != NULL) { SeqEntryToBioSource (sep, NULL, tmp, sizeof (tmp), NULL); if (! StringHasNoText (tmp)) { ptr = StringStr (tmp, "("); if (ptr != NULL) { *ptr = '\0'; } StringCat (str, " ["); StringCat (str, tmp); StringCat (str, "]"); } } StringCat (str, "\t"); sprintf (tmp, "%d %d %d", (int) gcp->entityID, (int) gcp->itemID, (int) gcp->thistype); StringCat (str, tmp); StringCat (str, "\n"); AppendText (afp->doc, str, &alignParFmt, alignColFmt, programFont); } BioseqUnlock (bsp); } return TRUE; default : break; } return TRUE; } static void PopulateAlignForm (ForM f, SeqEntryPtr sep) { AlignFormPtr afp; GatherScope gs; RecT r; Int2 width; if (f == NULL || sep == NULL) return; afp = (AlignFormPtr) GetObjectExtra (f); if (afp == NULL) return; Reset (afp->doc); SetDocAutoAdjust (afp->doc, FALSE); ObjectRect (afp->doc, &r); InsetRect (&r, 4, 4); width = r.right - r.left; alignColFmt [0].pixWidth = width / 5; alignColFmt [1].pixWidth = width - alignColFmt [0].pixWidth; bioseqColFmt [0].pixWidth = width; annotColFmt [0].pixWidth = width; 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_SEQALIGN] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQHIST] = FALSE; gs.ignore[OBJ_SEQHIST_ALIGN] = FALSE; gs.scope = sep; GatherEntity (afp->input_entityID, (Pointer) afp, AlignFormPopulateProc, &gs); AdjustDocScroll (afp->doc); } static void AlignMessageProc (ForM f, Int2 mssg) { FILE *fp; AlignFormPtr afp; Char path [PATH_MAX]; afp = (AlignFormPtr) GetObjectExtra (f); if (afp != NULL) { switch (mssg) { case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_PRINT : PrintDocument (afp->doc); break; case VIB_MSG_EXPORT : if (GetOutputFileName (path, sizeof (path), "align.txt")) { WatchCursor (); #ifdef WIN_MAC fp = FileOpen (path, "r"); if (fp != NULL) { FileClose (fp); } else { FileCreate (path, "TEXT", "ttxt"); } #endif fp = FileOpen (path, "w"); if (fp != NULL) { SaveDocument (afp->doc, fp); FileClose (fp); } ArrowCursor (); } break; default : if (afp->appmessage != NULL) { afp->appmessage (f, mssg); } break; } } } static void AlignFormActivate (WindoW w) { AlignFormPtr afp; IteM exportItm; IteM printItm; afp = (AlignFormPtr) GetObjectExtra (w); #ifdef WIN_MAC currentFormDataPtr = (VoidPtr) afp; #endif if (afp != NULL) { if (afp->activate != NULL) { afp->activate (w); } exportItm = FindFormMenuItem ((BaseFormPtr) afp, VIB_MSG_EXPORT); SafeSetTitle (exportItm, "Export Align Summary..."); SafeEnable (exportItm); printItm = FindFormMenuItem ((BaseFormPtr) afp, VIB_MSG_PRINT); SafeEnable (printItm); } } static void AlignNotifyProc (DoC d, Int2 item, Int2 row, Int2 col, Boolean dblClick) { unsigned int entityID; unsigned int itemID; unsigned int itemtype; CharPtr txt; if (d == NULL || item < 1 || row < 1 || col < 1) return; txt = GetDocText (d, item, row, 3); if (! StringHasNoText (txt)) { if (sscanf (txt, "%u %u %u", &entityID, &itemID, &itemtype) == 3) { if (shftKey) { ObjMgrAlsoSelect (entityID, itemID, itemtype, 0, NULL); } else { ObjMgrSelect (entityID, itemID, itemtype, 0, NULL); } } } MemFree (txt); } static ForM CreateAlignForm (Uint2 entityID) { AlignFormPtr afp; GrouP c; GrouP h; StdEditorProcsPtr sepp; WindoW w; #ifndef WIN_MAC MenU m; #endif w = NULL; afp = MemNew (sizeof (AlignForm)); if (afp != NULL) { w = FixedWindow (-50, -33, -10, -10, "Alignment Summary", StdCloseWindowProc); SetObjectExtra (w, afp, StdCleanupFormProc); afp->form = (ForM) w; afp->formmessage = AlignMessageProc; afp->input_entityID = entityID; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { afp->appmessage = sepp->handleMessages; } #ifndef WIN_MAC m = PulldownMenu (w, "File"); FormCommandItem (m, "Close", (BaseFormPtr) afp, VIB_MSG_CLOSE); SeparatorItem (m); FormCommandItem (m, "Export...", (BaseFormPtr) afp, VIB_MSG_EXPORT); SeparatorItem (m); FormCommandItem (m, "Print...", (BaseFormPtr) afp, VIB_MSG_PRINT); #endif h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); afp->doc = DocumentPanel (h, 35 * stdCharWidth, 20 * stdLineHeight); SetObjectExtra (afp->doc, afp, NULL); SetDocNotify (afp->doc, AlignNotifyProc); c = HiddenGroup (w, 4, 0, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) afp->doc, (HANDLE) c, NULL); RealizeWindow (w); SetActivate (w, AlignFormActivate); } return (ForM) w; } extern void ViewAlignmentSummary (IteM i) { BaseFormPtr bfp; ForM f; SeqEntryPtr sep; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL || bfp->input_entityID == 0) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; WatchCursor (); Update (); f = CreateAlignForm (bfp->input_entityID); PopulateAlignForm (f, sep); ArrowCursor (); Update (); Show (f); Select (f); } #define REMOVE_CDSET 1 #define CONVERT_CDSET 2 #define EDIT_CDSET 3 #define ADD_CDSET 4 static ENUM_ALIST(cds_gene_prot_field_alist) {" ", 0}, {"CDS comment", 1}, {"Gene locus", 2}, {"Gene description", 3}, {"Gene allele", 4}, {"Gene maploc", 5}, {"Gene synonym", 6}, {"Gene comment", 7}, {"Protein name", 8}, {"Protein description", 9}, {"Protein E.C. number", 10}, {"Protein activity", 11}, {"Protein comment", 12}, END_ENUM_ALIST static ENUM_ALIST(prot_subtype_alist) {" ", 5}, {"Product", 0}, {"Pre-protein", 1}, {"Mature", 2}, {"Signal peptide", 3}, {"Transit peptide", 4}, END_ENUM_ALIST typedef struct cdsetformdata { FEATURE_FORM_BLOCK Int2 type; PopuP fromfield; PopuP tofield; PrompT example; ButtoN leaveOn; Int2 fromval; Int2 toval; Boolean onlyGene; Boolean onlyProt; Boolean replaceOldAsked; Boolean doReplaceAll; TexT findthis; TexT replacewith; CharPtr findStr; CharPtr replaceStr; Char temp [128]; PopuP protSubType; GrouP protSubGrp; } CdsetFormData, PNTR CdsetFormPtr; typedef struct geneprotfind { SeqFeatPtr cds; SeqFeatPtr gene; SeqFeatPtr prot; SeqLocPtr location; SeqLocPtr product; Int4 mingene; Int4 minprot; } GeneProtFind, PNTR GeneProtPtr; static Boolean GeneProtFindFunc (GatherContextPtr gcp) { Int4 diff; GeneProtPtr gpp; SeqFeatPtr sfp; if (gcp == NULL) return TRUE; gpp = (GeneProtPtr) gcp->userdata; if (gpp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.value.ptrvalue == NULL) return TRUE; if (sfp->data.choice == SEQFEAT_GENE && gpp->location != NULL) { diff = SeqLocAinB (gpp->location, sfp->location); if (diff >= 0) { if (diff < gpp->mingene) { gpp->gene = sfp; gpp->mingene = diff; } } } else if (sfp->data.choice == SEQFEAT_PROT && gpp->product != NULL) { diff = SeqLocAinB (gpp->product, sfp->location); if (diff >= 0) { if (diff < gpp->minprot) { gpp->prot = sfp; gpp->minprot = diff; } } } return TRUE; } void FindGeneAndProtForCDS (Uint2 entityID, SeqFeatPtr cds, SeqFeatPtr PNTR gene, SeqFeatPtr PNTR prot) { GeneProtFind gpf; GatherScope gs; if (gene != NULL) { *gene = NULL; } if (prot != NULL) { *prot = NULL; } if (entityID == 0 || cds == NULL) return; MemSet ((Pointer) (&gpf), 0, sizeof (GeneProtFind)); gpf.cds = cds; gpf.gene = NULL; gpf.prot = NULL; gpf.location = cds->location; gpf.product = cds->product; gpf.mingene = INT4_MAX; gpf.minprot = INT4_MAX; 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 (entityID, (Pointer) &gpf, GeneProtFindFunc, &gs); if (gene != NULL) { *gene = gpf.gene; } if (prot != NULL) { *prot = gpf.prot; } } static Boolean ShouldReplaceString (CdsetFormPtr cfp) { MsgAnswer ans; if (cfp == NULL) return FALSE; if (cfp->type == EDIT_CDSET) { cfp->doReplaceAll = TRUE; cfp->replaceOldAsked = TRUE; } if (! cfp->replaceOldAsked) { cfp->replaceOldAsked = TRUE; ArrowCursor (); ans = Message (MSG_YN, "Do you wish to overwrite existing contents?"); WatchCursor (); Update (); cfp->doReplaceAll = (Boolean) (ans == ANS_YES); } return cfp->doReplaceAll; } static CharPtr SaveOrReplaceString (CdsetFormPtr cfp, CharPtr str, CharPtr current) { size_t len; CharPtr tmp; if (cfp == NULL) return str; if (StringHasNoText (str) && cfp->type != EDIT_CDSET) return current; if (current != NULL) { if (ShouldReplaceString (cfp)) { MemFree (current); } else { len = StringLen (str) + StringLen (current) + 4; tmp = MemNew (len); if (tmp != NULL) { StringCpy (tmp, current); StringCat (tmp, "; "); StringCat (tmp, str); MemFree (str); MemFree (current); return tmp; } } } return str; } static void EditCdsetString (CharPtr PNTR strptr, CdsetFormPtr cfp, CharPtr foundit) { size_t diff; size_t foundlen; size_t replen; CharPtr newstring; CharPtr tmp; CharPtr tmp2; if (cfp == NULL || strptr == NULL || foundit == NULL) return; foundlen = StringLen (cfp->findStr); replen = StringLen (cfp->replaceStr); if (replen > foundlen) { diff = replen - foundlen; } else { diff = foundlen - replen; } newstring = MemNew (StringLen (*strptr) + diff + 1); tmp = *strptr; tmp2 = newstring; while (tmp != foundit) { *tmp2 = *tmp; tmp++; tmp2++; } if (cfp->replaceStr != NULL) { tmp2 = MemCopy (tmp2, cfp->replaceStr, replen); } tmp2 += replen; tmp += foundlen; tmp2 = StringMove (tmp2, tmp); *strptr = MemFree (*strptr); *strptr = newstring; } static Boolean ProcessEachCDSFunc (GatherContextPtr gcp) { SeqFeatPtr cds; CdsetFormPtr cfp; CharPtr foundit; SeqFeatPtr gene; GeneRefPtr grp; SeqFeatPtr prot; ProtRefPtr prp; SeqFeatPtr sfp; CharPtr str; UIEnum val; ValNodePtr vnp; if (gcp == NULL) return TRUE; cfp = (CdsetFormPtr) gcp->userdata; if (cfp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.value.ptrvalue == NULL) return TRUE; cds = NULL; gene = NULL; grp = NULL; prot = NULL; prp = NULL; if (cfp->onlyGene) { if (sfp->data.choice == SEQFEAT_GENE) { gene = sfp; grp = (GeneRefPtr) gene->data.value.ptrvalue; } else return TRUE; } else if (cfp->onlyProt) { if (sfp->data.choice == SEQFEAT_PROT) { prot = sfp; prp = (ProtRefPtr) prot->data.value.ptrvalue; } else return TRUE; } else if (sfp->data.choice == SEQFEAT_CDREGION) { cds = sfp; FindGeneAndProtForCDS (cfp->input_entityID, cds, &gene, &prot); if (gene != NULL) { grp = (GeneRefPtr) gene->data.value.ptrvalue; } if (prot != NULL) { prp = (ProtRefPtr) prot->data.value.ptrvalue; } } else return TRUE; if (cfp->protSubType != NULL && prot != NULL && prp != NULL) { if (GetEnumPopup (cfp->protSubType, prot_subtype_alist, &val)) { if (val < 5 && (Uint1) val != prp->processed) { prot = NULL; prp = NULL; } } } str = NULL; switch (cfp->type) { case REMOVE_CDSET : break; case ADD_CDSET : str = StringSave (cfp->findStr); break; case EDIT_CDSET : case CONVERT_CDSET : switch (cfp->fromval) { case 1 : if (cds != NULL) { str = StringSave (cds->comment); } break; case 2 : if (grp != NULL) { str = StringSave (grp->locus); } break; case 3 : if (grp != NULL) { str = StringSave (grp->desc); } break; case 4 : if (grp != NULL) { str = StringSave (grp->allele); } break; case 5 : if (grp != NULL) { str = StringSave (grp->maploc); } break; case 6 : if (grp != NULL) { vnp = grp->syn; if (vnp != NULL) { str = StringSave (vnp->data.ptrvalue); } } break; case 7 : if (gene != NULL) { str = StringSave (gene->comment); } break; case 8 : if (prp != NULL) { vnp = prp->name; if (vnp != NULL) { str = StringSave (vnp->data.ptrvalue); } } break; case 9 : if (prp != NULL) { str = StringSave (prp->desc); } break; case 10 : if (prp != NULL) { vnp = prp->ec; if (vnp != NULL) { str = StringSave (vnp->data.ptrvalue); } } break; case 11 : if (prp != NULL) { vnp = prp->activity; if (vnp != NULL) { str = StringSave (vnp->data.ptrvalue); } } break; case 12 : if (prot != NULL) { str = StringSave (prot->comment); } break; default : break; } break; default : break; } if (cfp->type == EDIT_CDSET) { foundit = StringISearch (str, cfp->findStr); if (foundit != NULL) { EditCdsetString (&str, cfp, foundit); } } switch (cfp->type) { case REMOVE_CDSET : break; case CONVERT_CDSET : case ADD_CDSET : case EDIT_CDSET : switch (cfp->toval) { case 1 : if (cds != NULL) { cds->comment = SaveOrReplaceString (cfp, str, cds->comment); str = NULL; } break; case 2 : if (grp != NULL) { grp->locus = SaveOrReplaceString (cfp, str, grp->locus); str = NULL; } break; case 3 : if (grp != NULL) { grp->desc = SaveOrReplaceString (cfp, str, grp->desc); str = NULL; } break; case 4 : if (grp != NULL) { grp->allele = SaveOrReplaceString (cfp, str, grp->allele); str = NULL; } break; case 5 : if (grp != NULL) { grp->maploc = SaveOrReplaceString (cfp, str, grp->maploc); str = NULL; } break; case 6 : if (grp != NULL) { if (! StringHasNoText (str)) { if (grp->syn != NULL && ShouldReplaceString (cfp)) { vnp = grp->syn; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = str; str = NULL; } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = grp->syn; grp->syn = vnp; vnp->data.ptrvalue = str; str = NULL; } } } } break; case 7 : if (gene != NULL) { gene->comment = SaveOrReplaceString (cfp, str, gene->comment); str = NULL; } break; case 8 : if (prp != NULL) { if (! StringHasNoText (str)) { if (prp->name != NULL && ShouldReplaceString (cfp)) { vnp = prp->name; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = str; str = NULL; } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = prp->name; prp->name = vnp; vnp->data.ptrvalue = str; str = NULL; } } } } break; case 9 : if (prp != NULL) { prp->desc = SaveOrReplaceString (cfp, str, prp->desc); str = NULL; } break; case 10 : if (prp != NULL) { if (! StringHasNoText (str)) { if (prp->ec != NULL && ShouldReplaceString (cfp)) { vnp = prp->ec; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = str; str = NULL; } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = prp->ec; prp->ec = vnp; vnp->data.ptrvalue = str; str = NULL; } } } } break; case 11 : if (prp != NULL) { if (! StringHasNoText (str)) { if (prp->activity != NULL && ShouldReplaceString (cfp)) { vnp = prp->activity; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = str; str = NULL; } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = prp->activity; prp->activity = vnp; vnp->data.ptrvalue = str; str = NULL; } } } } break; case 12 : if (prot != NULL) { prot->comment = SaveOrReplaceString (cfp, str, prot->comment); str = NULL; } break; default : break; } break; default : break; } MemFree (str); return TRUE; } static Boolean CleanupEachCDSFunc (GatherContextPtr gcp) { SeqFeatPtr cds; CdsetFormPtr cfp; SeqFeatPtr gene; GeneRefPtr grp; SeqFeatPtr prot; ProtRefPtr prp; SeqFeatPtr sfp; if (gcp == NULL) return TRUE; cfp = (CdsetFormPtr) gcp->userdata; if (cfp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.value.ptrvalue == NULL) return TRUE; cds = NULL; gene = NULL; grp = NULL; prot = NULL; prp = NULL; if (sfp->data.choice == SEQFEAT_GENE) { gene = sfp; grp = (GeneRefPtr) gene->data.value.ptrvalue; } else if (sfp->data.choice == SEQFEAT_PROT) { prot = sfp; prp = (ProtRefPtr) prot->data.value.ptrvalue; } else if (sfp->data.choice == SEQFEAT_CDREGION) { cds = sfp; /* FindGeneAndProtForCDS (cfp->input_entityID, cds, &gene, &prot); if (gene != NULL) { grp = (GeneRefPtr) gene->data.value.ptrvalue; } if (prot != NULL) { prp = (ProtRefPtr) prot->data.value.ptrvalue; } */ } else return TRUE; switch (cfp->type) { case REMOVE_CDSET : case CONVERT_CDSET : switch (cfp->fromval) { case 1 : if (cds != NULL) { cds->comment = MemFree (cds->comment); } break; case 2 : if (grp != NULL) { grp->locus = MemFree (grp->locus); } break; case 3 : if (grp != NULL) { grp->desc = MemFree (grp->desc); } break; case 4 : if (grp != NULL) { grp->allele = MemFree (grp->allele); } break; case 5 : if (grp != NULL) { grp->maploc = MemFree (grp->maploc); } break; case 6 : if (grp != NULL) { grp->syn = ValNodeFreeData (grp->syn); } break; case 7 : if (gene != NULL) { gene->comment = MemFree (gene->comment); } break; case 8 : if (prp != NULL) { prp->name = ValNodeFreeData (prp->name); } break; case 9 : if (prp != NULL) { prp->desc = MemFree (prp->desc); } break; case 10 : if (prp != NULL) { prp->ec = ValNodeFreeData (prp->ec); } break; case 11 : if (prp != NULL) { prp->activity = ValNodeFreeData (prp->activity); } break; case 12 : if (prot != NULL) { prot->comment = MemFree (prot->comment); } break; default : break; } break; case ADD_CDSET : break; case EDIT_CDSET : break; default : break; } return TRUE; } static void AddProtFeatIfMissing (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; ProtRefPtr prp; SeqAnnotPtr sap; SeqFeatPtr sfp; if (sep == NULL) return; if (! IS_Bioseq (sep)) return; bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; if (! ISA_aa (bsp->mol)) return; sap = bsp->annot; while (sap != NULL) { if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { if (sfp->data.choice == SEQFEAT_PROT) { return; } } sfp = sfp->next; } sap = sap->next; } sfp = CreateNewFeature (sep, NULL, SEQFEAT_PROT, NULL); if (sfp == NULL) return; prp = ProtRefNew (); sfp->data.value.ptrvalue = (Pointer) prp; } CharPtr JustSaveStringFromText (TexT t) { size_t len; CharPtr str; len = TextLength (t); if (len > 0) { str = (CharPtr) MemNew(len + 1); if (str != NULL) { GetTitle (t, str, len + 1); /* TrimSpacesAroundString (str); */ if (StringHasNoText (str)) { str = (CharPtr) MemFree(str); } return str; } else { return NULL; } } else { return NULL; } } extern void CleanupEmptyFeatCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent); static void DoProcessCDSet (ButtoN b) { CdsetFormPtr cfp; GatherScope gs; SeqEntryPtr sep; UIEnum val; cfp = (CdsetFormPtr) GetObjectExtra (b); if (cfp == NULL || cfp->input_entityID == 0) return; Hide (cfp->form); WatchCursor (); Update (); cfp->fromval = 0; cfp->toval = 0; if (GetEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, &val)) { cfp->fromval = (Int2) val; } if (GetEnumPopup (cfp->tofield, cds_gene_prot_field_alist, &val)) { cfp->toval = (Int2) val; } if (cfp->type == ADD_CDSET || cfp->type == EDIT_CDSET) { cfp->toval = cfp->fromval; } cfp->onlyGene = (Boolean) ((cfp->toval >= 2 && cfp->toval <= 7) && (cfp->fromval >= 2 && cfp->fromval <= 7)); cfp->onlyProt = (Boolean) ((cfp->toval >= 8 && cfp->toval <= 12) && (cfp->fromval >= 8 && cfp->fromval <= 12)); if (cfp->type == ADD_CDSET || cfp->type == CONVERT_CDSET) { if (cfp->toval >= 8 && cfp->toval <= 12) { sep = GetTopSeqEntryForEntityID (cfp->input_entityID); SeqEntryExplore (sep, NULL, AddProtFeatIfMissing); } } cfp->replaceOldAsked = FALSE; cfp->doReplaceAll = FALSE; cfp->findStr = JustSaveStringFromText (cfp->findthis); cfp->replaceStr = JustSaveStringFromText (cfp->replacewith); if (cfp->type != EDIT_CDSET) { TrimSpacesAroundString (cfp->findStr); TrimSpacesAroundString (cfp->replaceStr); } 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; if (cfp->type != REMOVE_CDSET) { GatherEntity (cfp->input_entityID, (Pointer) cfp, ProcessEachCDSFunc, &gs); } if (cfp->type == REMOVE_CDSET || (cfp->type == CONVERT_CDSET && (! GetStatus (cfp->leaveOn)))) { GatherEntity (cfp->input_entityID, (Pointer) cfp, CleanupEachCDSFunc, &gs); } /* SeqEntryExplore (sep, (Pointer) cfp, CleanupEmptyFeatCallback); */ ArrowCursor (); Update (); if (indexerVersion && cfp->type == ADD_CDSET) { sep = GetTopSeqEntryForEntityID (cfp->input_entityID); if (CountSeqEntryComponents (sep) == 1) { switch (cfp->fromval) { case 1 : Message (MSG_OK, "When only one record present, edit the CdRgn feature directly"); break; case 2 : case 3 : case 4 : case 5 : case 6 : case 7 : Message (MSG_OK, "When only one record present, edit the gene feature directly"); break; case 8 : case 9 : case 10 : case 11 : case 12 : Message (MSG_OK, "When only one record present, edit the protein feature directly"); break; default : break; } } } ObjMgrSetDirtyFlag (cfp->input_entityID, TRUE); sep = GetTopSeqEntryForEntityID (cfp->input_entityID); SeqEntryExplore (sep, NULL, CleanupEmptyFeatCallback); ObjMgrSendMsg (OM_MSG_UPDATE, cfp->input_entityID, 0, 0); Remove (cfp->form); } static Boolean SetCDSExample (GatherContextPtr gcp) { SeqFeatPtr cds; CdsetFormPtr cfp; SeqFeatPtr gene; GeneRefPtr grp; size_t len; SeqFeatPtr prot; ProtRefPtr prp; SeqFeatPtr sfp; CharPtr str; CharPtr tmp; ValNodePtr vnp; if (gcp == NULL) return TRUE; cfp = (CdsetFormPtr) gcp->userdata; if (cfp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.value.ptrvalue == NULL) return TRUE; cds = NULL; gene = NULL; grp = NULL; prot = NULL; prp = NULL; if (sfp->data.choice == SEQFEAT_GENE) { gene = sfp; grp = (GeneRefPtr) gene->data.value.ptrvalue; } else if (sfp->data.choice == SEQFEAT_PROT) { prot = sfp; prp = (ProtRefPtr) prot->data.value.ptrvalue; } else if (sfp->data.choice == SEQFEAT_CDREGION) { cds = sfp; } else return TRUE; str = NULL; switch (cfp->fromval) { case 1 : if (cds != NULL) { str = cds->comment; } break; case 2 : if (grp != NULL) { str = grp->locus; } break; case 3 : if (grp != NULL) { str = grp->desc; } break; case 4 : if (grp != NULL) { str = grp->allele; } break; case 5 : if (grp != NULL) { str = grp->maploc; } break; case 6 : if (grp != NULL) { vnp = grp->syn; if (vnp != NULL) { str = vnp->data.ptrvalue; } } break; case 7 : if (gene != NULL) { str = gene->comment; } break; case 8 : if (prp != NULL) { vnp = prp->name; if (vnp != NULL) { str = vnp->data.ptrvalue; } } break; case 9 : if (prp != NULL) { str = prp->desc; } break; case 10 : if (prp != NULL) { vnp = prp->ec; if (vnp != NULL) { str = vnp->data.ptrvalue; } } break; case 11 : if (prp != NULL) { vnp = prp->activity; if (vnp != NULL) { str = vnp->data.ptrvalue; } } break; case 12 : if (prot != NULL) { str = prot->comment; } break; default : break; } if (str != NULL) { if (! StringHasNoText (str)) { if (cfp->type == EDIT_CDSET) { SafeSetTitle (cfp->findthis, str); } StringNCpy_0 (cfp->temp, str, sizeof (cfp->temp)); len = StringLen (str) + 12; tmp = MemNew (len); if (tmp != NULL) { StringCpy (tmp, "Example ("); StringCat (tmp, str); StringCat (tmp, ")"); SafeSetTitle (cfp->example, tmp); MemFree (tmp); return FALSE; } else { SafeSetTitle (cfp->example, str); return FALSE; } } } return TRUE; } static void ChangeCDSetExample (PopuP p) { CdsetFormPtr cfp; GatherScope gs; UIEnum val; cfp = (CdsetFormPtr) GetObjectExtra (p); if (cfp == NULL || cfp->input_entityID == 0) return; SafeSetTitle (cfp->example, ""); if (GetEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, &val)) { cfp->fromval = (Int2) val; 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 (cfp->input_entityID, (Pointer) cfp, SetCDSExample, &gs); if (cfp->fromval >= 8 && cfp->fromval <= 12) { SafeShow (cfp->protSubGrp); } else { SafeHide (cfp->protSubGrp); } } else { SafeSetTitle (cfp->findthis, ""); } Update (); } static void CDSetMessageProc (ForM f, Int2 mssg) { CdsetFormPtr cfp; cfp = (CdsetFormPtr) GetObjectExtra (f); if (cfp != NULL) { if (cfp->appmessage != NULL) { cfp->appmessage (f, mssg); } } } static CharPtr cdsetLegend = "\ CDS\n\ /gene=\"gene locus\"\n\ /map=\"gene maploc\" (moves to source with taxon fixup)\n\ /EC_number=\"protein E.C. number\"\n\ /function=\"protein activity\"\n\ /note=\"gene description; gene allele; gene synonym;\n\ cds comment; protein description; protein comment\"\n\ /product=\"protein name\"\n\ gene\n\ /gene=\"gene locus\"\n\ /allele=\"gene allele\"\n\ /note=\"gene comment; gene description; gene synonym\"\n\ /map=\"gene maploc\" (moves to source with taxon fixup)\n"; static void CDSetLegend (ButtoN b) { GrouP legend; WindoW w; w = FixedWindow (-90, -33, -10, -10, "CDS-Gene-Prot Legend", StdCloseWindowProc); legend = MultiLinePromptEx (w, cdsetLegend, stdCharWidth * 35, programFont, FALSE); b = PushButton (w, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) legend, (HANDLE) b, NULL); RealizeWindow (w); Show (w); Select (w); } static void CleanupCdsetForm (GraphiC g, VoidPtr data) { CdsetFormPtr cfp; cfp = (CdsetFormPtr) data; if (cfp != NULL) { MemFree (cfp->findStr); MemFree (cfp->replaceStr); } StdCleanupFormProc (g, data); } static void ProcessCDSet (IteM i, Int2 type) { EnumFieldAssocPtr ap; ButtoN b, b1; BaseFormPtr bfp; GrouP c; CdsetFormPtr cfp; GrouP g; GatherScope gs; GrouP h; GrouP samples; SeqEntryPtr sep; StdEditorProcsPtr sepp; CharPtr title; WindoW w; GrouP x; GrouP y; GrouP z; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; cfp = (CdsetFormPtr) MemNew (sizeof (CdsetFormData)); if (cfp == NULL) return; cfp->type = type; switch (type) { case REMOVE_CDSET : title = "CDS-Gene-Prot Removal"; break; case CONVERT_CDSET : title = "CDS-Gene-Prot Conversion"; break; case EDIT_CDSET : title = "Edit CDS-Gene-Prot"; break; case ADD_CDSET : title = "Add CDS-Gene-Prot"; break; default : title = "?"; break; } w = FixedWindow (-50, -33, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, cfp, CleanupCdsetForm); cfp->form = (ForM) w; cfp->formmessage = CDSetMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); cfp->appmessage = sepp->handleMessages; } cfp->input_entityID = bfp->input_entityID; cfp->input_itemID = bfp->input_itemID; cfp->input_itemtype = bfp->input_itemtype; z = HiddenGroup (w, -2, 0, NULL); if (indexerVersion) { samples = HiddenGroup (z, 2, 0, NULL); for (ap = cds_gene_prot_field_alist; ap->name != NULL; ap++) { if (ap->value != 0) { cfp->fromval = (Int2) ap->value; cfp->temp [0] = '\0'; 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 (cfp->input_entityID, (Pointer) cfp, SetCDSExample, &gs); StaticPrompt (samples, ap->name, 0, 0, programFont, 'l'); StaticPrompt (samples, cfp->temp, 14 * stdCharWidth, 0, programFont, 'l'); } } } h = HiddenGroup (z, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 4, 0, NULL); switch (type) { case ADD_CDSET : StaticPrompt (g, "Type", 0, popupMenuHeight, programFont, 'l'); cfp->fromfield = PopupList (g, TRUE, ChangeCDSetExample); SetObjectExtra (cfp->fromfield, cfp, NULL); InitEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, NULL); SetEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, 0); break; case REMOVE_CDSET : StaticPrompt (g, "Remove", 0, popupMenuHeight, programFont, 'l'); cfp->fromfield = PopupList (g, TRUE, ChangeCDSetExample); SetObjectExtra (cfp->fromfield, cfp, NULL); InitEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, NULL); SetEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, 0); break; case CONVERT_CDSET : StaticPrompt (g, "From", 0, popupMenuHeight, programFont, 'l'); cfp->fromfield = PopupList (g, TRUE, ChangeCDSetExample); SetObjectExtra (cfp->fromfield, cfp, NULL); InitEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, NULL); SetEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, 0); StaticPrompt (g, "To", 0, popupMenuHeight, programFont, 'l'); cfp->tofield = PopupList (g, TRUE, NULL); InitEnumPopup (cfp->tofield, cds_gene_prot_field_alist, NULL); SetEnumPopup (cfp->tofield, cds_gene_prot_field_alist, 0); break; case EDIT_CDSET : StaticPrompt (g, "Type", 0, popupMenuHeight, programFont, 'l'); cfp->fromfield = PopupList (g, TRUE, ChangeCDSetExample); SetObjectExtra (cfp->fromfield, cfp, NULL); InitEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, NULL); SetEnumPopup (cfp->fromfield, cds_gene_prot_field_alist, 0); break; default : break; } x = HiddenGroup (h, 4, 0, NULL); /*StaticPrompt (x, "Example", 0, 0, programFont, 'l');*/ cfp->example = StaticPrompt (x, "", 14 * stdCharWidth, 0, programFont, 'l'); y = NULL; cfp->protSubGrp = NULL; switch (type) { case REMOVE_CDSET : /* y = HiddenGroup (h, 2, 0, NULL); StaticPrompt (y, "Optional string constraint", 0, dialogTextHeight, programFont, 'c'); cfp->findthis = DialogText (y, "", 14, NULL); */ break; case CONVERT_CDSET : /* y = HiddenGroup (h, 2, 0, NULL); StaticPrompt (y, "Optional string constraint", 0, dialogTextHeight, programFont, 'c'); cfp->findthis = DialogText (y, "", 14, NULL); */ y = HiddenGroup (h, 2, 0, NULL); cfp->leaveOn = CheckBox (y, "Leave on original", NULL); break; case ADD_CDSET : y = HiddenGroup (h, 2, 0, NULL); StaticPrompt (y, "Text", 0, dialogTextHeight, programFont, 'c'); cfp->findthis = DialogText (y, "", 14, NULL); break; case EDIT_CDSET : cfp->protSubGrp = HiddenGroup (h, 2, 0, NULL); StaticPrompt (cfp->protSubGrp, "Protein subtype", 0, dialogTextHeight, programFont, 'l'); cfp->protSubType = PopupList (cfp->protSubGrp, TRUE, NULL); InitEnumPopup (cfp->protSubType, prot_subtype_alist, NULL); SetEnumPopup (cfp->protSubType, prot_subtype_alist, (UIEnum) 5); Hide (cfp->protSubGrp); y = HiddenGroup (h, 2, 0, NULL); StaticPrompt (y, "Find", 0, dialogTextHeight, programFont, 'c'); cfp->findthis = DialogText (y, "", 14, NULL); StaticPrompt (y, "Replace", 0, dialogTextHeight, programFont, 'c'); cfp->replacewith = DialogText (y, "", 14, NULL); break; default : break; } b1 = PushButton (h, "Legend", CDSetLegend); c = HiddenGroup (w, 4, 0, NULL); b = PushButton (c, "Accept", DoProcessCDSet); SetObjectExtra (b, cfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) b1, (HANDLE) y, (HANDLE) cfp->protSubGrp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) h, (HANDLE) c, NULL); RealizeWindow (w); Show (w); Select (cfp->findthis); Update (); } extern void AddCDSet (IteM i) { ProcessCDSet (i, ADD_CDSET); } extern void RemoveCDSet (IteM i) { ProcessCDSet (i, REMOVE_CDSET); } extern void EditCDSet (IteM i) { ProcessCDSet (i, EDIT_CDSET); } extern void ConvertCDSet (IteM i) { ProcessCDSet (i, CONVERT_CDSET); } #define FIND_ASN 1 #define FIND_FLAT 2 #define FIND_GENE 3 #define FIND_PROT 4 #define FIND_POS 5 typedef struct findform { FORM_MESSAGE_BLOCK TexT findTxt; TexT replaceTxt; ButtoN caseCounts; ButtoN wholeWord; ButtoN doSeqIdLocal; ButtoN findAllBtn; ButtoN replaceAllBtn; Int2 type; } FindForm, PNTR FindFormPtr; extern CharPtr CompressSpaces (CharPtr str) { Char ch; CharPtr dst; Char last; CharPtr ptr; if (str != NULL && str [0] != '\0') { dst = str; ptr = str; ch = *ptr; while (ch != '\0' && ch <= ' ') { ptr++; ch = *ptr; } while (ch != '\0') { *dst = ch; dst++; ptr++; last = ch; ch = *ptr; if (ch != '\0' && ch < ' ') { *ptr = ' '; ch = *ptr; } while (ch != '\0' && last <= ' ' && ch <= ' ') { ptr++; ch = *ptr; } } *dst = '\0'; dst = NULL; ptr = str; ch = *ptr; while (ch != '\0') { if (ch != ' ') { dst = NULL; } else if (dst == NULL) { dst = ptr; } ptr++; ch = *ptr; } if (dst != NULL) { *dst = '\0'; } } return str; } extern CharPtr SearchForString (CharPtr str, CharPtr sub, Boolean case_counts, Boolean whole_word) { CharPtr ptr = NULL; CharPtr tmp; if (case_counts) { ptr = StringSearch (str, sub); } else { ptr = StringISearch (str, sub); } if (ptr == NULL) return NULL; if (whole_word) { if (ptr > str) { tmp = ptr - 1; if (! IS_WHITESP (*tmp)) return NULL; } tmp = ptr + StringLen (sub); if (*tmp != '\0' && (! IS_WHITESP (*tmp))) return NULL; } return ptr; } static void FindInFlatFile (Uint2 entityID, Uint2 itemID, Uint2 itemtype, Uint1 format, Uint1 mode, CharPtr sub, Boolean case_counts, Boolean whole_word) { Asn2ffJobPtr ajp; Boolean already; BioseqPtr bsp; DescrStructPtr descr; unsigned int entID; Int4 index; unsigned int itmID; unsigned int itmtype; ErrSev level; SeqEntryPtr oldsep; FFPrintArrayPtr pap = NULL; Int4 pap_size; SeqEntryPtr sep = NULL; SelStructPtr sel; CharPtr string; SeqEntryPtr topsep; ajp = (Asn2ffJobPtr) MemNew (sizeof (Asn2ffJob)); if (ajp == NULL) return; if (itemID == 0) sep = GetTopSeqEntryForEntityID (entityID); else { bsp = GetBioseqGivenIDs (entityID, itemID, itemtype); if (bsp == NULL) return; sep = SeqMgrGetSeqEntryForData (bsp); if (bsp->repr == Seq_repr_seg) { sep = GetBestTopParentForData (entityID, bsp); } } if (sep == NULL) return; level = ErrSetMessageLevel (SEV_MAX); WatchCursor (); Update (); ajp->sep = sep; ajp->mode = mode; ajp->format = format; ajp->gb_style = TRUE; ajp->show_seq = TRUE; ajp->show_gi = TRUE; ajp->error_msgs = FALSE; ajp->non_strict = TRUE; ajp->Spop = spop; ajp->show_gene = TRUE; if (IsAGenomeRecord (sep)) { ajp->only_one = TRUE; ajp->genome_view = TRUE; } ajp->bankit = TRUE; topsep = GetTopSeqEntryForEntityID (entityID); oldsep = SeqEntrySetScope (topsep); pap_size = asn2ff_setup (ajp, &pap); if (pap_size > 0) { asn2ff_set_output (NULL, "\n"); for (index = 0; index < pap_size; index++) { string = FFPrint (pap, index, pap_size); if (string != NULL && *string != '\0') { CompressSpaces (string); if (SearchForString (string, sub, case_counts, whole_word) != NULL) { if (pap [index].descr) { descr = pap [index].descr; entID = descr->entityID; itmID = descr->itemID; itmtype = descr->itemtype; pap [index].descr = MemFree (pap [index].descr); already = FALSE; for (sel = ObjMgrGetSelected (); sel != NULL; sel = sel->next) { if (sel->entityID == entID && sel->itemID == itmID && sel->itemtype == itmtype) { already = TRUE; } } if (! already) { ObjMgrAlsoSelect (entID, itmID, itmtype, 0, NULL); } } } } MemFree (string); } MemFree (pap); } asn2ff_cleanup (ajp); SeqEntrySetScope (oldsep); MemFree (ajp); ErrSetMessageLevel (level); ArrowCursor (); Update (); } static void FindFlatProc (ButtoN b) { Boolean caseCounts; FindFormPtr ffp; CharPtr findme; Boolean wholeWord; ffp = (FindFormPtr) GetObjectExtra (b); if (ffp == NULL) return; findme = SaveStringFromText (ffp->findTxt); ObjMgrDeSelect (0, 0, 0, 0, NULL); caseCounts = GetStatus (ffp->caseCounts); wholeWord = GetStatus (ffp->wholeWord); CompressSpaces (findme); FindInFlatFile (ffp->input_entityID, ffp->input_itemID, ffp->input_itemtype, GENBANK_FMT, SEQUIN_MODE, findme, caseCounts, wholeWord); MemFree (findme); } static void FindTextProc (TexT t) { FindFormPtr ffp; ffp = (FindFormPtr) GetObjectExtra (t); if (ffp != NULL) { if (TextLength (t) > 0) { SafeEnable (ffp->findAllBtn); SafeEnable (ffp->replaceAllBtn); } else { SafeDisable (ffp->findAllBtn); SafeDisable (ffp->replaceAllBtn); } } } static void CommonFindReplaceProc (ButtoN b, Boolean replace, Boolean replaceAll) { Boolean caseCounts; CharPtr changeme; Boolean doSeqIdLocal; FindFormPtr ffp; CharPtr findme; Boolean wholeWord; ffp = (FindFormPtr) GetObjectExtra (b); if (ffp != NULL) { findme = SaveStringFromText (ffp->findTxt); ObjMgrDeSelect (0, 0, 0, 0, NULL); caseCounts = GetStatus (ffp->caseCounts); wholeWord = GetStatus (ffp->wholeWord); doSeqIdLocal = GetStatus (ffp->doSeqIdLocal); if (replace) { changeme = SaveStringFromText (ffp->replaceTxt); FindReplaceInEntity (ffp->input_entityID, findme, changeme, caseCounts, wholeWord, replaceAll, TRUE, UPDATE_ONCE, NULL, NULL, NULL, doSeqIdLocal); GetRidOfEmptyFeatsDescStrings (ffp->input_entityID, NULL); ObjMgrSetDirtyFlag (ffp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, ffp->input_entityID, 0, 0); MemFree (changeme); } else { FindReplaceInEntity (ffp->input_entityID, findme, NULL, caseCounts, wholeWord, FALSE, TRUE, UPDATE_ONCE, NULL, NULL, NULL, doSeqIdLocal); } MemFree (findme); Update (); } } static void FindAllProc (ButtoN b) { CommonFindReplaceProc (b, FALSE, FALSE); } static void ReplaceAllProc (ButtoN b) { CommonFindReplaceProc (b, TRUE, TRUE); } static void FindByLabelOrPosProc (ButtoN b) { Boolean already; BioseqPtr bsp; SeqMgrFeatContext context; FindFormPtr ffp; CharPtr findme; SelStructPtr sel; SeqEntryPtr sep = NULL; SeqFeatPtr sfp = NULL; Int4 val; ffp = (FindFormPtr) GetObjectExtra (b); if (ffp == NULL) return; if (ffp->input_itemID == 0) { sep = GetTopSeqEntryForEntityID (ffp->input_entityID); } else { bsp = GetBioseqGivenIDs (ffp->input_entityID, ffp->input_itemID, ffp->input_itemtype); if (bsp == NULL) return; sep = SeqMgrGetSeqEntryForData (bsp); if (bsp->repr == Seq_repr_seg) { sep = GetBestTopParentForData (ffp->input_entityID, bsp); } } if (sep == NULL) return; findme = SaveStringFromText (ffp->findTxt); ObjMgrDeSelect (0, 0, 0, 0, NULL); CompressSpaces (findme); switch (ffp->type) { case FIND_GENE : sfp = SeqMgrGetFeatureByLabel (bsp, findme, SEQFEAT_GENE, 0, &context); break; case FIND_PROT : sfp = SeqMgrGetFeatureByLabel (bsp, findme, SEQFEAT_CDREGION, 0, &context); break; case FIND_POS : if (StrToLong (findme, &val)) { if (val > 0 && val <= bsp->length) { val--; sfp = SeqMgrGetNextFeature (bsp, NULL, 0, 0, &context); while (sfp != NULL) { if (context.left >= val) break; sfp = SeqMgrGetNextFeature (bsp, sfp, 0, 0, &context); } } } break; default : break; } MemFree (findme); if (sfp == NULL) return; already = FALSE; for (sel = ObjMgrGetSelected (); sel != NULL; sel = sel->next) { if (sel->entityID == context.entityID && sel->itemID == context.itemID && sel->itemtype == OBJ_SEQFEAT) { already = TRUE; } } if (! already) { ObjMgrAlsoSelect (context.entityID, context.itemID, OBJ_SEQFEAT, 0, NULL); } Remove (ffp->form); } static void ClearFindTextProc (ButtoN b) { FindFormPtr ffp; ffp = (FindFormPtr) GetObjectExtra (b); if (ffp == NULL) return; SafeSetTitle (ffp->findTxt, ""); SafeSetTitle (ffp->replaceTxt, ""); Select (ffp->findTxt); } static void FindFormMessage (ForM f, Int2 mssg) { FindFormPtr ffp; ffp = (FindFormPtr) GetObjectExtra (f); if (ffp != 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 (ffp->appmessage != NULL) { ffp->appmessage (f, mssg); } break; } } } static ForM CreateFindForm (Int2 left, Int2 top, CharPtr title, Uint2 entityID, Uint2 itemID, Uint2 itemtype, Int2 type) { ButtoN b; GrouP c; GrouP g; FindFormPtr ffp; GrouP j; GrouP q = NULL; StdEditorProcsPtr sepp; WindoW w; w = NULL; ffp = MemNew (sizeof (FindForm)); if (ffp != NULL) { w = FixedWindow (left, top, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, ffp, StdCleanupFormProc); ffp->form = (ForM) w; ffp->formmessage = FindFormMessage; ffp->input_entityID = entityID; ffp->input_itemID = itemID; ffp->input_itemtype = itemtype; ffp->type = type; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); ffp->appmessage = sepp->handleMessages; } j = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (j, 10, 10); g = HiddenGroup (j, 2, 0, NULL); StaticPrompt (g, "Find", 0, dialogTextHeight, programFont, 'l'); ffp->findTxt = DialogText (g, "", 25, FindTextProc); SetObjectExtra (ffp->findTxt, ffp, NULL); if (type == FIND_ASN) { StaticPrompt (g, "Replace", 0, dialogTextHeight, programFont, 'l'); ffp->replaceTxt = DialogText (g, "", 25, NULL); SetObjectExtra (ffp->replaceTxt, ffp, NULL); } if (type == FIND_ASN || type == FIND_FLAT) { q = HiddenGroup (w, 3, 0, NULL); ffp->caseCounts = CheckBox (q, "Case Sensitive", NULL); ffp->wholeWord = CheckBox (q, "Entire Word", NULL); if (indexerVersion && type == FIND_ASN) { ffp->doSeqIdLocal = CheckBox (q, "SeqID LOCAL", NULL); } } c = HiddenGroup (w, 4, 0, NULL); SetGroupSpacing (c, 10, 2); if (type == FIND_ASN) { ffp->findAllBtn = DefaultButton (c, "Find All", FindAllProc); SetObjectExtra (ffp->findAllBtn, ffp, NULL); Disable (ffp->findAllBtn); ffp->replaceAllBtn = PushButton (c, "Replace All", ReplaceAllProc); SetObjectExtra (ffp->replaceAllBtn, ffp, NULL); Disable (ffp->replaceAllBtn); } else if (type == FIND_FLAT) { ffp->findAllBtn = DefaultButton (c, "Find All", FindFlatProc); SetObjectExtra (ffp->findAllBtn, ffp, NULL); Disable (ffp->findAllBtn); } else if (type == FIND_GENE) { ffp->findAllBtn = DefaultButton (c, "Find Gene", FindByLabelOrPosProc); SetObjectExtra (ffp->findAllBtn, ffp, NULL); Disable (ffp->findAllBtn); } else if (type == FIND_PROT) { ffp->findAllBtn = DefaultButton (c, "Find Protein", FindByLabelOrPosProc); SetObjectExtra (ffp->findAllBtn, ffp, NULL); Disable (ffp->findAllBtn); } else if (type == FIND_POS) { ffp->findAllBtn = DefaultButton (c, "Find by Position", FindByLabelOrPosProc); SetObjectExtra (ffp->findAllBtn, ffp, NULL); Disable (ffp->findAllBtn); } b = PushButton (c, "Clear", ClearFindTextProc); SetObjectExtra (b, ffp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) j, (HANDLE) c, (HANDLE) q, NULL); RealizeWindow (w); Select (ffp->findTxt); } return (ForM) w; } extern void FindStringProc (IteM i) { BaseFormPtr bfp; ForM w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp != NULL) { w = CreateFindForm (-90, -66, "Find", bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype, FIND_ASN); Show (w); Select (w); } } extern void FindFlatfileProc (IteM i) { BaseFormPtr bfp; ForM w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp != NULL) { w = CreateFindForm (-90, -66, "Flat File Find", bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype, FIND_FLAT); Show (w); Select (w); } } extern void FindGeneProc (IteM i) { BaseFormPtr bfp; ForM w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp != NULL) { w = CreateFindForm (-90, -66, "Find", bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype, FIND_GENE); Show (w); Select (w); } } extern void FindProtProc (IteM i) { BaseFormPtr bfp; ForM w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp != NULL) { w = CreateFindForm (-90, -66, "Find", bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype, FIND_PROT); Show (w); Select (w); } } extern void FindPosProc (IteM i) { BaseFormPtr bfp; ForM w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp != NULL) { w = CreateFindForm (-90, -66, "Find", bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype, FIND_POS); Show (w); Select (w); } } extern EnumFieldAssoc orgmod_subtype_alist []; extern EnumFieldAssoc subsource_subtype_alist []; static void RemoveRedundantSourceNote (CharPtr str, CharPtr keyword, CharPtr name) { Char ch; Boolean extract; CharPtr tmp1, tmp2; if (str == NULL || keyword == NULL || name == NULL) return; while (str != NULL && *str != '\0') { extract = TRUE; tmp1 = str; ch = *tmp1; while (ch == ' ' || ch == ';') { tmp1++; ch = *tmp1; } tmp2 = keyword; ch = TO_UPPER (*tmp1); while (ch != '\0' && ch == TO_UPPER (*tmp2)) { tmp1++; tmp2++; ch = TO_UPPER (*tmp1); } if (*tmp2 == '\0' && ch == ' ') { while (ch != '\0' && ch == ' ') { tmp1++; ch = *tmp1; } tmp2 = name; while (ch != '\0' && ch == *tmp2) { tmp1++; tmp2++; ch = *tmp1; } if (*tmp2 == '\0' && (ch == '\0' || ch == ' ' || ch == ';')) { while (ch != '\0' && ch == ' ') { tmp1++; ch = *tmp1; } /* now ready to extract */ } else { extract = FALSE; } } else { extract = FALSE; } if (extract) { while (ch == ' ' || ch == ';') { tmp1++; ch = *tmp1; } tmp2 = str; while (ch != '\0') { *tmp2 = ch; tmp1++; tmp2++; ch = *tmp1; } *tmp2 = '\0'; } else { ch = *tmp1; while (ch != '\0' && ch != ';') { tmp1++; ch = *tmp1; } if (ch == ';') { tmp1++; ch = *tmp1; } while (ch != '\0' && (ch == ' ' || ch == ';')) { tmp1++; ch = *tmp1; } str = tmp1; } } } static CharPtr TrimSpacesAndSemicolonsAroundString (CharPtr str) { Uchar ch; /* to use 8bit characters in multibyte languages */ CharPtr dst; CharPtr ptr; if (str != NULL && str [0] != '\0') { dst = str; ptr = str; ch = *ptr; while (ch != '\0' && (ch <= ' ' || ch == ';')) { ptr++; ch = *ptr; } while (ch != '\0') { *dst = ch; dst++; ptr++; ch = *ptr; } *dst = '\0'; dst = NULL; ptr = str; ch = *ptr; while (ch != '\0') { if (ch != ' ' && ch != ';') { dst = NULL; } else if (dst == NULL) { dst = ptr; } ptr++; ch = *ptr; } if (dst != NULL) { *dst = '\0'; } } return str; } extern void GetRidOfRedundantSourceNotes (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent); extern void GetRidOfRedundantSourceNotes (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { EnumFieldAssocPtr ap; BioSourcePtr biop; BioseqPtr bsp; BioseqSetPtr bssp; OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; ValNodePtr sdp; SubSourcePtr ssp; CharPtr str1, str2; if (sep == NULL || sep->data.ptrvalue == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sdp = bsp->descr; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sdp = bssp->descr; } else return; while (sdp != NULL) { if (sdp->choice == Seq_descr_source) { str1 = NULL; str2 = NULL; onp = NULL; biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop != NULL) { orp = biop->org; if (orp != NULL) { onp = orp->orgname; if (onp != NULL) { mod = onp->mod; while (mod != NULL) { if (mod->subtype == 255) { str1 = mod->subname; } mod = mod->next; } } } ssp = biop->subtype; while (ssp != NULL) { if (ssp->subtype == 255) { str2 = ssp->name; } ssp = ssp->next; } if (str1 != NULL || str2 != NULL) { if (onp != NULL) { mod = onp->mod; while (mod != NULL) { if (mod->subtype != 255) { for (ap = orgmod_subtype_alist; ap->name != NULL; ap++) { if (ap->value == mod->subtype) { RemoveRedundantSourceNote (str1, ap->name, mod->subname); RemoveRedundantSourceNote (str2, ap->name, mod->subname); } } } mod = mod->next; } } ssp = biop->subtype; while (ssp != NULL) { if (ssp->subtype != 255) { for (ap = subsource_subtype_alist; ap->name != NULL; ap++) { if (ap->value == ssp->subtype) { RemoveRedundantSourceNote (str1, ap->name, ssp->name); RemoveRedundantSourceNote (str2, ap->name, ssp->name); } } } ssp = ssp->next; } } } TrimSpacesAndSemicolonsAroundString (str1); TrimSpacesAndSemicolonsAroundString (str2); } sdp = sdp->next; } } typedef struct convaccdata { CharPtr currID; CharPtr newID; } ConvAccData, PNTR ConvAccPtr; static void ChangeSeqIdListToAccLocalID (SeqIdPtr sip, CharPtr currID, CharPtr newID) { ObjectIdPtr oip; while (sip != NULL) { switch (sip->choice) { case SEQID_LOCAL : oip = (ObjectIdPtr) sip->data.ptrvalue; if (oip != NULL) { if (StringCmp (oip->str, currID) == 0) { MemFree (oip->str); oip->str = StringSave (newID); } } break; default : break; } sip = sip->next; } } static void ChangeSeqLocListToAccLocalID (SeqLocPtr slp, CharPtr currID, CharPtr newID) { SeqLocPtr loc; PackSeqPntPtr psp; SeqBondPtr sbp; SeqIntPtr sinp; SeqIdPtr sip; SeqPntPtr spp; while (slp != NULL) { switch (slp->choice) { case SEQLOC_NULL : break; case SEQLOC_EMPTY : case SEQLOC_WHOLE : sip = (SeqIdPtr) slp->data.ptrvalue; ChangeSeqIdListToAccLocalID (sip, currID, newID); break; case SEQLOC_INT : sinp = (SeqIntPtr) slp->data.ptrvalue; if (sinp != NULL) { sip = sinp->id; ChangeSeqIdListToAccLocalID (sip, currID, newID); } break; case SEQLOC_PNT : spp = (SeqPntPtr) slp->data.ptrvalue; if (spp != NULL) { sip = spp->id; ChangeSeqIdListToAccLocalID (sip, currID, newID); } break; case SEQLOC_PACKED_PNT : psp = (PackSeqPntPtr) slp->data.ptrvalue; if (psp != NULL) { sip = psp->id; ChangeSeqIdListToAccLocalID (sip, currID, newID); } break; case SEQLOC_PACKED_INT : case SEQLOC_MIX : case SEQLOC_EQUIV : loc = (SeqLocPtr) slp->data.ptrvalue; while (loc != NULL) { ChangeSeqIdListToAccLocalID (loc, currID, newID); loc = loc->next; } break; case SEQLOC_BOND : sbp = (SeqBondPtr) slp->data.ptrvalue; if (sbp != NULL) { spp = (SeqPntPtr) sbp->a; if (spp != NULL) { sip = spp->id; ChangeSeqIdListToAccLocalID (sip, currID, newID); } spp = (SeqPntPtr) sbp->b; if (spp != NULL) { sip = spp->id; ChangeSeqIdListToAccLocalID (sip, currID, newID); } } break; case SEQLOC_FEAT : break; default : break; } slp = slp->next; } } static void ChangeAlignListToAccLocalID (SeqAlignPtr align, CharPtr currID, CharPtr newID) { DenseDiagPtr ddp; DenseSegPtr dsp; StdSegPtr ssp; if (align == NULL) return; if (align->segtype == 1) { ddp = (DenseDiagPtr) align->segs; if (ddp != NULL) { ChangeSeqIdListToAccLocalID (ddp->id, currID, newID); } } else if (align->segtype == 2) { dsp = (DenseSegPtr) align->segs; if (dsp != NULL) { ChangeSeqIdListToAccLocalID (dsp->ids, currID, newID); } } else if (align->segtype == 3) { ssp = (StdSegPtr) align->segs; if (ssp != NULL) { ChangeSeqLocListToAccLocalID (ssp->loc, currID, newID); } } } static void CopyAccToLocalCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; ConvAccPtr cap; SeqAlignPtr sal; SeqAnnotPtr sap; SeqFeatPtr sfp; SeqIdPtr sip; SeqLocPtr slp; if (sep == NULL || sep->data.ptrvalue == NULL) return; cap = (ConvAccPtr) mydata; if (cap == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sip = bsp->id; ChangeSeqIdListToAccLocalID (sip, cap->currID, cap->newID); SeqMgrReplaceInBioseqIndex (bsp); sap = bsp->annot; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; } else return; while (sap != NULL) { if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { slp = sfp->location; ChangeSeqLocListToAccLocalID (slp, cap->currID, cap->newID); slp = sfp->product; ChangeSeqLocListToAccLocalID (slp, cap->currID, cap->newID); sfp = sfp->next; } } else if (sap->type == 2) { sal = (SeqAlignPtr) sap->data; while (sal != NULL) { ChangeAlignListToAccLocalID (sal, cap->currID, cap->newID); sal = sal->next; } } sap = sap->next; } } static void RecordAccToConvert (ValNodePtr PNTR vnpp, BioseqPtr bsp, CharPtr newID) { ConvAccPtr cap; ObjectIdPtr oip; SeqIdPtr sip; if (vnpp == NULL || bsp == NULL || StringHasNoText (newID)) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_LOCAL) { oip = (ObjectIdPtr) sip->data.ptrvalue; if (oip != NULL) { if (! StringHasNoText (oip->str)) { cap = (ConvAccPtr) MemNew (sizeof (ConvAccData)); if (cap == NULL) return; cap->currID = StringSave (oip->str); cap->newID = StringSave (newID); ValNodeAddPointer (vnpp, 0, (Pointer) cap); return; } } } } } static Boolean IsLegalAccession (CharPtr acnum, Int2 i) { Int2 j; if (! isalpha (acnum [0])) return FALSE; if (!(isdigit(acnum[1]) && i == 6) && !(isalpha(acnum[1]) && i == 8)) return FALSE; for (j = 2; j < i; j++) { if (!(isdigit(acnum[j]))) return FALSE; } return TRUE; } static void FindAccInDefCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { Char acnum [17]; BioseqPtr bsp; Int2 i; CharPtr p; Char str [128]; ValNodePtr ttl; ValNodePtr PNTR vnpp; if (sep == NULL || sep->data.ptrvalue == NULL) return; if (! IS_Bioseq (sep)) return; vnpp = (ValNodePtr PNTR) mydata; if (vnpp == NULL) return; ttl = SeqEntryGetSeqDescr (sep, Seq_descr_title, NULL); while (ttl != NULL) { StringNCpy_0 (str, (CharPtr) ttl->data.ptrvalue, sizeof (str)); TrimSpacesAroundString (str); if (! StringHasNoText (str)) { if (str [0] == 'a' && str [1] == 'c' && str [2] == 'c') { p = str + 3; for (i = 0; isalnum (*p) && *p != '\0'; p++, i++) { acnum [i] = *p; } acnum [i] = '\0'; if (i == 6 || i == 8) { if (IsLegalAccession (acnum, i)) { bsp = (BioseqPtr) sep->data.ptrvalue; RecordAccToConvert (vnpp, bsp, str); } } } } ttl = SeqEntryGetSeqDescr (sep, Seq_descr_title, ttl); } } static void ConvertAccInDefToLocalIdProc (SeqEntryPtr sep) { ConvAccPtr cap; ValNodePtr head; ValNodePtr vnp; if (sep == NULL) return; head = NULL; SeqEntryExplore (sep, (Pointer) &head, FindAccInDefCallback); if (head == NULL) return; if (Message (MSG_YN, "Convert accLNNNNN or accLLNNNNNN in title to local ID?") == ANS_NO) return; for (vnp = head; vnp != NULL; vnp = vnp->next) { cap = (ConvAccPtr) vnp->data.ptrvalue; if (cap != NULL) { SeqEntryExplore (sep, (Pointer) cap, CopyAccToLocalCallback); } } for (vnp = head; vnp != NULL; vnp = vnp->next) { cap = (ConvAccPtr) vnp->data.ptrvalue; if (cap != NULL) { MemFree (cap->currID); MemFree (cap->newID); vnp->data.ptrvalue = MemFree (cap); } } ValNodeFree (head); } static Int2 taxonCount; static Int4 DoSeqEntryToAsn3 (SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean force, Boolean dotaxon, MonitorPtr mon) { BioseqSetPtr bssp; SeqEntryPtr oldscope; Int4 rsult; Char str [32]; rsult = 0; 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) { rsult += DoSeqEntryToAsn3 (sep, strip, correct, force, dotaxon, mon); } return rsult; } } /*#ifdef USE_TAXON*/ if (dotaxon && mon != NULL) { taxonCount++; sprintf (str, "Processing Component %d", (int) taxonCount); MonitorStrValue (mon, str); } /*#endif*/ /*#ifdef INTERNAL_NCBI_SEQUIN*/ if (indexerVersion) { if ((! force) && (! NoBiosourceOrTaxonId (sep))) return 0; } else { /*#else*/ if ((! force) && SeqEntryGetSeqDescr (sep, Seq_descr_source, NULL) != NULL) return 0; } /*#endif*/ oldscope = SeqEntrySetScope (sep); if (dotaxon) { rsult = SeqEntryToAsn3Ex (sep, strip, correct, TRUE, GetTaxserverOrg, TaxMergeBSinDescr); } else { rsult = SeqEntryToAsn3Ex (sep, strip, correct, FALSE, NULL, NULL); } SeqEntrySetScope (oldscope); return rsult; } /* CheckSeqAlignCallback copied from salsa.c */ static void CheckSeqAlignCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; SeqAnnotPtr sap, pre; if (sep != NULL && sep->data.ptrvalue) { if (IS_Bioseq(sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp!=NULL) { pre=NULL; sap=bsp->annot; while (sap!= NULL) { if (sap->type == 2) { if (is_dim1seqalign ((SeqAlignPtr) sap->data)) { if (pre==NULL) { bsp->annot=sap->next; sap->next=NULL; SeqAnnotFree (sap); sap=bsp->annot; } else { pre->next=sap->next; pre=sap->next; sap->next=NULL; SeqAnnotFree (sap); sap=pre; } } else { pre=sap; sap=sap->next; } } else { pre=sap; sap=sap->next; } } } } else if(IS_Bioseq_set(sep)) { bssp = (BioseqSetPtr)sep->data.ptrvalue; if (bssp!=NULL) { pre=NULL; sap=bssp->annot; while (sap!= NULL) { if (sap->type == 2) { if (is_dim1seqalign ((SeqAlignPtr) sap->data)) { if (pre==NULL) { bssp->annot=sap->next; sap->next=NULL; SeqAnnotFree (sap); sap=bssp->annot; } else { pre=sap->next; sap->next=NULL; SeqAnnotFree (sap); sap=sap->next; } } else { pre=sap; sap=sap->next; } } else { pre=sap; sap=sap->next; } } } } } } /* RemoveMultipleTitles currently removes FIRST title in chain */ static void RemoveMultipleTitles (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; SeqDescrPtr descr = NULL; SeqDescrPtr lasttitle = NULL; ObjValNodePtr ovp; SeqDescrPtr sdp; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; descr = bsp->descr; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; descr = bssp->descr; } else return; for (sdp = descr; sdp != NULL; sdp = sdp->next) { if (sdp->choice != Seq_descr_title) continue; if (lasttitle != NULL) { if (lasttitle->extended != 0) { ovp = (ObjValNodePtr) lasttitle; ovp->idx.deleteme = TRUE; } lasttitle = sdp; } else { lasttitle = sdp; } } } typedef struct featcount { Boolean is_mRNA; BioseqPtr bsp; Int2 numRNAs; SeqFeatPtr gene; Int4 numGene; Int4 numCDS; } FeatCount, PNTR FeatCountPtr; static void CountGenesAndCDSs (SeqFeatPtr sfp, Pointer userdata) { FeatCountPtr fcp; fcp = (FeatCountPtr) userdata; if (sfp->data.choice == SEQFEAT_GENE) { (fcp->numGene)++; fcp->gene = sfp; } else if (sfp->data.choice == SEQFEAT_CDREGION) { (fcp->numCDS)++; } } static void LookForMrna (BioseqPtr bsp, Pointer userdata) { FeatCountPtr fcp; MolInfoPtr mip; SeqDescrPtr sdp; if (bsp == NULL || bsp->length == 0) return; if (! ISA_na (bsp->mol)) return; fcp = (FeatCountPtr) userdata; for (sdp = bsp->descr; sdp != NULL; sdp = sdp->next) { if (sdp->choice != Seq_descr_molinfo) continue; mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL && mip->biomol == MOLECULE_TYPE_MRNA) { fcp->is_mRNA = TRUE; fcp->bsp = bsp; (fcp->numRNAs)++; return; } } } static void ExtendSingleGeneOnMRNA (SeqEntryPtr sep, Pointer userdata) { FeatCount fc; SeqIntPtr sintp; ValNodePtr vnp; fc.is_mRNA = FALSE; fc.bsp = NULL; fc.numRNAs = 0; VisitBioseqsInSep (sep, (Pointer) &fc, LookForMrna); if (! fc.is_mRNA) return; fc.gene = NULL; fc.numGene = 0; fc.numCDS = 0; VisitFeaturesInSep (sep, (Pointer) &fc, CountGenesAndCDSs); if (fc.numGene == 1 && fc.numCDS < 2 && fc.numRNAs == 1 && fc.bsp != NULL && fc.gene != NULL) { if (fc.bsp != BioseqFindFromSeqLoc (fc.gene->location)) return; for (vnp = fc.gene->location; vnp != NULL; vnp = vnp->next) { if (vnp->choice != SEQLOC_INT) continue; sintp = (SeqIntPtr) vnp->data.ptrvalue; if (sintp == NULL) continue; if (sintp->from != 0 || sintp->to != fc.bsp->length - 1) { sintp->from = 0; sintp->to = fc.bsp->length - 1; } } } } extern Int4 MySeqEntryToAsn3Ex (SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean force, Boolean dotaxon); extern Int4 MySeqEntryToAsn3Ex (SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean force, Boolean dotaxon) { Uint2 entityID; MonitorPtr mon; Boolean needstaxfix; Int4 rsult; ErrSev sev; rsult = 0; sev = ErrSetMessageLevel (SEV_FATAL); BasicSeqEntryCleanup (sep); EntryChangeImpFeat(sep); /* change any CDS ImpFeat to real CdRegion */ /* NormalizePeriodsOnInitials (sep); */ /* put periods on author initials */ /* MoveRnaGBQualProductToName (sep); */ /* move rna gbqual product to rna-ref.ext.name */ /* MoveProtGBQualProductToName (sep); */ /* move prot gbqual product to prot-ref.name */ /* MoveCdsGBQualProductToName (sep); */ /* move cds gbqual product to prot-ref.name */ /* MoveFeatGBQualsToFields (sep); */ /* move feature partial, exception to fields */ if (indexerVersion) { /* StripTitleFromProtsInNucProts (sep); */ move_cds (sep); /* move CDS features to nuc-prot set */ } /* ExtendGeneFeatIfOnMRNA (0, sep); */ /* gene on mRNA is full length */ VisitElementsInSep (sep, NULL, ExtendSingleGeneOnMRNA); /* needs < 2 CDS */ RemoveBioSourceOnPopSet (sep, NULL); /* SeqEntryExplore (sep, NULL, CleanupEmptyFeatCallback); */ SeqEntryExplore (sep, NULL, DeleteMultipleTitles); /* do it old way in Sequin */ /* SeqEntryExplore (sep, NULL, RemoveMultipleTitles); DeleteMarkedObjects (0, OBJ_SEQENTRY, (Pointer) sep); */ SeqEntryPack (sep); if (indexerVersion) { ConvertAccInDefToLocalIdProc (sep); /* if title is accXNNNNN, convert to seqID */ } if (useEntrez) { ValidateSeqAlignandACCInSeqEntry (sep, TRUE, FALSE, FALSE, TRUE, TRUE, FALSE); /* remove components with seqID accXNNNNN */ } SeqEntryExplore (sep, NULL, CheckSeqAlignCallback); /* remove alignments with single dimension */ needstaxfix = FALSE; if (! force) { needstaxfix = NoBiosourceOrTaxonId (sep); } if ((! force) && (! needstaxfix)) { ConvertFullLenSourceFeatToDesc (sep); ConvertFullLenPubFeatToDesc (sep); /* EntryStripSerialNumber(sep); */ /* strip citation serial numbers */ EntryChangeGBSource (sep); /* at least remove redundant information in GBBlocks */ EntryCheckGBBlock (sep); /* SeqEntryMoveDbxrefs (sep); */ /* db_xref gbqual to sfp->dbxref */ EntryMergeDupBioSources (sep); GetRidOfEmptyFeatsDescStrings (0, sep); GetRidOfLocusInSeqIds (0, sep); BasicSeqEntryCleanup (sep); ErrSetMessageLevel (sev); return rsult; } if (force && useTaxon) { dotaxon = TRUE; } mon = NULL; taxonCount = 0; /*#ifdef USE_TAXON*/ if (dotaxon) { WatchCursor (); mon = MonitorStrNewEx ("Taxonomy Lookup", 40, FALSE); MonitorStrValue (mon, "Connecting to Taxon"); Update (); if (! TaxArchInit ()) { ArrowCursor (); Update (); Message (MSG_ERROR, "Couldn't connect to Taxon"); MonitorFree (mon); Update (); BasicSeqEntryCleanup (sep); ErrSetMessageLevel (sev); return 0; } MonitorStrValue (mon, "Processing Organism Info"); Update (); } /*#endif*/ /* set dirty flag if no lineage or division in any biosource */ if (dotaxon && needstaxfix) { entityID = ObjMgrGetEntityIDForChoice (sep); ObjMgrSetDirtyFlag (entityID, TRUE); } EntryMergeDupBioSources (sep); /* do before and after SE2A3 */ rsult = DoSeqEntryToAsn3 (sep, strip, correct, force, dotaxon, mon); /*#ifdef USE_TAXON*/ if (dotaxon) { MonitorStrValue (mon, "Closing Taxon"); Update (); TaxArchFini (); MonitorFree (mon); ArrowCursor (); Update (); } /*#endif*/ ConvertFullLenSourceFeatToDesc (sep); ConvertFullLenPubFeatToDesc (sep); /* EntryStripSerialNumber(sep); */ /* strip citation serial numbers */ MovePopPhyMutPubs (sep); EntryChangeGBSource (sep); /* remove redundant information in GBBlocks again */ EntryCheckGBBlock (sep); /* SeqEntryMoveDbxrefs (sep); */ /* db_xref gbqual to sfp->dbxref */ EntryMergeDupBioSources (sep); GetRidOfEmptyFeatsDescStrings (0, sep); GetRidOfLocusInSeqIds (0, sep); BasicSeqEntryCleanup (sep); ErrSetMessageLevel (sev); ErrClear (); ErrShow (); return rsult; } typedef struct partialformdata { FEATURE_FORM_BLOCK ValNodePtr featlist; LisT feature; PopuP change5; PopuP change3; GrouP nucprotchoice; Int2 subtype; Int2 leftpolicy; Int2 rightpolicy; Int2 nucprotpolicy; ObjMgrPtr omp; ObjMgrTypePtr omtp; } PartialFormData, PNTR PartialFormPtr; static void PartialCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { Boolean atEnd; ByteStorePtr bs; BioseqPtr bsp; BioseqSetPtr bssp; Char ch; Boolean dash_at_end; SeqLocPtr firstSlp; SeqLocPtr lastSlp; ObjMgrTypePtr omtp; Boolean partial5; Boolean partial3; PartialFormPtr pfp; CharPtr prot; CharPtr ptr; SeqAnnotPtr sap; SeqFeatPtr sfp; SeqLocPtr slp; Boolean star_at_end; Uint1 strand; Uint2 subtype; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; pfp = (PartialFormPtr) mydata; if (pfp == NULL) return; omtp = pfp->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; while (sap != NULL) { if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { subtype = (*(omtp->subtypefunc)) ((Pointer) sfp); if (pfp->subtype == 0 || subtype == pfp->subtype) { CheckSeqLocForPartial (sfp->location, &partial5, &partial3); dash_at_end = FALSE; star_at_end = FALSE; if (subtype == FEATDEF_CDS) { bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE); if (bs != NULL) { prot = BSMerge (bs, NULL); bs = BSFree (bs); if (prot != NULL) { ptr = prot; ch = *ptr; if (ch == '-') { dash_at_end = TRUE; } while (ch != '\0') { /* *ptr = TO_UPPER (ch); */ if (ch == '*') { star_at_end = TRUE; } else { star_at_end = FALSE; } ptr++; ch = *ptr; } prot = MemFree (prot); } } } firstSlp = NULL; lastSlp = NULL; slp = SeqLocFindNext (sfp->location, NULL); while (slp != NULL) { if (firstSlp == NULL) { firstSlp = slp; } lastSlp = slp; slp = SeqLocFindNext (sfp->location, slp); } if (firstSlp != NULL) { bsp = BioseqFind (SeqLocId (firstSlp)); if (bsp != NULL) { if (((pfp->nucprotpolicy == 1 || pfp->nucprotpolicy == 2) && ISA_na (bsp->mol)) || ((pfp->nucprotpolicy == 1 || pfp->nucprotpolicy == 3) && ISA_aa (bsp->mol))) { strand = SeqLocStrand (firstSlp); atEnd = FALSE; if (strand == Seq_strand_minus) { if (GetOffsetInBioseq (firstSlp, bsp, SEQLOC_START) == bsp->length - 1) { atEnd = TRUE; } } else { if (GetOffsetInBioseq (firstSlp, bsp, SEQLOC_START) == 0) { atEnd = TRUE; } } switch (pfp->leftpolicy) { case 1 : partial5 = TRUE; break; case 2 : if (atEnd) { partial5 = TRUE; } break; case 3 : if (dash_at_end && subtype == FEATDEF_CDS) { partial5 = TRUE; } break; case 4 : partial5 = FALSE; break; case 5 : if (! atEnd) { partial5 = FALSE; } break; case 6 : if ((! dash_at_end) && subtype == FEATDEF_CDS) { partial5 = FALSE; } break; default : break; } } } } if (lastSlp != NULL) { bsp = BioseqFind (SeqLocId (firstSlp)); if (bsp != NULL) { if (((pfp->nucprotpolicy == 1 || pfp->nucprotpolicy == 2) && ISA_na (bsp->mol)) || ((pfp->nucprotpolicy == 1 || pfp->nucprotpolicy == 3) && ISA_aa (bsp->mol))) { strand = SeqLocStrand (firstSlp); atEnd = FALSE; if (strand == Seq_strand_minus) { if (GetOffsetInBioseq (lastSlp, bsp, SEQLOC_STOP) == 0) { atEnd = TRUE; } } else { if (GetOffsetInBioseq (lastSlp, bsp, SEQLOC_STOP) == bsp->length - 1) { atEnd = TRUE; } } switch (pfp->rightpolicy) { case 1 : partial3 = TRUE; break; case 2 : if (atEnd) { partial3 = TRUE; } break; case 3 : if ((! star_at_end) && subtype == FEATDEF_CDS) { partial3 = TRUE; } break; case 4 : partial3 = FALSE; break; case 5 : if (! atEnd) { partial3 = FALSE; } break; case 6 : if (star_at_end && subtype == FEATDEF_CDS) { partial3 = FALSE; } break; default : break; } } } } SetSeqLocPartial (sfp->location, partial5, partial3); sfp->partial = (/* sfp->partial || */ partial5 || partial3 || LocationHasNullsBetween (sfp->location)); } sfp = sfp->next; } } sap = sap->next; } } static void DoEditPartials (ButtoN b) { PartialFormPtr pfp; SeqEntryPtr sep; Int2 val; ValNodePtr vnp; pfp = (PartialFormPtr) GetObjectExtra (b); if (pfp == NULL) return; sep = GetTopSeqEntryForEntityID (pfp->input_entityID); if (sep == NULL) return; Hide (pfp->form); WatchCursor (); Update (); pfp->leftpolicy = GetValue (pfp->change5); pfp->rightpolicy = GetValue (pfp->change3); pfp->nucprotpolicy = GetValue (pfp->nucprotchoice); val = GetValue (pfp->feature); vnp = NULL; if (val > 0) { vnp = pfp->featlist; while (vnp != NULL && val > 1) { val--; vnp = vnp->next; } } if (vnp != NULL) { pfp->subtype = vnp->choice; } else { pfp->subtype = 0; } pfp->omp = ObjMgrGet (); pfp->omtp = NULL; if (pfp->omp != NULL) { pfp->omtp = ObjMgrTypeFind (pfp->omp, OBJ_SEQFEAT, NULL, NULL); } SeqEntryExplore (sep, (Pointer) pfp, PartialCallback); ArrowCursor (); Update (); ObjMgrSetDirtyFlag (pfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, pfp->input_entityID, 0, 0); Remove (pfp->form); } static void PartialMessageProc (ForM f, Int2 mssg) { PartialFormPtr pfp; pfp = (PartialFormPtr) GetObjectExtra (f); if (pfp != NULL) { if (pfp->appmessage != NULL) { pfp->appmessage (f, mssg); } } } static void CleanupPartialPage (GraphiC g, VoidPtr data) { PartialFormPtr pfp; pfp = (PartialFormPtr) data; if (pfp != NULL) { ValNodeFreeData (pfp->featlist); } StdCleanupFormProc (g, data); } extern void EditFeaturePartials (IteM i) { BaseFormPtr bfp; ButtoN b; GrouP c; FeatDefPtr curr; GrouP g; GrouP h; ValNodePtr head; GrouP k; Uint1 key; CharPtr label = NULL; Int2 listHeight; PartialFormPtr pfp; SeqEntryPtr sep; StdEditorProcsPtr sepp; Uint2 subtype; ValNodePtr vnp; WindoW w; GrouP x; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; pfp = (PartialFormPtr) MemNew (sizeof (PartialFormData)); if (pfp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Feature Partial Editor", StdCloseWindowProc); SetObjectExtra (w, pfp, CleanupPartialPage); pfp->form = (ForM) w; pfp->formmessage = PartialMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); pfp->appmessage = sepp->handleMessages; } pfp->input_entityID = bfp->input_entityID; pfp->input_itemID = bfp->input_itemID; pfp->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; } pfp->feature = 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 (pfp->feature, (CharPtr) vnp->data.ptrvalue); } } pfp->featlist = head; k = HiddenGroup (h, 2, 0, NULL); StaticPrompt (k, "5' policy", 0, stdLineHeight, programFont, 'l'); pfp->change5 = PopupList (k, TRUE, NULL); PopupItem (pfp->change5, "Set"); PopupItem (pfp->change5, "Set only if at 5' end"); PopupItem (pfp->change5, "Set if bad start codon"); PopupItem (pfp->change5, "Clear"); PopupItem (pfp->change5, "Clear if not at 5' end"); PopupItem (pfp->change5, "Clear if good start codon"); PopupItem (pfp->change5, "Do not change"); SetValue (pfp->change5, 7); StaticPrompt (k, "3' policy", 0, stdLineHeight, programFont, 'l'); pfp->change3 = PopupList (k, TRUE, NULL); PopupItem (pfp->change3, "Set"); PopupItem (pfp->change3, "Set only if at 3' end"); PopupItem (pfp->change3, "Set if bad stop codon"); PopupItem (pfp->change3, "Clear"); PopupItem (pfp->change3, "Clear if not at 3' end"); PopupItem (pfp->change3, "Clear if good stop codon"); PopupItem (pfp->change3, "Do not change"); SetValue (pfp->change3, 7); x = HiddenGroup (h, 2, 0, NULL); /* StaticPrompt (x, "Constraints", 0, stdLineHeight, programFont, 'l'); */ pfp->nucprotchoice = HiddenGroup (x, 4, 0, NULL); RadioButton (pfp->nucprotchoice, "All Sequences"); RadioButton (pfp->nucprotchoice, "Nucleotides"); RadioButton (pfp->nucprotchoice, "Proteins"); SetValue (pfp->nucprotchoice, 1); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoEditPartials); SetObjectExtra (b, pfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) k, (HANDLE) x, (HANDLE) c, NULL); RealizeWindow (w); Show (w); Update (); } /* static Boolean AddOrgToDefGatherFunc (GatherContextPtr gcp) { CharPtr def; CharPtr ptr; ValNodePtr sdp; CharPtr str; CharPtr text; if (gcp == NULL || gcp->thisitem == NULL) return TRUE; if (gcp->thistype != OBJ_SEQDESC) return TRUE; text = (CharPtr) gcp->userdata; if (text == NULL || StringHasNoText (text)) return TRUE; sdp = (ValNodePtr) gcp->thisitem; if (sdp->choice != Seq_descr_title) return TRUE; def = (CharPtr) sdp->data.ptrvalue; if (StringHasNoText (def)) return TRUE; ptr = StringISearch (def, text); if (ptr != NULL && ptr == def) return TRUE; str = MemNew ((StringLen (text) + StringLen (def) + 4) * sizeof (Char)); if (str != NULL) { StringCpy (str, text); StringCat (str, " "); StringCat (str, def); sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue); sdp->data.ptrvalue = str; ObjMgrSetDirtyFlag (gcp->entityID, TRUE); } return TRUE; } */ static void AppendOrgToString (Uint2 entityID, SeqDescrPtr sdp, CharPtr text) { CharPtr def; CharPtr ptr; CharPtr str; def = (CharPtr) sdp->data.ptrvalue; if (StringHasNoText (def)) return; ptr = StringISearch (def, text); if (ptr != NULL && ptr == def) return; str = MemNew ((StringLen (text) + StringLen (def) + 4) * sizeof (Char)); if (str != NULL) { StringCpy (str, text); StringCat (str, " "); StringCat (str, def); sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue); sdp->data.ptrvalue = str; ObjMgrSetDirtyFlag (entityID, TRUE); } } static void AddOrgToDefElement (Uint2 entityID, SeqEntryPtr sep, Int2 orgmod, Int2 subsource) { EnumFieldAssocPtr ap; BioSourcePtr biop; BioseqPtr bsp; BioseqSetPtr bssp; Char ch; SeqMgrDescContext dcontext; OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; CharPtr ptr; SeqDescrPtr sdp; SubSourcePtr ssp; Char str [96]; Char text [64]; CharPtr title; if (sep == NULL) return; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && (bssp->_class == 1 || bssp->_class == 2 || bssp->_class == 4)) { for (sep = bssp->seq_set; sep != NULL; sep = sep->next) { AddOrgToDefElement (entityID, sep, orgmod, subsource); } return; } } if (! IS_Bioseq (sep)) return; bsp = (BioseqPtr) sep->data.ptrvalue; biop = NULL; text [0] = '\0'; str [0] = '\0'; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext); if (sdp != NULL) { biop = (BioSourcePtr) sdp->data.ptrvalue; } if (biop == NULL) return; /* SeqEntryToBioSource (sep, NULL, str, sizeof (str) - 1, &biop); */ if (orgmod == 0 && subsource == 0) { orp = biop->org; if (orp == NULL) return; StringNCpy_0 (str, orp->taxname, sizeof (str)); ptr = StringSearch (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]); } else if (biop != NULL && biop->org != NULL) { text [0] = '\0'; str [0] = '\0'; orp = biop->org; if (orgmod > 0) { onp = orp->orgname; if (onp != NULL) { mod = onp->mod; while (mod != NULL) { if (mod->subtype == orgmod) { StringNCpy_0 (text, mod->subname, sizeof (text)); for (ap = orgmod_subtype_alist; ap->name != NULL; ap++) { if (ap->value == orgmod) { StringNCpy_0 (str, ap->name, sizeof (str)); } } } mod = mod->next; } } } else if (subsource > 0) { ssp = biop->subtype; while (ssp != NULL) { if (ssp->subtype == subsource) { StringNCpy_0 (text, ssp->name, sizeof (text)); for (ap = subsource_subtype_alist; ap->name != NULL; ap++) { if (ap->value == subsource) { StringNCpy_0 (str, ap->name, sizeof (str)); } } } ssp = ssp->next; } } if (StringHasNoText (text)) { str [0] = '\0'; text [0] = '\0'; } else { StringCat (str, " "); ptr = str; while (*ptr != '\0') { ch = *ptr; *ptr = TO_LOWER (ch); ptr++; } StringCat (str, text); } } /* 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_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQDESC] = FALSE; gs.scope = sep; GatherSeqEntry (sep, (Pointer) str, AddOrgToDefGatherFunc, &gs); */ sdp = SeqEntryGetSeqDescr (sep, Seq_descr_title, NULL); if (sdp == NULL) { sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_title, &dcontext); if (sdp == NULL) return; title = (CharPtr) sdp->data.ptrvalue; if (title == NULL) return; sdp = SeqDescrAdd (&(bsp->descr)); if (sdp == NULL) return; sdp->choice = Seq_descr_title; sdp->data.ptrvalue = StringSave (title); } if (sdp == NULL) return; AppendOrgToString (entityID, sdp, str); } static void AddOrgToDef (Uint2 entityID, SeqEntryPtr sep, Int2 orgmod, Int2 subsource) { BioseqSetPtr bssp; 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) { AddOrgToDef (entityID, sep, orgmod, subsource); } return; } } AddOrgToDefElement (entityID, sep, orgmod, subsource); } extern void CommonAddOrgOrModsToDefLines (IteM i, Int2 orgmod, Int2 subsource, ButtoN b) { BaseFormPtr bfp; SeqEntryPtr sep; 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; WatchCursor (); Update (); AddOrgToDef (bfp->input_entityID, sep, orgmod, subsource); ArrowCursor (); Update (); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); } static void RemoveAlignmentCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; SeqAlignPtr nextsalp; SeqAnnotPtr nextsap; Pointer PNTR prevsalp; Pointer PNTR prevsap; SeqAlignPtr salp; SeqAnnotPtr sap; if (sep == NULL || sep->data.ptrvalue == 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; while (sap != NULL) { nextsap = sap->next; if (sap->type == 2) { salp = (SeqAlignPtr) sap->data; prevsalp = (Pointer PNTR) &(sap->data); while (salp != NULL) { nextsalp = salp->next; if (salp->type <= 255) { *(prevsalp) = salp->next; salp->next = NULL; SeqAlignFree (salp); } else { prevsalp = (Pointer PNTR) &(salp->next); } salp = nextsalp; } } if (sap->data == NULL) { *(prevsap) = sap->next; sap->next = NULL; SeqAnnotFree (sap); } else { prevsap = (Pointer PNTR) &(sap->next); } sap = nextsap; } } extern void RemoveAlignment (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; SeqEntryExplore (sep, NULL, RemoveAlignmentCallback); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); ObjMgrDeSelect (0, 0, 0, 0, NULL); Update (); } static void RemoveGraphCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; SeqAnnotPtr nextsap; SeqGraphPtr nextsgp; Pointer PNTR prevsap; Pointer PNTR prevsgp; SeqAnnotPtr sap; SeqGraphPtr sgp; if (sep == NULL || sep->data.ptrvalue == 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; while (sap != NULL) { nextsap = sap->next; if (sap->type == 3) { sgp = (SeqGraphPtr) sap->data; prevsgp = (Pointer PNTR) &(sap->data); while (sgp != NULL) { nextsgp = sgp->next; if (sgp->flags [2] >= 1 && sgp->flags [2] <= 3) { *(prevsgp) = sgp->next; sgp->next = NULL; SeqGraphFree (sgp); } else { prevsgp = (Pointer PNTR) &(sgp->next); } sgp = nextsgp; } } if (sap->data == NULL) { *(prevsap) = sap->next; sap->next = NULL; SeqAnnotFree (sap); } else { prevsap = (Pointer PNTR) &(sap->next); } sap = nextsap; } } extern void RemoveGraph (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; SeqEntryExplore (sep, NULL, RemoveGraphCallback); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); ObjMgrDeSelect (0, 0, 0, 0, NULL); Update (); } static void MarkProteinCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; ValNodePtr PNTR vnpp; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; vnpp = (ValNodePtr PNTR) mydata; if (vnpp == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (ISA_aa (bsp->mol)) { ValNodeAddPointer (vnpp, 0, (Pointer) bsp); } } } extern void RemoveProteins (IteM i) { BaseFormPtr bfp; BioseqPtr bsp; Uint2 itemID; ObjMgrDataPtr omdptop; ObjMgrData omdata; OMProcControl ompc; Uint2 parenttype; Pointer parentptr; SeqEntryPtr sep; ValNodePtr tmp; ValNodePtr vnp; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; SaveSeqEntryObjMgrData (sep, &omdptop, &omdata); GetSeqEntryParent (sep, &parentptr, &parenttype); vnp = NULL; SeqEntryExplore (sep, (Pointer) &vnp, MarkProteinCallback); for (tmp = vnp; tmp != NULL; tmp = tmp->next) { bsp = (BioseqPtr) tmp->data.ptrvalue; itemID = GetItemIDGivenPointer (bfp->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 = bfp->input_entityID; ompc.input_itemID = itemID; ompc.input_itemtype = OBJ_BIOSEQ; if (! DetachDataForProc (&ompc, FALSE)) { Message (MSG_POSTERR, "DetachDataForProc failed"); } } } ValNodeFree (vnp); SeqMgrLinkSeqEntry (sep, parenttype, parentptr); RestoreSeqEntryObjMgrData (sep, omdptop, &omdata); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); ObjMgrDeSelect (0, 0, 0, 0, NULL); Update (); }