/* sequin6.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: sequin6.c * * Author: Jonathan Kans * * Version Creation Date: 11/12/97 * * $Revision: 6.58 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include "sequin.h" #include #include #include #include #include #include static ENUM_ALIST(target_field_alist) {" ", 0}, {"Gene", 1}, {"CDS", 2}, {"Prot", 3}, {"RNA", 4}, {"BioSource", 5}, {"OrgMod", 6}, {"SubSource", 7}, END_ENUM_ALIST static ENUM_ALIST(ext_target_field_alist) {" ", 0}, {"Gene", 1}, {"CDS", 2}, {"Prot", 3}, {"RNA", 4}, {"BioSource", 5}, {"OrgMod", 6}, {"SubSource", 7}, {"Feature Note", 8}, END_ENUM_ALIST static ENUM_ALIST(gene_field_alist) {" ", 0}, {"Gene locus", 1}, {"Gene description", 2}, {"Gene allele", 3}, {"Gene maploc", 4}, {"Gene synonym", 5}, {"Gene comment", 6}, END_ENUM_ALIST static ENUM_ALIST(cds_field_alist) {" ", 0}, {"CDS comment", 1}, {"gene xref", 2}, {"db_xref", 3}, END_ENUM_ALIST static ENUM_ALIST(prot_field_alist) {" ", 0}, {"Protein name", 1}, {"Protein description", 2}, {"Protein E.C. number", 3}, {"Protein activity", 4}, {"Protein comment", 5}, END_ENUM_ALIST static ENUM_ALIST(rnax_field_alist) {" ", 0}, {"RNA Name", 1}, {"RNA Comment", 2}, {"gene xref", 3}, END_ENUM_ALIST static ENUM_ALIST(orgref_field_alist) {" ", 0}, {"Scientific Name", 1}, {"Common Name", 2}, {"Lineage", 3}, {"Division", 4}, END_ENUM_ALIST static ENUM_ALIST(orgmod_note_subtype_alist) {" ", 0}, {"Strain", 2}, {"Substrain", 3}, {"Type", 4}, {"Subtype", 5}, {"Variety", 6}, {"Serotype", 7}, {"Serogroup", 8}, {"Serovar", 9}, {"Cultivar", 10}, {"Pathovar", 11}, {"Chemovar", 12}, {"Biovar", 13}, {"Biotype", 14}, {"Group", 15}, {"Subgroup", 16}, {"Isolate", 17}, {"Common", 18}, {"Acronym", 19}, {"Dosage", 20}, {"Natural-host", 21}, {"Sub-species", 22}, {"Specimen-voucher", 23}, {"Authority", 24}, {"Forma", 25}, {"Forma-specialis", 26}, {"Ecotype", 27}, {"Synonym", 28}, {"Anamorph", 29}, {"Teleomorph", 30}, {"Breed", 31}, {"Old Lineage", 253}, {"Old Name", 254}, {"Note", 255}, END_ENUM_ALIST static ENUM_ALIST(subsource_note_subtype_alist) {" ", 0}, {"Chromosome", 1}, {"Map", 2}, {"Clone", 3}, {"Subclone", 4}, {"Haplotype", 5}, {"Genotype", 6}, {"Sex", 7}, {"Cell-line", 8}, {"Cell-type", 9}, {"Tissue-type", 10}, {"Clone-lib", 11}, {"Dev-stage", 12}, {"Frequency", 13}, {"Germline", 14}, {"Rearranged", 15}, {"Lab-host", 16}, {"Pop-variant", 17}, {"Tissue-lib", 18}, {"Plasmid-name", 19}, {"Transposon-name", 20}, {"Ins-seq-name", 21}, {"Plastid-name", 22}, {"Country", 23}, {"Segment", 24}, {"Endogenous-virus-name", 25}, {"Transgenic", 26}, {"Environmental-sample", 27}, {"Isolation-source", 28}, {"Note", 255}, END_ENUM_ALIST extern EnumFieldAssoc orgmod_subtype_alist []; extern EnumFieldAssoc subsource_subtype_alist []; #define NUM_SUBTARGET_POPUPS 10 typedef struct convertformdata { FEATURE_FORM_BLOCK GrouP asnOrFlat; TexT atleft; TexT atright; PopuP target; PopuP subtarget [NUM_SUBTARGET_POPUPS]; EnumFieldAssocPtr alists [NUM_SUBTARGET_POPUPS]; ButtoN accept; Int2 report; Int2 type; Int2 subtype; CharPtr leftstr; CharPtr rightstr; CharPtr foundstr; GrouP leftbehav; GrouP rightbehav; Boolean includeleft; Boolean includeright; Boolean replaceOldAsked; Boolean doReplaceAll; Int2 index; } ConvertFormData, PNTR ConvertFormPtr; static Boolean ShouldReplaceParsedString (ConvertFormPtr cfp) { MsgAnswer ans; if (cfp == NULL) return FALSE; if (! cfp->replaceOldAsked) { cfp->replaceOldAsked = TRUE; ArrowCursor (); Update (); ans = Message (MSG_YN, "Do you wish to overwrite existing contents?"); WatchCursor (); Update (); cfp->doReplaceAll = (Boolean) (ans == ANS_YES); } return cfp->doReplaceAll; } static CharPtr SaveOrReplaceStringCopy (ConvertFormPtr cfp, CharPtr str, CharPtr current) { size_t len; CharPtr tmp; if (cfp == NULL) return NULL; if (StringHasNoText (str)) return current; if (current != NULL) { if (ShouldReplaceParsedString (cfp)) { MemFree (current); } else { len = StringLen (str) + StringLen (current) + 4; tmp = MemNew (len); if (tmp != NULL) { StringCpy (tmp, current); StringCat (tmp, "; "); StringCat (tmp, str); /* str is within asn2ff string, so must not MemFree (str); */ MemFree (current); return tmp; } } } return StringSave (str); } static void ConvertAFeatureField (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; ConvertFormPtr cfp; GBQualPtr gbq; GeneRefPtr grp; ProtRefPtr prp; RnaRefPtr rrp; SeqAnnotPtr sap; SeqFeatPtr sfp; ValNodePtr vnp; SeqFeatXrefPtr xref; if (sep == NULL || sep->data.ptrvalue == NULL) return; cfp = (ConvertFormPtr) mydata; if (cfp == 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) { if (sfp->data.choice == SEQFEAT_GENE && cfp->type == 1) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp != NULL) { switch (cfp->subtype) { case 1 : grp->locus = SaveOrReplaceStringCopy (cfp, cfp->foundstr, grp->locus); break; case 2 : grp->desc = SaveOrReplaceStringCopy (cfp, cfp->foundstr, grp->desc); break; case 3 : grp->allele = SaveOrReplaceStringCopy (cfp, cfp->foundstr, grp->allele); break; case 4 : grp->maploc = SaveOrReplaceStringCopy (cfp, cfp->foundstr, grp->maploc); break; case 5 : if (! StringHasNoText (cfp->foundstr)) { if (grp->syn != NULL && ShouldReplaceParsedString (cfp)) { vnp = grp->syn; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = StringSave (cfp->foundstr); } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = grp->syn; grp->syn = vnp; vnp->data.ptrvalue = StringSave (cfp->foundstr);; } } } break; case 6 : sfp->comment = SaveOrReplaceStringCopy (cfp, cfp->foundstr, sfp->comment); break; default : break; } } } else if (sfp->data.choice == SEQFEAT_CDREGION && cfp->type == 2) { switch (cfp->subtype) { case 1 : sfp->comment = SaveOrReplaceStringCopy (cfp, cfp->foundstr, sfp->comment); break; case 2 : if (! StringHasNoText (cfp->foundstr)) { xref = SeqFeatXrefNew (); if (xref != NULL) { grp = CreateNewGeneRef (cfp->foundstr, NULL, NULL, FALSE); if (grp != NULL) { xref->data.choice = SEQFEAT_GENE; xref->data.value.ptrvalue = grp; xref->next = sfp->xref; sfp->xref = xref; } } } break; case 3 : gbq = GBQualNew (); if (gbq != NULL) { /* BasicSeqEntryCleanup will convert to real sfp->dbxref */ gbq->qual = StringSave ("db_xref"); gbq->val = StringSave (cfp->foundstr); gbq->next = sfp->qual; sfp->qual = gbq; } break; default : break; } } else if (sfp->data.choice == SEQFEAT_PROT && cfp->type == 3) { prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp != NULL) { switch (cfp->subtype) { case 1 : if (! StringHasNoText (cfp->foundstr)) { if (prp->name != NULL && ShouldReplaceParsedString (cfp)) { vnp = prp->name; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = StringSave (cfp->foundstr); } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = prp->name; prp->name = vnp; vnp->data.ptrvalue = StringSave (cfp->foundstr); } } } break; case 2 : prp->desc = SaveOrReplaceStringCopy (cfp, cfp->foundstr, prp->desc); break; case 3 : if (! StringHasNoText (cfp->foundstr)) { if (prp->ec != NULL && ShouldReplaceParsedString (cfp)) { vnp = prp->ec; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = StringSave (cfp->foundstr); } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = prp->ec; prp->ec = vnp; vnp->data.ptrvalue = StringSave (cfp->foundstr); } } } break; case 4 : if (! StringHasNoText (cfp->foundstr)) { if (prp->activity != NULL && ShouldReplaceParsedString (cfp)) { vnp = prp->activity; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = StringSave (cfp->foundstr); } else { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->next = prp->activity; prp->activity = vnp; vnp->data.ptrvalue = StringSave (cfp->foundstr); } } } break; case 5 : sfp->comment = SaveOrReplaceStringCopy (cfp, cfp->foundstr, sfp->comment); break; default : break; } } } else if (sfp->data.choice == SEQFEAT_RNA && cfp->type == 4) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp != NULL) { switch (cfp->subtype) { case 1 : if (rrp->ext.choice == 0 || rrp->ext.choice == 1) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = SaveOrReplaceStringCopy (cfp, cfp->foundstr, rrp->ext.value.ptrvalue); } break; case 2 : sfp->comment = SaveOrReplaceStringCopy (cfp, cfp->foundstr, sfp->comment); break; case 3 : if (! StringHasNoText (cfp->foundstr)) { xref = SeqFeatXrefNew (); if (xref != NULL) { grp = CreateNewGeneRef (cfp->foundstr, NULL, NULL, FALSE); if (grp != NULL) { xref->data.choice = SEQFEAT_GENE; xref->data.value.ptrvalue = grp; xref->next = sfp->xref; sfp->xref = xref; } } } default : break; } } } else if (cfp->type == 8) { if (cfp->subtype == sfp->idx.subtype) { sfp->comment = SaveOrReplaceStringCopy (cfp, cfp->foundstr, sfp->comment); } } sfp = sfp->next; } } sap = sap->next; } } static void ConvertASourceField (BioSourcePtr biop, ConvertFormPtr cfp) { OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; SubSourcePtr ssp; OrgModPtr tmpmod; SubSourcePtr tmpssp; if (biop == NULL || cfp == NULL) return; switch (cfp->type) { case 5 : orp = biop->org; if (orp == NULL) return; switch (cfp->subtype) { case 1 : orp->taxname = SaveOrReplaceStringCopy (cfp, cfp->foundstr, orp->taxname); break; case 2 : orp->common = SaveOrReplaceStringCopy (cfp, cfp->foundstr, orp->common); break; case 3 : onp = orp->orgname; if (onp == NULL) { onp = OrgNameNew (); orp->orgname = onp; } if (onp != NULL) { onp->lineage = SaveOrReplaceStringCopy (cfp, cfp->foundstr, onp->lineage); } break; case 4 : onp = orp->orgname; if (onp == NULL) { onp = OrgNameNew (); orp->orgname = onp; } if (onp != NULL) { onp->div = SaveOrReplaceStringCopy (cfp, cfp->foundstr, onp->div); } break; default : break; } break; case 6 : orp = biop->org; if (orp == NULL) { orp = OrgRefNew (); biop->org = orp; } if (orp != NULL) { onp = orp->orgname; if (onp == NULL) { onp = OrgNameNew (); orp->orgname = onp; } if (onp != NULL) { mod = onp->mod; while (mod != NULL && mod->subtype != cfp->subtype) { mod = mod->next; } if (mod == NULL) { mod = OrgModNew (); if (onp->mod == NULL) { onp->mod = mod; } else { tmpmod = onp->mod; while (tmpmod->next != NULL) { tmpmod = tmpmod->next; } tmpmod->next = mod; } } if (mod != NULL) { mod->subtype = cfp->subtype; mod->subname = SaveOrReplaceStringCopy (cfp, cfp->foundstr, mod->subname); } } } break; case 7 : ssp = biop->subtype; while (ssp != NULL && ssp->subtype != cfp->subtype) { ssp = ssp->next; } if (ssp == NULL) { ssp = SubSourceNew (); if (biop->subtype == NULL) { biop->subtype = ssp; } else { tmpssp = biop->subtype; while (tmpssp->next != NULL) { tmpssp = tmpssp->next; } tmpssp->next = ssp; } } if (ssp != NULL) { ssp->subtype = cfp->subtype; ssp->name = SaveOrReplaceStringCopy (cfp, cfp->foundstr, ssp->name); } break; default : break; } } static void FoundStringForConversion (Uint2 entityID, SeqEntryPtr sep, ConvertFormPtr cfp, CharPtr str) { BioSourcePtr biop; OrgRefPtr orp; ValNodePtr vnp; cfp->foundstr = str; switch (cfp->type) { case 1 : case 2 : case 3 : case 4 : SeqEntryExplore (sep, (Pointer) cfp, ConvertAFeatureField); break; case 5 : SeqEntryToBioSource (sep, NULL, NULL, 0, &biop); if (biop == NULL && cfp->subtype == 1) { biop = BioSourceNew (); if (biop == NULL) return; orp = OrgRefNew (); biop->org = orp; vnp = CreateNewDescriptor (sep, Seq_descr_source); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) biop; } } ConvertASourceField (biop, cfp); break; case 6 : case 7 : SeqEntryToBioSource (sep, NULL, NULL, 0, &biop); ConvertASourceField (biop, cfp); break; case 8 : SeqEntryExplore (sep, (Pointer) cfp, ConvertAFeatureField); break; default : break; } } static void ConvertFromFlatFile (Uint2 entityID, SeqEntryPtr sep, ConvertFormPtr cfp, Uint1 format) { Asn2ffJobPtr ajp; Boolean goOn; Int4 index; ErrSev level; CharPtr lft = NULL; Boolean okay; FFPrintArrayPtr pap = NULL; Int4 pap_size; CharPtr rgt = NULL; CharPtr string; CharPtr tmp; ajp = (Asn2ffJobPtr) MemNew (sizeof (Asn2ffJob)); if (ajp == NULL) return; level = ErrSetMessageLevel (SEV_MAX); ajp->sep = sep; ajp->mode = SEQUIN_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) || IsSegmentedBioseqWithoutParts (sep)) { ajp->only_one = TRUE; ajp->genome_view = TRUE; } ajp->bankit = TRUE; pap_size = asn2ff_setup (ajp, &pap); if (pap_size > 0) { asn2ff_set_output (NULL, "\n"); goOn = TRUE; for (index = 0; index < pap_size && goOn; index++) { string = FFPrint (pap, index, pap_size); if (string != NULL && *string != '\0') { CompressSpaces (string); okay = TRUE; tmp = string; if (cfp->leftstr != NULL && cfp->leftstr [0] != '\0') { lft = SearchForString (string, cfp->leftstr, FALSE, FALSE); if (lft != NULL) { if (! cfp->includeleft) { lft += StringLen (cfp->leftstr); } tmp = lft; } else { okay = FALSE; } } if (cfp->rightstr != NULL && cfp->rightstr [0] != '\0') { rgt = SearchForString (tmp, cfp->rightstr, FALSE, FALSE); if (rgt != NULL) { if (cfp->includeright) { rgt += StringLen (cfp->rightstr); } *rgt = '\0'; } else { okay = FALSE; } } if (okay) { if (lft != NULL) { lft = tmp; } else { lft = string; } if (! StringHasNoText (lft)) { FoundStringForConversion (entityID, sep, cfp, lft); goOn = FALSE; } } } MemFree (string); } MemFree (pap); } asn2ff_cleanup (ajp); MemFree (ajp); ErrSetMessageLevel (level); } static void DoOneConvert (Uint2 entityID, SeqEntryPtr sep, ConvertFormPtr cfp, MonitorPtr mon) { BioseqSetPtr bssp; Char str [64]; if (sep == NULL || cfp == 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) { DoOneConvert (entityID, sep, cfp, mon); } return; } } (cfp->index)++; if (mon != NULL) { sprintf (str, "Parsing component %d", (int) cfp->index); MonitorStrValue (mon, str); } switch (cfp->report) { case 1 : ConvertFromFlatFile (entityID, sep, cfp, GENBANK_FMT); break; case 2 : ConvertFromFlatFile (entityID, sep, cfp, EMBL_FMT); break; default : break; } } static void SearchAndExciseText (CharPtr PNTR strptr, ConvertFormPtr cfp) { Char ch; CharPtr lft = NULL; CharPtr rgt = NULL; CharPtr string; CharPtr tmp; if (strptr == NULL || cfp == NULL) return; string = *strptr; if (string == NULL) return; tmp = string; if (cfp->leftstr != NULL && cfp->leftstr [0] != '\0') { lft = SearchForString (string, cfp->leftstr, FALSE, FALSE); if (lft == NULL) return; if (! cfp->includeleft) { lft += StringLen (cfp->leftstr); } tmp = lft; } if (cfp->rightstr != NULL && cfp->rightstr [0] != '\0') { rgt = SearchForString (tmp, cfp->rightstr, FALSE, FALSE); if (rgt == NULL) return; if (cfp->includeright) { rgt += StringLen (cfp->rightstr); } } if (lft != NULL) { *tmp = '\0'; lft = tmp; } else { lft = string; } if (rgt != NULL) { ch = *rgt; while (ch != '\0') { *lft = ch; rgt++; lft++; ch = *rgt; } *lft = '\0'; } } static void RemoveAFeatureText (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; ConvertFormPtr cfp; GeneRefPtr grp; ProtRefPtr prp; RnaRefPtr rrp; SeqAnnotPtr sap; SeqFeatPtr sfp; CharPtr PNTR strp; ValNodePtr vnp; if (sep == NULL || sep->data.ptrvalue == NULL) return; cfp = (ConvertFormPtr) mydata; if (cfp == 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) { if (sfp->data.choice == SEQFEAT_GENE && cfp->type == 1) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp != NULL) { switch (cfp->subtype) { case 1 : SearchAndExciseText (&grp->locus, cfp); break; case 2 : SearchAndExciseText (&grp->desc, cfp); break; case 3 : SearchAndExciseText (&grp->allele, cfp); break; case 4 : SearchAndExciseText (&grp->maploc, cfp); break; case 5 : for (vnp = grp->syn; vnp != NULL; vnp = vnp->next) { strp = (CharPtr PNTR) &vnp->data.ptrvalue; SearchAndExciseText (strp, cfp); } break; case 6 : SearchAndExciseText (&sfp->comment, cfp); break; default : break; } } } else if (sfp->data.choice == SEQFEAT_CDREGION && cfp->type == 2) { switch (cfp->subtype) { case 1 : SearchAndExciseText (&sfp->comment, cfp); break; case 2 : break; default : break; } } else if (sfp->data.choice == SEQFEAT_PROT && cfp->type == 3) { prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp != NULL) { switch (cfp->subtype) { case 1 : for (vnp = prp->name; vnp != NULL; vnp = vnp->next) { strp = (CharPtr PNTR) &vnp->data.ptrvalue; SearchAndExciseText (strp, cfp); } break; case 2 : SearchAndExciseText (&prp->desc, cfp); break; case 3 : for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { strp = (CharPtr PNTR) &vnp->data.ptrvalue; SearchAndExciseText (strp, cfp); } break; case 4 : for (vnp = prp->activity; vnp != NULL; vnp = vnp->next) { strp = (CharPtr PNTR) &vnp->data.ptrvalue; SearchAndExciseText (strp, cfp); } break; case 5 : SearchAndExciseText (&sfp->comment, cfp); break; default : break; } } } else if (sfp->data.choice == SEQFEAT_RNA && cfp->type == 4) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp != NULL) { switch (cfp->subtype) { case 1 : if (rrp->ext.choice == 0 || rrp->ext.choice == 1) { rrp->ext.choice = 1; strp = (CharPtr PNTR) &rrp->ext.value.ptrvalue; SearchAndExciseText (strp, cfp); } break; case 2 : SearchAndExciseText (&sfp->comment, cfp); break; case 3 : default : break; } } } sfp = sfp->next; } } sap = sap->next; } } static void RemoveASourceText (BioSourcePtr biop, ConvertFormPtr cfp) { OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; SubSourcePtr ssp; if (biop == NULL || cfp == NULL) return; switch (cfp->type) { case 5 : orp = biop->org; if (orp == NULL) return; switch (cfp->subtype) { case 1 : SearchAndExciseText (&orp->taxname, cfp); break; case 2 : SearchAndExciseText (&orp->common, cfp); break; case 3 : onp = orp->orgname; if (onp == NULL) { onp = OrgNameNew (); orp->orgname = onp; } if (onp != NULL) { SearchAndExciseText (&onp->lineage, cfp); } break; case 4 : onp = orp->orgname; if (onp == NULL) { onp = OrgNameNew (); orp->orgname = onp; } if (onp != NULL) { SearchAndExciseText (&onp->div, cfp); } break; default : break; } break; case 6 : orp = biop->org; if (orp == NULL) { orp = OrgRefNew (); biop->org = orp; } if (orp != NULL) { onp = orp->orgname; if (onp == NULL) { onp = OrgNameNew (); orp->orgname = onp; } if (onp != NULL) { mod = onp->mod; while (mod != NULL && mod->subtype != cfp->subtype) { mod = mod->next; } if (mod != NULL) { SearchAndExciseText (&mod->subname, cfp); } } } break; case 7 : ssp = biop->subtype; while (ssp != NULL && ssp->subtype != cfp->subtype) { ssp = ssp->next; } if (ssp != NULL) { SearchAndExciseText (&ssp->name, cfp); } break; default : break; } } static void DoOneRemoveText (Uint2 entityID, SeqEntryPtr sep, ConvertFormPtr cfp, MonitorPtr mon) { BioSourcePtr biop; BioseqSetPtr bssp; Char str [64]; if (sep == NULL || cfp == 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) { DoOneRemoveText (entityID, sep, cfp, mon); } return; } } (cfp->index)++; if (mon != NULL) { sprintf (str, "Processing component %d", (int) cfp->index); MonitorStrValue (mon, str); } switch (cfp->type) { case 1 : case 2 : case 3 : case 4 : SeqEntryExplore (sep, (Pointer) cfp, RemoveAFeatureText); break; case 5 : SeqEntryToBioSource (sep, NULL, NULL, 0, &biop); RemoveASourceText (biop, cfp); break; case 6 : case 7 : SeqEntryToBioSource (sep, NULL, NULL, 0, &biop); RemoveASourceText (biop, cfp); break; default : break; } } static CharPtr SaveStringFromTextNoStripSpaces (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); return str; } else { return NULL; } } else { return NULL; } } static void DoConvertProc (ButtoN b) { ConvertFormPtr cfp; MonitorPtr mon; SeqEntryPtr sep; UIEnum val; cfp = (ConvertFormPtr) GetObjectExtra (b); if (cfp == NULL || cfp->input_entityID == 0) return; sep = GetTopSeqEntryForEntityID (cfp->input_entityID); if (sep == NULL) return; Hide (cfp->form); WatchCursor (); Update (); if (GetEnumPopup (cfp->target, ext_target_field_alist, &val) && val > 0) { cfp->type = (Int2) val; if (GetEnumPopup (cfp->subtarget [cfp->type], cfp->alists [cfp->type], &val) && val > 0) { cfp->subtype = (Int2) val; cfp->report = GetValue (cfp->asnOrFlat); if (cfp->report > 0) { cfp->leftstr = SaveStringFromTextNoStripSpaces (cfp->atleft); cfp->rightstr = SaveStringFromTextNoStripSpaces (cfp->atright); cfp->includeleft = (Boolean) (GetValue (cfp->leftbehav) == 2); cfp->includeright = (Boolean) (GetValue (cfp->rightbehav) == 2); mon = MonitorStrNewEx ("Parsing Text From FlatFile", 20, FALSE); cfp->index = 0; DoOneConvert (cfp->input_entityID, sep, cfp, mon); MonitorFree (mon); cfp->leftstr = MemFree (cfp->leftstr); cfp->rightstr = MemFree (cfp->rightstr); } } } ArrowCursor (); Update (); ObjMgrSetDirtyFlag (cfp->input_entityID, TRUE); BasicSeqEntryCleanup (sep); ObjMgrSendMsg (OM_MSG_UPDATE, cfp->input_entityID, 0, 0); Remove (cfp->form); } static void DoRemoveTextProc (ButtoN b) { ConvertFormPtr cfp; MonitorPtr mon; SeqEntryPtr sep; UIEnum val; cfp = (ConvertFormPtr) GetObjectExtra (b); if (cfp == NULL || cfp->input_entityID == 0) return; sep = GetTopSeqEntryForEntityID (cfp->input_entityID); if (sep == NULL) return; Hide (cfp->form); WatchCursor (); Update (); if (GetEnumPopup (cfp->target, ext_target_field_alist, &val) && val > 0) { cfp->type = (Int2) val; if (GetEnumPopup (cfp->subtarget [cfp->type], cfp->alists [cfp->type], &val) && val > 0) { cfp->subtype = (Int2) val; cfp->leftstr = SaveStringFromTextNoStripSpaces (cfp->atleft); cfp->rightstr = SaveStringFromTextNoStripSpaces (cfp->atright); cfp->includeleft = (Boolean) (GetValue (cfp->leftbehav) == 2); cfp->includeright = (Boolean) (GetValue (cfp->rightbehav) == 2); mon = MonitorStrNewEx ("Removing Text From String", 20, FALSE); cfp->index = 0; DoOneRemoveText (cfp->input_entityID, sep, cfp, mon); MonitorFree (mon); cfp->leftstr = MemFree (cfp->leftstr); cfp->rightstr = MemFree (cfp->rightstr); } } ArrowCursor (); Update (); ObjMgrSetDirtyFlag (cfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, cfp->input_entityID, 0, 0); Remove (cfp->form); } static void SetConvertAcceptButton (Handle a) { ConvertFormPtr cfp; UIEnum val; cfp = (ConvertFormPtr) GetObjectExtra (a); if (cfp == NULL) return; if (GetEnumPopup (cfp->target, ext_target_field_alist, &val) && val > 0) { cfp->type = (Int2) val; if (GetEnumPopup (cfp->subtarget [cfp->type], cfp->alists [cfp->type], &val) && val > 0) { if (GetValue (cfp->asnOrFlat) > 0) { if ((! TextHasNoText (cfp->atleft)) || (! TextHasNoText (cfp->atright))) { SafeEnable (cfp->accept); return; } } if (cfp->asnOrFlat == NULL) { if ((! TextHasNoText (cfp->atleft)) || (! TextHasNoText (cfp->atright))) { SafeEnable (cfp->accept); return; } } } } SafeDisable (cfp->accept); } static void ChangeSubtarget (PopuP p) { ConvertFormPtr cfp; Int2 i; UIEnum val; cfp = (ConvertFormPtr) GetObjectExtra (p); if (cfp == NULL) return; if (GetEnumPopup (cfp->target, ext_target_field_alist, &val) && val > 0) { for (i = 0; i < NUM_SUBTARGET_POPUPS; i++) { if (i != (Int2) val) { SafeHide (cfp->subtarget [i]); } } SafeShow (cfp->subtarget [(Int2) val]); } SetConvertAcceptButton ((Handle) p); } static void ConvertMessageProc (ForM f, Int2 mssg) { StdEditorProcsPtr sepp; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { if (sepp->handleMessages != NULL) { sepp->handleMessages (f, mssg); } } } static void CleanupParseForm (GraphiC g, VoidPtr data) { ConvertFormPtr cfp; cfp = (ConvertFormPtr) data; if (cfp != NULL) { if (cfp->alists [8] != NULL) { FreeEnumFieldAlist (cfp->alists [8]); } } StdCleanupFormProc (g, data); } extern void ParseAsnOrFlatfileToAnywhere (IteM i) { EnumFieldAssocPtr ap; BaseFormPtr bfp; GrouP c; ConvertFormPtr cfp; GrouP g; GrouP h; Int2 j; GrouP p; GrouP q; SeqEntryPtr sep; StdEditorProcsPtr sepp; 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; cfp = (ConvertFormPtr) MemNew (sizeof (ConvertFormData)); if (cfp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "General Field Conversion", StdCloseWindowProc); SetObjectExtra (w, cfp, CleanupParseForm); cfp->form = (ForM) w; cfp->formmessage = ConvertMessageProc; 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; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); q = HiddenGroup (h, 4, 0, NULL); StaticPrompt (q, "File format to parse", 0, stdLineHeight, programFont, 'l'); cfp->asnOrFlat = HiddenGroup (q, 3, 0, (GrpActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->asnOrFlat, cfp, NULL); RadioButton (cfp->asnOrFlat, "GenBank"); RadioButton (cfp->asnOrFlat, "EMBL"); SetValue (cfp->asnOrFlat, 1); g = HiddenGroup (h, 3, 0, NULL); StaticPrompt (g, "Get text between", 0, dialogTextHeight, programFont, 'l'); cfp->leftbehav = HiddenGroup (g, 2, 0, NULL); RadioButton (cfp->leftbehav, "just after"); RadioButton (cfp->leftbehav, "starting at"); SetValue (cfp->leftbehav, 1); cfp->atleft = DialogText (g, "", 10, (TxtActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->atleft, cfp, NULL); StaticPrompt (g, "and", 0, dialogTextHeight, programFont, 'l'); cfp->rightbehav = HiddenGroup (g, 2, 0, NULL); RadioButton (cfp->rightbehav, "up to"); RadioButton (cfp->rightbehav, "including"); SetValue (cfp->rightbehav, 1); cfp->atright = DialogText (g, "", 10, (TxtActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->atright, cfp, NULL); p = HiddenGroup (h, 6, 0, NULL); StaticPrompt (p, "Place in", 0, popupMenuHeight, programFont, 'l'); cfp->target = PopupList (p, TRUE, ChangeSubtarget); SetObjectExtra (cfp->target, cfp, NULL); InitEnumPopup (cfp->target, ext_target_field_alist, NULL); SetEnumPopup (cfp->target, ext_target_field_alist, 0); cfp->alists [1] = gene_field_alist; cfp->alists [2] = cds_field_alist; cfp->alists [3] = prot_field_alist; cfp->alists [4] = rnax_field_alist; cfp->alists [5] = orgref_field_alist; cfp->alists [6] = orgmod_note_subtype_alist; cfp->alists [7] = subsource_note_subtype_alist; cfp->alists [8] = import_featdef_alist (TRUE, FALSE, FALSE); cfp->replaceOldAsked = FALSE; cfp->doReplaceAll = FALSE; x = HiddenGroup (p, 0, 0, NULL); for (j = 1; j <= 7; j++) { cfp->subtarget [j] = PopupList (x, TRUE, (PupActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->subtarget [j], cfp, NULL); InitEnumPopup (cfp->subtarget [j], cfp->alists [j], NULL); SetEnumPopup (cfp->subtarget [j], cfp->alists [j], 0); Hide (cfp->subtarget [j]); } cfp->subtarget [8] = (PopuP) SingleList (x, 10, 8, (LstActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->subtarget [8], cfp, NULL); for (ap = cfp->alists [8]; ap->name != NULL; ap++) { ListItem ((LisT) cfp->subtarget [8], ap->name); } Hide (cfp->subtarget [8]); c = HiddenGroup (h, 4, 0, NULL); cfp->accept = PushButton (c, "Accept", DoConvertProc); SetObjectExtra (cfp->accept, cfp, NULL); Disable (cfp->accept); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) g, NULL); RealizeWindow (w); Show (w); Select (w); Select (cfp->atleft); Update (); } extern void RemoveTextInsideString (IteM i) { BaseFormPtr bfp; GrouP c; ConvertFormPtr cfp; GrouP g; GrouP h; Int2 j; GrouP p; SeqEntryPtr sep; StdEditorProcsPtr sepp; 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; cfp = (ConvertFormPtr) MemNew (sizeof (ConvertFormData)); if (cfp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "General Text Excision", StdCloseWindowProc); SetObjectExtra (w, cfp, StdCleanupFormProc); cfp->form = (ForM) w; cfp->formmessage = ConvertMessageProc; 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; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 3, 0, NULL); StaticPrompt (g, "Remove text between", 0, dialogTextHeight, programFont, 'l'); cfp->leftbehav = HiddenGroup (g, 2, 0, NULL); RadioButton (cfp->leftbehav, "just after"); RadioButton (cfp->leftbehav, "starting at"); SetValue (cfp->leftbehav, 1); cfp->atleft = DialogText (g, "", 10, (TxtActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->atleft, cfp, NULL); StaticPrompt (g, "and", 0, dialogTextHeight, programFont, 'l'); cfp->rightbehav = HiddenGroup (g, 2, 0, NULL); RadioButton (cfp->rightbehav, "up to"); RadioButton (cfp->rightbehav, "including"); SetValue (cfp->rightbehav, 1); cfp->atright = DialogText (g, "", 10, (TxtActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->atright, cfp, NULL); p = HiddenGroup (h, 6, 0, NULL); StaticPrompt (p, "Perform excision in", 0, popupMenuHeight, programFont, 'l'); cfp->target = PopupList (p, TRUE, ChangeSubtarget); SetObjectExtra (cfp->target, cfp, NULL); InitEnumPopup (cfp->target, target_field_alist, NULL); SetEnumPopup (cfp->target, target_field_alist, 0); cfp->alists [1] = gene_field_alist; cfp->alists [2] = cds_field_alist; cfp->alists [3] = prot_field_alist; cfp->alists [4] = rnax_field_alist; cfp->alists [5] = orgref_field_alist; cfp->alists [6] = orgmod_note_subtype_alist; cfp->alists [7] = subsource_note_subtype_alist; cfp->replaceOldAsked = FALSE; cfp->doReplaceAll = FALSE; x = HiddenGroup (p, 0, 0, NULL); for (j = 1; j <= 7; j++) { cfp->subtarget [j] = PopupList (x, TRUE, (PupActnProc) SetConvertAcceptButton); SetObjectExtra (cfp->subtarget [j], cfp, NULL); InitEnumPopup (cfp->subtarget [j], cfp->alists [j], NULL); SetEnumPopup (cfp->subtarget [j], cfp->alists [j], 0); Hide (cfp->subtarget [j]); } c = HiddenGroup (h, 4, 0, NULL); cfp->accept = PushButton (c, "Accept", DoRemoveTextProc); SetObjectExtra (cfp->accept, cfp, NULL); Disable (cfp->accept); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) g, NULL); RealizeWindow (w); Show (w); Select (w); Select (cfp->atleft); Update (); } /* AAForCodon is extern in seqport.c */ /* NLM_EXTERN Uint1 AAForCodon (Uint1Ptr codon, CharPtr codes); */ /* static Boolean CorrectStartCodonCallback (GatherContextPtr gcp) { Uint1 aa; Boolean bad_base; CodeBreakPtr cbp; Uint1 codon [3]; CharPtr codes; CdRegionPtr crp; GeneticCodePtr gc; Int2 i; Uint1 residue; SeqEntryPtr sep; SeqFeatPtr sfp; SeqLocPtr slp; SeqPntPtr spntp; SeqPortPtr spp; ValNodePtr vnp; if (gcp == NULL) return TRUE; sep = (SeqEntryPtr) gcp->userdata; if (sep == NULL ) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return TRUE; crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp == NULL) return TRUE; if (crp->code_break != NULL) return TRUE; gc = NULL; if (crp->genetic_code != NULL) { vnp = (ValNodePtr)(crp->genetic_code->data.ptrvalue); while ((vnp != NULL) && (gcp == NULL)) { switch (vnp->choice) { case 1: gc = GeneticCodeFind(0, (CharPtr)vnp->data.ptrvalue); break; case 2: gc = GeneticCodeFind(vnp->data.intvalue, NULL); break; case 3: case 6: case 4: case 5: case 7: case 8: default: break; } vnp = vnp->next; } } if (gc == NULL) gc = GeneticCodeFind(1, NULL); if (gc == NULL) return TRUE; codes = NULL; for (vnp = (ValNodePtr)gc->data.ptrvalue; vnp != NULL; vnp = vnp->next) { if (vnp->choice == 3) codes = (CharPtr)vnp->data.ptrvalue; } if (codes == NULL) return TRUE; if (crp->frame == 2 || crp->frame == 3) return TRUE; spp = SeqPortNewByLoc (sfp->location, Seq_code_ncbi4na); if (spp == NULL) return TRUE; bad_base = FALSE; for (i = 0; i < 3; i++) { residue = SeqPortGetResidue (spp); if (residue == SEQPORT_EOF) break; if (residue == INVALID_RESIDUE) bad_base = TRUE; codon[i] = residue; } SeqPortFree (spp); if (i != 3 || bad_base) return TRUE; aa = AAForCodon (codon, codes); spp = SeqPortNewByLoc (sfp->product, Seq_code_ncbieaa); if (spp == NULL) return TRUE; residue = SeqPortGetResidue (spp); SeqPortFree (spp); if (residue == SEQPORT_EOF || residue == INVALID_RESIDUE) return TRUE; if (residue != aa) { cbp = CodeBreakNew (); if (cbp != NULL) { spntp = SeqPntNew (); slp = ValNodeNew (NULL); slp->choice = SEQLOC_PNT; slp->data.ptrvalue = (Pointer) spntp; spntp->point = (Int4) 0; spntp->id = SeqIdStripLocus (SeqIdDup (SeqLocId (sfp->product))); cbp->loc = slp; slp = aaLoc_to_dnaLoc (sfp, cbp->loc); cbp->loc = SeqLocFree (cbp->loc); cbp->loc = slp; cbp->aa.value.intvalue = aa; cbp->aa.choice = 1; cbp->next = crp->code_break; crp->code_break = cbp; } } return TRUE; } static void CorrectStartCodon (SeqEntryPtr sep, Uint2 entityID) { BioseqSetPtr bssp; GatherScope gs; if (sep == NULL) return; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && (bssp->_class == 7 || bssp->_class == 13 || bssp->_class == 14 || bssp->_class == 15)) { for (sep = bssp->seq_set; sep != NULL; sep = sep->next) { CorrectStartCodon (sep, entityID); } return; } } MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = FALSE; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.scope = sep; GatherEntity (entityID, (Pointer) sep, CorrectStartCodonCallback, &gs); } extern void CorrectCDSStartCodon (IteM i); extern void CorrectCDSStartCodon (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; CorrectStartCodon (sep, bfp->input_entityID); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); } */ static void CountComponentFunc (SeqEntryPtr sep, Int2Ptr cp) { BioseqSetPtr bssp; if (sep == NULL || cp == 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) { CountComponentFunc (sep, cp); } return; } } (*cp)++; } extern Int2 CountSeqEntryComponents (SeqEntryPtr sep) { Int2 count; count = 0; if (sep != NULL) { CountComponentFunc (sep, &count); } return count; } static ENUM_ALIST(rnax_subtype_alist) {" ", 7}, {"unknown", 0}, {"preRna", 1}, {"mRNA", 2}, {"tRNA", 3}, {"rRNA", 4}, {"snRNA", 5}, {"scRNA", 6}, {"Other RNA", 255}, END_ENUM_ALIST typedef struct applyformdata { FEATURE_FORM_BLOCK Int2 type; Int2 errcount; Boolean noLeft; Boolean noRight; ButtoN applyToParts; ButtoN partial5; ButtoN partial3; TexT onlyThisPart; TexT geneName; TexT protName; TexT rnaName; TexT featcomment; TexT defline; LisT key; PopuP rnaSubType; Uint1 rnatype; EnumFieldAssoc PNTR realalist; EnumFieldAssoc PNTR alist; } ApplyFormData, PNTR ApplyFormPtr; typedef struct alreadyhas { Boolean rsult; Uint1 featchoice; Uint1 descchoice; Uint1 rnatype; } AlreadyHas, PNTR AlreadyHasPtr; static Boolean SeeIfAlreadyHasGatherFunc (GatherContextPtr gcp) { AlreadyHasPtr ahp; RnaRefPtr rrp; ValNodePtr sdp; SeqFeatPtr sfp; if (gcp == NULL) return TRUE; ahp = (AlreadyHasPtr) gcp->userdata; if (ahp == NULL ) return TRUE; if (gcp->thistype == OBJ_SEQFEAT && ahp->featchoice != 0) { sfp = (SeqFeatPtr) gcp->thisitem; if (sfp != NULL && sfp->data.choice == ahp->featchoice && sfp->data.value.ptrvalue != NULL) { if (sfp->data.choice == SEQFEAT_RNA) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp->type != ahp->rnatype) return TRUE; } ahp->rsult = TRUE; return FALSE; } } else if (gcp->thistype == OBJ_SEQDESC && ahp->descchoice != 0) { sdp = (ValNodePtr) gcp->thisitem; if (sdp != NULL && sdp->choice == ahp->descchoice && sdp->data.ptrvalue != NULL) { ahp->rsult = TRUE; return FALSE; } } return TRUE; } static Boolean AlreadyHasFeatOrDesc (SeqEntryPtr sep, Uint1 featchoice, Uint1 descchoice, Uint1 rnatype) { AlreadyHas ah; BioseqPtr bsp; GatherScope gs; SeqEntryPtr nsep; SeqIdPtr sip; SeqLocPtr slp; ah.rsult = FALSE; ah.featchoice = featchoice; ah.descchoice = descchoice; ah.rnatype = rnatype; if (sep == NULL) return FALSE; 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_SEQDESC] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.scope = sep; if (descchoice != 0) { nsep = FindNucSeqEntry (sep); if (nsep != NULL && IS_Bioseq (nsep)) { bsp = (BioseqPtr) nsep->data.ptrvalue; if (bsp != NULL) { slp = ValNodeNew (NULL); slp->choice = SEQLOC_WHOLE; sip = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); slp->data.ptrvalue = sip; gs.target = slp; } } } GatherSeqEntry (sep, (Pointer) (&ah), SeeIfAlreadyHasGatherFunc, &gs); gs.target = SeqLocFree (gs.target); return ah.rsult; } static void RealApplyBioFeatToAll (Uint2 entityID, SeqEntryPtr sep, SeqEntryPtr nsep, ApplyFormPtr afp, Boolean suppressDups) { EnumFieldAssocPtr ap; ByteStorePtr bs; BioseqPtr bsp; BioseqSetPtr bssp; Char ch; CdRegionPtr crp; ValNodePtr descr; Uint1 frame; Int2 genCode; GeneRefPtr grp; Int2 i; ImpFeatPtr ifp; Int4 len; Int4 lens [4]; Int4 max; MolInfoPtr mip; SeqEntryPtr old; CharPtr prot; ProtRefPtr prp; SeqEntryPtr psep; CharPtr ptr; RnaRefPtr rrp; ValNodePtr sdp; SeqFeatPtr sfp; Char str [128]; Int2 val; ValNodePtr vnp; if (sep == NULL || nsep == NULL || afp == NULL) return; if (afp->type == ADD_TITLE) { if (suppressDups && entityID > 0 && AlreadyHasFeatOrDesc (sep, 0, Seq_descr_title, 0)) return; if (entityID == 0 && SeqEntryGetTitle (sep) != NULL) return; if (! TextHasNoText (afp->defline)) { if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == 1 && bssp->seq_set != NULL) { sep = bssp->seq_set; } } sdp = CreateNewDescriptor (sep, Seq_descr_title); if (sdp != NULL) { sdp->data.ptrvalue = (Pointer) SaveStringFromTextAndStripNewlines (afp->defline); } } return; } else if (afp->type == ADD_CDS) { if (suppressDups && entityID > 0 && AlreadyHasFeatOrDesc (sep, SEQFEAT_CDREGION, 0, 0)) return; genCode = SeqEntryToGeneticCode (sep, NULL, NULL, 0); crp = CreateNewCdRgn (1, FALSE, genCode); if (crp != NULL) { sfp = CreateNewFeature (nsep, NULL, SEQFEAT_CDREGION, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) crp; SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); sfp->partial = (afp->noLeft || afp->noRight); if (! TextHasNoText (afp->featcomment)) { sfp->comment = SaveStringFromTextAndStripNewlines (afp->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) { (afp->errcount)++; } } crp->frame = frame; bs = ProteinFromCdRegionEx (sfp, TRUE, FALSE); if (bs != NULL) { prot = BSMerge (bs, NULL); bs = BSFree (bs); if (prot != NULL) { 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)); } } bsp = BioseqNew (); if (bsp != NULL) { 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 (afp->noLeft && afp->noRight) { mip->completeness = 5; } else if (afp->noLeft) { mip->completeness = 3; } else if (afp->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 (afp->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, afp->noLeft, afp->noRight); sfp->partial = (afp->noLeft || afp->noRight); } } } } } } } } GetTitle (afp->geneName, str, sizeof (str)); if (! StringHasNoText (str)) { if (entityID > 0 && AlreadyHasFeatOrDesc (sep, SEQFEAT_GENE, 0, 0)) return; grp = CreateNewGeneRef (str, NULL, NULL, FALSE); if (grp != NULL) { sfp = CreateNewFeature (nsep, NULL, SEQFEAT_GENE, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) grp; SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); sfp->partial = (afp->noLeft || afp->noRight); } } } } else if (afp->type == ADD_RRNA) { if (suppressDups && entityID > 0 && AlreadyHasFeatOrDesc (sep, SEQFEAT_RNA, 0, afp->rnatype)) return; rrp = RnaRefNew (); if (rrp != NULL) { rrp->type = afp->rnatype; if (! TextHasNoText (afp->rnaName)) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = SaveStringFromText (afp->rnaName); } sfp = CreateNewFeature (nsep, NULL, SEQFEAT_RNA, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) rrp; SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); sfp->partial = (afp->noLeft || afp->noRight); if (! TextHasNoText (afp->featcomment)) { sfp->comment = SaveStringFromTextAndStripNewlines (afp->featcomment); } } } GetTitle (afp->geneName, str, sizeof (str)); if (! StringHasNoText (str)) { if (entityID > 0 && AlreadyHasFeatOrDesc (sep, SEQFEAT_GENE, 0, 0)) return; grp = CreateNewGeneRef (str, NULL, NULL, FALSE); if (grp != NULL) { sfp = CreateNewFeature (nsep, NULL, SEQFEAT_GENE, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) grp; SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); sfp->partial = (afp->noLeft || afp->noRight); } } } } else if (afp->type == ADD_IMP) { val = GetValue (afp->key); if (val > 0) { ifp = ImpFeatNew (); if (ifp != NULL) { if (val > 1) { for (i = 1, ap = afp->alist; ap->name != NULL; i++, ap++) { if (i == val) { ifp->key = StringSave (ap->name); } } } else { ifp->key = StringSave ("misc_feature"); } sfp = CreateNewFeature (nsep, NULL, SEQFEAT_IMP, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) ifp; SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); sfp->partial = (afp->noLeft || afp->noRight); if (! TextHasNoText (afp->featcomment)) { sfp->comment = SaveStringFromTextAndStripNewlines (afp->featcomment); } sfp->qual = DialogToPointer (afp->gbquals); } } } GetTitle (afp->geneName, str, sizeof (str)); if (! StringHasNoText (str)) { if (entityID > 0 && AlreadyHasFeatOrDesc (sep, SEQFEAT_GENE, 0, 0)) return; grp = CreateNewGeneRef (str, NULL, NULL, FALSE); if (grp != NULL) { sfp = CreateNewFeature (nsep, NULL, SEQFEAT_GENE, NULL); if (sfp != NULL) { sfp->data.value.ptrvalue = (Pointer) grp; SetSeqLocPartial (sfp->location, afp->noLeft, afp->noRight); sfp->partial = (afp->noLeft || afp->noRight); if (val == 0 && (! TextHasNoText (afp->featcomment))) { sfp->comment = SaveStringFromTextAndStripNewlines (afp->featcomment); } } } } } } static void ApplyBioFeatToRaw (Uint2 entityID, SeqEntryPtr sep, SeqEntryPtr tmp, ApplyFormPtr afp, Int2 onlythis) { BioseqPtr bsp; BioseqSetPtr bssp; Int2 count; SeqEntryPtr nsep; if (tmp == NULL || afp == NULL) return; if (IS_Bioseq_set (tmp)) { bssp = (BioseqSetPtr) tmp->data.ptrvalue; if (bssp != NULL) { if (onlythis != 0 && bssp->_class == BioseqseqSet_class_parts) { for (tmp = bssp->seq_set, count = 1; tmp != NULL && count != onlythis; tmp = tmp->next, count++) continue; if (tmp != NULL) { ApplyBioFeatToRaw (entityID, sep, tmp, afp, onlythis); } } else { for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { ApplyBioFeatToRaw (entityID, sep, tmp, afp, onlythis); } } return; } } nsep = FindNucSeqEntry (tmp); if (nsep == NULL) return; bsp = (BioseqPtr) nsep->data.ptrvalue; if (bsp == NULL) return; if (bsp->repr == Seq_repr_raw) { RealApplyBioFeatToAll (entityID, nsep, nsep, afp, FALSE); /* RealApplyBioFeatToAll (entityID, sep, nsep, afp, FALSE); */ } } static void ApplyBioFeatToAll (Uint2 entityID, SeqEntryPtr sep, ApplyFormPtr afp) { BioseqSetPtr bssp; SeqEntryPtr nsep; Int2 onlythis; Char str [32]; if (sep == NULL || afp == 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) { ApplyBioFeatToAll (entityID, sep, afp); } return; } } nsep = FindNucSeqEntry (sep); if (nsep == NULL) return; if (afp->applyToParts != NULL && GetStatus (afp->applyToParts)) { GetTitle (afp->onlyThisPart, str, sizeof (str)); if (! StrToInt (str, &onlythis)) { onlythis = 0; } ApplyBioFeatToRaw (entityID, sep, sep, afp, onlythis); } else { RealApplyBioFeatToAll (entityID, sep, nsep, afp, TRUE); } } Int2 ApplyAnnotationToAll (Int2 type, SeqEntryPtr sep, ButtoN partialLft, ButtoN partialRgt, TexT geneName, TexT protName, TexT rnaName, TexT featcomment, TexT defline) { ApplyFormData afd; MemSet ((Pointer) (&afd), 0, sizeof (ApplyFormData)); afd.type = type; afd.errcount = 0; afd.partial5 = partialLft; afd.partial3 = partialRgt; afd.noLeft = GetStatus (afd.partial5); afd.noRight = GetStatus (afd.partial3); afd.geneName = geneName; afd.protName = protName; afd.rnaName = rnaName; afd.featcomment = featcomment; afd.defline = defline; ApplyBioFeatToAll (0, sep, &afd); if (afd.type == ADD_CDS) { return afd.errcount; } return 0; } static void NowReadyToApplyToAll (ApplyFormPtr afp, DialoG gbquals) { Uint2 parenttype; Pointer parentptr; CharPtr plural; SeqEntryPtr sep; SeqEntryPtr top; UIEnum val; if (afp == NULL) return; afp->gbquals = gbquals; sep = GetTopSeqEntryForEntityID (afp->input_entityID); if (sep == NULL) return; Hide (afp->form); WatchCursor (); Update (); afp->noLeft = GetStatus (afp->partial5); afp->noRight = GetStatus (afp->partial3); top = sep; if (afp->type == ADD_CDS) { GetSeqEntryParent (top, &parentptr, &parenttype); } afp->rnatype = 0; if (afp->rnaSubType != NULL) { if (GetEnumPopup (afp->rnaSubType, rnax_subtype_alist, &val)) { afp->rnatype = val; } } ApplyBioFeatToAll (afp->input_entityID, sep, afp); ArrowCursor (); Update (); if (afp->errcount > 0 && afp->type == ADD_CDS) { if (afp->errcount > 1) { plural = "records"; } else { plural = "record"; } Message (MSG_ERROR, "Possible ambiguous frames detected in %d %s", (int) afp->errcount, plural); } if (indexerVersion) { if (CountSeqEntryComponents (sep) == 1) { switch (afp->type) { case ADD_TITLE : Message (MSG_OK, "When only one record present, add a title descriptor directly"); break; case ADD_RRNA : Message (MSG_OK, "When only one record present, add an rRNA feature directly"); break; case ADD_CDS : Message (MSG_OK, "When only one record present, add a CdRgn feature directly"); break; case ADD_IMP : Message (MSG_OK, "When only one record present, add the feature directly"); break; default : break; } } } ObjMgrSetDirtyFlag (afp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, afp->input_entityID, 0, 0); Remove (afp->form); } typedef struct qualsform { FEATURE_FORM_BLOCK ApplyFormPtr afp; } QualsForm, PNTR QualsFormPtr; static void CallNowReady (ButtoN b) { QualsFormPtr qfp; qfp = (QualsFormPtr) GetObjectExtra (b); if (qfp == NULL) return; Hide (qfp->form); NowReadyToApplyToAll (qfp->afp, qfp->gbquals); Remove (qfp->form); } static void DoTheApplyToAllProc (ButtoN b) { ApplyFormPtr afp; EnumFieldAssocPtr ap; Int2 i; CharPtr name; QualsFormPtr qfp; Int2 val; WindoW w; afp = GetObjectExtra (b); if (afp == NULL) { Remove (ParentWindow (b)); return; } if (afp->type == ADD_IMP) { val = GetValue (afp->key); if (val > 0) { qfp = (QualsFormPtr) MemNew (sizeof (QualsForm)); if (qfp != NULL) { Hide (afp->form); Update (); name = NULL; if (val > 1) { for (i = 1, ap = afp->alist; ap->name != NULL; i++, ap++) { if (i == val) { name = ap->name; } } } else { name = "misc_feature"; } qfp->afp = afp; w = FixedWindow (-50, -33, -10, -10, "Qualifiers", StdCloseWindowProc); SetObjectExtra (w, qfp, StdCleanupFormProc); qfp->form = (ForM) w; qfp->gbquals = CreateImportFields (w, name, NULL, FALSE); b = PushButton (w, "Okay", CallNowReady); SetObjectExtra (b, qfp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) qfp->gbquals, (HANDLE) b, NULL); RealizeWindow (w); Show (w); Select (w); } } else { NowReadyToApplyToAll (afp, NULL); } } else { NowReadyToApplyToAll (afp, NULL); } } static void ApplyToPartsProc (ButtoN b) { ApplyFormPtr afp; afp = (ApplyFormPtr) GetObjectExtra (b); if (afp == NULL) return; if (GetStatus (b)) { SafeEnable (afp->onlyThisPart); } else { SafeDisable (afp->onlyThisPart); } } static void LookForParts (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqSetPtr bssp; BoolPtr rsult; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts) { rsult = (BoolPtr) mydata; if (rsult != NULL) { *rsult = TRUE; } } } } extern Boolean HasPartsSet (SeqEntryPtr sep); extern Boolean HasPartsSet (SeqEntryPtr sep) { Boolean rsult = FALSE; SeqEntryExplore (sep, (Pointer) (&rsult), LookForParts); return rsult; } static void ApplyMessageProc (ForM f, Int2 mssg) { ApplyFormPtr afp; afp = (ApplyFormPtr) GetObjectExtra (f); if (afp != NULL) { if (afp->appmessage != NULL) { afp->appmessage (f, mssg); } } } static void CleanupApplyToAllForm (GraphiC g, VoidPtr data) { Int2 j; ApplyFormPtr afp; afp = (ApplyFormPtr) data; if (afp != NULL) { if (afp->realalist != NULL) { for (j = 0; afp->realalist [j].name != NULL; j++) { MemFree (afp->realalist [j].name); } } MemFree (afp->realalist); } StdCleanupFormProc (g, data); } static void CommonApplyToAllProc (IteM i, Int2 type) { ApplyFormPtr afp; EnumFieldAssocPtr ap; BaseFormPtr bfp; ButtoN b; GrouP c; GrouP g; GrouP h; GrouP p; GrouP q; SeqEntryPtr sep; StdEditorProcsPtr sepp; WindoW w; GrouP x; 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; afp = (ApplyFormPtr) MemNew (sizeof (ApplyFormData)); if (afp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Automatic Processing", StdCloseWindowProc); SetObjectExtra (w, afp, CleanupApplyToAllForm); afp->form = (ForM) w; afp->formmessage = ApplyMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); afp->appmessage = sepp->handleMessages; } afp->input_entityID = bfp->input_entityID; afp->input_itemID = bfp->input_itemID; afp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); afp->type = type; afp->errcount = 0; z = HiddenGroup (h, 1, 0, NULL); if (HasPartsSet (sep)) { afp->applyToParts = CheckBox (z, "Apply to segmented parts, not segmented sequence", ApplyToPartsProc); SetObjectExtra (afp->applyToParts, afp, NULL); x = HiddenGroup (z, 2, 0, NULL); StaticPrompt (x, "Apply only to particular numbered segment", 0, dialogTextHeight, programFont, 'l'); afp->onlyThisPart = DialogText (x, "", 4, NULL); Disable (afp->onlyThisPart); } g = HiddenGroup (h, 2, 0, NULL); if (type == ADD_CDS || type == ADD_RRNA || type == ADD_IMP) { afp->partial5 = CheckBox (g, "Incomplete at 5' end", NULL); afp->partial3 = CheckBox (g, "Incomplete at 3' end", NULL); } if (type == ADD_TITLE) { p = HiddenGroup (h, 0, 2, NULL); StaticPrompt (p, "Title", 0, 0, programFont, 'c'); afp->defline = ScrollText (p, 20, 4, programFont, TRUE, NULL); } else { p = HiddenGroup (h, 2, 0, NULL); if (type == ADD_CDS) { StaticPrompt (p, "Gene Symbol", 0, dialogTextHeight, programFont, 'l'); afp->geneName = DialogText (p, "", 20, NULL); StaticPrompt (p, "Protein Name", 0, dialogTextHeight, programFont, 'l'); afp->protName = DialogText (p, "", 20, NULL); } else if (type == ADD_RRNA) { StaticPrompt (p, "RNA Name", 0, dialogTextHeight, programFont, 'l'); afp->rnaName = DialogText (p, "", 20, NULL); StaticPrompt (p, "Gene Symbol", 0, dialogTextHeight, programFont, 'l'); afp->geneName = DialogText (p, "", 20, NULL); } else if (type == ADD_IMP) { ap = import_featdef_alist (FALSE, FALSE, FALSE); afp->realalist = ap; ap++; afp->alist = ap; StaticPrompt (p, "Type", 0, 6 * Nlm_stdLineHeight, programFont, 'l'); afp->key = SingleList (p, 12, 6, NULL); for (ap = afp->alist; ap->name != NULL; ap++) { ListItem (afp->key, ap->name); } SetValue (afp->key, 0); StaticPrompt (p, "Gene Symbol", 0, dialogTextHeight, programFont, 'l'); afp->geneName = DialogText (p, "", 20, NULL); } StaticPrompt (p, "Comment", 0, 4 * Nlm_stdLineHeight, programFont, 'l'); afp->featcomment = ScrollText (p, 20, 4, programFont, TRUE, NULL); } afp->gbquals = NULL; q = NULL; if (type == ADD_RRNA) { q = HiddenGroup (h, 2, 0, NULL); StaticPrompt (q, "RNA subtype", 0, dialogTextHeight, programFont, 'l'); afp->rnaSubType = PopupList (q, TRUE, NULL); InitEnumPopup (afp->rnaSubType, rnax_subtype_alist, NULL); SetEnumPopup (afp->rnaSubType, rnax_subtype_alist, (UIEnum) 4); } c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoTheApplyToAllProc); SetObjectExtra (b, afp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) p, (HANDLE) c, (HANDLE) z, (HANDLE) q, NULL); RealizeWindow (w); Show (w); if (type == ADD_TITLE) { Select (afp->defline); } else if (type == ADD_RRNA) { Select (afp->rnaName); } else { Select (afp->geneName); } Update (); } extern void ApplyTitle (IteM i) { CommonApplyToAllProc (i, ADD_TITLE); } extern void ApplyCDS (IteM i) { CommonApplyToAllProc (i, ADD_CDS); } extern void ApplyRRNA (IteM i) { CommonApplyToAllProc (i, ADD_RRNA); } extern void ApplyImpFeat (IteM i) { CommonApplyToAllProc (i, ADD_IMP); } #define SUBMISSION_PAGE 0 #define CONTACT_PAGE 1 #define AUTHOR_PAGE 2 #define AFFILIATION_PAGE 3 typedef struct submitform { FORM_MESSAGE_BLOCK GrouP pages [4]; Int2 currentPage; DialoG tbs; GrouP hup; GrouP dateGrp; TexT title; DialoG reldate; TexT firstname; TexT middleinit; TexT lastname; TexT suffix; DialoG phonefaxemail; DialoG authors; DialoG affil; Boolean visitedContact; Boolean visitedAuthor; ButtoN nextBtn; ButtoN prevBtn; BtnActnProc goToNext; BtnActnProc goToPrev; } SubmitForm, PNTR SubmitFormPtr; static void SequinBlockPtrToSubmitForm (ForM f, Pointer data) { AuthorPtr ap; DatePtr dp; NameStdPtr nsp; PersonIdPtr pid; SubmitFormPtr sbfp; SequinBlockPtr sbp; CharPtr str; CharPtr txt; sbfp = (SubmitFormPtr) GetObjectExtra (f); sbp = (SequinBlockPtr) data; if (sbfp != NULL) { if (sbp != NULL) { SafeSetTitle (sbfp->title, sbp->citsubtitle); PointerToDialog (sbfp->reldate, (Pointer) sbp->releasedate); ap = sbp->contactperson; if (ap != NULL) { pid = ap->name; if (pid != NULL && pid->choice == 2) { nsp = pid->data; if (nsp != NULL) { str = NameStdPtrToAuthorSpreadsheetString (nsp); if (str != NULL) { txt = ExtractTagListColumn (str, 0); SafeSetTitle (sbfp->firstname, txt); MemFree (txt); txt = ExtractTagListColumn (str, 1); SafeSetTitle (sbfp->middleinit, txt); MemFree (txt); txt = ExtractTagListColumn (str, 2); SafeSetTitle (sbfp->lastname, txt); MemFree (txt); txt = ExtractTagListColumn (str, 3); SafeSetTitle (sbfp->suffix, txt); MemFree (txt); MemFree (str); } } } PointerToDialog (sbfp->phonefaxemail, (Pointer) ap->affil); } PointerToDialog (sbfp->authors, (Pointer) sbp->citsubauthors); PointerToDialog (sbfp->affil, (Pointer) sbp->citsubaffil); if (sbp->holduntilpublished) { SafeSetValue (sbfp->hup, 2); SafeShow (sbfp->dateGrp); } else { SafeSetValue (sbfp->hup, 1); SafeHide (sbfp->dateGrp); } sbfp->visitedAuthor = TRUE; SetValue (sbfp->tbs, 0); } else { SafeSetTitle (sbfp->title, NULL); dp = DateCurr (); if (dp != NULL) { dp->data [3] = 0; /* force to end of month */ dp = DateAdvance (dp, 12); /* (dp->data [1])++; if (dp->data [2] == 2 && dp->data [3] > 28) { dp->data [3] = 28; } */ PointerToDialog (sbfp->reldate, (Pointer) dp); } else { PointerToDialog (sbfp->reldate, NULL); } DateFree (dp); SafeSetTitle (sbfp->firstname, ""); SafeSetTitle (sbfp->middleinit, ""); SafeSetTitle (sbfp->lastname, ""); SafeSetTitle (sbfp->suffix, ""); PointerToDialog (sbfp->phonefaxemail, NULL); PointerToDialog (sbfp->authors, NULL); PointerToDialog (sbfp->affil, NULL); SafeSetValue (sbfp->hup, 1); SafeHide (sbfp->dateGrp); SetValue (sbfp->tbs, 0); } } } static Pointer SubmitFormToSequinBlockPtr (ForM f) { AffilPtr affil; AuthorPtr ap; NameStdPtr nsp; PersonIdPtr pid; SubmitFormPtr sbfp; SequinBlockPtr sbp; Char str [128]; CharPtr txt; sbp = NULL; sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { sbp = (SequinBlockPtr) MemNew (sizeof (SequinBlock)); if (sbp != NULL) { sbp->citsubtitle = SaveStringFromTextAndStripNewlines (sbfp->title); ap = AuthorNew (); if (ap != NULL) { pid = PersonIdNew (); ap->name = pid; if (pid != NULL) { pid->choice = 2; str [0] = '\0'; txt = SaveStringFromText (sbfp->firstname); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->middleinit); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->lastname); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->suffix); StringCat (str, txt); StringCat (str, "\n"); MemFree (txt); txt = StringSave (str); nsp = AuthorSpreadsheetStringToNameStdPtr (txt); MemFree (txt); pid->data = nsp; if (nsp != NULL) { if (StringHasNoText (nsp->names [0])) { ap = AuthorFree (ap); } } } affil = (AffilPtr) DialogToPointer (sbfp->phonefaxemail); if (affil != NULL) { if (affil->choice == 2) { affil->affil = MemFree (affil->affil); affil->div = MemFree (affil->div); affil->city = MemFree (affil->city); affil->sub = MemFree (affil->sub); affil->country = MemFree (affil->country); affil->street = MemFree (affil->street); affil->postal_code = MemFree (affil->postal_code); if (affil->phone == NULL && affil->fax == NULL && affil->email == NULL) { affil = AffilFree (affil); } } else { affil = AffilFree (affil); } } ap->affil = affil; } sbp->contactperson = ap; sbp->citsubauthors = (AuthListPtr) DialogToPointer (sbfp->authors); sbp->citsubaffil = (AffilPtr) DialogToPointer (sbfp->affil); if (GetValue (sbfp->hup) == 2) { sbp->holduntilpublished = TRUE; sbp->releasedate = (DatePtr) DialogToPointer (sbfp->reldate); } if (sbp->contactperson == NULL && sbp->citsubauthors == NULL && sbp->citsubaffil == NULL) { sbp = SequinBlockFree (sbp); } } } return (Pointer) sbp; } static void SubmitBlockPtrToSubmitForm (ForM f, Pointer data) { AuthorPtr ap; AuthListPtr authors; ContactInfoPtr cip; CitSubPtr csp; DatePtr dp; NameStdPtr nsp; PersonIdPtr pid; SubmitFormPtr sbfp; SubmitBlockPtr sbp; CharPtr str; CharPtr txt; sbfp = (SubmitFormPtr) GetObjectExtra (f); sbp = (SubmitBlockPtr) data; if (sbfp != NULL) { if (sbp != NULL) { PointerToDialog (sbfp->reldate, (Pointer) sbp->reldate); cip = sbp->contact; if (cip != NULL) { ap = cip->contact; if (ap != NULL) { pid = ap->name; if (pid != NULL && pid->choice == 2) { nsp = pid->data; if (nsp != NULL) { str = NameStdPtrToAuthorSpreadsheetString (nsp); if (str != NULL) { txt = ExtractTagListColumn (str, 0); SafeSetTitle (sbfp->firstname, txt); MemFree (txt); txt = ExtractTagListColumn (str, 1); SafeSetTitle (sbfp->middleinit, txt); MemFree (txt); txt = ExtractTagListColumn (str, 2); SafeSetTitle (sbfp->lastname, txt); MemFree (txt); txt = ExtractTagListColumn (str, 3); SafeSetTitle (sbfp->suffix, txt); MemFree (txt); MemFree (str); } } } PointerToDialog (sbfp->phonefaxemail, (Pointer) ap->affil); } } csp = sbp->cit; if (csp != NULL) { authors = csp->authors; if (authors != NULL) { PointerToDialog (sbfp->authors, (Pointer) authors); PointerToDialog (sbfp->affil, (Pointer) authors->affil); } } if (sbp->hup) { SafeSetValue (sbfp->hup, 2); SafeShow (sbfp->dateGrp); } else { SafeSetValue (sbfp->hup, 1); SafeHide (sbfp->dateGrp); } sbfp->visitedAuthor = TRUE; SetValue (sbfp->tbs, 0); } else { SafeSetTitle (sbfp->title, NULL); dp = DateCurr (); if (dp != NULL) { dp->data [3] = 0; /* force to end of month */ dp = DateAdvance (dp, 12); /* (dp->data [1])++; if (dp->data [2] == 2 && dp->data [3] > 28) { dp->data [3] = 28; } */ PointerToDialog (sbfp->reldate, (Pointer) dp); } else { PointerToDialog (sbfp->reldate, NULL); } DateFree (dp); SafeSetTitle (sbfp->firstname, ""); SafeSetTitle (sbfp->middleinit, ""); SafeSetTitle (sbfp->lastname, ""); SafeSetTitle (sbfp->suffix, ""); PointerToDialog (sbfp->phonefaxemail, NULL); PointerToDialog (sbfp->authors, NULL); PointerToDialog (sbfp->affil, NULL); SafeSetValue (sbfp->hup, 1); SafeHide (sbfp->dateGrp); SetValue (sbfp->tbs, 0); } } } static ValNodePtr TestSubmitForm (ForM f) { AffilPtr affil; AuthListPtr authors; DatePtr dp; ValNodePtr head; SubmitFormPtr sbfp; head = NULL; sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (TextHasNoText (sbfp->firstname)) { head = AddStringToValNodeChain (head, "first name", 1); } if (TextHasNoText (sbfp->lastname)) { head = AddStringToValNodeChain (head, "last name", 1); } affil = DialogToPointer (sbfp->phonefaxemail); if (affil != NULL) { if (StringHasNoText (affil->phone)) { head = AddStringToValNodeChain (head, "telephone number", 0); } if (StringHasNoText (affil->fax)) { head = AddStringToValNodeChain (head, "fax number", 0); } if (StringHasNoText (affil->email)) { head = AddStringToValNodeChain (head, "e-mail address", 0); } } else { head = AddStringToValNodeChain (head, "telephone number", 0); head = AddStringToValNodeChain (head, "fax number", 0); head = AddStringToValNodeChain (head, "e-mail address", 0); } affil = AffilFree (affil); if (GetValue (sbfp->hup) == 2) { dp = DialogToPointer (sbfp->reldate); if (dp == NULL) { head = AddStringToValNodeChain (head, "release date", 1); } dp = DateFree (dp); } if (TextHasNoText (sbfp->title)) { head = AddStringToValNodeChain (head, "manuscript title", 1); } authors = DialogToPointer (sbfp->authors); if (authors == NULL) { head = AddStringToValNodeChain (head, "author names", 1); } authors = AuthListFree (authors); affil = DialogToPointer (sbfp->affil); if (affil == NULL) { head = AddStringToValNodeChain (head, "affiliation", 1); } affil = AffilFree (affil); } return head; } /* static Boolean ReadSubmitBlock (ForM f, CharPtr filename) { AsnIoPtr aip; Char path [PATH_MAX]; SubmitFormPtr sbfp; SubmitBlockPtr sbp; path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetInputFileName (path, sizeof (path), "", "TEXT")) { aip = AsnIoOpen (path, "r"); if (aip != NULL) { sbp = SubmitBlockAsnRead (aip, NULL); AsnIoClose (aip); if (sbp != NULL) { SubmitBlockPtrToSubmitForm (f, (Pointer) sbp); sbp = SubmitBlockFree (sbp); Update (); return TRUE; } } } } return FALSE; } */ static Boolean ReadSubmitBlock (ForM f, CharPtr filename) { Pointer dataptr; Uint2 datatype; Uint2 entityID; SubmitFormPtr sbfp; SubmitBlockPtr sbp; SeqSubmitPtr ssp; Char path [PATH_MAX]; path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetInputFileName (path, sizeof (path), "", "TEXT")) { dataptr = ObjMgrGenericAsnTextFileRead (path, &datatype, &entityID); if (dataptr != NULL && entityID > 0) { sbp = NULL; switch (datatype) { case OBJ_SUBMIT_BLOCK : sbp = (SubmitBlockPtr) dataptr; break; case OBJ_SEQSUB : ssp = (SeqSubmitPtr) dataptr; if (ssp != NULL) { sbp = ssp->sub; } break; default : break; } if (sbp != NULL) { SubmitBlockPtrToSubmitForm (f, sbp); } ObjMgrDelete (datatype, dataptr); if (sbp != NULL) { Update (); return TRUE; } } } } return FALSE; } static Boolean ReadContactPage (ForM f, CharPtr filename) { AsnIoPtr aip; AuthorPtr ap; ContactInfoPtr cip; NameStdPtr nsp; Char path [PATH_MAX]; PersonIdPtr pid; SubmitFormPtr sbfp; CharPtr str; CharPtr txt; path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetInputFileName (path, sizeof (path), "", "TEXT")) { aip = AsnIoOpen (path, "r"); if (aip != NULL) { cip = ContactInfoAsnRead (aip, NULL); AsnIoClose (aip); if (cip != NULL) { ap = cip->contact; if (ap != NULL) { pid = ap->name; if (pid != NULL && pid->choice == 2) { nsp = pid->data; if (nsp != NULL) { str = NameStdPtrToAuthorSpreadsheetString (nsp); if (str != NULL) { txt = ExtractTagListColumn (str, 0); SafeSetTitle (sbfp->firstname, txt); MemFree (txt); txt = ExtractTagListColumn (str, 1); SafeSetTitle (sbfp->middleinit, txt); MemFree (txt); txt = ExtractTagListColumn (str, 2); SafeSetTitle (sbfp->lastname, txt); MemFree (txt); txt = ExtractTagListColumn (str, 3); SafeSetTitle (sbfp->suffix, txt); MemFree (txt); MemFree (str); } } } PointerToDialog (sbfp->phonefaxemail, (Pointer) ap->affil); } cip = ContactInfoFree (cip); Update (); return TRUE; } } } } return FALSE; } static Boolean WriteContactPage (ForM f, CharPtr filename) { AffilPtr affil; AsnIoPtr aip; AuthorPtr ap; ContactInfoPtr cip; NameStdPtr nsp; Char path [PATH_MAX]; PersonIdPtr pid; SubmitFormPtr sbfp; Char str [128]; CharPtr txt; #ifdef WIN_MAC FILE *fp; #endif path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetOutputFileName (path, sizeof (path), NULL)) { #ifdef WIN_MAC fp = FileOpen (path, "r"); if (fp != NULL) { FileClose (fp); } else { FileCreate (path, "TEXT", "ttxt"); } #endif aip = AsnIoOpen (path, "w"); if (aip != NULL) { cip = ContactInfoNew (); if (cip != NULL) { ap = AuthorNew (); if (ap != NULL) { pid = PersonIdNew (); ap->name = pid; if (pid != NULL) { pid->choice = 2; str [0] = '\0'; txt = SaveStringFromText (sbfp->firstname); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->middleinit); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->lastname); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->suffix); StringCat (str, txt); StringCat (str, "\n"); MemFree (txt); txt = StringSave (str); nsp = AuthorSpreadsheetStringToNameStdPtr (txt); MemFree (txt); pid->data = nsp; if (nsp != NULL) { if (StringHasNoText (nsp->names [0])) { ap = AuthorFree (ap); } } } affil = (AffilPtr) DialogToPointer (sbfp->phonefaxemail); if (affil != NULL) { if (affil->choice == 2) { affil->affil = MemFree (affil->affil); affil->div = MemFree (affil->div); affil->city = MemFree (affil->city); affil->sub = MemFree (affil->sub); affil->country = MemFree (affil->country); affil->street = MemFree (affil->street); affil->postal_code = MemFree (affil->postal_code); if (affil->phone == NULL && affil->fax == NULL && affil->email == NULL) { affil = AffilFree (affil); } } else { affil = AffilFree (affil); } } ap->affil = affil; } cip->contact = ap; ContactInfoAsnWrite (cip, aip, NULL); AsnIoClose (aip); cip = ContactInfoFree (cip); return TRUE; } } } } return FALSE; } static Boolean ReadAuthListPage (ForM f, CharPtr filename) { AsnIoPtr aip; AuthListPtr alp; Char path [PATH_MAX]; SubmitFormPtr sbfp; path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetInputFileName (path, sizeof (path), "", "TEXT")) { aip = AsnIoOpen (path, "r"); if (aip != NULL) { alp = AuthListAsnRead (aip, NULL); AsnIoClose (aip); if (alp != NULL) { PointerToDialog (sbfp->authors, alp); alp = AuthListFree (alp); Update (); return TRUE; } } } } return FALSE; } static Boolean WriteAuthListPage (ForM f, CharPtr filename) { AsnIoPtr aip; AuthListPtr alp; Char path [PATH_MAX]; SubmitFormPtr sbfp; #ifdef WIN_MAC FILE *fp; #endif path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetOutputFileName (path, sizeof (path), NULL)) { #ifdef WIN_MAC fp = FileOpen (path, "r"); if (fp != NULL) { FileClose (fp); } else { FileCreate (path, "TEXT", "ttxt"); } #endif aip = AsnIoOpen (path, "w"); if (aip != NULL) { alp = DialogToPointer (sbfp->authors); AuthListAsnWrite (alp, aip, NULL); AsnIoClose (aip); alp = AuthListFree (alp); return TRUE; } } } return FALSE; } static Boolean ReadAffilPage (ForM f, CharPtr filename) { AffilPtr affil; AsnIoPtr aip; Char path [PATH_MAX]; SubmitFormPtr sbfp; path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetInputFileName (path, sizeof (path), "", "TEXT")) { aip = AsnIoOpen (path, "r"); if (aip != NULL) { affil = AffilAsnRead (aip, NULL); AsnIoClose (aip); if (affil != NULL) { affil->phone = MemFree (affil->phone); affil->fax = MemFree (affil->fax); affil->email = MemFree (affil->email); PointerToDialog (sbfp->affil, affil); affil = AffilFree (affil); Update (); return TRUE; } } } } return FALSE; } static Boolean WriteAffilPage (ForM f, CharPtr filename) { AffilPtr affil; AsnIoPtr aip; Char path [PATH_MAX]; SubmitFormPtr sbfp; #ifdef WIN_MAC FILE *fp; #endif path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { if (path [0] != '\0' || GetOutputFileName (path, sizeof (path), NULL)) { #ifdef WIN_MAC fp = FileOpen (path, "r"); if (fp != NULL) { FileClose (fp); } else { FileCreate (path, "TEXT", "ttxt"); } #endif aip = AsnIoOpen (path, "w"); if (aip != NULL) { affil = DialogToPointer (sbfp->affil); affil->phone = MemFree (affil->phone); affil->fax = MemFree (affil->fax); affil->email = MemFree (affil->email); AffilAsnWrite (affil, aip, NULL); AsnIoClose (aip); affil = AffilFree (affil); return TRUE; } } } return FALSE; } static Boolean ImportSubmitForm (ForM f, CharPtr filename) { SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { switch (sbfp->currentPage) { case SUBMISSION_PAGE : return ReadSubmitBlock (f, filename); case CONTACT_PAGE : return ReadContactPage (f, filename); case AUTHOR_PAGE : return ReadAuthListPage (f, filename); case AFFILIATION_PAGE : return ReadAffilPage (f, filename); default : break; } } return FALSE; } static Boolean ExportSubmitForm (ForM f, CharPtr filename) { SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { switch (sbfp->currentPage) { case SUBMISSION_PAGE : return FALSE; case CONTACT_PAGE : return WriteContactPage (f, filename); case AUTHOR_PAGE : return WriteAuthListPage (f, filename); case AFFILIATION_PAGE : return WriteAffilPage (f, filename); default : break; } } return FALSE; } static void CopyContactToAuthors (SubmitFormPtr sbfp) { AuthListPtr alp; AuthorPtr ap; ValNodePtr names; NameStdPtr nsp; PersonIdPtr pid; Char str [128]; CharPtr txt; if (sbfp == NULL) return; ap = NULL; alp = AuthListNew (); if (alp != NULL) { alp->choice = 1; names = ValNodeNew (NULL); alp->choice = 1; alp->names = names; if (names != NULL) { ap = AuthorNew (); if (ap != NULL) { pid = PersonIdNew (); ap->name = pid; if (pid != NULL) { pid->choice = 2; str [0] = '\0'; txt = SaveStringFromText (sbfp->firstname); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->middleinit); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->lastname); StringCat (str, txt); StringCat (str, "\t"); MemFree (txt); txt = SaveStringFromText (sbfp->suffix); StringCat (str, txt); StringCat (str, "\n"); MemFree (txt); txt = StringSave (str); nsp = AuthorSpreadsheetStringToNameStdPtr (txt); MemFree (txt); pid->data = nsp; if (nsp != NULL) { if (StringHasNoText (nsp->names [0])) { ap = AuthorFree (ap); } } } } names->choice = 1; names->data.ptrvalue = ap; } if (ap == NULL) { alp = AuthListFree (alp); } if (alp != NULL) { PointerToDialog (sbfp->authors, (Pointer) alp); } } alp = AuthListFree (alp); } static void SetSubmitterImportExportItems (SubmitFormPtr sbfp) { IteM exportItm; IteM importItm; if (sbfp != NULL) { importItm = FindFormMenuItem ((BaseFormPtr) sbfp, VIB_MSG_IMPORT); exportItm = FindFormMenuItem ((BaseFormPtr) sbfp, VIB_MSG_EXPORT); switch (sbfp->currentPage) { case SUBMISSION_PAGE : SafeSetTitle (importItm, "Import Submitter Info..."); SafeSetTitle (exportItm, "Export..."); SafeEnable (importItm); SafeDisable (exportItm); break; case CONTACT_PAGE : SafeSetTitle (importItm, "Import Contact..."); SafeSetTitle (exportItm, "Export Contact..."); SafeEnable (importItm); SafeEnable (exportItm); break; case AUTHOR_PAGE : SafeSetTitle (importItm, "Import Authors..."); SafeSetTitle (exportItm, "Export Authors..."); SafeEnable (importItm); SafeEnable (exportItm); break; case AFFILIATION_PAGE : SafeSetTitle (importItm, "Import Affiliation..."); SafeSetTitle (exportItm, "Export Affiliation..."); SafeEnable (importItm); SafeEnable (exportItm); break; default : break; } } } static void EnterSubmitPage (SubmitFormPtr sbfp, Int2 page) { AuthListPtr alp; if (sbfp != NULL) { switch (page) { case SUBMISSION_PAGE : Select (sbfp->title); SafeSetTitle (sbfp->prevBtn, "<< Prev Form"); SafeSetTitle (sbfp->nextBtn, "Next Page >>"); break; case CONTACT_PAGE : Select (sbfp->firstname); sbfp->visitedContact = TRUE; SafeSetTitle (sbfp->prevBtn, "<< Prev Page"); SafeSetTitle (sbfp->nextBtn, "Next Page >>"); break; case AUTHOR_PAGE : alp = (AuthListPtr) DialogToPointer (sbfp->authors); if (sbfp->visitedContact && alp == NULL) { CopyContactToAuthors (sbfp); } AuthListFree (alp); /* if (sbfp->visitedContact && (! sbfp->visitedAuthor)) { CopyContactToAuthors (sbfp); } */ SendMessageToDialog (sbfp->authors, VIB_MSG_ENTER); sbfp->visitedAuthor = TRUE; SafeSetTitle (sbfp->prevBtn, "<< Prev Page"); SafeSetTitle (sbfp->nextBtn, "Next Page >>"); break; case AFFILIATION_PAGE : SendMessageToDialog (sbfp->affil, VIB_MSG_ENTER); SafeSetTitle (sbfp->prevBtn, "<< Prev Page"); SafeSetTitle (sbfp->nextBtn, "Next Form >>"); break; default : break; } } } static void ChangeSubmitFormPage (VoidPtr data, Int2 newval, Int2 oldval) { SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) data; if (sbfp != NULL) { sbfp->currentPage = newval; SafeHide (sbfp->pages [oldval]); Update (); #ifdef WIN_MAC EnterSubmitPage (sbfp, newval); #endif SetSubmitterImportExportItems (sbfp); SafeShow (sbfp->pages [newval]); #ifndef WIN_MAC EnterSubmitPage (sbfp, newval); #endif Update (); switch (newval) { case SUBMISSION_PAGE : SendHelpScrollMessage (helpForm, "Submitting Authors Form", "Submission Page"); break; case CONTACT_PAGE : SendHelpScrollMessage (helpForm, "Submitting Authors Form", "Contact Page"); break; case AUTHOR_PAGE : SendHelpScrollMessage (helpForm, "Submitting Authors Form", "Authors Page"); break; case AFFILIATION_PAGE : SendHelpScrollMessage (helpForm, "Submitting Authors Form", "Affiliation Page"); break; default : break; } } } static void NextSubmitFormBtn (ButtoN b) { SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) GetObjectExtra (b); if (sbfp != NULL) { if (sbfp->currentPage < 3) { SetValue (sbfp->tbs, sbfp->currentPage + 1); } else if (sbfp->goToNext != NULL) { (sbfp->goToNext) (b); } } } static void PrevSubmitFormBtn (ButtoN b) { SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) GetObjectExtra (b); if (sbfp != NULL) { if (sbfp->currentPage > 0) { SetValue (sbfp->tbs, sbfp->currentPage - 1); } else if (sbfp->goToPrev != NULL) { (sbfp->goToPrev) (b); } } } static void ChangeHup (GrouP g) { Boolean hup; SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) GetObjectExtra (g); if (sbfp != NULL) { hup = (Boolean) (GetValue (sbfp->hup) == 2); if (hup) { SafeShow (sbfp->dateGrp); } else { SafeHide (sbfp->dateGrp); } } } static CharPtr submitFormTabs [] = { "Submission", "Contact", "Authors", "Affiliation", NULL }; static void SubmitFormMessage (ForM f, Int2 mssg) { SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) GetObjectExtra (f); if (sbfp != NULL) { switch (mssg) { case VIB_MSG_IMPORT : ImportSubmitForm (f, NULL); break; case VIB_MSG_EXPORT : ExportSubmitForm (f, NULL); 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 (sbfp->appmessage != NULL) { sbfp->appmessage (f, mssg); } break; } } } static void InitSubmitterFormActivate (WindoW w) { SubmitFormPtr sbfp; sbfp = (SubmitFormPtr) GetObjectExtra (w); if (sbfp != NULL) { if (sbfp->activate != NULL) { sbfp->activate (w); } SetSubmitterImportExportItems (sbfp); } } extern ForM CreateInitSubmitterForm (Int2 left, Int2 top, CharPtr title, BtnActnProc goToNext, BtnActnProc goBack, WndActnProc activateForm) { GrouP c; GrouP g; GrouP h; GrouP j; GrouP m; GrouP n; GrouP q; SubmitFormPtr sbfp; StdEditorProcsPtr sepp; GrouP t; WindoW w; GrouP x; w = NULL; sbfp = MemNew (sizeof (SubmitForm)); if (sbfp != NULL) { w = FixedWindow (left, top, -10, -10, title, NULL); SetObjectExtra (w, sbfp, StdCleanupFormProc); sbfp->form = (ForM) w; sbfp->toform = SequinBlockPtrToSubmitForm; sbfp->fromform = SubmitFormToSequinBlockPtr; sbfp->testform = TestSubmitForm; sbfp->importform = ImportSubmitForm; sbfp->exportform = ExportSubmitForm; sbfp->formmessage = SubmitFormMessage; #ifndef WIN_MAC CreateSqnInitialFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { sbfp->appmessage = sepp->handleMessages; } SetGroupSpacing (w, 10, 10); j = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (j, 10, 10); sbfp->tbs = CreateFolderTabs (j, submitFormTabs, 0, 0, 0, SYSTEM_FOLDER_TAB, ChangeSubmitFormPage, (Pointer) sbfp); sbfp->currentPage = SUBMISSION_PAGE; sbfp->visitedContact = FALSE; sbfp->visitedAuthor = FALSE; h = HiddenGroup (w, 0, 0, NULL); q = HiddenGroup (h, -1, 0, NULL); SetGroupSpacing (q, 10, 20); m = HiddenGroup (q, -1, 0, NULL); g = HiddenGroup (m, 0, -4, NULL); SetGroupSpacing (g, 3, 10); StaticPrompt (g, "When may we release your sequence record?", 0, stdLineHeight, programFont, 'l'); sbfp->hup = HiddenGroup (g, 0, -2, ChangeHup); SetObjectExtra (sbfp->hup, sbfp, NULL); RadioButton (sbfp->hup, "Immediately After Processing"); RadioButton (sbfp->hup, "Release Date:"); SetValue (sbfp->hup, 1); sbfp->dateGrp = HiddenGroup (m, 10, 0, NULL); /* StaticPrompt (sbfp->dateGrp, "Release Date: ", 0, popupMenuHeight, programFont, 'l'); */ sbfp->reldate = CreateDateDialog (sbfp->dateGrp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) sbfp->dateGrp, NULL); Hide (sbfp->dateGrp); t = HiddenGroup (q, 1, 0, NULL); StaticPrompt (t, "Tentative title for manuscript", 0, 0, programFont, 'c'); sbfp->title = ScrollText (t, 25, 4, programFont, TRUE, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) sbfp->reldate, (HANDLE) sbfp->title, (HANDLE) t, NULL); sbfp->pages [SUBMISSION_PAGE] = q; Hide (sbfp->pages [SUBMISSION_PAGE]); q = HiddenGroup (h, -1, 0, NULL); SetGroupSpacing (q, 10, 20); n = HiddenGroup (q, 4, 0, NULL); SetGroupSpacing (n, -1, 2); StaticPrompt (n, "First Name", 0, 0, programFont, 'c'); StaticPrompt (n, "M.I.", 0, 0, programFont, 'c'); StaticPrompt (n, "Last Name", 0, 0, programFont, 'c'); StaticPrompt (n, "Sfx", 0, 0, programFont, 'c'); sbfp->firstname = DialogText (n, "", 8, NULL); sbfp->middleinit = DialogText (n, "", 4, NULL); sbfp->lastname = DialogText (n, "", 9, NULL); sbfp->suffix = DialogText (n, "", 3, NULL); sbfp->phonefaxemail = CreateExtAffilDialog (q, NULL, NULL, &x); Show (x); Show (sbfp->phonefaxemail); AlignObjects (ALIGN_CENTER, (HANDLE) n, (HANDLE) sbfp->phonefaxemail, NULL); sbfp->pages [CONTACT_PAGE] = q; Hide (sbfp->pages [CONTACT_PAGE]); q = HiddenGroup (h, -1, 0, NULL); SetGroupSpacing (q, 10, 20); sbfp->authors = CreateAuthorDialog (q, 3, -1); sbfp->pages [AUTHOR_PAGE] = q; Hide (sbfp->pages [AUTHOR_PAGE]); q = HiddenGroup (h, -1, 0, NULL); SetGroupSpacing (q, 10, 20); sbfp->affil = CreateExtAffilDialog (q, NULL, &g, NULL); Show (g); Show (sbfp->affil); sbfp->pages [AFFILIATION_PAGE] = q; Hide (sbfp->pages [AFFILIATION_PAGE]); c = HiddenGroup (w, 4, 0, NULL); SetGroupSpacing (c, 10, 2); sbfp->goToPrev = goBack; sbfp->prevBtn = PushButton (c, " << Prev Form ", PrevSubmitFormBtn); SetObjectExtra (sbfp->prevBtn, sbfp, NULL); sbfp->goToNext = goToNext; sbfp->nextBtn = PushButton (c, " Next Page >> ", NextSubmitFormBtn); SetObjectExtra (sbfp->nextBtn, sbfp, NULL); AlignObjects (ALIGN_CENTER, (HANDLE) sbfp->pages [SUBMISSION_PAGE], (HANDLE) sbfp->pages [CONTACT_PAGE], (HANDLE) sbfp->pages [AUTHOR_PAGE], (HANDLE) sbfp->pages [AFFILIATION_PAGE], (HANDLE) sbfp->tbs, (HANDLE) c, NULL); RealizeWindow (w); SafeSetTitle (sbfp->prevBtn, "<< Prev Form"); SafeSetTitle (sbfp->nextBtn, "Next Page >>"); sbfp->activate = activateForm; SetActivate (w, InitSubmitterFormActivate); Show (sbfp->pages [sbfp->currentPage]); EnterSubmitPage (sbfp, sbfp->currentPage); } return (ForM) w; } #define REMOVE_RNA 1 #define CONVERT_RNA 2 #define ADD_RNA 3 #define EDIT_RNA 4 static ENUM_ALIST(rna_field_alist) {" ", 0}, {"Name", 1}, {"Comment", 2}, {"Product GBQUAL", 3}, END_ENUM_ALIST static ENUM_ALIST(rna_subtype_alist) {" ", 7}, {"unknown", 0}, {"preRna", 1}, {"mRNA", 2}, {"tRNA", 3}, {"rRNA", 4}, {"snRNA", 5}, {"scRNA", 6}, {"Other RNA", 255}, END_ENUM_ALIST typedef struct rnaformdata { FEATURE_FORM_BLOCK Int2 type; PopuP fromfield; PopuP tofield; Int2 fromval; Int2 toval; Boolean replaceOldAsked; Boolean doReplaceAll; TexT findthis; Char findStr [256]; PopuP rnaSubType; PopuP rnaDestType; GrouP txtGrp; CharPtr replaceStr; TexT replacewith; } RnaFormData, PNTR RnaFormPtr; static Boolean ShouldReplaceRnaString (RnaFormPtr rfp) { MsgAnswer ans; if (rfp == NULL) return FALSE; if (! rfp->replaceOldAsked) { rfp->replaceOldAsked = TRUE; ArrowCursor (); ans = Message (MSG_YN, "Do you wish to overwrite existing contents?"); WatchCursor (); Update (); rfp->doReplaceAll = (Boolean) (ans == ANS_YES); } return rfp->doReplaceAll; } static CharPtr SaveOrReplaceRnaString (RnaFormPtr rfp, CharPtr str, CharPtr current) { size_t len; CharPtr tmp; if (rfp == NULL) return str; if (StringHasNoText (str)) return current; if (current != NULL) { if (ShouldReplaceRnaString (rfp)) { 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 EditRnaString (CharPtr PNTR strptr, RnaFormPtr rfp, CharPtr findStr, CharPtr foundit) { size_t diff; size_t foundlen; size_t replen; CharPtr newstring; CharPtr tmp; CharPtr tmp2; if (rfp == NULL || strptr == NULL || findStr == NULL || foundit == NULL) return; foundlen = StringLen (findStr); replen = StringLen (rfp->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 (rfp->replaceStr != NULL) { tmp2 = MemCopy (tmp2, rfp->replaceStr, replen); } tmp2 += replen; tmp += foundlen; tmp2 = StringMove (tmp2, tmp); *strptr = MemFree (*strptr); *strptr = newstring; } /* EditRnaString */ static Boolean ProcessEachRNAFunc (GatherContextPtr gcp) { GBQualPtr gbqual; RnaFormPtr rfp; RnaRefPtr rrp; SeqFeatPtr sfp; CharPtr str, foundit; UIEnum val; if (gcp == NULL) return TRUE; rfp = (RnaFormPtr) gcp->userdata; if (rfp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.value.ptrvalue == NULL) return TRUE; rrp = NULL; if (sfp->data.choice == SEQFEAT_RNA) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; } else return TRUE; str = NULL; if (rfp->rnaSubType != NULL) { if (GetEnumPopup (rfp->rnaSubType, rna_subtype_alist, &val)) { if (val != 7 && (Uint1) val != rrp->type) { rrp = NULL; } } } if (rrp == NULL) return TRUE; switch (rfp->type) { case REMOVE_RNA : break; case CONVERT_RNA : switch (rfp->fromval) { case 1 : if (rrp->ext.choice == 1 && rrp->ext.value.ptrvalue != NULL) { str = StringSave ((CharPtr) rrp->ext.value.ptrvalue); } break; case 2 : str = StringSave (sfp->comment); break; case 3 : gbqual = sfp->qual; while (gbqual != NULL) { if (StringICmp (gbqual->qual, "product") == 0) { str = StringSave (gbqual->val); } gbqual = gbqual->next; } break; default : break; } break; case ADD_RNA : str = StringSave (rfp->findStr); break; case EDIT_RNA : str = JustSaveStringFromText (rfp->findthis); break; default : break; } if (str == NULL) return TRUE; switch (rfp->type) { case REMOVE_RNA : break; case CONVERT_RNA : case ADD_RNA : switch (rfp->toval) { case 1 : if (rrp->ext.choice == 0 || rrp->ext.choice == 1) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = SaveOrReplaceRnaString (rfp, str, rrp->ext.value.ptrvalue); } str = NULL; break; case 2 : sfp->comment = SaveOrReplaceRnaString (rfp, str, sfp->comment); str = NULL; break; case 3 : gbqual = GBQualNew (); if (gbqual != NULL) { gbqual->qual = StringSave ("product"); gbqual->val = str; str = NULL; gbqual->next = sfp->qual; sfp->qual = gbqual; } break; default : break; } break; case EDIT_RNA : rfp->replaceStr = JustSaveStringFromText (rfp->replacewith); foundit = StringISearch (rrp->ext.value.ptrvalue, str); if (foundit) { if (rrp->ext.choice == 0 || rrp->ext.choice == 1) { rrp->ext.choice = 1; EditRnaString ((CharPtr PNTR) &(rrp->ext.value.ptrvalue), rfp, str, foundit); } } MemFree (str); break; default : break; } MemFree (str); return TRUE; } static Boolean CleanupEachRNAFunc (GatherContextPtr gcp) { Uint1 desttype; GBQualPtr gbqual; GBQualPtr nextqual; GBQualPtr PNTR prevqual; RnaFormPtr rfp; RnaRefPtr rrp; SeqFeatPtr sfp; UIEnum val; if (gcp == NULL) return TRUE; rfp = (RnaFormPtr) gcp->userdata; if (rfp == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT) return TRUE; sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.value.ptrvalue == NULL) return TRUE; rrp = NULL; if (sfp->data.choice == SEQFEAT_RNA) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; } else return TRUE; if (rfp->rnaSubType != NULL) { if (GetEnumPopup (rfp->rnaSubType, rna_subtype_alist, &val)) { if (val != 7 && (Uint1) val != rrp->type) { rrp = NULL; } } } if (rrp == NULL) return TRUE; desttype = 7; if (rfp->rnaDestType != NULL) { if (GetEnumPopup (rfp->rnaDestType, rna_subtype_alist, &val)) { if (val != 7 && (Uint1) val != rrp->type) { desttype = (Uint1) val; } } } switch (rfp->type) { case REMOVE_RNA : case CONVERT_RNA : switch (rfp->fromval) { case 1 : if (rrp->ext.choice == 1 && rrp->ext.value.ptrvalue != NULL) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.choice = 0; } break; case 2 : sfp->comment = MemFree (sfp->comment); break; case 3 : gbqual = sfp->qual; prevqual = (GBQualPtr PNTR) &(sfp->qual); while (gbqual != NULL) { nextqual = gbqual->next; if (StringICmp (gbqual->qual, "product") == 0) { *(prevqual) = gbqual->next; gbqual->next = NULL; gbqual->qual = MemFree (gbqual->qual); gbqual->val = MemFree (gbqual->val); GBQualFree (gbqual); } else { prevqual = (GBQualPtr PNTR) &(gbqual->next); } gbqual = nextqual; } break; default : break; } if (desttype != 7) { rrp->type = desttype; } break; case ADD_RNA : break; default : break; } return TRUE; } static void DoProcessRnaProc (ButtoN b) { GatherScope gs; RnaFormPtr rfp; UIEnum val; rfp = (RnaFormPtr) GetObjectExtra (b); if (rfp == NULL || rfp->input_entityID == 0) return; Hide (rfp->form); WatchCursor (); Update (); rfp->fromval = 0; rfp->toval = 0; if (GetEnumPopup (rfp->fromfield, rna_field_alist, &val)) { rfp->fromval = (Int2) val; } if (GetEnumPopup (rfp->tofield, rna_field_alist, &val)) { rfp->toval = (Int2) val; } if (rfp->type == ADD_RNA) { rfp->toval = rfp->fromval; } rfp->replaceOldAsked = FALSE; rfp->doReplaceAll = FALSE; rfp->findStr [0] = '\0'; GetTitle (rfp->findthis, rfp->findStr, sizeof (rfp->findStr) - 1); TrimSpacesAroundString (rfp->findStr); 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 (rfp->type != REMOVE_RNA) { GatherEntity (rfp->input_entityID, (Pointer) rfp, ProcessEachRNAFunc, &gs); } if (rfp->type == CONVERT_RNA || rfp->type == REMOVE_RNA) { GatherEntity (rfp->input_entityID, (Pointer) rfp, CleanupEachRNAFunc, &gs); } ArrowCursor (); Update (); ObjMgrSetDirtyFlag (rfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, rfp->input_entityID, 0, 0); Remove (rfp->form); } static void ProcessRNAMessageProc (ForM f, Int2 mssg) { StdEditorProcsPtr sepp; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { if (sepp->handleMessages != NULL) { sepp->handleMessages (f, mssg); } } } static void ProcessRNA (IteM i, Int2 type) { ButtoN b; BaseFormPtr bfp; GrouP c; GrouP g; GrouP h; GrouP p; RnaFormPtr rfp; SeqEntryPtr sep; StdEditorProcsPtr sepp; CharPtr title; WindoW w; GrouP y; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; rfp = (RnaFormPtr) MemNew (sizeof (RnaFormData)); if (rfp == NULL) return; rfp->type = type; switch (type) { case REMOVE_RNA : title = "RNA Removal"; break; case CONVERT_RNA : title = "RNA Conversion"; break; case ADD_RNA : title = "Add RNA Qualifier"; break; case EDIT_RNA : title = "Edit RNA Qualifier"; break; default : title = "?"; break; } w = FixedWindow (-50, -33, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, rfp, StdCleanupFormProc); rfp->form = (ForM) w; rfp->formmessage = ProcessRNAMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); rfp->appmessage = sepp->handleMessages; } rfp->input_entityID = bfp->input_entityID; rfp->input_itemID = bfp->input_itemID; rfp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, 4, 0, NULL); switch (type) { case REMOVE_RNA : StaticPrompt (g, "Remove", 0, popupMenuHeight, programFont, 'l'); rfp->fromfield = PopupList (g, TRUE, NULL); SetObjectExtra (rfp->fromfield, rfp, NULL); InitEnumPopup (rfp->fromfield, rna_field_alist, NULL); SetEnumPopup (rfp->fromfield, rna_field_alist, 0); break; case CONVERT_RNA : StaticPrompt (g, "From", 0, popupMenuHeight, programFont, 'l'); rfp->fromfield = PopupList (g, TRUE, NULL); SetObjectExtra (rfp->fromfield, rfp, NULL); InitEnumPopup (rfp->fromfield, rna_field_alist, NULL); SetEnumPopup (rfp->fromfield, rna_field_alist, 0); StaticPrompt (g, "To", 0, popupMenuHeight, programFont, 'l'); rfp->tofield = PopupList (g, TRUE, NULL); InitEnumPopup (rfp->tofield, rna_field_alist, NULL); SetEnumPopup (rfp->tofield, rna_field_alist, 0); break; case ADD_RNA : StaticPrompt (g, "Type", 0, popupMenuHeight, programFont, 'l'); rfp->fromfield = PopupList (g, TRUE, NULL); SetObjectExtra (rfp->fromfield, rfp, NULL); InitEnumPopup (rfp->fromfield, rna_field_alist, NULL); SetEnumPopup (rfp->fromfield, rna_field_alist, 0); break; case EDIT_RNA : break; default : break; } y = NULL; switch (type) { case REMOVE_RNA : break; case CONVERT_RNA : break; case ADD_RNA : y = HiddenGroup (h, 2, 0, NULL); StaticPrompt (y, "Text", 0, dialogTextHeight, programFont, 'c'); rfp->findthis = DialogText (y, "", 14, NULL); break; case EDIT_RNA : break; default : break; } p = HiddenGroup (h, 4, 0, NULL); StaticPrompt (p, "RNA subtype", 0, popupMenuHeight, programFont, 'l'); rfp->rnaSubType = PopupList (p, TRUE, NULL); InitEnumPopup (rfp->rnaSubType, rna_subtype_alist, NULL); SetEnumPopup (rfp->rnaSubType, rna_subtype_alist, (UIEnum) 7); rfp->rnaDestType = NULL; if (type == CONVERT_RNA) { StaticPrompt (p, "Change to", 0, popupMenuHeight, programFont, 'l'); rfp->rnaDestType = PopupList (p, TRUE, NULL); InitEnumPopup (rfp->rnaDestType, rna_subtype_alist, NULL); SetEnumPopup (rfp->rnaDestType, rna_subtype_alist, (UIEnum) 7); } rfp->txtGrp = NULL; if (type == EDIT_RNA) { rfp->txtGrp = HiddenGroup (h, 2, 0, NULL); StaticPrompt (rfp->txtGrp, "Find", 0, dialogTextHeight, programFont, 'l'); rfp->findthis = DialogText (rfp->txtGrp, "", 14, NULL); StaticPrompt (rfp->txtGrp, "Replace", 0, dialogTextHeight, programFont, 'l'); rfp->replacewith = DialogText (rfp->txtGrp, "", 14, NULL); } c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoProcessRnaProc); SetObjectExtra (b, rfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) p, (HANDLE) c, (HANDLE) y, NULL); RealizeWindow (w); Show (w); Update (); } extern void RemoveRNA (IteM i) { ProcessRNA (i, REMOVE_RNA); } extern void ConvertRNA (IteM i) { ProcessRNA (i, CONVERT_RNA); } extern void AddRNA (IteM i) { ProcessRNA (i, ADD_RNA); } extern void EditRNA (IteM i) { ProcessRNA (i, EDIT_RNA); } typedef struct parseformdata { FEATURE_FORM_BLOCK TexT atleft; TexT atright; PopuP orgmod; PopuP subsource; PopuP taxname; Boolean parsedef; Char path [PATH_MAX]; FILE *fp; } ParseFormData, PNTR ParseFormPtr; static void DoOneParseItem (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, BioSourcePtr topbiop, CharPtr useme, SeqEntryPtr nps) { BioSourcePtr biop; BioseqPtr bsp; BioseqSetPtr bssp; OrgModPtr mod; SeqEntryPtr nsep; OrgNamePtr onp; Uint1 orgmodtype; OrgRefPtr orp; CharPtr ptr; SeqIdPtr sip; SubSourcePtr ssp; Char str [256]; Uint1 subsourcetype; Uint1 subtype; Int2 taxnameval; SeqEntryPtr tmp; OrgModPtr tmpmod; SubSourcePtr tmpssp; ValNodePtr ttl; Char txt [128]; UIEnum val; ValNodePtr vnp; if (sep == NULL || pfp == NULL) return; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL) { /* if nucprot set, look for biosource here */ biop = NULL; SeqEntryToBioSource (sep, NULL, NULL, 0, &biop); if (biop != NULL && topbiop != NULL) { topbiop = biop; } for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { DoOneParseItem (entityID, tmp, pfp, topbiop, useme, sep); } return; } } nsep = FindNucSeqEntry (sep); if (nsep != NULL && nsep->data.ptrvalue != NULL) { str [0] = '\0'; if (useme != NULL) { StringNCpy_0 (str, useme, sizeof (str)); } else if (pfp->parsedef) { ttl = SeqEntryGetSeqDescr (nsep, Seq_descr_title, NULL); if (ttl == NULL && nps != NULL) { ttl = SeqEntryGetSeqDescr (nps, Seq_descr_title, NULL); } if (ttl == NULL || ttl->data.ptrvalue == NULL) return; StringNCpy_0 (str, (CharPtr) ttl->data.ptrvalue, sizeof (str)); GetTitle (pfp->atleft, txt, sizeof (txt)); if (! StringHasNoText (txt)) { ptr = StringISearch (str, txt); if (ptr != NULL) { StringNCpy_0 (str, ptr + StringLen (txt), sizeof (str)); } } GetTitle (pfp->atright, txt, sizeof (txt)); if (txt [0] != '\0' /* ! StringHasNoText (txt) */) { ptr = StringISearch (str, txt); if (ptr != NULL) { *ptr = '\0'; } } } else { bsp = (BioseqPtr) nsep->data.ptrvalue; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_LOCAL) { SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str)); if (StringNICmp (str, "tmpseq_", 7) == 0 || StringNICmp (str, "segseq_", 7) == 0 || StringNICmp (str, "SEG_dna", 7) == 0) return; } } } if (StringHasNoText (str)) return; biop = NULL; SeqEntryToBioSource (sep, NULL, NULL, 0, &biop); taxnameval = GetValue (pfp->taxname); if (taxnameval == 2) { if (biop == NULL) { biop = BioSourceNew (); if (biop != NULL) { orp = OrgRefNew (); biop->org = orp; vnp = CreateNewDescriptor (sep, Seq_descr_source); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) biop; } } } if (biop == NULL) return; orp = biop->org; if (orp == NULL) return; orp->taxname = MemFree (orp->taxname); orp->taxname = StringSave (str); return; } if (biop == NULL && topbiop != NULL) { biop = (BioSourcePtr) AsnIoMemCopy ((Pointer) topbiop, (AsnReadFunc) BioSourceAsnRead, (AsnWriteFunc) BioSourceAsnWrite); if (biop != NULL) { vnp = CreateNewDescriptor (sep, Seq_descr_source); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) biop; } } } if (biop == NULL) return; orgmodtype = 0; subsourcetype = 0; if (taxnameval == 3) { orgmodtype = 255; } else if (taxnameval == 4) { subsourcetype = 255; } else if (GetEnumPopup (pfp->orgmod, orgmod_subtype_alist, &val) && val > 0) { orgmodtype = val; } else if (GetEnumPopup (pfp->subsource, subsource_subtype_alist, &val) && val > 0) { subsourcetype = val; } if (! StringHasNoText (str)) { if (orgmodtype > 0) { subtype = orgmodtype; orp = biop->org; if (orp == NULL) { orp = OrgRefNew (); biop->org = orp; } if (orp != NULL) { onp = orp->orgname; if (onp == NULL) { onp = OrgNameNew (); orp->orgname = onp; } if (onp != NULL) { mod = onp->mod; while (mod != NULL && mod->subtype != subtype) { mod = mod->next; } if (mod == NULL) { mod = OrgModNew (); if (onp->mod == NULL) { onp->mod = mod; } else { tmpmod = onp->mod; while (tmpmod->next != NULL) { tmpmod = tmpmod->next; } tmpmod->next = mod; } } if (mod != NULL) { mod->subtype = subtype; mod->subname = MemFree (mod->subname); mod->subname = StringSave (str); } } } } else if (subsourcetype > 0) { subtype = subsourcetype; ssp = biop->subtype; while (ssp != NULL && ssp->subtype != subtype) { ssp = ssp->next; } if (ssp == NULL) { ssp = SubSourceNew (); if (biop->subtype == NULL) { biop->subtype = ssp; } else { tmpssp = biop->subtype; while (tmpssp->next != NULL) { tmpssp = tmpssp->next; } tmpssp->next = ssp; } } if (ssp != NULL) { ssp->subtype = subtype; ssp->name = MemFree (ssp->name); ssp->name = StringSave (str); } } } } } static void DoOneParse (Uint2 entityID, SeqEntryPtr sep, ParseFormPtr pfp, BioSourcePtr topbiop) { BioseqPtr bsp; BioseqSetPtr bssp; Char gb [256]; CharPtr ptr; SeqIdPtr sip; Char str [250]; SeqEntryPtr tmp; if (sep == NULL || pfp == NULL) return; if (pfp->fp != NULL) { ReadLine (pfp->fp, str, sizeof (str)); /* FileGets on Mac sometimes sees '\r' instead of '\n' */ while (Nlm_fileDone) { if (! StringHasNoText (str)) { ptr = StringChr (str, '\t'); if (ptr != NULL) { *ptr = '\0'; ptr++; TrimSpacesAroundString (str); TrimSpacesAroundString (ptr); sip = MakeSeqID (str); bsp = BioseqFind (sip); SeqIdFree (sip); if (bsp == NULL) { sprintf (gb, "gb|%s|", str); sip = MakeSeqID (gb); bsp = BioseqFind (sip); SeqIdFree (sip); } if (bsp != NULL) { tmp = GetBestTopParentForData (entityID, bsp); DoOneParseItem (entityID, tmp, pfp, topbiop, ptr, NULL); } } } ReadLine (pfp->fp, str, sizeof (str)); } return; } if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && (bssp->_class == 7 || (bssp->_class >= 13 && bssp->_class <= 16))) { for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { DoOneParse (entityID, tmp, pfp, topbiop); } return; } } DoOneParseItem (entityID, sep, pfp, topbiop, NULL, NULL); } static void DoParseDeflineProc (ButtoN b) { BioSourcePtr topbiop; ParseFormPtr pfp; SeqEntryPtr sep; pfp = (ParseFormPtr) GetObjectExtra (b); if (pfp == NULL || pfp->input_entityID == 0) return; sep = GetTopSeqEntryForEntityID (pfp->input_entityID); if (sep == NULL) return; Hide (pfp->form); WatchCursor (); Update (); /* if popset, look for top biosource */ SeqEntryToBioSource (sep, NULL, NULL, 0, &topbiop); if (! StringHasNoText (pfp->path)) { pfp->fp = FileOpen (pfp->path, "r"); } DoOneParse (pfp->input_entityID, sep, pfp, topbiop); FileClose (pfp->fp); ArrowCursor (); Update (); ObjMgrSetDirtyFlag (pfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, pfp->input_entityID, 0, 0); Remove (pfp->form); } static void ParseDeflineMessageProc (ForM f, Int2 mssg) { StdEditorProcsPtr sepp; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { if (sepp->handleMessages != NULL) { sepp->handleMessages (f, mssg); } } } static void ParseDefOrLocalIDToSource (IteM i, Boolean parsedef, CharPtr path) { ButtoN b; BaseFormPtr bfp; GrouP c; GrouP g; GrouP h; GrouP p; ParseFormPtr pfp; SeqEntryPtr sep; StdEditorProcsPtr sepp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; pfp = (ParseFormPtr) MemNew (sizeof (ParseFormData)); if (pfp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "Parse Def Line", StdCloseWindowProc); SetObjectExtra (w, pfp, StdCleanupFormProc); pfp->form = (ForM) w; pfp->formmessage = ParseDeflineMessageProc; 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; pfp->parsedef = parsedef; StringNCpy_0 (pfp->path, path, sizeof (pfp->path)); pfp->fp = NULL; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = NULL; if (parsedef) { g = HiddenGroup (h, 4, 0, NULL); StaticPrompt (g, "Get text between", 0, dialogTextHeight, programFont, 'l'); pfp->atleft = DialogText (g, "", 10, NULL); StaticPrompt (g, "and", 0, dialogTextHeight, programFont, 'l'); pfp->atright = DialogText (g, "", 10, NULL); } p = HiddenGroup (h, 6, 0, NULL); if (parsedef || path != NULL) { StaticPrompt (p, "Place in", 0, popupMenuHeight, programFont, 'l'); } else { StaticPrompt (p, "Place localID in", 0, popupMenuHeight, programFont, 'l'); } pfp->taxname = PopupList (p, TRUE, NULL); SetObjectExtra (pfp->taxname, pfp, NULL); PopupItem (pfp->taxname, " "); PopupItem (pfp->taxname, "Taxname"); PopupItem (pfp->taxname, "OrgMod Note"); PopupItem (pfp->taxname, "SubSource Note"); SetValue (pfp->taxname, 1); StaticPrompt (p, "or", 0, popupMenuHeight, programFont, 'l'); pfp->orgmod = PopupList (p, TRUE, NULL); SetObjectExtra (pfp->orgmod, pfp, NULL); InitEnumPopup (pfp->orgmod, orgmod_subtype_alist, NULL); SetEnumPopup (pfp->orgmod, orgmod_subtype_alist, 0); StaticPrompt (p, "or", 0, popupMenuHeight, programFont, 'l'); pfp->subsource = PopupList (p, TRUE, NULL); SetObjectExtra (pfp->subsource, pfp, NULL); InitEnumPopup (pfp->subsource, subsource_subtype_alist, NULL); SetEnumPopup (pfp->subsource, subsource_subtype_alist, 0); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoParseDeflineProc); SetObjectExtra (b, pfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) p, (HANDLE) c, (HANDLE) g, NULL); RealizeWindow (w); Show (w); Select (w); Select (pfp->atleft); Update (); } extern void ParseDefToSource (IteM i) { ParseDefOrLocalIDToSource (i, TRUE, NULL); } extern void ParseLocalIDToSource (IteM i) { ParseDefOrLocalIDToSource (i, FALSE, NULL); } extern void ParseFileToSource (IteM i) { Char path [PATH_MAX]; if (GetInputFileName (path, sizeof (path), "", "TEXT")) { ParseDefOrLocalIDToSource (i, FALSE, path); } } static Boolean AddStrainGatherFunc (GatherContextPtr gcp) { BioSourcePtr biop; Boolean influenza; size_t len; OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; CharPtr ptr; ValNodePtr sdp; SeqFeatPtr sfp; CharPtr str; CharPtr strain; if (gcp == NULL || gcp->thisitem == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT && gcp->thistype != OBJ_SEQDESC) return TRUE; orp = NULL; biop = NULL; switch (gcp->thistype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; switch (sfp->data.choice) { case SEQFEAT_ORG : orp = (OrgRefPtr) sfp->data.value.ptrvalue; break; case SEQFEAT_BIOSRC : biop = (BioSourcePtr) sfp->data.value.ptrvalue; break; default : break; } break; case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; switch (sdp->choice) { case Seq_descr_org : orp = (OrgRefPtr) sdp->data.ptrvalue; break; case Seq_descr_source : biop = (BioSourcePtr) sdp->data.ptrvalue; break; default : break; } break; default : break; } if (orp == NULL && biop != NULL) { orp = biop->org; } if (orp != NULL) { onp = orp->orgname; if (onp != NULL) { mod = onp->mod; strain = NULL; while (mod != NULL) { if (mod->subtype == 2) { strain = mod->subname; } mod = mod->next; } if (strain != NULL) { ptr = StringStr (orp->taxname, " ("); if (ptr != NULL) { *ptr = '\0'; } else { ptr = StringStr (orp->taxname, " ("); if (ptr != NULL) { *ptr = '\0'; } } influenza = FALSE; if (StringICmp (orp->taxname, "Influenza A virus") == 0 || StringICmp (orp->taxname, "Influenza B virus") == 0) { influenza = TRUE; } len = StringLen (orp->taxname) + StringLen (strain) + 6; if (influenza) { len += 2; } str = MemNew (len); if (str != NULL) { StringCpy (str, orp->taxname); StringCat (str, " "); if (influenza) { StringCat (str, "("); } StringCat (str, strain); if (influenza) { StringCat (str, ")"); } orp->taxname = MemFree (orp->taxname); orp->taxname = str; } } } } return TRUE; } extern void AddStrainToOrg (IteM i) { BaseFormPtr bfp; GatherScope gs; 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; 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.ignore[OBJ_SEQDESC] = FALSE; GatherEntity (bfp->input_entityID, (Pointer) NULL, AddStrainGatherFunc, &gs); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); Update (); } static Boolean AddSubspeciesGatherFunc (GatherContextPtr gcp) { BioSourcePtr biop; size_t len; OrgModPtr mod; OrgNamePtr onp; OrgRefPtr orp; CharPtr ptr; ValNodePtr sdp; SeqFeatPtr sfp; CharPtr str; CharPtr subspecies; if (gcp == NULL || gcp->thisitem == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT && gcp->thistype != OBJ_SEQDESC) return TRUE; orp = NULL; biop = NULL; switch (gcp->thistype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; switch (sfp->data.choice) { case SEQFEAT_ORG : orp = (OrgRefPtr) sfp->data.value.ptrvalue; break; case SEQFEAT_BIOSRC : biop = (BioSourcePtr) sfp->data.value.ptrvalue; break; default : break; } break; case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; switch (sdp->choice) { case Seq_descr_org : orp = (OrgRefPtr) sdp->data.ptrvalue; break; case Seq_descr_source : biop = (BioSourcePtr) sdp->data.ptrvalue; break; default : break; } break; default : break; } if (orp == NULL && biop != NULL) { orp = biop->org; } if (orp != NULL) { onp = orp->orgname; if (onp != NULL) { mod = onp->mod; subspecies = NULL; while (mod != NULL) { if (mod->subtype == 22) { subspecies = mod->subname; } mod = mod->next; } if (subspecies != NULL) { ptr = StringStr (orp->taxname, " ("); if (ptr != NULL) { *ptr = '\0'; } else { ptr = StringStr (orp->taxname, " ("); if (ptr != NULL) { *ptr = '\0'; } } len = StringLen (orp->taxname) + StringLen (subspecies) + 6; str = MemNew (len); if (str != NULL) { StringCpy (str, orp->taxname); StringCat (str, " "); StringCat (str, subspecies); orp->taxname = MemFree (orp->taxname); orp->taxname = str; } } } } return TRUE; } extern void AddSubspeciesToOrg (IteM i) { BaseFormPtr bfp; GatherScope gs; 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; 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.ignore[OBJ_SEQDESC] = FALSE; GatherEntity (bfp->input_entityID, (Pointer) NULL, AddSubspeciesGatherFunc, &gs); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); Update (); } static Boolean AddCloneGatherFunc (GatherContextPtr gcp) { BioSourcePtr biop; CharPtr clone; size_t len; OrgRefPtr orp; CharPtr ptr; ValNodePtr sdp; SeqFeatPtr sfp; SubSourcePtr ssp; CharPtr str; if (gcp == NULL || gcp->thisitem == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT && gcp->thistype != OBJ_SEQDESC) return TRUE; orp = NULL; biop = NULL; switch (gcp->thistype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; switch (sfp->data.choice) { case SEQFEAT_ORG : orp = (OrgRefPtr) sfp->data.value.ptrvalue; break; case SEQFEAT_BIOSRC : biop = (BioSourcePtr) sfp->data.value.ptrvalue; break; default : break; } break; case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; switch (sdp->choice) { case Seq_descr_org : orp = (OrgRefPtr) sdp->data.ptrvalue; break; case Seq_descr_source : biop = (BioSourcePtr) sdp->data.ptrvalue; break; default : break; } break; default : break; } if (orp == NULL && biop != NULL) { orp = biop->org; } if (orp != NULL && biop != NULL) { if (biop->subtype != NULL) { ssp = biop->subtype; clone = NULL; while (ssp != NULL) { if (ssp->subtype == 3) { clone = ssp->name; } ssp = ssp->next; } if (clone != NULL) { ptr = StringStr (orp->taxname, " ("); if (ptr != NULL) { *ptr = '\0'; } else { ptr = StringStr (orp->taxname, " ("); if (ptr != NULL) { *ptr = '\0'; } } len = StringLen (orp->taxname) + StringLen (clone) + 6; str = MemNew (len); if (str != NULL) { StringCpy (str, orp->taxname); /* StringCat (str, " ("); */ StringCat (str, " "); StringCat (str, clone); /* StringCat (str, ")"); */ orp->taxname = MemFree (orp->taxname); orp->taxname = str; } } } } return TRUE; } extern void AddCloneToOrg (IteM i) { BaseFormPtr bfp; GatherScope gs; 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; 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.ignore[OBJ_SEQDESC] = FALSE; GatherEntity (bfp->input_entityID, (Pointer) NULL, AddCloneGatherFunc, &gs); ObjMgrSetDirtyFlag (bfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, bfp->input_entityID, 0, 0); Update (); } typedef struct descformdata { FEATURE_FORM_BLOCK Uint2 oldEntityID; Uint2 oldItemID; Uint2 oldItemtype; Uint2 lookfor; Boolean found; ObjMgrProcPtr ompp; BioseqPtr bsp; BioseqSetPtr bssp; SeqEntryPtr sep; Handle target; Boolean usePopupForTarget; Boolean hasMutPopPhySet; Int2 targetScratchSpace; Int2 nucProtCount; Int2 segSetCount; Uint2 descsubtype; ButtoN createNewBtn; } DescFormData, PNTR DescFormPtr; static Boolean FindDescrFunc (GatherContextPtr gcp) { DescFormPtr dfp; ValNodePtr vnp; if (gcp == NULL) return TRUE; dfp = (DescFormPtr) gcp->userdata; if (dfp == NULL) return TRUE; if (gcp->thistype == OBJ_SEQDESC) { vnp = (ValNodePtr) gcp->thisitem; if (vnp != NULL && vnp->choice == dfp->lookfor) { dfp->oldEntityID = gcp->entityID; dfp->oldItemID = gcp->itemID; dfp->oldItemtype = gcp->thistype; dfp->found = TRUE; return FALSE; } } return TRUE; } static CharPtr segClassList [] = { " ", "Nucleotide-Protein Set", "Segmented Nucleotide Set", "conset", "parts", "gibb", "gi", "genbank", "pir", "pub-set", "equiv", "swissprot", "pdb-entry", "MUTATION SET", "POPULATION SET", "PHYLOGENETIC SET", "ENVIRONMENTAL SAMPLES", "genomic product set", "other", NULL }; static Int4 AllButPartsList (SeqEntryPtr sep, Pointer mydata, SeqEntryFunc mycallback, Int4 index, Int2 indent) { BioseqSetPtr bssp; if (sep == NULL) return index; if (IS_Bioseq (sep)) { if (mycallback != NULL) (*mycallback) (sep, mydata, index, indent); return index + 1; } if (Bioseq_set_class (sep) != 4) { if (mycallback != NULL) (*mycallback) (sep, mydata, index, indent); index++; } bssp = (BioseqSetPtr) sep->data.ptrvalue; sep = bssp->seq_set; indent++; while (sep != NULL) { index = AllButPartsList (sep, mydata, mycallback, index, indent); sep = sep->next; } return index; } #define AllButPartsCount( a ) AllButPartsList( a ,NULL,NULL,0,0); #define AllButPartsExplore(a,b,c) AllButPartsList(a, b, c, 0L, 0); static void PopTargetProc (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { DescFormPtr dfp; BioseqPtr bsp; BioseqSetPtr bssp; Uint1 _class; CharPtr ptr; SeqIdPtr sip; Char str [128]; dfp = (DescFormPtr) mydata; if (sep != NULL && sep->data.ptrvalue != NULL) { if (sep->choice == 1) { bsp = (BioseqPtr) sep->data.ptrvalue; sip = SeqIdFindWorst (bsp->id); SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str)); ptr = StringChr (str, '|'); if (ptr == NULL) { ptr = str; } else { ptr++; } if (dfp->usePopupForTarget) { PopupItem (dfp->target, ptr); } else { ListItem (dfp->target, ptr); } if (bsp == dfp->bsp) { dfp->targetScratchSpace = index + 1; } } else if (sep->choice == 2) { bssp = (BioseqSetPtr) sep->data.ptrvalue; _class = bssp->_class; if (_class > 17) { _class = 18; } if (_class == 7 || (_class >= 13 && _class <= 16)) { dfp->hasMutPopPhySet = TRUE; } if (! dfp->hasMutPopPhySet) { sprintf (str, "[%s]", segClassList [_class]); } else if (_class == 1) { (dfp->nucProtCount)++; sprintf (str, "[%s %d]", segClassList [_class], (int) dfp->nucProtCount); (dfp->segSetCount)++; } else if (_class == 2) { sprintf (str, "[%s %d]", segClassList [_class], (int) dfp->segSetCount); } else { sprintf (str, "[%s]", segClassList [_class]); } if (dfp->usePopupForTarget) { PopupItem (dfp->target, str); } else { ListItem (dfp->target, str); } } } } static Int2 PopulateTarget (DescFormPtr dfp, BioseqPtr bsp, Uint2 entityID) { SeqEntryPtr sep; Int2 val; val = 0; if (dfp != NULL) { if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForPointer (sep); } sep = GetTopSeqEntryForEntityID (entityID); dfp->sep = sep; if (sep != NULL) { dfp->hasMutPopPhySet = FALSE; dfp->targetScratchSpace = 1; dfp->nucProtCount = 0; dfp->segSetCount = 0; AllButPartsExplore (sep, (Pointer) dfp, PopTargetProc); val = dfp->targetScratchSpace; } } return val; } static void FindNewTargetProc (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { DescFormPtr dfp; dfp = (DescFormPtr) mydata; if (sep != NULL && sep->data.ptrvalue != NULL) { if (index + 1 == dfp->targetScratchSpace) { if (sep->choice == 1) { dfp->bsp = (BioseqPtr) sep->data.ptrvalue; } else if (sep->choice == 2) { dfp->bssp = (BioseqSetPtr) sep->data.ptrvalue; } } } } static Boolean ChangeTargetItemID (GatherContextPtr gcp) { DescFormPtr dfp; if (gcp == NULL) return TRUE; dfp = (DescFormPtr) gcp->userdata; if (dfp == NULL) return TRUE; if (gcp->thistype == OBJ_BIOSEQ) { if (dfp->bsp == (BioseqPtr) gcp->thisitem) { dfp->input_entityID = gcp->entityID; dfp->input_itemID = gcp->itemID; dfp->input_itemtype = gcp->thistype; return FALSE; } } else if (gcp->thistype == OBJ_BIOSEQSET) { if (dfp->bssp == (BioseqSetPtr) gcp->thisitem) { dfp->input_entityID = gcp->entityID; dfp->input_itemID = gcp->itemID; dfp->input_itemtype = gcp->thistype; return FALSE; } } return TRUE; } static void PreventDupTitleCreation (DescFormPtr dfp) { ValNodePtr sdp; if (dfp == NULL) return; if (dfp->bsp != NULL) { sdp = dfp->bsp->descr; } else if (dfp->bssp != NULL) { sdp = dfp->bssp->descr; } else return; if (dfp->descsubtype != Seq_descr_title) return; while (sdp != NULL) { if (sdp->choice == Seq_descr_title) { SafeDisable (dfp->createNewBtn); return; } sdp = sdp->next; } SafeEnable (dfp->createNewBtn); } static void ChangeNewDescTarget (Handle obj) { DescFormPtr dfp; GatherScope gs; dfp = (DescFormPtr) GetObjectExtra (obj); if (dfp != NULL) { dfp->bsp = NULL; dfp->bssp = NULL; dfp->targetScratchSpace = GetValue (dfp->target); AllButPartsExplore (dfp->sep, (Pointer) dfp, FindNewTargetProc); MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 0; MemSet((Pointer) (gs.ignore), (int) (TRUE), (size_t) (OBJ_MAX * sizeof (Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQSET] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; GatherEntity (dfp->input_entityID, (Pointer) dfp, ChangeTargetItemID, &gs); PreventDupTitleCreation (dfp); } } static void CreateNewDescProc (ButtoN b) { DescFormPtr dfp; OMProcControl ompc; ObjMgrProcPtr ompp; Int2 retval; dfp = (DescFormPtr) GetObjectExtra (b); if (dfp != NULL) { Hide (dfp->form); ompp = dfp->ompp; MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl)); ompc.input_entityID = dfp->input_entityID; ompc.input_itemID = dfp->input_itemID; ompc.input_itemtype = dfp->input_itemtype; GatherDataForProc (&ompc, FALSE); ompc.proc = ompp; retval = (*(ompp->func)) (&ompc); if (retval == OM_MSG_RET_ERROR) { ErrShow (); } Update (); Remove (dfp->form); } } static void EditOldDescProc (ButtoN b) { DescFormPtr dfp; Int2 handled; dfp = (DescFormPtr) GetObjectExtra (b); if (dfp != NULL) { Hide (dfp->form); if (dfp->oldEntityID > 0 && dfp->oldItemID > 0 && dfp->oldItemtype > 0) { WatchCursor (); handled = GatherProcLaunch (OMPROC_EDIT, FALSE, dfp->oldEntityID, dfp->oldItemID, dfp->oldItemtype, 0, 0, dfp->oldItemtype, 0); ArrowCursor (); if (handled != OM_MSG_RET_DONE || handled == OM_MSG_RET_NOPROC) { Message (MSG_ERROR, "Unable to edit existing descriptor."); } } Update (); Remove (dfp->form); } } static CharPtr newDescMsg = "\ Descriptors may apply to a single sequence or to a set of \ sequences. Please set the target control to the desired \ set or sequence."; static CharPtr editOldMsg = "\ A descriptor of this type already exists at or above the \ displayed target. You may want to edit it instead of \ creating a new descriptor."; static void NewDescriptorMessageProc (ForM f, Int2 mssg) { DescFormPtr dfp; dfp = (DescFormPtr) GetObjectExtra (f); if (dfp != NULL) { if (dfp->appmessage != NULL) { dfp->appmessage (f, mssg); } } } extern void NewDescriptorMenuFunc (ObjMgrProcPtr ompp, BaseFormPtr bfp, Uint2 descsubtype) { ButtoN b; BioseqPtr bsp; GrouP c; Int4 count; DescFormPtr dfp; Uint2 entityID; GrouP g; GatherScope gs; GrouP h; GrouP p1, p2; SeqEntryPtr sep; StdEditorProcsPtr sepp; SeqIdPtr sip; SeqLocPtr slp; Int2 val; WindoW w; #ifdef WIN_MAC bfp = (BaseFormPtr) currentFormDataPtr; #endif if (bfp == NULL) return; if (ompp == NULL || ompp->func == NULL) return; if (ompp->inputtype != OBJ_SEQDESC) return; dfp = (DescFormPtr) MemNew (sizeof (DescFormData)); if (dfp == NULL) return; dfp->ompp = ompp; dfp->lookfor = ompp->subinputtype; dfp->found = FALSE; dfp->descsubtype = descsubtype; bsp = GetBioseqGivenIDs (bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype); MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 0; 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_BIOSEQSET] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQDESC] = FALSE; if (bsp != NULL) { slp = ValNodeNew (NULL); slp->choice = SEQLOC_WHOLE; sip = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); slp->data.ptrvalue = sip; gs.target = slp; } dfp->bsp = bsp; GatherEntity (bfp->input_entityID, (Pointer) dfp, FindDescrFunc, &gs); SeqLocFree (gs.target); w = FixedWindow (-50, -33, -10, -10, "Descriptor Target Control", StdCloseWindowProc); SetObjectExtra (w, dfp, StdCleanupFormProc); dfp->form = (ForM) w; dfp->formmessage = NewDescriptorMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); dfp->appmessage = sepp->handleMessages; } dfp->input_entityID = bfp->input_entityID; dfp->input_itemID = bfp->input_itemID; dfp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); p1 = MultiLinePrompt (h, newDescMsg, 25 * stdCharWidth, programFont); entityID = bfp->input_entityID; if (bsp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); entityID = ObjMgrGetEntityIDForChoice (sep); } sep = GetTopSeqEntryForEntityID (entityID); count = AllButPartsCount (sep); if (count < 32) { g = HiddenGroup (h, 2, 0, NULL); StaticPrompt (g, "Target", 0, popupMenuHeight, programFont, 'l'); dfp->usePopupForTarget = TRUE; dfp->target = PopupList (g, TRUE, (PupActnProc) ChangeNewDescTarget); } else { g = HiddenGroup (h, 0, 2, NULL); StaticPrompt (g, "Target", 0, 0, programFont, 'c'); dfp->usePopupForTarget = FALSE; dfp->target = SingleList (g, 14, 3, (LstActnProc) ChangeNewDescTarget); } SetObjectExtra (dfp->target, dfp, NULL); val = PopulateTarget (dfp, bsp, bfp->input_entityID); SetValue (dfp->target, val); ChangeNewDescTarget ((Handle) dfp->target); p2 = NULL; if (dfp->found) { p2 = MultiLinePrompt (h, editOldMsg, 25 * stdCharWidth, programFont); } c = HiddenGroup (h, 4, 0, NULL); SetGroupSpacing (c, 10, 2); dfp->createNewBtn = PushButton (c, "Create New", CreateNewDescProc); SetObjectExtra (dfp->createNewBtn, dfp, NULL); if (dfp->found) { b = DefaultButton (c, "Edit Old", EditOldDescProc); SetObjectExtra (b, dfp, NULL); } PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) p1, (HANDLE) g, (HANDLE) c, (HANDLE) p2, NULL); RealizeWindow (w); PreventDupTitleCreation (dfp); Show (w); Update (); } static void NewDescriptorMenuProc (IteM i) { NewObjectPtr nop; nop = (NewObjectPtr) GetObjectExtra (i); if (nop == NULL) return; NewDescriptorMenuFunc (nop->ompp, nop->bfp, nop->descsubtype); } extern void SetupNewDescriptorsMenu (MenU m, BaseFormPtr bfp) { Boolean allowgenbank; IteM i; NewObjectPtr nop; ObjMgrPtr omp; ObjMgrProcPtr ompp; ObjMgrTypePtr omtp; if (m == NULL) return; omp = ObjMgrGet (); if (omp == NULL) return; ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, 0, 0, NULL); if (ompp == NULL) return; omtp = NULL; allowgenbank = FALSE; /*#ifdef EXTRA_SERVICES*/ if (extraServices) { allowgenbank = TRUE; } /*#endif*/ while ((omtp = ObjMgrTypeFindNext (omp, omtp)) != NULL) { ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, NULL); if (ompp != NULL) { switch (omtp->datatype) { case OBJ_SEQDESC : ompp = NULL; while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, ompp)) != NULL) { if (ompp->subinputtype != Seq_descr_pub) { if (allowgenbank || ompp->subinputtype != Seq_descr_genbank) { i = CommandItem (m, ompp->proclabel, NewDescriptorMenuProc); nop = (NewObjectPtr) MemNew (sizeof (NewObjectData)); if (nop != NULL) { nop->ompp = ompp; nop->bfp = bfp; nop->descsubtype = ompp->subinputtype; } SetObjectExtra (i, (Pointer) nop, StdCleanupExtraProc); } } } break; default : break; } } } } static CharPtr editOldDescMsg = "\ You may really want to edit an existing BioSource descriptor instead.\n\ Proceed anyway?"; static void NewFeatureMenuProc (IteM i) { MsgAnswer ans; BaseFormPtr bfp; NewObjectPtr nop; OMProcControl ompc; ObjMgrProcPtr ompp; Int2 retval; nop = (NewObjectPtr) GetObjectExtra (i); if (nop == NULL) return; #ifdef WIN_MAC bfp = (BaseFormPtr) currentFormDataPtr; #else bfp = nop->bfp; #endif if (bfp == NULL) return; ompp = nop->ompp; if (ompp == NULL || ompp->func == NULL) return; if (ompp->subinputtype == FEATDEF_BIOSRC) { ans = Message (MSG_YN, editOldDescMsg); if (ans == ANS_NO) return; } MemSet ((Pointer) (&ompc), 0, sizeof (OMProcControl)); ompc.input_entityID = bfp->input_entityID; ompc.input_itemID = bfp->input_itemID; ompc.input_itemtype = bfp->input_itemtype; GatherDataForProc (&ompc, FALSE); ompc.proc = ompp; retval = (*(ompp->func)) (&ompc); if (retval == OM_MSG_RET_ERROR) { ErrShow (); } } #ifdef WIN_MAC VoidPtr macUserDataPtr = NULL; #endif extern void EnableFeaturesPerTarget (BaseFormPtr bfp) { BioseqPtr bsp; Uint1 mol; NewObjectPtr nop; if (bfp == NULL) return; #ifdef WIN_MAC nop = (NewObjectPtr) macUserDataPtr; #else nop = (NewObjectPtr) bfp->userDataPtr; #endif bsp = GetBioseqGivenIDs (bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype); mol = 0; if (bsp != NULL) { mol = bsp->mol; } while (nop != NULL) { if (nop->kind == 2) { /* analysis menu item, ignore it */ } else if (mol == 0) { SafeDisable (nop->item); } else if (ISA_na (mol) && (nop->molgroup == 2 || nop->molgroup == 3)) { SafeEnable (nop->item); } else if (ISA_aa (mol) && (nop->molgroup == 1 || nop->molgroup == 3)) { SafeEnable (nop->item); } else { SafeDisable (nop->item); } nop = nop->next; } } static VoidPtr LinkNewObjectLists (NewObjectPtr list1, NewObjectPtr list2) { NewObjectPtr nop; if (list1 == NULL) return list2; nop = list1; while (nop->next != NULL) { nop = nop->next; } nop->next = list2; return list1; } extern void SetupNewFeaturesMenu (MenU m, BaseFormPtr bfp) { FeatDispGroupPtr fdgp; FeatDefPtr fdp; NewObjectPtr first; IteM i; Uint1 key; CharPtr label; NewObjectPtr last; NewObjectPtr nop; ObjMgrPtr omp; ObjMgrProcPtr ompp; ObjMgrTypePtr omtp; MenU sub; Uint2 subtype; if (m == NULL) return; omp = ObjMgrGet (); if (omp == NULL) return; ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, 0, 0, NULL); if (ompp == NULL) return; omtp = NULL; first = NULL; last = NULL; while ((omtp = ObjMgrTypeFindNext (omp, omtp)) != NULL) { ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, NULL); if (ompp != NULL) { switch (omtp->datatype) { case OBJ_SEQFEAT : fdgp = NULL; while ((fdgp = DispGroupFindNext (fdgp, &key, &label)) != NULL) { if (fdgp->groupkey != 0) { sub = SubMenu (m, fdgp->groupname); fdp = NULL; label = NULL; while ((fdp = FeatDefFindNext (fdp, &key, &label, fdgp->groupkey, FALSE)) != NULL) { if (key != FEATDEF_BAD) { ompp = NULL; while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, ompp)) != NULL) { if (ompp->subinputtype == fdp->featdef_key && ompp->subinputtype != FEATDEF_PUB) { i = CommandItem (sub, ompp->proclabel, NewFeatureMenuProc); nop = (NewObjectPtr) MemNew (sizeof (NewObjectData)); if (nop != NULL) { nop->kind = 1; /* feature creation item */ nop->ompp = ompp; nop->bfp = bfp; nop->item = i; nop->molgroup = fdp->molgroup; } if (first == NULL) { first = nop; } if (last != NULL) { last->next = nop; } last = nop; SetObjectExtra (i, (Pointer) nop, StdCleanupExtraProc); } } } } } } /* if (indexerVersion) { */ sub = SubMenu (m, "Remaining Features"); fdp = NULL; label = NULL; while ((fdp = FeatDefFindNext (fdp, &key, &label, 0, FALSE)) != NULL) { if (key != FEATDEF_BAD) { ompp = NULL; while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, ompp)) != NULL) { subtype = ompp->subinputtype; if (subtype == fdp->featdef_key && subtype != FEATDEF_PUB && subtype != FEATDEF_Imp_CDS && subtype != FEATDEF_misc_RNA && subtype != FEATDEF_precursor_RNA && subtype != FEATDEF_mat_peptide && subtype != FEATDEF_sig_peptide && subtype != FEATDEF_transit_peptide && subtype != FEATDEF_source && subtype != FEATDEF_virion && subtype != FEATDEF_mutation && subtype != FEATDEF_allele && subtype != FEATDEF_site_ref) { i = CommandItem (sub, ompp->proclabel, NewFeatureMenuProc); nop = (NewObjectPtr) MemNew (sizeof (NewObjectData)); if (nop != NULL) { nop->kind = 1; /* feature creation item */ nop->ompp = ompp; nop->bfp = bfp; nop->item = i; nop->molgroup = fdp->molgroup; } if (first == NULL) { first = nop; } if (last != NULL) { last->next = nop; } last = nop; SetObjectExtra (i, (Pointer) nop, StdCleanupExtraProc); } } } } /* } */ break; default : break; } } } #ifdef WIN_MAC macUserDataPtr = LinkNewObjectLists (macUserDataPtr, first); #else bfp->userDataPtr = LinkNewObjectLists (bfp->userDataPtr, first); #endif } extern void SetupNewPublicationsMenu (MenU m, BaseFormPtr bfp) { NewObjectPtr first; IteM i; NewObjectPtr nop; ObjMgrPtr omp; ObjMgrProcPtr ompp; ObjMgrTypePtr omtp; if (m == NULL) return; omp = ObjMgrGet (); if (omp == NULL) return; ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, 0, 0, NULL); if (ompp == NULL) return; omtp = NULL; while ((omtp = ObjMgrTypeFindNext (omp, omtp)) != NULL) { ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, NULL); if (ompp != NULL) { switch (omtp->datatype) { case OBJ_SEQFEAT : ompp = NULL; while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, ompp)) != NULL) { if (ompp->subinputtype == FEATDEF_PUB) { i = CommandItem (m, "Publication Feature", NewFeatureMenuProc); nop = (NewObjectPtr) MemNew (sizeof (NewObjectData)); if (nop != NULL) { nop->kind = 1; /* feature creation item */ nop->ompp = ompp; nop->bfp = bfp; nop->item = i; nop->molgroup = 3; #ifdef WIN_MAC first = (NewObjectPtr) macUserDataPtr; #else first = (NewObjectPtr) bfp->userDataPtr; #endif if (first != NULL) { while (first->next != NULL) { first = first->next; } first->next = nop; } } SetObjectExtra (i, (Pointer) nop, StdCleanupExtraProc); } } break; case OBJ_SEQDESC : ompp = NULL; while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, ompp)) != NULL) { if (ompp->subinputtype == Seq_descr_pub) { i = CommandItem (m, "Publication Descriptor", NewDescriptorMenuProc); nop = (NewObjectPtr) MemNew (sizeof (NewObjectData)); if (nop != NULL) { nop->ompp = ompp; nop->bfp = bfp; } SetObjectExtra (i, (Pointer) nop, StdCleanupExtraProc); } } break; default : break; } } } } #ifdef WIN_MAC extern IteM addSecondaryItem; #endif extern void SetupEditSecondary (MenU m, BaseFormPtr bfp) { IteM i; NewObjectPtr nop; ObjMgrPtr omp; ObjMgrProcPtr ompp; ObjMgrTypePtr omtp; if (m == NULL) return; omp = ObjMgrGet (); if (omp == NULL) return; ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, 0, 0, NULL); if (ompp == NULL) return; omtp = NULL; while ((omtp = ObjMgrTypeFindNext (omp, omtp)) != NULL) { ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, NULL); if (ompp != NULL) { switch (omtp->datatype) { case OBJ_SEQDESC : ompp = NULL; while ((ompp = ObjMgrProcFindNext (omp, OMPROC_EDIT, omtp->datatype, 0, ompp)) != NULL) { if (ompp->subinputtype != Seq_descr_pub) { if (ompp->subinputtype == Seq_descr_genbank) { i = CommandItem (m, "Add Secondary", NewDescriptorMenuProc); nop = (NewObjectPtr) MemNew (sizeof (NewObjectData)); if (nop != NULL) { nop->ompp = ompp; nop->bfp = bfp; } SetObjectExtra (i, (Pointer) nop, StdCleanupExtraProc); #ifdef WIN_MAC if (addSecondaryItem == NULL) { addSecondaryItem = i; } #endif return; } } } break; default : break; } } } } typedef struct gbformdata { FEATURE_FORM_BLOCK ButtoN clearExtraAccns; ButtoN clearSource; ButtoN clearKeywords; ButtoN clearOrigin; ButtoN clearOldDate; ButtoN clearEntryDate; ButtoN clearDivision; ButtoN clearTaxonomy; } GbeditFormData, PNTR GbeditFormPtr; static void EditGenbankCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; Boolean empty; GBBlockPtr gbp; GbeditFormPtr gfp; ValNodePtr nextsdp; Pointer PNTR prevsdp; ValNodePtr sdp; if (mydata == NULL) return; if (sep == NULL || sep->data.ptrvalue == NULL) return; gfp = (GbeditFormPtr) mydata; if (gfp == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sdp = bsp->descr; prevsdp = (Pointer PNTR) &(bsp->descr); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sdp = bssp->descr; prevsdp = (Pointer PNTR) &(bssp->descr); } else return; while (sdp != NULL) { nextsdp = sdp->next; empty = FALSE; if (sdp->choice == Seq_descr_genbank && sdp->data.ptrvalue != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; if (GetStatus (gfp->clearExtraAccns)) { gbp->extra_accessions = ValNodeFreeData (gbp->extra_accessions); } if (GetStatus (gfp->clearSource)) { gbp->source = MemFree (gbp->source); } if (GetStatus (gfp->clearKeywords)) { gbp->keywords = ValNodeFreeData (gbp->keywords); } if (GetStatus (gfp->clearOrigin)) { gbp->origin = MemFree (gbp->origin); } if (GetStatus (gfp->clearOldDate)) { gbp->date = MemFree (gbp->date); } if (GetStatus (gfp->clearEntryDate)) { gbp->entry_date = DateFree (gbp->entry_date); } if (GetStatus (gfp->clearDivision)) { gbp->div = MemFree (gbp->div); } if (GetStatus (gfp->clearTaxonomy)) { gbp->taxonomy = MemFree (gbp->taxonomy); } if (gbp->extra_accessions == NULL && gbp->source == NULL && gbp->keywords == NULL && gbp->origin == NULL && gbp->date == NULL && gbp->entry_date == NULL && gbp->div == NULL && gbp->taxonomy == NULL) { empty = TRUE; ObjMgrDeSelect (0, 0, 0, 0, NULL); } } if (empty) { *(prevsdp) = sdp->next; sdp->next = NULL; SeqDescFree (sdp); } else { prevsdp = (Pointer PNTR) &(sdp->next); } sdp = nextsdp; } } static void DoEditGenbank (ButtoN b) { GbeditFormPtr gfp; SeqEntryPtr sep; gfp = GetObjectExtra (b); if (gfp == NULL) return; sep = GetTopSeqEntryForEntityID (gfp->input_entityID); if (sep == NULL) return; Hide (gfp->form); WatchCursor (); Update (); SeqEntryExplore (sep, (Pointer) gfp, EditGenbankCallback); ArrowCursor (); Update (); ObjMgrSetDirtyFlag (gfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, gfp->input_entityID, 0, 0); Remove (gfp->form); } static void EditGenbankMessageProc (ForM f, Int2 mssg) { GbeditFormPtr gfp; gfp = (GbeditFormPtr) GetObjectExtra (f); if (gfp != NULL) { if (gfp->appmessage != NULL) { gfp->appmessage (f, mssg); } } } extern void EditGenbankElements (Handle i) { BaseFormPtr bfp; ButtoN b; GrouP c; GrouP g; GbeditFormPtr gfp; GrouP h; SeqEntryPtr sep; StdEditorProcsPtr sepp; WindoW w; #ifdef WIN_MAC bfp = currentFormDataPtr; #else bfp = GetObjectExtra (i); #endif if (bfp == NULL) return; sep = GetTopSeqEntryForEntityID (bfp->input_entityID); if (sep == NULL) return; gfp = (GbeditFormPtr) MemNew (sizeof (GbeditFormData)); if (gfp == NULL) return; w = FixedWindow (-50, -33, -10, -10, "GenBank Block Removal", StdCloseWindowProc); SetObjectExtra (w, gfp, StdCleanupFormProc); gfp->form = (ForM) w; gfp->formmessage = EditGenbankMessageProc; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); gfp->appmessage = sepp->handleMessages; } gfp->input_entityID = bfp->input_entityID; gfp->input_itemID = bfp->input_itemID; gfp->input_itemtype = bfp->input_itemtype; h = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (h, 10, 10); g = HiddenGroup (h, -1, 0, NULL); gfp->clearExtraAccns = CheckBox (g, "Clear Secondary Accessions", NULL); gfp->clearSource = CheckBox (g, "Clear Source Line", NULL); gfp->clearKeywords = CheckBox (g, "Clear Keywords", NULL); gfp->clearOrigin = CheckBox (g, "Clear Origin", NULL); gfp->clearOldDate = CheckBox (g, "Clear Old Date", NULL); gfp->clearEntryDate = CheckBox (g, "Clear Entry Date", NULL); gfp->clearDivision = CheckBox (g, "Clear Division", NULL); gfp->clearTaxonomy = CheckBox (g, "Clear Lineage", NULL); c = HiddenGroup (h, 4, 0, NULL); b = PushButton (c, "Accept", DoEditGenbank); SetObjectExtra (b, gfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); Show (w); Update (); } typedef struct helpindex { Int2 item; CharPtr heading; CharPtr section; CharPtr combined; } HelpIndex, PNTR HelpIndexPtr; typedef struct helpform { FORM_MESSAGE_BLOCK DoC doc; DoC list; TexT findTxt; ButtoN findBtn; GrouP dismissGrp; ValNodePtr mainStrings; ValNodePtr indexStrings; ValNodePtr index; Char file [PATH_MAX]; } HelpForm, PNTR HelpFormPtr; #define TBL_FMT 1 #define TXT_FMT 2 #define HDG_FMT 3 #define SUB_FMT 4 /* and beyond, encoding indent */ static ParData lstParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData lstColFmt = {0, 0, 80, 0, NULL, 'l', FALSE, FALSE, FALSE, FALSE, TRUE}; static ParData hdgParFmt = {TRUE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData hdgColFmt = {0, 0, 80, 0, NULL, 'c', TRUE, FALSE, FALSE, FALSE, TRUE}; static ParData subParFmt = {TRUE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData subColFmt = {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}; static ParData tblParFmt = {TRUE, FALSE, FALSE, FALSE, TRUE, 0, 0}; static ColData tblColFmt = {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}; static ParData txtParFmt = {TRUE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData txtColFmt = {0, 0, 80, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}; static void ResetHelpLists (HelpFormPtr hfp) { HelpIndexPtr hip; ValNodePtr vnp; if (hfp != NULL) { hfp->mainStrings = ValNodeFreeData (hfp->mainStrings); hfp->indexStrings = ValNodeFreeData (hfp->indexStrings); vnp = hfp->index; while (vnp != NULL) { hip = (HelpIndexPtr) vnp->data.ptrvalue; if (hip != NULL) { hip->heading = MemFree (hip->heading); hip->section = MemFree (hip->section); hip->combined = MemFree (hip->combined); } vnp = vnp->next; } hfp->index = ValNodeFreeData (hfp->index); } } static void TrimTrailingSpaces (CharPtr str) { size_t len; if (str != NULL && str [0] != '\0') { len = StringLen (str); while (len > 0 && str [len - 1] == ' ') { len--; } str [len] = '\0'; } } static Boolean ParseHelpFile (HelpFormPtr hfp, Boolean printPath) { Char ch; Uint1 choice; FILE *fp; Boolean goOn; Char heading [64]; HelpIndexPtr hip; Boolean inTable; Int2 level; ValNodePtr list; Int2 numItems; Char path [PATH_MAX]; CharPtr ptr; Char section [64]; Char str [256]; ValNodePtr vnp; if (hfp == NULL || hfp->doc == NULL) return FALSE; Hide (hfp->list); Hide (hfp->doc); Update (); Reset (hfp->list); Reset (hfp->doc); ResetHelpLists (hfp); if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE; numItems = 0; ProgramPath (path, sizeof (path)); ptr = StringRChr (path, DIRDELIMCHR); if (ptr != NULL) { *ptr = '\0'; } FileBuildPath (path, NULL, hfp->file); fp = FileOpen (path, "r"); if (fp == NULL) { if (GetAppParam ("NCBI", "ErrorProcessing", "MsgPath", NULL, path, sizeof (path))) { FileBuildPath (path, NULL, hfp->file); fp = FileOpen (path, "r"); } } if (fp == NULL) { if (GetAppParam ("NCBI", "NCBI", "DATA", NULL, path, sizeof (path))) { FileBuildPath (path, NULL, hfp->file); fp = FileOpen (path, "r"); } } if (fp != NULL) { if (printPath) { SetTitle (hfp->form, path); } list = NULL; heading [0] = '\0'; section [0] = '\0'; inTable = FALSE; goOn = (fgets (str, sizeof (str), fp) != NULL); while (goOn) { ptr = str; ch = *ptr; while (ch != '\n' && ch != '\r' && ch != '\0') { ptr++; ch = *ptr; } *ptr = '\0'; if (inTable) { TrimTrailingSpaces (str); } else { TrimSpacesAroundString (str); } ch = str [0]; if (ch == '>' || ch == '*' || ch == '#' || ch == '!') { if (list != NULL) { ptr = MergeValNodeStrings (list, inTable); if (inTable) { choice = TBL_FMT; } else { choice = TXT_FMT; } numItems++; vnp = ValNodeAdd (&(hfp->mainStrings)); if (vnp != NULL) { vnp->choice = choice; vnp->data.ptrvalue = ptr; } /* ptr = MemFree (ptr); */ list = ValNodeFreeData (list); } ch = str [0]; if (ch == '>') { StringNCpy_0 (heading, str + 1, sizeof (heading)); numItems++; vnp = ValNodeAdd (&(hfp->mainStrings)); if (vnp != NULL) { vnp->choice = HDG_FMT; vnp->data.ptrvalue = StringSave (heading); } vnp = ValNodeAdd (&(hfp->indexStrings)); if (vnp != NULL) { vnp->choice = 0; vnp->data.ptrvalue = StringSave (heading); } vnp = ValNodeAdd (&(hfp->index)); if (vnp != NULL) { hip = (HelpIndexPtr) MemNew (sizeof (HelpIndex)); vnp->data.ptrvalue = (Pointer) hip; if (hip != NULL) { hip->item = numItems; hip->heading = StringSave (heading); } } } else if (ch == '*') { level = 1; ch = str [level]; while (ch == '*') { level++; ch = str [level]; } StringNCpy_0 (section, str + level, sizeof (section)); numItems++; vnp = ValNodeAdd (&(hfp->mainStrings)); if (vnp != NULL) { if (level < 2) { vnp->choice = SUB_FMT; } else { vnp->choice = 5 * (level - 1); } vnp->data.ptrvalue = StringSave (section); } vnp = ValNodeAdd (&(hfp->indexStrings)); if (vnp != NULL) { vnp->choice = 5 * level; vnp->data.ptrvalue = StringSave (section); } vnp = ValNodeAdd (&(hfp->index)); if (vnp != NULL) { hip = (HelpIndexPtr) MemNew (sizeof (HelpIndex)); vnp->data.ptrvalue = (Pointer) hip; if (hip != NULL) { hip->item = numItems; hip->heading = StringSave (heading); hip->section = StringSave (section); sprintf (str, "%s|%s", heading, section); hip->combined = StringSave (str); } } } else if (ch == '#' || ch == '!') { inTable = (Boolean) (ch == '!'); vnp = ValNodeAdd (&list); if (vnp != NULL) { if (! StringHasNoText (str + 1)) { vnp->data.ptrvalue = StringSave (str + 1); } } } } else if (ch == '<') { } else if (ch != '\0') { vnp = ValNodeAdd (&list); if (vnp != NULL) { if (! StringHasNoText (str)) { vnp->data.ptrvalue = StringSave (str); } } } goOn = (Boolean) (goOn && (fgets (str, sizeof (str), fp) != NULL)); } if (list != NULL) { ptr = MergeValNodeStrings (list, inTable); if (inTable) { choice = TBL_FMT; } else { choice = TXT_FMT; } numItems++; vnp = ValNodeAdd (&(hfp->mainStrings)); if (vnp != NULL) { vnp->choice = choice; vnp->data.ptrvalue = ptr; } /* ptr = MemFree (ptr); */ list = ValNodeFreeData (list); } FileClose (fp); return TRUE; } else { return FALSE; } } static Int2 GetSequinAppParam (CharPtr section, CharPtr type, CharPtr dflt, CharPtr buf, Int2 buflen) { Int2 rsult; rsult = GetAppParam ("SEQUINCUSTOM", section, type, NULL, buf, buflen); if (rsult) return rsult; rsult = GetAppParam ("SEQUIN", section, type, dflt, buf, buflen); return rsult; } static FonT GetHelpFontFromConfig (CharPtr param, FonT dfault) { FonT f; Char str [128]; f = dfault; if (GetSequinAppParam ("SCREEN", param, NULL, str, sizeof (str))) { f = Nlm_ParseFontEx (str, NULL); } if (f == NULL) { f = dfault; } return f; } static void SetupHelpFonts (void) { if (IsJapanese()) { #ifdef WIN_MAC /* Osaka is common font for Japanese on Macintosh. */ hdgColFmt.font = Nlm_ParseFontEx ("Osaka,14,b", NULL); subColFmt.font = Nlm_ParseFontEx ("Osaka,10,b", NULL); txtColFmt.font = Nlm_ParseFontEx ("Osaka,10", NULL); lstColFmt.font = Nlm_ParseFontEx ("Osaka\x81\x7c\x93\x99\x95\x9d,12", NULL); tblColFmt.font = Nlm_ParseFontEx ("Osaka\x81\x7c\x93\x99\x95\x9d,12", NULL); /* hdgColFmt.font = GetResidentFont (Nlm_Minchou(14, STYLE_BOLD)); */ /* subColFmt.font = GetResidentFont (Nlm_Minchou(10, STYLE_BOLD)); */ /* txtColFmt.font = GetResidentFont (Nlm_Gothic(10, STYLE_REGULAR)); */ /* lstColFmt.font = GetResidentFont (Nlm_MinchouFixed(12, STYLE_REGULAR)); */ /* tblColFmt.font = GetResidentFont (Nlm_MinchouFixed(12, STYLE_REGULAR)); */ #endif #ifdef WIN_MSWIN hdgColFmt.font = Nlm_ParseFontEx ("\x82\x6c\x82\x72\x20\x82\x6f\x96\xbe\x92\xa9,14,b,Kanji", NULL); subColFmt.font = Nlm_ParseFontEx ("\x82\x6c\x82\x72\x20\x82\x6f\x96\xbe\x92\xa9,11,b,Kanji", NULL); txtColFmt.font = Nlm_ParseFontEx ("\x82\x6c\x82\x72\x20\x82\x6f\x83\x53\x83\x56\x83\x62\x83\x4e,11,,Kanji", NULL); lstColFmt.font = Nlm_ParseFontEx ("\x82\x6c\x82\x72\x20\x96\xbe\x92\xa9,12,f,Kanji", NULL); tblColFmt.font = Nlm_ParseFontEx ("\x82\x6c\x82\x72\x20\x96\xbe\x92\xa9,12,f,Kanji", NULL); /* hdgColFmt.font = GetResidentFont (Nlm_Minchou(14, STYLE_BOLD)); */ /* subColFmt.font = GetResidentFont (Nlm_Minchou(11, STYLE_BOLD)); */ /* txtColFmt.font = GetResidentFont (Nlm_Gothic(11, STYLE_REGULAR)); */ /* lstColFmt.font = GetResidentFont (Nlm_MinchouFixed(12, STYLE_REGULAR)); */ /* tblColFmt.font = GetResidentFont (Nlm_MinchouFixed(12, STYLE_REGULAR)); */ #endif #ifdef WIN_MOTIF hdgColFmt.font = ParseFont ("Times,18,b"); subColFmt.font = ParseFont ("Helvetica,12,b"); txtColFmt.font = ParseFont ("fixed,13"); lstColFmt.font = programFont; tblColFmt.font = programFont; #endif } else if (IsEnglish() || IsFrench() || IsGerman() || IsItalian() || IsSystemLang()) { #ifdef WIN_MAC hdgColFmt.font = ParseFont ("Times,14,b"); subColFmt.font = ParseFont ("Geneva,10,b"); txtColFmt.font = ParseFont ("Geneva,10"); #endif /*WIN_MAC*/ #ifdef WIN_MSWIN hdgColFmt.font = ParseFont ("Times New Roman,14,b"); subColFmt.font = ParseFont ("Arial,11,b"); txtColFmt.font = ParseFont ("Times New Roman,11"); #endif /*WIN_MSWIN*/ #ifdef WIN_MOTIF hdgColFmt.font = ParseFont ("Times,18,b"); subColFmt.font = ParseFont ("Helvetica,12,b"); txtColFmt.font = ParseFont ("Times,14"); #endif /*WIN_MOTIF*/ lstColFmt.font = programFont; tblColFmt.font = programFont; } else { /* above call to IsSystemLang should override this section */ /* default system font is often native character set */ /* because native character sets have a set of ascii letters, english help file can also be drawn as well as native letters. */ hdgColFmt.font = systemFont; subColFmt.font = systemFont; txtColFmt.font = systemFont; lstColFmt.font = systemFont; tblColFmt.font = systemFont; } /* now allow override by sequin config file */ hdgColFmt.font = GetHelpFontFromConfig ("HEADING", hdgColFmt.font); subColFmt.font = GetHelpFontFromConfig ("SUBHEAD", subColFmt.font); txtColFmt.font = GetHelpFontFromConfig ("TEXT", txtColFmt.font); lstColFmt.font = GetHelpFontFromConfig ("LIST", lstColFmt.font); tblColFmt.font = GetHelpFontFromConfig ("TABLE", tblColFmt.font); } static Boolean PopulateHelpForm (HelpFormPtr hfp) { Int2 firstLine; Int2 firstShown; RecT r; BaR sb; Int4 startsAt; CharPtr text; ValNodePtr vnp; if (hfp == NULL || hfp->doc == NULL) return FALSE; Hide (hfp->list); Hide (hfp->doc); Update (); if (! GetScrlParams4 (hfp->doc, NULL, &firstShown, &firstLine)) { firstShown = 0; firstLine = 0; } sb = GetSlateVScrollBar ((SlatE) hfp->doc); Reset (hfp->list); Reset (hfp->doc); if (hfp->file == NULL || hfp->file [0] == '\0') return FALSE; if (hfp->mainStrings == NULL || hfp->indexStrings == NULL) return FALSE; ObjectRect (hfp->doc, &r); InsetRect (&r, 4, 4); lstColFmt.pixWidth = r.right - r.left; hdgColFmt.pixWidth = r.right - r.left; subColFmt.pixWidth = r.right - r.left; /* tblColFmt.pixWidth = screenRect.right - screenRect.left; */ tblColFmt.pixWidth = r.right - r.left; tblColFmt.pixInset = 10; txtColFmt.pixWidth = r.right - r.left; txtColFmt.pixInset = 10; for (vnp = hfp->indexStrings; vnp != NULL; vnp = vnp->next) { lstColFmt.pixInset = vnp->choice; AppendText (hfp->list, vnp->data.ptrvalue, &lstParFmt, &lstColFmt, programFont); } for (vnp = hfp->mainStrings; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case TBL_FMT : AppendText (hfp->doc, vnp->data.ptrvalue, &tblParFmt, &tblColFmt, programFont); break; case TXT_FMT : AppendText (hfp->doc, vnp->data.ptrvalue, &txtParFmt, &txtColFmt, programFont); break; case HDG_FMT : AppendText (hfp->doc, vnp->data.ptrvalue, &hdgParFmt, &hdgColFmt, systemFont); break; case SUB_FMT : subColFmt.pixInset = 0; AppendText (hfp->doc, vnp->data.ptrvalue, &subParFmt, &subColFmt, programFont); break; default : subColFmt.pixInset = vnp->choice; AppendText (hfp->doc, vnp->data.ptrvalue, &subParFmt, &subColFmt, programFont); break; } } UpdateDocument (hfp->list, 0, 0); /* UpdateDocument (hfp->doc, 0, 0); */ text = GetDocText (hfp->doc, firstShown, 0, 0); MemFree (text); AdjustDocScroll (hfp->doc); GetItemParams4 (hfp->doc, firstShown, &startsAt, NULL, NULL, NULL, NULL); CorrectBarValue (sb, startsAt + firstLine); Show (hfp->list); Show (hfp->doc); Update (); return TRUE; } static void RefreshHelpForm (ButtoN b) { HelpFormPtr hfp; hfp = (HelpFormPtr) GetObjectExtra (b); if (hfp == NULL) return; ParseHelpFile (hfp, TRUE); PopulateHelpForm (hfp); Update (); } static void CleanupHelpForm (GraphiC g, VoidPtr data) { ResetHelpLists ((HelpFormPtr) data); StdCleanupFormProc (g, data); } static void HelpListNotify (DoC d, Int2 item, Int2 row, Int2 col, Boolean dblclick) { HelpFormPtr hfp; HelpIndexPtr hip; BaR sb; Int2 startsAt; ValNodePtr vnp; hfp = (HelpFormPtr) GetObjectExtra (d); if (hfp == NULL || hfp->doc == NULL) return; if (item == 0 || row == 0 || col == 0) return; vnp = hfp->index; while (vnp != NULL && item > 1) { item--; vnp = vnp->next; } if (vnp != NULL) { hip = (HelpIndexPtr) vnp->data.ptrvalue; if (hip != NULL) { GetItemParams (hfp->doc, hip->item, &startsAt, NULL, NULL, NULL, NULL); ResetClip (); sb = GetSlateVScrollBar ((SlatE) hfp->doc); SetValue (sb, startsAt); Update (); } } } static void ResizeHelpForm (WindoW w) { Int2 delta; Int2 diff; Int2 gap; Int2 height; HelpFormPtr hfp; RecT r; RecT s; RecT t; Int2 width; hfp = (HelpFormPtr) GetObjectExtra (w); if (hfp != NULL) { ObjectRect (w, &r); width = r.right - r.left; height = r.bottom - r.top; GetPosition (hfp->doc, &s); GetPosition (hfp->dismissGrp, &t); diff = t.bottom - t.top; gap = t.top - s.bottom; t.bottom = height - s.left; t.top = t.bottom - diff; delta = (width - t.right - t.left) / 2; t.left += delta; t.right += delta; s.right = width - s.left; /* s.bottom = height - s.left; */ s.bottom = t.top - gap; SetPosition (hfp->dismissGrp, &t); SetPosition (hfp->doc, &s); AdjustPrnt (hfp->doc, &s, FALSE); PopulateHelpForm (hfp); Update (); } } static Boolean ScrollToTextInDoc (DoC d, Int2 item, CharPtr text) { Pointer data; Boolean found; RecT rct; BaR sb; Int4 startsAt; CharPtr str; WindoW tempPort; found = FALSE; GetItemParams4 (d, item, &startsAt, NULL, NULL, NULL, &data); str = (CharPtr) data; if (StringISearch (str, text) != NULL) { found = TRUE; } if (found) { tempPort = SavePort (d); Select (d); sb = GetSlateVScrollBar ((SlatE) d); CorrectBarValue (sb, startsAt); ObjectRect (d, &rct); InsetRect (&rct, 4, 4); InsetRect (&rct, -1, -1); InvalRect (&rct); RestorePort (tempPort); Update (); } return found; } static void FindHelpBtnProc (ButtoN b) { Int2 firstShown; HelpFormPtr hfp; Int2 i; Int2 numItems; Char str [256]; hfp = (HelpFormPtr) GetObjectExtra (b); if (hfp == NULL) return; GetTitle (hfp->findTxt, str, sizeof (str) - 1); GetDocParams (hfp->doc, &numItems, NULL); if (GetScrlParams (hfp->doc, NULL, &firstShown, NULL)) { for (i = firstShown + 1; i <= numItems; i++) { if (ScrollToTextInDoc (hfp->doc, i, str)) { return; } } for (i = 1; i < firstShown; i++) { if (ScrollToTextInDoc (hfp->doc, i, str)) { return; } } } } static void FindHelpTextProc (TexT t) { HelpFormPtr hfp; hfp = (HelpFormPtr) GetObjectExtra (t); if (hfp == NULL) return; if (TextLength (t) > 0) { SafeEnable (hfp->findBtn); } else { SafeDisable (hfp->findBtn); } } static void HelpFormMessage (ForM f, Int2 mssg) { FILE *fp; HelpFormPtr hfp; Char path [PATH_MAX]; hfp = (HelpFormPtr) GetObjectExtra (f); if (hfp != NULL) { switch (mssg) { case VIB_MSG_CLOSE : Hide (f); break; case VIB_MSG_PRINT : PrintDocument (hfp->doc); break; case VIB_MSG_EXPORT : if (GetOutputFileName (path, sizeof (path), "help.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 (hfp->doc, fp); FileClose (fp); } ArrowCursor (); } break; default : if (hfp->appmessage != NULL) { hfp->appmessage (f, mssg); } break; } } } static void HelpFormActivate (WindoW w) { IteM exportItm; HelpFormPtr hfp; hfp = (HelpFormPtr) GetObjectExtra (w); if (hfp != NULL) { if (hfp->activate != NULL) { hfp->activate (w); } exportItm = FindFormMenuItem ((BaseFormPtr) hfp, VIB_MSG_EXPORT); SafeSetTitle (exportItm, "Export Help..."); } } extern ForM CreateHelpForm (Int2 left, Int2 top, CharPtr title, CharPtr file, BtnActnProc closeForm, WndActnProc activateForm) { ButtoN b; GrouP c; GrouP h; Int2 height; HelpFormPtr hfp; StdEditorProcsPtr sepp; WindoW w; #ifndef WIN_MAC MenU m; #endif w = NULL; hfp = MemNew (sizeof (HelpForm)); if (hfp != NULL) { w = DocumentWindow (left, top, -10, -10, title, StdSendCloseWindowMessageProc, ResizeHelpForm); SetObjectExtra (w, hfp, CleanupHelpForm); hfp->form = (ForM) w; hfp->formmessage = HelpFormMessage; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { hfp->appmessage = sepp->handleMessages; } StringNCpy_0 (hfp->file, file, sizeof (hfp->file)); #ifndef WIN_MAC m = PulldownMenu (w, "File"); FormCommandItem (m, "Export", (BaseFormPtr) hfp, VIB_MSG_EXPORT); SeparatorItem (m); #ifdef WIN_MSWIN FormCommandItem (m, "Print", (BaseFormPtr) hfp, VIB_MSG_PRINT); SeparatorItem (m); #endif FormCommandItem (m, "Close", (BaseFormPtr) hfp, VIB_MSG_CLOSE); #endif c = HiddenGroup (w, 4, 0, NULL); StaticPrompt (c, "Find", 0, dialogTextHeight, programFont, 'l'); hfp->findTxt = DialogText (c, "", 20, FindHelpTextProc); SetObjectExtra (hfp->findTxt, hfp, NULL); hfp->findBtn = PushButton (c, "Find", FindHelpBtnProc); SetObjectExtra (hfp->findBtn, hfp, NULL); Disable (hfp->findBtn); h = HiddenGroup (w, -1, 0, NULL); SelectFont (programFont); height = LineHeight (); SelectFont (systemFont); hfp->list = DocumentPanel (h, stdCharWidth * 28, height * 5); SetDocAutoAdjust (hfp->list, FALSE); SetObjectExtra (hfp->list, hfp, NULL); SetDocNotify (hfp->list, HelpListNotify); hfp->doc = DocumentPanel (h, stdCharWidth * 33, stdLineHeight * 20); SetDocAutoAdjust (hfp->doc, FALSE); SetObjectExtra (hfp->doc, hfp, NULL); hfp->dismissGrp = HiddenGroup (w, 2, 0, NULL); PushButton (hfp->dismissGrp, "Dismiss", closeForm); if (indexerVersion) { b = PushButton (hfp->dismissGrp, "Refresh", RefreshHelpForm); SetObjectExtra (b, hfp, NULL); } AlignObjects (ALIGN_CENTER, (HANDLE) hfp->doc, (HANDLE) hfp->dismissGrp, NULL); RealizeWindow (w); SetupHelpFonts (); if (activateForm != NULL) { hfp->activate = activateForm; } else { if (sepp != NULL) { hfp->activate = sepp->activateForm; } } SetActivate (w, HelpFormActivate); HelpFormActivate ((WindoW) hfp->form); if (ParseHelpFile (hfp, FALSE)) { if (! PopulateHelpForm (hfp)) { w = Remove (w); } } else { w = Remove (w); } } return (ForM) w; } extern void SendHelpScrollMessage (ForM f, CharPtr heading, CharPtr section) { HelpFormPtr hfp; HelpIndexPtr hip; BaR sb; Int2 startsAt; CharPtr str; Char txt [256]; Boolean useBoth; Boolean useHeading; Boolean useSection; ValNodePtr vnp; hfp = (HelpFormPtr) GetObjectExtra (f); if (hfp != NULL) { vnp = hfp->index; txt [0] = '\0'; useBoth = FALSE; useHeading = FALSE; useSection = FALSE; if (heading != NULL && *heading != '\0' && section != NULL && *section != '\0') { useBoth = TRUE; if (StringLen (heading) + StringLen (section) < sizeof (txt) - 2) { StringCpy (txt, heading); StringCat (txt, "|"); StringCat (txt, section); } } else if (heading != NULL && *heading != '\0') { useHeading = TRUE; StringNCpy_0 (txt, heading, sizeof (txt)); } else if (section != NULL && *section != '\0') { useSection = TRUE; StringNCpy_0 (txt, section, sizeof (txt)); } while (vnp != NULL) { hip = (HelpIndexPtr) vnp->data.ptrvalue; if (hip != NULL) { if (useBoth) { str = hip->combined; } else if (useHeading) { str = hip->heading; } else if (useSection) { str = hip->section; } else { str = NULL; } if (str != NULL && StringICmp (txt, str) == 0) { GetItemParams (hfp->doc, hip->item, &startsAt, NULL, NULL, NULL, NULL); sb = GetSlateVScrollBar ((SlatE) hfp->doc); ResetClip (); SetValue (sb, startsAt); Update (); return; } } vnp = vnp->next; } } }