/* import.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: import.c * * Author: Jonathan Kans * * Version Creation Date: 6/18/95 * * $Revision: 6.29 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #include #include #include #include #include /* TOPOLOGY_xxx definitions */ #define IMPORT_PAGE 0 #define ENUM_PAGE 0 #define REGION_PAGE 0 #define COMMON_PAGE 1 #define LOCATION_PAGE 2 #define NUM_PAGES 8 typedef struct imprtform { FEATURE_FORM_BLOCK SeqEntryPtr sep; GrouP pages [NUM_PAGES]; DialoG foldertabs; Int2 currentPage; } ImprtForm, PNTR ImprtFormPtr; typedef struct importpage { DIALOG_MESSAGE_BLOCK ImprtFormPtr ifp; Handle key; TexT loc; EnumFieldAssoc PNTR alist; } ImportPage, PNTR ImportPagePtr; extern EnumFieldAssocPtr import_featdef_alist (Boolean notJustImpFeats, Boolean allowPeptideFeats, Boolean allowRnaImpFeats) { EnumFieldAssocPtr alist; EnumFieldAssocPtr ap; FeatDefPtr curr; Int2 fdn; Int2 i; Uint1 key; CharPtr label = NULL; CharPtr str; Uint2 subtype; fdn = FeatDefNum (); alist = MemNew (sizeof (EnumFieldAssoc) * (fdn + 2)); if (alist == NULL) { Message (MSG_ERROR, "in import_featdef_alist: no room"); } else { i = 0; ap = alist; ap->name = StringSave (" "); ap->value = (UIEnum) 0; ap++; i++; curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE); while (curr != NULL) { if (key != FEATDEF_BAD) { if (notJustImpFeats || curr->seqfeat_key == SEQFEAT_IMP) { subtype = curr->featdef_key; if (subtype != FEATDEF_Imp_CDS && subtype != FEATDEF_source && subtype != FEATDEF_virion && subtype != FEATDEF_mutation && subtype != FEATDEF_allele && subtype != FEATDEF_site_ref) { if (allowPeptideFeats || (subtype != FEATDEF_mat_peptide && subtype != FEATDEF_sig_peptide && subtype != FEATDEF_transit_peptide)) { if (allowRnaImpFeats || (subtype != FEATDEF_misc_RNA && subtype != FEATDEF_precursor_RNA)) { str = StringSave (curr->typelabel); if (*str == '-') { *str = '~'; } ap->name = str; ap->value = key; ap++; i++; } } } } } curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE); } ap->name = NULL; } return alist; } static void ImpFeatPtrToImportPage (DialoG d, Pointer data) { EnumFieldAssocPtr ap; Int2 i; ImportPagePtr ipp; ImpFeatPtr ifp; ipp = (ImportPagePtr) GetObjectExtra (d); ifp = (ImpFeatPtr) data; if (ipp != NULL) { if (ifp != NULL) { for (i = 1, ap = ipp->alist; ap->name != NULL; i++, ap++) { if (StringCmp (ap->name, ifp->key) == 0) { SetValue (ipp->key, i); SetTitle (ipp->loc, ifp->loc); return; } } } SetValue (ipp->key, 1); SetTitle (ipp->loc, ""); } } static Pointer ImportPageToImpFeatPtr (DialoG d) { EnumFieldAssocPtr ap; Int2 i; ImportPagePtr ipp; ImpFeatPtr ifp; UIEnum val; ifp = NULL; ipp = (ImportPagePtr) GetObjectExtra (d); if (ipp != NULL) { ifp = ImpFeatNew (); if (ifp != NULL) { ifp->loc = SaveStringFromText (ipp->loc); val = GetValue (ipp->key); if (val > 1) { for (i = 1, ap = ipp->alist; ap->name != NULL; i++, ap++) { if (i == val) { ifp->key = StringSave (ap->name); return (Pointer) ifp; } } } else { ifp->key = StringSave ("misc_feature"); } } } return (Pointer) ifp; } static void CleanupImportPage (GraphiC g, VoidPtr data) { ImportPagePtr ipp; Int2 j; ipp = (ImportPagePtr) data; if (ipp != NULL) { if (ipp->alist != NULL) { for (j = 0; ipp->alist [j].name != NULL; j++) { MemFree (ipp->alist [j].name); } } MemFree (ipp->alist); } MemFree (data); } static void ChangeKey (Handle obj) { Char ch; Int2 expev; Int2 geneval; HelpMessageFunc helpfunc; ImprtFormPtr ifp; ImpFeatPtr imp; ImprtFormPtr newifp; ObjMgrPtr omp; ObjMgrTypePtr omtp; CharPtr ptr; SeqEntryPtr sep; SeqFeatPtr sfp; Char title [128]; WindoW w; ifp = (ImprtFormPtr) GetObjectExtra (obj); if (ifp != NULL) { sfp = SeqFeatNew (); if (sfp != NULL) { sfp->data.choice = FindFeatFromFeatDefType (ifp->this_subtype); sfp->data.value.ptrvalue = DialogToPointer (ifp->data); sfp->comment = SaveStringFromText (ifp->comment); ptr = sfp->comment; if (ptr != NULL) { ch = *ptr; while (ch != '\0') { if (ch < ' ' || ch > '~') { *ptr = '~'; } ptr++; ch = *ptr; } } expev = GetValue (ifp->evidence); if (expev > 0 && expev <= 3) { sfp->exp_ev = expev - 1; } else { sfp->exp_ev = 0; } sfp->partial = GetStatus (ifp->partial); sfp->excpt = GetStatus (ifp->exception); sfp->title = NULL; sfp->product = DialogToPointer (ifp->product); sfp->location = DialogToPointer (ifp->location); sfp->cit = DialogToPointer (ifp->featcits); sfp->dbxref = DialogToPointer (ifp->dbxrefs); sfp->qual = DialogToPointer (ifp->gbquals); geneval = GetValue (ifp->gene); sep = GetTopSeqEntryForEntityID (ifp->input_entityID); StringCpy (title, "Feature"); if (sfp != NULL && sfp->data.value.ptrvalue != NULL) { imp = (ImpFeatPtr) sfp->data.value.ptrvalue; StringNCpy_0 (title, imp->key, sizeof (title)); if (StringHasNoText (title)) { StringCpy (title, "Feature"); } } w = (WindoW) CreateImportForm (-50, -33, title, sfp, sep, StdFeatFormActnProc); newifp = (ImprtFormPtr) GetObjectExtra (w); if (newifp != NULL) { newifp->input_entityID = ifp->input_entityID; newifp->input_itemID = ifp->input_itemID; newifp->input_itemtype = ifp->input_itemtype; newifp->this_itemtype = ifp->this_itemtype; newifp->this_subtype = ifp->this_subtype; if (sfp != NULL) { omp = ObjMgrGet (); if (omp != NULL) { omtp = ObjMgrTypeFind (omp, OBJ_SEQFEAT, NULL, NULL); if (omtp != NULL && omtp->subtypefunc != NULL) { newifp->this_subtype = (*(omtp->subtypefunc)) (sfp); } } } SendMessageToForm (newifp->form, VIB_MSG_INIT); SetValue (newifp->gene, geneval); if (sfp != NULL) { PointerToForm (newifp->form, (Pointer) sfp); } } Remove (ifp->form); Show (w); Select (w); helpfunc = (HelpMessageFunc) GetAppProperty ("HelpMessageProc"); if (helpfunc != NULL) { helpfunc ("Features", title); } } SeqFeatFree (sfp); Update (); } } static DialoG CreateImportDialog (GrouP h, CharPtr title, ImprtFormPtr ifp, Boolean allowPeptideFeats) { EnumFieldAssocPtr ap; GrouP f; ImportPagePtr ipp; GrouP m; GrouP p; PrompT ppt; GrouP s; CharPtr str; Boolean usePopup; PrompT x; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); ipp = (ImportPagePtr) MemNew (sizeof (ImportPage)); if (ipp != NULL) { SetObjectExtra (p, ipp, CleanupImportPage); ipp->dialog = (DialoG) p; ipp->todialog = ImpFeatPtrToImportPage; ipp->fromdialog = ImportPageToImpFeatPtr; ipp->testdialog = NULL; if (title != NULL && title [0] != '\0') { s = NormalGroup (p, 0, -2, title, systemFont, NULL); } else { s = HiddenGroup (p, 0, -2, NULL); } m = HiddenGroup (s, -1, 0, NULL); /* SetGroupSpacing (m, 10, 10); */ ipp->ifp = ifp; ipp->alist = import_featdef_alist (FALSE, allowPeptideFeats, FALSE); ppt = StaticPrompt (m, "Changing feature key will recreate the window.", 0, 0, programFont, 'c'); f = HiddenGroup (m, -2, 0, NULL); #ifdef WIN_MOTIF usePopup = FALSE; #else usePopup = TRUE; #endif x = NULL; #ifndef WIN_MOTIF x = StaticPrompt (f, "Key", 0, 0, programFont, 'l'); #endif if (usePopup) { ipp->key = (Handle) PopupList (f, TRUE, (PupActnProc) ChangeKey); SetObjectExtra (ipp->key, ifp, NULL); InitEnumPopup ((PopuP) ipp->key, ipp->alist, NULL); SetEnumPopup ((PopuP) ipp->key, ipp->alist, (UIEnum) 0); } else { ipp->key = (Handle) SingleList (f, 12, 3, (LstActnProc) ChangeKey); SetObjectExtra (ipp->key, ifp, NULL); for (ap = ipp->alist; ap->name != NULL; ap++) { ListItem ((LisT) ipp->key, ap->name); } SetValue (ipp->key, 0); } if (Nlm_GetAppProperty ("SequinUseImpFeatLocField") != NULL) { StaticPrompt (f, "Loc", 0, dialogTextHeight, programFont, 'l'); ipp->loc = DialogText (f, "", 15, NULL); } AlignObjects (ALIGN_VERTICAL, (HANDLE) ipp->key, (HANDLE) x, NULL); for (ap = ipp->alist; ap->name != NULL; ap++) { str = ap->name; if (*str == '~') { *str = '-'; } } AlignObjects (ALIGN_CENTER, (HANDLE) ppt, (HANDLE) f, NULL); } return (DialoG) p; } static void SetImportImportExportItems (ImprtFormPtr ifp) { IteM exportItm; IteM importItm; if (ifp != NULL) { importItm = FindFormMenuItem ((BaseFormPtr) ifp, VIB_MSG_IMPORT); exportItm = FindFormMenuItem ((BaseFormPtr) ifp, VIB_MSG_EXPORT); switch (ifp->currentPage) { case IMPORT_PAGE : SafeSetTitle (importItm, "Import..."); SafeSetTitle (exportItm, "Export..."); SafeDisable (importItm); SafeDisable (exportItm); break; case COMMON_PAGE : SafeSetTitle (importItm, "Import..."); SafeSetTitle (exportItm, "Export..."); SafeDisable (importItm); SafeDisable (exportItm); break; case LOCATION_PAGE : SafeSetTitle (importItm, "Import SeqLoc..."); SafeSetTitle (exportItm, "Export SeqLoc..."); SafeEnable (importItm); SafeEnable (exportItm); break; default : break; } } } static void ChangeImportPage (VoidPtr data, Int2 newval, Int2 oldval) { ImprtFormPtr ifp; ifp = (ImprtFormPtr) data; if (ifp != NULL) { ifp->currentPage = newval; SafeHide (ifp->pages [oldval]); SafeShow (ifp->pages [newval]); switch (newval) { case IMPORT_PAGE : SendMessageToDialog (ifp->data, VIB_MSG_ENTER); break; case COMMON_PAGE : break; case LOCATION_PAGE : SendMessageToDialog (ifp->location, VIB_MSG_ENTER); break; default : break; } SetImportImportExportItems (ifp); Update (); } } static Boolean ImportImportForm (ForM f, CharPtr filename) { ImprtFormPtr ifp; ifp = (ImprtFormPtr) GetObjectExtra (f); if (ifp != NULL) { switch (ifp->currentPage) { case LOCATION_PAGE : return ImportDialog (ifp->location, filename); default : break; } } return FALSE; } static Boolean ExportImportForm (ForM f, CharPtr filename) { ImprtFormPtr ifp; ifp = (ImprtFormPtr) GetObjectExtra (f); if (ifp != NULL) { switch (ifp->currentPage) { case LOCATION_PAGE : return ExportDialog (ifp->location, filename); default : break; } } return FALSE; } static CharPtr importFormTabs [] = { NULL, "Properties", "Location", NULL }; extern DialoG CreateQualsDialog (GrouP h, Uint2 rows, Int2 spacing, Int2 width1, Int2 width2); static void ImportFormMessage (ForM f, Int2 mssg) { ImprtFormPtr ifp; ifp = (ImprtFormPtr) GetObjectExtra (f); if (ifp != NULL) { switch (mssg) { case VIB_MSG_INIT : StdInitFeatFormProc (f); break; case VIB_MSG_IMPORT : ImportImportForm (f, NULL); break; case VIB_MSG_EXPORT : ExportImportForm (f, NULL); break; case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : if (ifp->currentPage == LOCATION_PAGE) { PointerToDialog (ifp->location, NULL); } else { StdDeleteTextProc (NULL); } break; default : if (ifp->appmessage != NULL) { ifp->appmessage (f, mssg); } break; } } } static void ImportFormActivate (WindoW w) { ImprtFormPtr ifp; ifp = (ImprtFormPtr) GetObjectExtra (w); if (ifp != NULL) { if (ifp->activate != NULL) { ifp->activate (w); } SetImportImportExportItems (ifp); } } extern ForM CreateImportForm (Int2 left, Int2 top, CharPtr title, SeqFeatPtr sfp, SeqEntryPtr sep, FormActnFunc actproc) { Boolean allowPeptideFeats; Boolean allowProductGBQual; ButtoN b; GrouP c; GrouP g; GrouP h; ImprtFormPtr ifp; ImpFeatPtr imp; GrouP s; StdEditorProcsPtr sepp; WindoW w; GrouP x; GrouP z; w = NULL; ifp = (ImprtFormPtr) MemNew (sizeof (ImprtForm)); if (ifp != NULL) { w = FixedWindow (left, top, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, ifp, StdFeatFormCleanupProc); ifp->form = (ForM) w; ifp->actproc = actproc; ifp->toform = StdSeqFeatPtrToFeatFormProc; ifp->fromform = NULL; ifp->formmessage = ImportFormMessage; ifp->testform = NULL; ifp->importform = ImportImportForm; ifp->exportform = ExportImportForm; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif ifp->activate = NULL; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { ifp->activate = sepp->activateForm; ifp->appmessage = sepp->handleMessages; } SetActivate (w, ImportFormActivate); g = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (g, 3, 10); ifp->sep = sep; importFormTabs [0] = NULL; if (title != NULL && *title != '\0') { importFormTabs [0] = title; } else { importFormTabs [0] = "misc_feature"; } ifp->foldertabs = CreateFolderTabs (g, importFormTabs, IMPORT_PAGE, 0, 0, SYSTEM_FOLDER_TAB, ChangeImportPage, (Pointer) ifp); ifp->currentPage = IMPORT_PAGE; h = HiddenGroup (g, 0, 0, NULL); s = HiddenGroup (h, -1, 0, NULL); SetGroupSpacing (s, 3, 10); allowPeptideFeats = FALSE; allowProductGBQual = FALSE; if (sfp != NULL && sfp->data.choice == SEQFEAT_IMP) { imp = (ImpFeatPtr) sfp->data.value.ptrvalue; if (imp != NULL) { if (StringICmp (imp->key, "mat_peptide") == 0 || StringICmp (imp->key, "sig_peptide") == 0 || StringICmp (imp->key, "transit_peptide") == 0) { allowPeptideFeats = TRUE; allowProductGBQual = TRUE; } } } ifp->data = CreateImportDialog (s, NULL, ifp, allowPeptideFeats); x = HiddenGroup (s, -1, 0, NULL); if (StringICmp (importFormTabs [0], "source") == 0) { z = HiddenGroup (x, -4, 0, NULL); SetGroupSpacing (z, -1, 0); StaticPrompt (z, "Qualifier", 7 * stdCharWidth, 0, programFont, 'c'); StaticPrompt (z, "Value", 10 * stdCharWidth, 0, programFont, 'c'); ifp->gbquals = CreateQualsDialog (x, 5, -1, 7, 10); } else { ifp->gbquals = CreateImportFields (x, importFormTabs [0], sfp, allowProductGBQual); } AlignObjects (ALIGN_CENTER, (HANDLE) ifp->data, (HANDLE) x, NULL); ifp->pages [IMPORT_PAGE] = s; Hide (ifp->pages [IMPORT_PAGE]); importFormTabs [0] = NULL; s = HiddenGroup (h, -1, 0, NULL); CreateCommonFeatureGroup (s, (FeatureFormPtr) ifp, sfp, TRUE, TRUE); ifp->pages [COMMON_PAGE] = s; Hide (ifp->pages [COMMON_PAGE]); s = HiddenGroup (h, -1, 0, NULL); ifp->location = CreateIntervalEditorDialogEx (s, NULL, 4, 2, sep, TRUE, FALSE, TRUE, TRUE, FALSE, (FeatureFormPtr) ifp, StdFeatIntEdPartialCallback); ifp->pages [LOCATION_PAGE] = s; Hide (ifp->pages [LOCATION_PAGE]); AlignObjects (ALIGN_CENTER, (HANDLE) ifp->pages [IMPORT_PAGE], (HANDLE) ifp->pages [COMMON_PAGE], (HANDLE) ifp->pages [LOCATION_PAGE], NULL); AlignObjects (ALIGN_CENTER, (HANDLE) ifp->foldertabs, (HANDLE) h, NULL); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdFeatFormAcceptButtonProc); SetObjectExtra (b, ifp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); SendMessageToDialog (ifp->data, VIB_MSG_INIT); SendMessageToDialog (ifp->location, VIB_MSG_INIT); Show (ifp->pages [ifp->currentPage]); SendMessageToDialog (ifp->data, VIB_MSG_ENTER); Update (); } return (ForM) w; } extern Int2 LIBCALLBACK ImportGenFunc (Pointer data) { EnumFieldAssocPtr ap; FeatDefPtr curr; HelpMessageFunc helpfunc; Int2 i; ImprtFormPtr ifp; ImpFeatPtr imp; ImportPagePtr ipp; Uint1 key; CharPtr label = NULL; ObjMgrPtr omp; OMProcControlPtr ompcp; ObjMgrTypePtr omtp; OMUserDataPtr omudp; ObjMgrProcPtr proc; SeqEntryPtr sep; SeqFeatPtr sfp; Uint2 subtype; Char title [64]; WindoW w; ompcp = (OMProcControlPtr) data; sfp = NULL; sep = NULL; imp = NULL; subtype = FEATDEF_IMP; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; proc = ompcp->proc; switch (ompcp->input_itemtype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) ompcp->input_data; if (sfp != NULL && sfp->data.choice != SEQFEAT_IMP) { return OM_MSG_RET_ERROR; } break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { ifp = (ImprtFormPtr) omudp->userdata.ptrvalue; if (ifp != NULL) { Select (ifp->form); } return OM_MSG_RET_DONE; } sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); StringCpy (title, "Feature"); if (sfp != NULL && sfp->data.value.ptrvalue != NULL) { imp = (ImpFeatPtr) sfp->data.value.ptrvalue; StringNCpy_0 (title, imp->key, sizeof (title)); if (StringHasNoText (title)) { StringCpy (title, "Feature"); } } else if (proc->subinputtype > 0) { subtype = proc->subinputtype; curr = FeatDefFindNext (NULL, &key, &label, FEATDEF_ANY, TRUE); while (curr != NULL) { if (key != FEATDEF_BAD && curr->seqfeat_key == SEQFEAT_IMP) { if (subtype == curr->featdef_key) { StringNCpy_0 (title, curr->typelabel, sizeof (title)); break; } } curr = FeatDefFindNext (curr, &key, &label, FEATDEF_ANY, TRUE); } } w = (WindoW) CreateImportForm (-50, -33, title, sfp, sep, StdFeatFormActnProc); ifp = (ImprtFormPtr) GetObjectExtra (w); if (ifp != NULL) { ifp->input_entityID = ompcp->input_entityID; ifp->input_itemID = ompcp->input_itemID; ifp->input_itemtype = ompcp->input_itemtype; ifp->this_itemtype = OBJ_SEQFEAT; ifp->this_subtype = subtype; ifp->procid = ompcp->proc->procid; ifp->proctype = ompcp->proc->proctype; ifp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, ifp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) ifp; omudp->messagefunc = StdVibrantEditorMsgFunc; } if (sfp != NULL) { omp = ObjMgrGet (); if (omp != NULL) { omtp = ObjMgrTypeFind (omp, OBJ_SEQFEAT, NULL, NULL); if (omtp != NULL && omtp->subtypefunc != NULL) { ifp->this_subtype = (*(omtp->subtypefunc)) (sfp); } } } SendMessageToForm (ifp->form, VIB_MSG_INIT); if (sfp != NULL) { PointerToForm (ifp->form, (Pointer) sfp); SetClosestParentIfDuplicating ((BaseFormPtr) ifp); } else { ipp = (ImportPagePtr) GetObjectExtra (ifp->data); if (ipp != NULL) { for (i = 1, ap = ipp->alist; ap->name != NULL; i++, ap++) { if (StringCmp (ap->name, title) == 0) { SetValue (ipp->key, i); SetTitle (ipp->loc, ""); break; } } } SetNewFeatureDefaultInterval ((FeatureFormPtr) ifp); } } Show (w); Select (w); helpfunc = (HelpMessageFunc) GetAppProperty ("HelpMessageProc"); if (helpfunc != NULL) { helpfunc ("Features", title); } return OM_MSG_RET_DONE; } typedef struct enumpage { DIALOG_MESSAGE_BLOCK PopuP key; EnumFieldAssocPtr alist; } EnumPage, PNTR EnumPagePtr; typedef struct enumform { FEATURE_FORM_BLOCK SeqEntryPtr sep; GrouP pages [NUM_PAGES]; DialoG foldertabs; Int2 currentPage; } EnumForm, PNTR EnumFormPtr; extern EnumFieldAssoc enum_bond_alist []; ENUM_ALIST(enum_bond_alist) {"Disulfide", 1}, {"Thioester", 2}, {"Crosslink", 3}, {"Thioether", 4}, {"Other", 255}, END_ENUM_ALIST extern EnumFieldAssoc enum_site_alist []; ENUM_ALIST(enum_site_alist) {"Active", 1}, {"Binding", 2}, {"Cleavage", 3}, {"Inhibit", 4}, {"Modified", 5}, {"Glycosylation", 6}, {"Myristoylation", 7}, {"Mutagenized", 8}, {"Metal-binding", 9}, {"Phosphorylation", 10}, {"Acetylation", 11}, {"Amidation", 12}, {"Methylation", 13}, {"Hydroxylation", 14}, {"Sulfatation", 15}, {"Oxidative-deamination", 16}, {"Pyrrolidone-carboxylic-acid", 17}, {"Gamma-carboxyglutamic-acid", 18}, {"Blocked", 19}, {"Lipid-binding", 20}, {"np-binding", 21}, {"DNA-binding", 22}, {"Signal-peptide", 23}, {"Transit-peptide", 24}, {"Transmembrane-region", 25}, {"Other", 255}, END_ENUM_ALIST static ENUM_ALIST(enum_psec_alist) {"Helix", 1}, {"Sheet", 2}, {"Turn", 3}, END_ENUM_ALIST static void EnumFeatPtrToEnumPage (DialoG d, Pointer data) { EnumPagePtr epp; Int4Ptr intptr; Int4 val; epp = (EnumPagePtr) GetObjectExtra (d); intptr = (Int4Ptr) data; if (epp != NULL) { val = *intptr; SetEnumPopup (epp->key, epp->alist, (UIEnum) val); } } static Pointer EnumPageToEnumFeatPtr (DialoG d) { EnumPagePtr epp; Int4Ptr intptr; UIEnum val; intptr = NULL; epp = (EnumPagePtr) GetObjectExtra (d); if (epp != NULL) { if (GetEnumPopup (epp->key, epp->alist, &val)) { epp->intvalue = (Int4) val; intptr = (&epp->intvalue); } } return (Pointer) intptr; } static DialoG CreateEnumDialog (GrouP h, CharPtr title, Uint2 subtype) { EnumPagePtr epp; GrouP f; GrouP m; GrouP p; GrouP s; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); epp = (EnumPagePtr) MemNew (sizeof (EnumPage)); if (epp != NULL) { SetObjectExtra (p, epp, StdCleanupExtraProc); epp->dialog = (DialoG) p; epp->todialog = EnumFeatPtrToEnumPage; epp->fromdialog = EnumPageToEnumFeatPtr; epp->testdialog = NULL; if (title != NULL && title [0] != '\0') { s = NormalGroup (p, 0, -2, title, systemFont, NULL); } else { s = HiddenGroup (p, 0, -2, NULL); } m = HiddenGroup (s, -1, 0, NULL); /* SetGroupSpacing (m, 10, 10); */ switch (subtype) { case FEATDEF_BOND : epp->alist = enum_bond_alist; break; case FEATDEF_SITE : epp->alist = enum_site_alist; break; case FEATDEF_PSEC_STR : epp->alist = enum_psec_alist; break; default : Message (MSG_FATAL, "Unknown enumerated feature type"); return NULL; } f = HiddenGroup (m, -2, 0, NULL); StaticPrompt (f, "Type", 0, popupMenuHeight, programFont, 'l'); epp->key = PopupList (f, TRUE, NULL); SetObjectExtra (epp->key, epp, NULL); InitEnumPopup (epp->key, epp->alist, NULL); /* SetEnumPopup (epp->key, epp->alist, (UIEnum) 0); */ } return (DialoG) p; } static void SetEnumImportExportItems (EnumFormPtr efp) { IteM exportItm; IteM importItm; if (efp != NULL) { importItm = FindFormMenuItem ((BaseFormPtr) efp, VIB_MSG_IMPORT); exportItm = FindFormMenuItem ((BaseFormPtr) efp, VIB_MSG_EXPORT); switch (efp->currentPage) { case ENUM_PAGE : SafeSetTitle (importItm, "Import..."); SafeSetTitle (exportItm, "Export..."); SafeDisable (importItm); SafeDisable (exportItm); break; case COMMON_PAGE : SafeSetTitle (importItm, "Import..."); SafeSetTitle (exportItm, "Export..."); SafeDisable (importItm); SafeDisable (exportItm); break; case LOCATION_PAGE : SafeSetTitle (importItm, "Import SeqLoc..."); SafeSetTitle (exportItm, "Export SeqLoc..."); SafeEnable (importItm); SafeEnable (exportItm); break; default : break; } } } static void ChangeEnumPage (VoidPtr data, Int2 newval, Int2 oldval) { EnumFormPtr efp; efp = (EnumFormPtr) data; if (efp != NULL) { efp->currentPage = newval; SafeHide (efp->pages [oldval]); SafeShow (efp->pages [newval]); switch (newval) { case ENUM_PAGE : SendMessageToDialog (efp->data, VIB_MSG_ENTER); break; case COMMON_PAGE : break; case LOCATION_PAGE : SendMessageToDialog (efp->location, VIB_MSG_ENTER); break; default : break; } SetEnumImportExportItems (efp); Update (); } } static Boolean ImportEnumForm (ForM f, CharPtr filename) { EnumFormPtr efp; efp = (EnumFormPtr) GetObjectExtra (f); if (efp != NULL) { switch (efp->currentPage) { case LOCATION_PAGE : return ImportDialog (efp->location, filename); default : break; } } return FALSE; } static Boolean ExportEnumForm (ForM f, CharPtr filename) { EnumFormPtr efp; efp = (EnumFormPtr) GetObjectExtra (f); if (efp != NULL) { switch (efp->currentPage) { case LOCATION_PAGE : return ExportDialog (efp->location, filename); default : break; } } return FALSE; } static CharPtr enumFormTabs [] = { NULL, "Properties", "Location", NULL }; static void EnumFormMessage (ForM f, Int2 mssg) { EnumFormPtr efp; efp = (EnumFormPtr) GetObjectExtra (f); if (efp != NULL) { switch (mssg) { case VIB_MSG_INIT : StdInitFeatFormProc (f); break; case VIB_MSG_IMPORT : ImportEnumForm (f, NULL); break; case VIB_MSG_EXPORT : ExportEnumForm (f, NULL); break; case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : if (efp->currentPage == LOCATION_PAGE) { PointerToDialog (efp->location, NULL); } else { StdDeleteTextProc (NULL); } break; default : if (efp->appmessage != NULL) { efp->appmessage (f, mssg); } break; } } } static void EnumFormActivate (WindoW w) { EnumFormPtr efp; efp = (EnumFormPtr) GetObjectExtra (w); if (efp != NULL) { if (efp->activate != NULL) { efp->activate (w); } SetEnumImportExportItems (efp); } } extern DialoG CreateBondEditorDialog (GrouP h, CharPtr title, SeqEntryPtr sep); extern ForM CreateEnumForm (Int2 left, Int2 top, CharPtr title, SeqFeatPtr sfp, SeqEntryPtr sep, Uint2 subtype, FormActnFunc actproc) { ButtoN b; GrouP c; EnumFormPtr efp; GrouP g; GrouP h; GrouP s; StdEditorProcsPtr sepp; WindoW w; w = NULL; efp = (EnumFormPtr) MemNew (sizeof (EnumForm)); if (efp != NULL) { w = FixedWindow (left, top, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, efp, StdFeatFormCleanupProc); efp->form = (ForM) w; efp->actproc = actproc; efp->toform = StdSeqFeatPtrToFeatFormProc; efp->fromform = NULL; efp->formmessage = EnumFormMessage; efp->testform = NULL; efp->importform = ImportEnumForm; efp->exportform = ExportEnumForm; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif efp->activate = NULL; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { efp->activate = sepp->activateForm; efp->appmessage = sepp->handleMessages; } SetActivate (w, EnumFormActivate); g = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (g, 3, 10); efp->sep = sep; enumFormTabs [0] = NULL; if (title != NULL && *title != '\0') { enumFormTabs [0] = title; } else if (subtype == FEATDEF_BOND) { enumFormTabs [0] = "Bond"; } else if (subtype == FEATDEF_SITE) { enumFormTabs [0] = "Site"; } else if (subtype == FEATDEF_PSEC_STR) { enumFormTabs [0] = "Secondary Structure"; } efp->foldertabs = CreateFolderTabs (g, enumFormTabs, ENUM_PAGE, 0, 0, SYSTEM_FOLDER_TAB, ChangeEnumPage, (Pointer) efp); efp->currentPage = ENUM_PAGE; h = HiddenGroup (g, 0, 0, NULL); s = HiddenGroup (h, -1, 0, NULL); SetGroupSpacing (s, 3, 10); efp->data = CreateEnumDialog (s, NULL, subtype); efp->pages [ENUM_PAGE] = s; Hide (efp->pages [ENUM_PAGE]); enumFormTabs [0] = NULL; s = HiddenGroup (h, -1, 0, NULL); CreateCommonFeatureGroup (s, (FeatureFormPtr) efp, sfp, TRUE, TRUE); efp->pages [COMMON_PAGE] = s; Hide (efp->pages [COMMON_PAGE]); s = HiddenGroup (h, -1, 0, NULL); if (subtype == FEATDEF_BOND) { efp->location = CreateBondEditorDialog (s, NULL, sep); } else { efp->location = CreateIntervalEditorDialogEx (s, NULL, 4, 2, sep, TRUE, TRUE, TRUE, TRUE, FALSE, (FeatureFormPtr) efp, StdFeatIntEdPartialCallback); } efp->pages [LOCATION_PAGE] = s; Hide (efp->pages [LOCATION_PAGE]); AlignObjects (ALIGN_CENTER, (HANDLE) efp->pages [ENUM_PAGE], (HANDLE) efp->pages [COMMON_PAGE], (HANDLE) efp->pages [LOCATION_PAGE], NULL); AlignObjects (ALIGN_CENTER, (HANDLE) efp->foldertabs, (HANDLE) h, NULL); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdFeatFormAcceptButtonProc); SetObjectExtra (b, efp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); SendMessageToDialog (efp->data, VIB_MSG_INIT); SendMessageToDialog (efp->location, VIB_MSG_INIT); Show (efp->pages [efp->currentPage]); SendMessageToDialog (efp->data, VIB_MSG_ENTER); Update (); } return (ForM) w; } extern Int2 LIBCALLBACK EnumGenFunc (Pointer data) { EnumFormPtr efp; HelpMessageFunc helpfunc; OMProcControlPtr ompcp; OMUserDataPtr omudp; ObjMgrProcPtr proc; SeqEntryPtr sep; SeqFeatPtr sfp; Uint2 subtype; WindoW w; ompcp = (OMProcControlPtr) data; w = NULL; sfp = NULL; sep = NULL; subtype = 0; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; proc = ompcp->proc; switch (ompcp->input_itemtype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) ompcp->input_data; if (sfp != NULL && (sfp->data.choice != SEQFEAT_BOND && sfp->data.choice != SEQFEAT_SITE && sfp->data.choice != SEQFEAT_PSEC_STR)) { return OM_MSG_RET_ERROR; } if (sfp->data.choice == SEQFEAT_BOND) { subtype = FEATDEF_BOND; } else if (sfp->data.choice == SEQFEAT_SITE) { subtype = FEATDEF_SITE; } else if (sfp->data.choice == SEQFEAT_PSEC_STR) { subtype = FEATDEF_PSEC_STR; } else { return OM_MSG_RET_ERROR; } break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { efp = (EnumFormPtr) omudp->userdata.ptrvalue; if (efp != NULL) { Select (efp->form); } return OM_MSG_RET_DONE; } sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); if (sfp == NULL) { subtype = proc->subinputtype; } if (subtype == FEATDEF_BOND) { w = (WindoW) CreateEnumForm (-50, -33, "Bond", sfp, sep, subtype, StdFeatFormActnProc); } else if (subtype == FEATDEF_SITE) { w = (WindoW) CreateEnumForm (-50, -33, "Site", sfp, sep, subtype, StdFeatFormActnProc); } else if (subtype == FEATDEF_PSEC_STR) { w = (WindoW) CreateEnumForm (-50, -33, "Secondary Structure", sfp, sep, subtype, StdFeatFormActnProc); } else { return OM_MSG_RET_ERROR; } efp = (EnumFormPtr) GetObjectExtra (w); if (efp != NULL) { efp->input_entityID = ompcp->input_entityID; efp->input_itemID = ompcp->input_itemID; efp->input_itemtype = ompcp->input_itemtype; efp->this_itemtype = OBJ_SEQFEAT; efp->this_subtype = subtype; efp->procid = ompcp->proc->procid; efp->proctype = ompcp->proc->proctype; efp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, efp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) efp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToForm (efp->form, VIB_MSG_INIT); if (sfp != NULL) { PointerToForm (efp->form, (Pointer) sfp); SetClosestParentIfDuplicating ((BaseFormPtr) efp); } else { SetNewFeatureDefaultInterval ((FeatureFormPtr) efp); } } Show (w); Select (w); helpfunc = (HelpMessageFunc) GetAppProperty ("HelpMessageProc"); if (helpfunc != NULL) { if (subtype == FEATDEF_BOND) { helpfunc ("Features", "Bond"); } else if (subtype == FEATDEF_SITE) { helpfunc ("Features", "Site"); } else if (subtype == FEATDEF_PSEC_STR) { helpfunc ("Features", "Secondary Structure"); } } return OM_MSG_RET_DONE; } typedef struct regionform { FEATURE_FORM_BLOCK SeqEntryPtr sep; GrouP pages [NUM_PAGES]; DialoG foldertabs; Int2 currentPage; } RegionForm, PNTR RegionFormPtr; typedef struct regionpage { DIALOG_MESSAGE_BLOCK TexT region; ButtoN convertToMiscFeat; RegionFormPtr rfp; } RegionPage, PNTR RegionPagePtr; static void CharPtrToRegionPage (DialoG d, Pointer data) { RegionFormPtr rfp; RegionPagePtr rpp; CharPtr str; rpp = (RegionPagePtr) GetObjectExtra (d); str = (CharPtr) data; if (rpp != NULL) { rfp = rpp->rfp; if (rfp->this_subtype == FEATDEF_COMMENT) return; if (rfp->this_subtype == FEATDEF_misc_feature) return; if (str != NULL) { SafeSetTitle (rpp->region, str); } else { SafeSetTitle (rpp->region, ""); } } } static Pointer RegionPageToCharPtr (DialoG d) { ImpFeatPtr ifp; RegionFormPtr rfp; RegionPagePtr rpp; CharPtr str; str = NULL; rpp = (RegionPagePtr) GetObjectExtra (d); if (rpp != NULL) { rfp = rpp->rfp; if (rfp->this_subtype == FEATDEF_misc_feature) { if (GetStatus (rpp->convertToMiscFeat)) { ifp = ImpFeatNew (); if (ifp != NULL) { ifp->key = StringSave ("misc_feature"); } return (Pointer) ifp; } else { return NULL; } } if (rfp->this_subtype == FEATDEF_COMMENT) return NULL; str = SaveStringFromText (rpp->region); if (str == NULL) { str = StringSave (""); } } return (Pointer) str; } static DialoG CreateRegionDialog (GrouP h, CharPtr title, CharPtr str, Uint2 subtype, RegionFormPtr rfp) { GrouP m; GrouP p; RegionPagePtr rpp; GrouP s; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); rpp = (RegionPagePtr) MemNew (sizeof (RegionPage)); if (rpp != NULL) { SetObjectExtra (p, rpp, StdCleanupExtraProc); rpp->dialog = (DialoG) p; rpp->todialog = CharPtrToRegionPage; rpp->fromdialog = RegionPageToCharPtr; rpp->testdialog = NULL; rpp->rfp = rfp; if (title != NULL && title [0] != '\0') { s = NormalGroup (p, 0, -2, title, systemFont, NULL); } else { s = HiddenGroup (p, 0, -2, NULL); } m = HiddenGroup (s, 2, 0, NULL); if (subtype == FEATDEF_REGION) { StaticPrompt (m, "Name", 0, dialogTextHeight, programFont, 'c'); rpp->region = DialogText (m, "", 20, NULL); } else if (subtype == FEATDEF_COMMENT) { StaticPrompt (m, "Enter comment in Properties page", 0, 0, programFont, 'c'); } if (GetAppProperty ("InternalNcbiSequin") != NULL) { rpp->convertToMiscFeat = CheckBox (p, "Convert to misc_feat", NULL); AlignObjects (ALIGN_CENTER, (HANDLE) s, (HANDLE) rpp->convertToMiscFeat, NULL); } } return (DialoG) p; } static void SetRegionImportExportItems (RegionFormPtr rfp) { IteM exportItm; IteM importItm; if (rfp != NULL) { importItm = FindFormMenuItem ((BaseFormPtr) rfp, VIB_MSG_IMPORT); exportItm = FindFormMenuItem ((BaseFormPtr) rfp, VIB_MSG_EXPORT); switch (rfp->currentPage) { case REGION_PAGE : SafeSetTitle (importItm, "Import..."); SafeSetTitle (exportItm, "Export..."); SafeDisable (importItm); SafeDisable (exportItm); break; case COMMON_PAGE : SafeSetTitle (importItm, "Import..."); SafeSetTitle (exportItm, "Export..."); SafeDisable (importItm); SafeDisable (exportItm); break; case LOCATION_PAGE : SafeSetTitle (importItm, "Import SeqLoc..."); SafeSetTitle (exportItm, "Export SeqLoc..."); SafeEnable (importItm); SafeEnable (exportItm); break; default : break; } } } static void ChangeRegionPage (VoidPtr data, Int2 newval, Int2 oldval) { RegionFormPtr rfp; rfp = (RegionFormPtr) data; if (rfp != NULL) { rfp->currentPage = newval; SafeHide (rfp->pages [oldval]); SafeShow (rfp->pages [newval]); switch (newval) { case REGION_PAGE : break; case COMMON_PAGE : break; case LOCATION_PAGE : SendMessageToDialog (rfp->location, VIB_MSG_ENTER); break; default : break; } SetRegionImportExportItems (rfp); Update (); } } static Boolean ImportRegionForm (ForM f, CharPtr filename) { RegionFormPtr rfp; rfp = (RegionFormPtr) GetObjectExtra (f); if (rfp != NULL) { switch (rfp->currentPage) { case LOCATION_PAGE : return ImportDialog (rfp->location, filename); default : break; } } return FALSE; } static Boolean ExportRegionForm (ForM f, CharPtr filename) { RegionFormPtr rfp; rfp = (RegionFormPtr) GetObjectExtra (f); if (rfp != NULL) { switch (rfp->currentPage) { case LOCATION_PAGE : return ExportDialog (rfp->location, filename); default : break; } } return FALSE; } static CharPtr regionFormTabs [] = { "Region", "Properties", "Location", NULL }; static CharPtr commentFormTabs [] = { "Comment", "Properties", "Location", NULL }; static void RegionFormMessage (ForM f, Int2 mssg) { RegionFormPtr rfp; rfp = (RegionFormPtr) GetObjectExtra (f); if (rfp != NULL) { switch (mssg) { case VIB_MSG_INIT : StdInitFeatFormProc (f); break; case VIB_MSG_IMPORT : ImportRegionForm (f, NULL); break; case VIB_MSG_EXPORT : ExportRegionForm (f, NULL); break; case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : if (rfp->currentPage == LOCATION_PAGE) { PointerToDialog (rfp->location, NULL); } else { StdDeleteTextProc (NULL); } break; default : if (rfp->appmessage != NULL) { rfp->appmessage (f, mssg); } break; } } } static void RegionFormActivate (WindoW w) { RegionFormPtr rfp; rfp = (RegionFormPtr) GetObjectExtra (w); if (rfp != NULL) { if (rfp->activate != NULL) { rfp->activate (w); } SetRegionImportExportItems (rfp); } } extern ForM CreateRegionOrCommentForm (Int2 left, Int2 top, CharPtr title, SeqFeatPtr sfp, SeqEntryPtr sep, Uint2 subtype, FormActnFunc actproc) { ButtoN b; GrouP c; GrouP g; GrouP h; RegionFormPtr rfp; GrouP s; StdEditorProcsPtr sepp; CharPtr str; WindoW w; w = NULL; rfp = (RegionFormPtr) MemNew (sizeof (RegionForm)); if (rfp != NULL) { w = FixedWindow (left, top, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, rfp, StdFeatFormCleanupProc); rfp->form = (ForM) w; rfp->actproc = actproc; rfp->toform = StdSeqFeatPtrToFeatFormProc; rfp->fromform = NULL; rfp->formmessage = RegionFormMessage; rfp->testform = NULL; rfp->importform = ImportRegionForm; rfp->exportform = ExportRegionForm; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif rfp->activate = NULL; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { rfp->activate = sepp->activateForm; rfp->appmessage = sepp->handleMessages; } SetActivate (w, RegionFormActivate); g = HiddenGroup (w, -1, 0, NULL); SetGroupSpacing (g, 3, 10); rfp->sep = sep; if (subtype == FEATDEF_REGION) { rfp->foldertabs = CreateFolderTabs (g, regionFormTabs, REGION_PAGE, 0, 0, SYSTEM_FOLDER_TAB, ChangeRegionPage, (Pointer) rfp); } else if (subtype == FEATDEF_COMMENT) { rfp->foldertabs = CreateFolderTabs (g, commentFormTabs, REGION_PAGE, 0, 0, SYSTEM_FOLDER_TAB, ChangeRegionPage, (Pointer) rfp); } else { Message (MSG_FATAL, "Region or Comment Feature error"); } rfp->currentPage = REGION_PAGE; h = HiddenGroup (g, 0, 0, NULL); s = HiddenGroup (h, -1, 0, NULL); str = NULL; if (sfp != NULL && sfp->data.choice == SEQFEAT_REGION) { str = sfp->data.value.ptrvalue; } rfp->data = CreateRegionDialog (s, NULL, str, subtype, rfp); /* if (subtype == FEATDEF_COMMENT) { rfp->data = NULL; } */ rfp->pages [REGION_PAGE] = s; Hide (rfp->pages [REGION_PAGE]); s = HiddenGroup (h, -1, 0, NULL); CreateCommonFeatureGroup (s, (FeatureFormPtr) rfp, sfp, TRUE, TRUE); rfp->pages [COMMON_PAGE] = s; Hide (rfp->pages [COMMON_PAGE]); s = HiddenGroup (h, -1, 0, NULL); rfp->location = CreateIntervalEditorDialogEx (s, NULL, 4, 2, sep, TRUE, TRUE, TRUE, TRUE, FALSE, (FeatureFormPtr) rfp, StdFeatIntEdPartialCallback); rfp->pages [LOCATION_PAGE] = s; Hide (rfp->pages [LOCATION_PAGE]); AlignObjects (ALIGN_CENTER, (HANDLE) rfp->pages [REGION_PAGE], (HANDLE) rfp->pages [COMMON_PAGE], (HANDLE) rfp->pages [LOCATION_PAGE], NULL); AlignObjects (ALIGN_CENTER, (HANDLE) rfp->foldertabs, (HANDLE) h, NULL); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdFeatFormAcceptButtonProc); SetObjectExtra (b, rfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); SendMessageToDialog (rfp->data, VIB_MSG_INIT); SendMessageToDialog (rfp->location, VIB_MSG_INIT); Show (rfp->pages [rfp->currentPage]); SendMessageToDialog (rfp->data, VIB_MSG_ENTER); Update (); } return (ForM) w; } static void RegionOrCommentFeatFormActnProc (ForM f) { RegionFormPtr rfp; RegionPagePtr rpp; rfp = (RegionFormPtr) GetObjectExtra (f); if (rfp != NULL) { rpp = (RegionPagePtr) GetObjectExtra (rfp->data); if (rpp != NULL && GetStatus (rpp->convertToMiscFeat)) { rfp->this_subtype = FEATDEF_misc_feature; } } if (FeatFormReplaceWithoutUpdateProc (f)) { if (rfp != NULL) { GetRidOfEmptyFeatsDescStrings (rfp->input_entityID, NULL); if (GetAppProperty ("InternalNcbiSequin") != NULL) { ExtendGeneFeatIfOnMRNA (rfp->input_entityID, NULL); } ObjMgrSendMsg (OM_MSG_UPDATE, rfp->input_entityID, rfp->input_itemID, rfp->input_itemtype); } } } extern Int2 LIBCALLBACK RegionOrCommentGenFunc (Pointer data) { OMProcControlPtr ompcp; OMUserDataPtr omudp; ObjMgrProcPtr proc; RegionFormPtr rfp; SeqEntryPtr sep; SeqFeatPtr sfp; Uint2 subtype; CharPtr title; WindoW w; ompcp = (OMProcControlPtr) data; sfp = NULL; sep = NULL; subtype = 0; title = NULL; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; proc = ompcp->proc; switch (ompcp->input_itemtype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) ompcp->input_data; if (sfp != NULL && (sfp->data.choice != SEQFEAT_REGION && sfp->data.choice != SEQFEAT_COMMENT)) { return OM_MSG_RET_ERROR; } break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { rfp = (RegionFormPtr) omudp->userdata.ptrvalue; if (rfp != NULL) { Select (rfp->form); } return OM_MSG_RET_DONE; } if (sfp != NULL) { if (sfp->data.choice == SEQFEAT_REGION) { subtype = FEATDEF_REGION; } else if (sfp->data.choice == SEQFEAT_COMMENT) { subtype = FEATDEF_COMMENT; } } else if (proc->subinputtype > 0) { subtype = proc->subinputtype; } if (subtype == FEATDEF_REGION) { title = "Region"; } else if (subtype == FEATDEF_COMMENT) { title = "Comment"; } else { return OM_MSG_RET_ERROR; } sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); w = (WindoW) CreateRegionOrCommentForm (-50, -33, title, sfp, sep, subtype, RegionOrCommentFeatFormActnProc); rfp = (RegionFormPtr) GetObjectExtra (w); if (rfp != NULL) { rfp->input_entityID = ompcp->input_entityID; rfp->input_itemID = ompcp->input_itemID; rfp->input_itemtype = ompcp->input_itemtype; rfp->this_itemtype = OBJ_SEQFEAT; rfp->this_subtype = subtype; rfp->procid = ompcp->proc->procid; rfp->proctype = ompcp->proc->proctype; rfp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, rfp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) rfp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToForm (rfp->form, VIB_MSG_INIT); if (sfp != NULL) { PointerToForm (rfp->form, (Pointer) sfp); SetClosestParentIfDuplicating ((BaseFormPtr) rfp); } else { SetNewFeatureDefaultInterval ((FeatureFormPtr) rfp); } } Show (w); Select (w); return OM_MSG_RET_DONE; } typedef struct molinfopage { DIALOG_MESSAGE_BLOCK PopuP moltype; PopuP technique; PopuP complete; GrouP expGrp; TexT explain; EnumFieldAssoc PNTR moltypeAlist; EnumFieldAssoc PNTR techniqueAlist; EnumFieldAssoc PNTR completeAlist; } MolInfoPage, PNTR MolInfoPagePtr; typedef struct molinfoform { DESCRIPTOR_FORM_BLOCK PopuP molPopup; PopuP topologyPopup; PopuP strandPopup; } MolInfoForm, PNTR MolInfoFormPtr; static ENUM_ALIST(molinfo_biomol_alist) {" ", 0}, {"Genomic DNA or RNA", 1}, {"Precursor RNA", 2}, {"mRNA [cDNA]", 3}, {"Ribosomal RNA", 4}, {"Transfer RNA", 5}, {"Small nuclear RNA", 6}, {"Small cytoplasmic RNA", 7}, {"Peptide", 8}, {"Other-Genetic", 9}, {"Genomic-mRNA", 10}, {"cRNA", 11}, {"Small nucleolar RNA", 12}, {"Transcribed RNA", 13}, {"Other", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_biomol_nuc_alist) {" ", 0}, {"Genomic DNA or RNA", 1}, {"Precursor RNA", 2}, {"mRNA [cDNA]", 3}, {"Ribosomal RNA", 4}, {"Transfer RNA", 5}, {"Small nuclear RNA", 6}, {"Small cytoplasmic RNA", 7}, {"Other-Genetic", 9}, {"Genomic-mRNA", 10}, {"cRNA", 11}, {"Small nucleolar RNA", 12}, {"Transcribed RNA", 13}, {"Other", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_biomol_nucX_alist) {" ", 0}, {"Genomic DNA", 253}, {"Genomic RNA", 254}, {"Precursor RNA", 2}, {"mRNA [cDNA]", 3}, {"Ribosomal RNA", 4}, {"Transfer RNA", 5}, {"Small nuclear RNA", 6}, {"Small cytoplasmic RNA", 7}, {"Other-Genetic", 9}, {"Genomic-mRNA", 10}, {"cRNA", 11}, {"Small nucleolar RNA", 12}, {"Other", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_biomol_prot_alist) {" ", 0}, {"Peptide", 8}, {"Other", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_tech_alist) {" ", 0}, {"Standard", 1}, {"EST", 2}, {"STS", 3}, {"Survey", 4}, {"Genetic Map", 5}, {"Physical Map", 6}, {"Derived", 7}, {"Concept-Trans", 8}, {"Seq-Pept", 9}, {"Both", 10}, {"Seq-Pept-Overlap", 11}, {"Seq-Pept-Homol", 12}, {"Concept-Trans-A", 13}, {"HTGS 0", 18}, {"HTGS 1", 14}, {"HTGS 2", 15}, {"HTGS 3", 16}, {"FLI_cDNA", 17}, {"HTC", 19}, {"Other:", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_tech_nuc_alist) {" ", 0}, {"Standard", 1}, {"EST", 2}, {"STS", 3}, {"Survey", 4}, {"Genetic Map", 5}, {"Physical Map", 6}, {"Derived", 7}, {"HTGS 0", 18}, {"HTGS 1", 14}, {"HTGS 2", 15}, {"HTGS 3", 16}, {"FLI_cDNA", 17}, {"HTC", 19}, {"Other:", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_tech_prot_alist) {" ", 0}, {"Concept-Trans", 8}, {"Seq-Pept", 9}, {"Both", 10}, {"Seq-Pept-Overlap", 11}, {"Seq-Pept-Homol", 12}, {"Concept-Trans-A", 13}, {"Other:", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_complete_alist) {" ", 0}, {"Complete", 1}, {"Partial", 2}, {"No Left", 3}, {"No Right", 4}, {"No Ends", 5}, {"Has Left", 6}, {"Has Right", 7}, {"Other", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_complete_nuc_alist) {" ", 0}, {"Complete", 1}, {"Partial", 2}, {"No 5'", 3}, {"No 3'", 4}, {"No Ends", 5}, {"Has 5'", 6}, {"Has 3'", 7}, {"Other", 255}, END_ENUM_ALIST static ENUM_ALIST(molinfo_complete_prot_alist) {" ", 0}, {"Complete", 1}, {"Partial", 2}, {"No NH3", 3}, {"No CO2", 4}, {"No Ends", 5}, {"Has NH3", 6}, {"Has CO2", 7}, {"Other", 255}, END_ENUM_ALIST static Uint1 check_biomol (Uint1 biomol) { if (biomol > 12 && biomol < 253) return 0; return biomol; } static Uint1 check_technique (Uint1 tech) { if (tech > 19 && tech != 255) return 0; return tech; } static Uint1 check_complete (Uint1 completeness) { if (completeness > 7 && completeness != 255) return 0; return completeness; } static void MolInfoPtrToMolInfoPage (DialoG d, Pointer data) { MolInfoPtr mip; MolInfoPagePtr mpp; mpp = (MolInfoPagePtr) GetObjectExtra (d); mip = (MolInfoPtr) data; if (mpp != NULL) { SetEnumPopup (mpp->moltype, mpp->moltypeAlist, (UIEnum) check_biomol (mip->biomol)); SetEnumPopup (mpp->technique, mpp->techniqueAlist, (UIEnum) check_technique (mip->tech)); SetEnumPopup (mpp->complete, mpp->completeAlist, (UIEnum) check_complete (mip->completeness)); SetTitle (mpp->explain, mip->techexp); if (mip->tech == 255) { SafeShow (mpp->expGrp); } else { SafeHide (mpp->expGrp); } } } static Pointer MolInfoPageToMolInfoPtr (DialoG d) { MolInfoPtr mip; MolInfoPagePtr mpp; UIEnum val; mip = NULL; mpp = (MolInfoPagePtr) GetObjectExtra (d); if (mpp != NULL) { mip = MolInfoNew (); if (mip != NULL) { if (GetEnumPopup (mpp->moltype, mpp->moltypeAlist, &val)) { mip->biomol = (Uint1) val; } if (GetEnumPopup (mpp->technique, mpp->techniqueAlist, &val)) { mip->tech = (Uint1) val; } if (GetEnumPopup (mpp->complete, mpp->completeAlist, &val)) { mip->completeness = (Uint1) val; } if (mip->tech == 255) { mip->techexp = SaveStringFromText (mpp->explain); } } } return (Pointer) mip; } static void ChangeTech (PopuP p) { MolInfoPagePtr mpp; UIEnum val; mpp = (MolInfoPagePtr) GetObjectExtra (p); if (mpp != NULL) { if (GetEnumPopup (mpp->technique, mpp->techniqueAlist, &val)) { if (val == 255) { SafeShow (mpp->expGrp); } else { SafeHide (mpp->expGrp); } } } } static CharPtr labels [] = { "Molecule", "Technique", NULL }; extern DialoG CreateMolInfoDialog (GrouP h, CharPtr title, Uint1 biomol, Uint1 tech, Boolean showComplete, Boolean nucsOK, Boolean protsOK, Boolean separateGenomicDNAandRNA) { GrouP f; GrouP m; MolInfoPagePtr mpp; GrouP p; GrouP s; Int2 wid; GrouP x; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); mpp = (MolInfoPagePtr) MemNew (sizeof (MolInfoPage)); if (mpp != NULL) { SetObjectExtra (p, mpp, StdCleanupExtraProc); mpp->dialog = (DialoG) p; mpp->todialog = MolInfoPtrToMolInfoPage; mpp->fromdialog = MolInfoPageToMolInfoPtr; mpp->testdialog = NULL; if (title != NULL && title [0] != '\0') { s = NormalGroup (p, 0, -2, title, systemFont, NULL); } else { s = HiddenGroup (p, 0, -2, NULL); } m = HiddenGroup (s, -1, 0, NULL); /* SetGroupSpacing (m, 10, 10); */ if (showComplete) { f = HiddenGroup (m, -3, 0, NULL); } else { f = HiddenGroup (m, -2, 0, NULL); } SelectFont (programFont); wid = MaxStringWidths (labels); if (nucsOK && protsOK) { mpp->moltypeAlist = molinfo_biomol_alist; mpp->techniqueAlist = molinfo_tech_alist; mpp->completeAlist = molinfo_complete_alist; } else if (nucsOK) { if (separateGenomicDNAandRNA) { mpp->moltypeAlist = molinfo_biomol_nucX_alist; mpp->techniqueAlist = molinfo_tech_nuc_alist; mpp->completeAlist = molinfo_complete_nuc_alist; } else { mpp->moltypeAlist = molinfo_biomol_nuc_alist; mpp->techniqueAlist = molinfo_tech_nuc_alist; mpp->completeAlist = molinfo_complete_nuc_alist; } } else if (protsOK) { mpp->moltypeAlist = molinfo_biomol_prot_alist; mpp->techniqueAlist = molinfo_tech_prot_alist; mpp->completeAlist = molinfo_complete_prot_alist; } else { mpp->moltypeAlist = molinfo_biomol_alist; mpp->techniqueAlist = molinfo_tech_alist; mpp->completeAlist = molinfo_complete_alist; } StaticPrompt (f, "Molecule", wid, popupMenuHeight, programFont, 'l'); mpp->moltype = PopupList (f, TRUE, NULL); SetObjectExtra (mpp->moltype, mpp, NULL); InitEnumPopup (mpp->moltype, mpp->moltypeAlist, NULL); SetEnumPopup (mpp->moltype, mpp->moltypeAlist, biomol); x = NULL; if (showComplete) { x = HiddenGroup (f, 2, 0, NULL); StaticPrompt (x, "Completedness", 0, popupMenuHeight, programFont, 'l'); mpp->complete = PopupList (x, TRUE, NULL); SetObjectExtra (mpp->complete, mpp, NULL); InitEnumPopup (mpp->complete, mpp->completeAlist, NULL); SetEnumPopup (mpp->complete, mpp->completeAlist, 0); } StaticPrompt (f, "Technique", wid, popupMenuHeight, programFont, 'l'); mpp->technique = PopupList (f, TRUE, ChangeTech); SetObjectExtra (mpp->technique, mpp, NULL); InitEnumPopup (mpp->technique, mpp->techniqueAlist, NULL); SetEnumPopup (mpp->technique, mpp->techniqueAlist, 0); SetEnumPopup (mpp->technique, mpp->techniqueAlist, tech); mpp->expGrp = HiddenGroup (f, -2, 0, NULL); SetGroupSpacing (mpp->expGrp, 0, 0); /* StaticPrompt (mpp->expGrp, "Explanation", 0, dialogTextHeight, programFont, 'l'); */ mpp->explain = DialogText (mpp->expGrp, "", 10, NULL); SetObjectExtra (mpp->explain, mpp, NULL); if (showComplete) { AlignObjects (ALIGN_LEFT, (HANDLE) mpp->explain, (HANDLE) x, NULL); AlignObjects (ALIGN_RIGHT, (HANDLE) mpp->explain, (HANDLE) mpp->complete, NULL); AlignObjects (ALIGN_RIGHT, (HANDLE) mpp->explain, (HANDLE) x, NULL); } else { AlignObjects (ALIGN_RIGHT, (HANDLE) mpp->technique, (HANDLE) mpp->explain, NULL); AlignObjects (ALIGN_LEFT, (HANDLE) mpp->technique, (HANDLE) mpp->explain, NULL); } Hide (mpp->expGrp); } return (DialoG) p; } /************ Bioseq field editors ************/ static ENUM_ALIST(mol_alist) {" ", 0}, /* Unknown? */ {"DNA", Seq_mol_dna}, /* 1 */ {"RNA", Seq_mol_rna}, /* 2 */ {"Protein", Seq_mol_aa}, /* 3 */ {"Nucleotide", Seq_mol_na}, /* 4 */ {"Other", Seq_mol_other}, /* 255 */ END_ENUM_ALIST static ENUM_ALIST(topology_alist) {" ", 0}, /* Unknown? */ {"Linear", TOPOLOGY_LINEAR}, /* 1 */ {"Circular", TOPOLOGY_CIRCULAR}, /* 2 */ {"Tandem", TOPOLOGY_TANDEM}, /* 3 */ {"Other", 255}, /* Other? */ END_ENUM_ALIST static ENUM_ALIST(strand_alist) {" ", Seq_strand_unknown}, /* 0 */ {"Single", Seq_strand_plus}, /* 1 */ {"Double", Seq_strand_minus}, /* 2 */ {"Mixed", Seq_strand_both}, /* 3 */ {"Mixed Rev", Seq_strand_both_rev}, /* 4 */ {"Other", Seq_strand_other}, /* 255 */ END_ENUM_ALIST static Uint1 check_mol (Uint1 mol) { if (mol > Seq_mol_na && mol != Seq_mol_other) return 0; return mol; } static Uint1 check_topology (Uint1 topology) { if (topology > TOPOLOGY_TANDEM && topology != 255) return 0; return topology; } static Uint1 check_strand (Uint1 strand) { /* if (strand == Seq_strand_both_rev) return Seq_strand_other; ??? */ if (strand > Seq_strand_both_rev && strand != Seq_strand_other) return Seq_strand_unknown; return strand; } static Boolean UpdateSeqInstGatherFunc (GatherContextPtr gcp) { BioseqPtr bsp; MolInfoFormPtr mfp; UIEnum val; if (gcp == NULL) return TRUE; mfp = (MolInfoFormPtr) gcp->userdata; if (mfp == NULL) return TRUE; if (gcp->thistype == OBJ_BIOSEQ && gcp->thisitem != NULL) { bsp = (BioseqPtr) gcp->thisitem; if (GetEnumPopup (mfp->molPopup, mol_alist, &val)) { bsp->mol = (Uint1) val; } if (GetEnumPopup (mfp->strandPopup, strand_alist, &val)) { bsp->strand = (Uint1) val; } if (GetEnumPopup (mfp->topologyPopup, topology_alist, &val)) { bsp->topology = (Uint1) val; } } return TRUE; } static Boolean UpdateSeqInstFlags (GatherContextPtr gcp) { GatherScope gs; MolInfoFormPtr mfp; SeqEntryPtr sep; if (gcp == NULL || gcp->userdata == NULL) return TRUE; mfp = (MolInfoFormPtr) gcp->userdata; if (gcp->parenttype == OBJ_BIOSEQ || gcp->parenttype == OBJ_BIOSEQSET) { sep = SeqMgrGetSeqEntryForData (gcp->parentitem); if (sep != NULL) { MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.scope = sep; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQDESC] = FALSE; GatherEntity (mfp->input_entityID, (Pointer) mfp, UpdateSeqInstGatherFunc, &gs); } } return TRUE; } static Boolean CollectSeqInstGatherFunc (GatherContextPtr gcp) { BioseqPtr bsp; MolInfoFormPtr mfp; if (gcp == NULL) return TRUE; mfp = (MolInfoFormPtr) gcp->userdata; if (mfp == NULL) return TRUE; if (gcp->thistype == OBJ_BIOSEQ && gcp->thisitem != NULL) { bsp = (BioseqPtr) gcp->thisitem; SetEnumPopup (mfp->molPopup, mol_alist, (UIEnum) check_mol (bsp->mol)); SetEnumPopup (mfp->strandPopup, strand_alist, (UIEnum) check_strand (bsp->strand)); SetEnumPopup (mfp->topologyPopup, topology_alist, (UIEnum) check_topology (bsp->topology)); } return TRUE; } static Boolean CollectSeqInstFlags (GatherContextPtr gcp) { GatherScope gs; MolInfoFormPtr mfp; SeqEntryPtr sep; if (gcp == NULL || gcp->userdata == NULL) return TRUE; mfp = (MolInfoFormPtr) gcp->userdata; if (gcp->parenttype == OBJ_BIOSEQ || gcp->parenttype == OBJ_BIOSEQSET) { sep = SeqMgrGetSeqEntryForData (gcp->parentitem); if (sep != NULL) { MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.scope = sep; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQDESC] = FALSE; GatherEntity (mfp->input_entityID, (Pointer) mfp, CollectSeqInstGatherFunc, &gs); } } return TRUE; } static void MolInfoDescFormActnProc (ForM f) { MolInfoFormPtr mfp; mfp = (MolInfoFormPtr) GetObjectExtra (f); if (mfp != NULL) { DescFormReplaceWithoutUpdateProc (f); if (mfp->input_itemtype == OBJ_SEQDESC) { GatherItem (mfp->input_entityID, mfp->input_itemID, mfp->input_itemtype, (Pointer) mfp, UpdateSeqInstFlags); } GetRidOfEmptyFeatsDescStrings (mfp->input_entityID, NULL); if (GetAppProperty ("InternalNcbiSequin") != NULL) { ExtendGeneFeatIfOnMRNA (mfp->input_entityID, NULL); } ObjMgrSendMsg (OM_MSG_UPDATE, mfp->input_entityID, mfp->input_itemID, mfp->input_itemtype); } } static void MolInfoFormMessage (ForM f, Int2 mssg) { MolInfoFormPtr mfp; mfp = (MolInfoFormPtr) GetObjectExtra (f); if (mfp != NULL) { switch (mssg) { case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : StdDeleteTextProc (NULL); break; default : if (mfp->appmessage != NULL) { mfp->appmessage (f, mssg); } break; } } } extern ForM CreateMolInfoForm (Int2 left, Int2 top, Int2 width, Int2 height, CharPtr title, Uint1 biomol, Uint1 tech, Boolean nucsOK, Boolean protsOK, FormActnFunc actproc) { ButtoN b; GrouP c; GrouP g; MolInfoFormPtr mfp; PrompT p; GrouP q; StdEditorProcsPtr sepp; WindoW w; w = NULL; mfp = (MolInfoFormPtr) MemNew (sizeof (MolInfoForm)); if (mfp != NULL) { w = FixedWindow (left, top, width, height, title, StdCloseWindowProc); SetObjectExtra (w, mfp, StdDescFormCleanupProc); mfp->form = (ForM) w; mfp->actproc = actproc; mfp->formmessage = MolInfoFormMessage; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); mfp->appmessage = sepp->handleMessages; } g = HiddenGroup (w, -1, 0, NULL); mfp->data = CreateMolInfoDialog (g, NULL, biomol, tech, TRUE, nucsOK, protsOK, FALSE); p = StaticPrompt (w, "Biological characteristics of sequences:", 0, stdLineHeight, programFont, 'c'); q = HiddenGroup (w, 6, 0, NULL); StaticPrompt (q, "Class", 0, popupMenuHeight, programFont, 'c'); mfp->molPopup = PopupList (q, TRUE, NULL); InitEnumPopup (mfp->molPopup, mol_alist, NULL); StaticPrompt (q, "Topology", 0, popupMenuHeight, programFont, 'c'); mfp->topologyPopup = PopupList (q, TRUE, NULL); InitEnumPopup (mfp->topologyPopup, topology_alist, NULL); StaticPrompt (q, "Strand", 0, popupMenuHeight, programFont, 'c'); mfp->strandPopup = PopupList (q, TRUE, NULL); InitEnumPopup (mfp->strandPopup, strand_alist, NULL); SetGroupSpacing (q, 15, 2); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdAcceptFormButtonProc); SetObjectExtra (b, mfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) p, (HANDLE) q, (HANDLE) c, NULL); RealizeWindow (w); } return (ForM) w; } extern Int2 LIBCALLBACK MolInfoGenFunc (Pointer data) { MolInfoFormPtr mfp; OMProcControlPtr ompcp; OMUserDataPtr omudp; ValNodePtr sdp; WindoW w; ompcp = (OMProcControlPtr) data; sdp = NULL; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; switch (ompcp->input_itemtype) { case OBJ_SEQDESC : sdp = (ValNodePtr) ompcp->input_data; if (sdp != NULL && sdp->choice != Seq_descr_molinfo) { return OM_MSG_RET_ERROR; } break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { mfp = (MolInfoFormPtr) omudp->userdata.ptrvalue; if (mfp != NULL) { Select (mfp->form); } return OM_MSG_RET_DONE; } w = (WindoW) CreateMolInfoForm (-50, -33, -10, -10, "Molecule Information", 0, 0, TRUE, TRUE, MolInfoDescFormActnProc); mfp = (MolInfoFormPtr) GetObjectExtra (w); if (mfp != NULL) { mfp->input_entityID = ompcp->input_entityID; mfp->input_itemID = ompcp->input_itemID; mfp->input_itemtype = ompcp->input_itemtype; mfp->this_itemtype = OBJ_SEQDESC; mfp->this_subtype = Seq_descr_molinfo; mfp->procid = ompcp->proc->procid; mfp->proctype = ompcp->proc->proctype; mfp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, mfp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) mfp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToDialog (mfp->data, VIB_MSG_INIT); if (sdp != NULL) { PointerToDialog (mfp->data, (Pointer) sdp->data.ptrvalue); if (mfp->input_itemtype == OBJ_SEQDESC) { GatherItem (mfp->input_entityID, mfp->input_itemID, mfp->input_itemtype, (Pointer) mfp, CollectSeqInstFlags); } SetClosestParentIfDuplicating ((BaseFormPtr) mfp); } } Show (w); Select (w); return OM_MSG_RET_DONE; } typedef struct gbblockpage { DIALOG_MESSAGE_BLOCK TexT source; TexT origin; TexT date; TexT div; TexT taxonomy; ButtoN htgsDraft; ButtoN htgsFulltop; ButtoN htgsActivefin; ButtoN htgsCancelled; DialoG kywds; DialoG xaccns; DialoG entryDate; } GenBankPage, PNTR GenBankPagePtr; typedef struct gbblockform { DESCRIPTOR_FORM_BLOCK DialoG gbppxaccns; ButtoN xaccnstohistory; } GenBankForm, PNTR GenBankFormPtr; static void GBBlockPtrToGenBankPage (DialoG d, Pointer data) { GBBlockPtr gbp; GenBankPagePtr gpp; ValNodePtr head; Boolean isActivefin = FALSE; Boolean isCancelled = FALSE; Boolean isDraft = FALSE; Boolean isFulltop = FALSE; CharPtr str; ValNodePtr vnp; gpp = (GenBankPagePtr) GetObjectExtra (d); gbp = (GBBlockPtr) data; if (gpp != NULL) { SetTitle (gpp->source, gbp->source); SetTitle (gpp->origin, gbp->origin); SetTitle (gpp->date, gbp->date); SetTitle (gpp->div, gbp->div); SetTitle (gpp->taxonomy, gbp->taxonomy); for (head = NULL, vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringICmp (str, "HTGS_DRAFT") != 0 && StringICmp (str, "HTGS_FULLTOP") != 0 && StringICmp (str, "HTGS_ACTIVEFIN") != 0 && StringICmp (str, "HTGS_CANCELLED") != 0) { ValNodeCopyStr (&head, 0, str); } } PointerToDialog (gpp->kywds, head); ValNodeFreeData (head); PointerToDialog (gpp->xaccns, gbp->extra_accessions); PointerToDialog (gpp->entryDate, gbp->entry_date); isDraft = FALSE; for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_DRAFT") == 0) { isDraft = TRUE; } else if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_FULLTOP") == 0) { isFulltop = TRUE; } else if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_ACTIVEFIN") == 0) { isActivefin = TRUE; } else if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_CANCELLED") == 0) { isCancelled = TRUE; } } SafeSetStatus (gpp->htgsDraft, isDraft); SafeSetStatus (gpp->htgsFulltop, isFulltop); SafeSetStatus (gpp->htgsActivefin, isActivefin); SafeSetStatus (gpp->htgsCancelled, isCancelled); } } static Pointer GenBankPageToGBBlockPtr (DialoG d) { GBBlockPtr gbp; GenBankPagePtr gpp; Boolean noActivefin; Boolean noCancelled; Boolean noDraft; Boolean noFulltop; ValNodePtr vnp; gbp = NULL; gpp = (GenBankPagePtr) GetObjectExtra (d); if (gpp != NULL) { gbp = GBBlockNew (); if (gbp != NULL) { gbp->source = SaveStringFromText (gpp->source); gbp->origin = SaveStringFromText (gpp->origin); gbp->date = SaveStringFromText (gpp->date); gbp->div = SaveStringFromText (gpp->div); gbp->taxonomy = SaveStringFromTextAndStripNewlines (gpp->taxonomy); gbp->keywords = DialogToPointer (gpp->kywds); gbp->extra_accessions = DialogToPointer (gpp->xaccns); gbp->entry_date = DialogToPointer (gpp->entryDate); if (GetStatus (gpp->htgsDraft)) { noDraft = TRUE; for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_DRAFT") == 0) { noDraft = FALSE; } } if (noDraft) { ValNodeCopyStr (&(gbp->keywords), 0, "HTGS_DRAFT"); } } if (GetStatus (gpp->htgsFulltop)) { noFulltop = TRUE; for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_FULLTOP") == 0) { noFulltop = FALSE; } } if (noFulltop) { ValNodeCopyStr (&(gbp->keywords), 0, "HTGS_FULLTOP"); } } if (GetStatus (gpp->htgsActivefin)) { noActivefin = TRUE; for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_ACTIVEFIN") == 0) { noActivefin = FALSE; } } if (noActivefin) { ValNodeCopyStr (&(gbp->keywords), 0, "HTGS_ACTIVEFIN"); } } if (GetStatus (gpp->htgsCancelled)) { noCancelled = TRUE; for (vnp = gbp->keywords; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_CANCELLED") == 0) { noCancelled = FALSE; } } if (noCancelled) { ValNodeCopyStr (&(gbp->keywords), 0, "HTGS_CANCELLED"); } } } } return (Pointer) gbp; } static void DeleteKeywordProc (ButtoN b) { GenBankPagePtr gpp; gpp = (GenBankPagePtr) GetObjectExtra (b); if (gpp != NULL) { PointerToDialog (gpp->kywds, NULL); SafeSetStatus (gpp->htgsDraft, FALSE); SafeSetStatus (gpp->htgsFulltop, FALSE); SafeSetStatus (gpp->htgsActivefin, FALSE); SafeSetStatus (gpp->htgsCancelled, FALSE); } } static DialoG CreateGenBankDialog (GrouP h, CharPtr title, ValNodePtr sdp, GenBankFormPtr gfp) { ButtoN b; GrouP f1, f2, f3, f4, f5; GBBlockPtr gbp; Boolean genome; GenBankPagePtr gpp; Boolean internal; GrouP m; GrouP p; GrouP s; Boolean showKeywords; ValNodePtr vnp; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); gpp = (GenBankPagePtr) MemNew (sizeof (GenBankPage)); if (gpp) { SetObjectExtra (p, gpp, StdCleanupExtraProc); gpp->dialog = (DialoG) p; gpp->todialog = GBBlockPtrToGenBankPage; gpp->fromdialog = GenBankPageToGBBlockPtr; gpp->testdialog = NULL; if (title != NULL && title [0] != '\0') { s = NormalGroup (p, 0, -2, title, systemFont, NULL); } else { s = HiddenGroup (p, 0, -2, NULL); } m = HiddenGroup (s, -1, 0, NULL); /* SetGroupSpacing (m, 10, 10); */ gbp = NULL; if (sdp != NULL && sdp->choice == Seq_descr_genbank && sdp->data.ptrvalue != NULL) { gbp = (GBBlockPtr) sdp->data.ptrvalue; } internal = (Boolean) (GetAppProperty ("InternalNcbiSequin") != NULL); genome = (Boolean) (GetAppProperty ("GenomeCenterSequin") != NULL); f1 = HiddenGroup (m, 1, 0, NULL); if ((! genome) || (gbp != NULL && gbp->div != NULL)) { StaticPrompt (f1, "Division", 0, 0, programFont, 'c'); gpp->div = DialogText (f1, "", 15, NULL); } if (internal || (gbp != NULL && gbp->origin != NULL)) { StaticPrompt (f1, "Origin", 0, 0, programFont, 'c'); gpp->origin = DialogText (f1, "", 15, NULL); } if (internal || (gbp != NULL && gbp->date != NULL)) { StaticPrompt (f1, "(Old Date)", 0, 0, programFont, 'c'); gpp->date = DialogText (f1, "", 15, NULL); } if (internal || (gbp != NULL && gbp->source != NULL)) { StaticPrompt (f1, "Source", 0, 0, programFont, 'c'); gpp->source = DialogText (f1, "", 15, NULL); } if (internal || (gbp != NULL && gbp->taxonomy != NULL)) { StaticPrompt (f1, "Taxonomy", 0, 0, programFont, 'c'); gpp->taxonomy = ScrollText (f1, 15, 5, programFont, TRUE, NULL); } f3 = HiddenGroup (m, 0, 3, NULL); if (internal || genome || (gbp != NULL && gbp->extra_accessions != NULL)) { StaticPrompt (f3, "Secondary Accessions", 0, 0, programFont, 'c'); gpp->xaccns = CreateVisibleStringDialog (f3, 3, -1, 15); if (internal || genome) { gfp->gbppxaccns = gpp->xaccns; gfp->xaccnstohistory = CheckBox (f3, "Copy to Bioseq-history.replaces", NULL); if (genome) { SetStatus (gfp->xaccnstohistory, TRUE); Hide (gfp->xaccnstohistory); } } } b = NULL; f2 = HiddenGroup (m, 0, 3, NULL); showKeywords = FALSE; if (gbp != NULL && gbp->keywords != NULL) { vnp = gbp->keywords; if (vnp->next != NULL || StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_DRAFT") != 0 || StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_FULLTOP") != 0 || StringICmp ((CharPtr) vnp->data.ptrvalue, "HTGS_ACTIVEFIN") != 0) { showKeywords = TRUE; } } if (internal || showKeywords) { StaticPrompt (f2, "Keywords", 0, 0, programFont, 'c'); gpp->kywds = CreateVisibleStringDialog (f2, 3, -1, 15); } if (internal || genome || (gbp != NULL && gbp->keywords != NULL)) { f5 = HiddenGroup (f2, 2, 0, NULL); gpp->htgsDraft = CheckBox (f5, "HTGS_DRAFT", NULL); gpp->htgsFulltop = CheckBox (f5, "HTGS_FULLTOP", NULL); gpp->htgsActivefin = CheckBox (f5, "HTGS_ACTIVEFIN", NULL); gpp->htgsCancelled = CheckBox (f5, "HTGS_CANCELLED", NULL); } if (internal) { b = PushButton (m, "Delete All Keywords", DeleteKeywordProc); SetObjectExtra (b, gpp, NULL); } f4 = HiddenGroup (m, 2, 0, NULL); if (internal || (gbp != NULL && gbp->entry_date != NULL)) { gpp->entryDate = CreateDateDialog (f4, ""); } AlignObjects (ALIGN_CENTER, (HANDLE) f1, (HANDLE) f2, (HANDLE) f3, (HANDLE) f4, (HANDLE) b, NULL); } return (DialoG) p; } static void GenBankFormMessage (ForM f, Int2 mssg) { GenBankFormPtr gfp; gfp = (GenBankFormPtr) GetObjectExtra (f); if (gfp != NULL) { switch (mssg) { case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : StdDeleteTextProc (NULL); break; default : if (gfp->appmessage != NULL) { gfp->appmessage (f, mssg); } break; } } } extern ForM CreateGenBankForm (Int2 left, Int2 top, CharPtr title, ValNodePtr sdp, SeqEntryPtr sep, FormActnFunc actproc) { ButtoN b; GrouP c; GrouP g; GenBankFormPtr gfp; StdEditorProcsPtr sepp; WindoW w; w = NULL; gfp = (GenBankFormPtr) MemNew (sizeof (GenBankForm)); if (gfp != NULL) { w = FixedWindow (left, top, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, gfp, StdDescFormCleanupProc); gfp->form = (ForM) w; gfp->actproc = actproc; gfp->formmessage = GenBankFormMessage; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); gfp->appmessage = sepp->handleMessages; } g = HiddenGroup (w, -1, 0, NULL); gfp->xaccnstohistory = NULL; gfp->gbppxaccns = NULL; gfp->data = CreateGenBankDialog (g, NULL, sdp, gfp); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdAcceptFormButtonProc); SetObjectExtra (b, gfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); } return (ForM) w; } static Boolean GetLowestStackSeqEntryForGBB (GatherContextPtr gcp) { BaseFormPtr bfp; Int2 i; if (gcp == NULL) return TRUE; bfp = (BaseFormPtr) gcp->userdata; if (bfp == NULL) return TRUE; if (gcp->gatherstack != NULL && gcp->numstack > 0) { for (i = 0; i < gcp->numstack; i++) { if (gcp->gatherstack [i].itemtype == OBJ_BIOSEQ || gcp->gatherstack [i].itemtype == OBJ_BIOSEQSET) { bfp->input_itemID = gcp->gatherstack [i].itemID; bfp->input_itemtype = gcp->gatherstack [i].itemtype; } } } return FALSE; } static void GenBankFormActnProc (ForM f) { BioseqPtr bsp; Boolean changehist; GenBankFormPtr gfp; SeqHistPtr hist; Char prefix [20]; SeqIdPtr sip; TextSeqIdPtr tsip; ValNodePtr tmp; ValNodePtr vnp; Uint4 whichdb; gfp = (GenBankFormPtr) GetObjectExtra (f); if (gfp != NULL) { vnp = NULL; changehist = (Boolean) (gfp->xaccnstohistory != NULL && GetStatus (gfp->xaccnstohistory)); if (changehist) { vnp = DialogToPointer (gfp->gbppxaccns); } if (DescFormReplaceWithoutUpdateProc (f)) { GetRidOfEmptyFeatsDescStrings (gfp->input_entityID, NULL); if (GetAppProperty ("InternalNcbiSequin") != NULL) { ExtendGeneFeatIfOnMRNA (gfp->input_entityID, NULL); } if (changehist) { GatherItem (gfp->input_entityID, gfp->input_itemID, gfp->input_itemtype, (Pointer) gfp, GetLowestStackSeqEntryForGBB); bsp = GetBioseqGivenIDs (gfp->input_entityID, gfp->input_itemID, gfp->input_itemtype); if (bsp != NULL) { hist = bsp->hist; if (hist != NULL) { hist->replace_ids = SeqIdSetFree (hist->replace_ids); } else { hist = SeqHistNew (); bsp->hist = hist; } if (hist != NULL && vnp != NULL) { for (tmp = vnp; tmp != NULL; tmp = tmp->next) { sip = ValNodeNew (hist->replace_ids); if (hist->replace_ids == NULL) { hist->replace_ids = sip; } if (sip != NULL) { tsip = TextSeqIdNew (); StringNCpy_0 (prefix, (CharPtr) tmp->data.ptrvalue, sizeof (prefix)); /* ptr = &(prefix [0]); ch = *ptr; while (ch != '\0' && IS_ALPHA (ch)) { ptr++; ch = *ptr; } *ptr = '\0'; */ whichdb = WHICH_db_accession (prefix); if (ACCN_IS_EMBL (whichdb)) { sip->choice = SEQID_EMBL; } else if (ACCN_IS_DDBJ (whichdb)) { sip->choice = SEQID_DDBJ; } else { sip->choice = SEQID_GENBANK; } sip->data.ptrvalue = (Pointer) tsip; if (tsip != NULL) { tsip->accession = StringSave (tmp->data.ptrvalue); } } } } if (hist != NULL) { if (hist->assembly == NULL && hist->replace_date == NULL && hist->replace_ids == NULL && hist->replaced_by_date == NULL && hist->replaced_by_ids == NULL && hist->deleted_date == NULL && (! hist->deleted)) { bsp->hist = SeqHistFree (bsp->hist); } } } ValNodeFreeData (vnp); } ObjMgrSendMsg (OM_MSG_UPDATE, gfp->input_entityID, gfp->input_itemID, gfp->input_itemtype); } } } extern Int2 LIBCALLBACK GenBankGenFunc (Pointer data) { GenBankFormPtr gfp; OMProcControlPtr ompcp; OMUserDataPtr omudp; ValNodePtr sdp; SeqEntryPtr sep; WindoW w; ompcp = (OMProcControlPtr) data; sdp = NULL; sep = NULL; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; switch (ompcp->input_itemtype) { case OBJ_SEQDESC : sdp = (ValNodePtr) ompcp->input_data; if (sdp != NULL && sdp->choice != Seq_descr_genbank) { return OM_MSG_RET_ERROR; } break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { gfp = (GenBankFormPtr) omudp->userdata.ptrvalue; if (gfp != NULL) { Select (gfp->form); } return OM_MSG_RET_DONE; } sep = GetTopSeqEntryForEntityID (ompcp->input_entityID); w = (WindoW) CreateGenBankForm (-50, -33, "GenBank Block", sdp, sep, GenBankFormActnProc); gfp = (GenBankFormPtr) GetObjectExtra (w); if (gfp != NULL) { gfp->input_entityID = ompcp->input_entityID; gfp->input_itemID = ompcp->input_itemID; gfp->input_itemtype = ompcp->input_itemtype; gfp->this_itemtype = OBJ_SEQDESC; gfp->this_subtype = Seq_descr_genbank; gfp->procid = ompcp->proc->procid; gfp->proctype = ompcp->proc->proctype; gfp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, gfp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) gfp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToDialog (gfp->data, VIB_MSG_INIT); if (sdp != NULL) { PointerToDialog (gfp->data, (Pointer) sdp->data.ptrvalue); SetClosestParentIfDuplicating ((BaseFormPtr) gfp); } } Show (w); Select (w); return OM_MSG_RET_DONE; } typedef struct visstrpage { DIALOG_MESSAGE_BLOCK TexT title; } VisStrPage, PNTR VisStrPagePtr; typedef struct visstrform { DESCRIPTOR_FORM_BLOCK Uint2 subtype; } VisStrForm, PNTR VisStrFormPtr; static void CharPtrToVisStrPage (DialoG d, Pointer data) { CharPtr title; VisStrPagePtr vpp; vpp = (VisStrPagePtr) GetObjectExtra (d); title = (CharPtr) data; if (vpp != NULL) { SetTitle (vpp->title, title); } } static Pointer VisStrPageToCharPtr (DialoG d) { CharPtr title; VisStrPagePtr vpp; title = NULL; vpp = (VisStrPagePtr) GetObjectExtra (d); if (vpp != NULL) { title = SaveStringFromTextAndStripNewlines (vpp->title); } return (Pointer) title; } static void VisStrDialogMessage (DialoG d, Int2 mssg) { VisStrPagePtr vpp; vpp = (VisStrPagePtr) GetObjectExtra (d); if (vpp != NULL) { switch (mssg) { case VIB_MSG_ENTER : Select (vpp->title); break; default : break; } } } static DialoG CreateVisStrDialog (GrouP h, CharPtr title, Uint2 subtype) { GrouP f; CharPtr label; GrouP m; GrouP p; GrouP s; VisStrPagePtr vpp; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); vpp = (VisStrPagePtr) MemNew (sizeof (VisStrPage)); if (vpp) { SetObjectExtra (p, vpp, StdCleanupExtraProc); vpp->dialog = (DialoG) p; vpp->todialog = CharPtrToVisStrPage; vpp->fromdialog = VisStrPageToCharPtr; vpp->testdialog = NULL; vpp->dialogmessage = VisStrDialogMessage; if (title != NULL && title [0] != '\0') { s = NormalGroup (p, 0, -2, title, systemFont, NULL); } else { s = HiddenGroup (p, 0, -2, NULL); } m = HiddenGroup (s, -1, 0, NULL); /* SetGroupSpacing (m, 10, 10); */ f = HiddenGroup (m, 0, 2, NULL); if (subtype == Seq_descr_title) { label = "Title"; } else if (subtype == Seq_descr_comment) { label = "Comment"; } else if (subtype == Seq_descr_name) { label = "Name"; } else if (subtype == Seq_descr_region) { label = "Region"; } else { label = "Title"; } StaticPrompt (f, label, 0, 0, programFont, 'c'); vpp->title = ScrollText (f, 25, 15, programFont, TRUE, NULL); } return (DialoG) p; } static void VisStrFormMessage (ForM f, Int2 mssg) { VisStrFormPtr vfp; vfp = (VisStrFormPtr) GetObjectExtra (f); if (vfp != NULL) { switch (mssg) { case VIB_MSG_ENTER : SendMessageToDialog (vfp->data, VIB_MSG_ENTER); break; case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : StdDeleteTextProc (NULL); break; default : if (vfp->appmessage != NULL) { vfp->appmessage (f, mssg); } break; } } } extern ForM CreateVisStrForm (Int2 left, Int2 top, CharPtr title, Uint2 subtype, FormActnFunc actproc) { ButtoN b; GrouP c; GrouP g; StdEditorProcsPtr sepp; VisStrFormPtr vfp; WindoW w; w = NULL; vfp = (VisStrFormPtr) MemNew (sizeof (VisStrForm)); if (vfp != NULL) { w = FixedWindow (left, top, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, vfp, StdDescFormCleanupProc); vfp->form = (ForM) w; vfp->actproc = actproc; vfp->formmessage = VisStrFormMessage; vfp->subtype = subtype; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); vfp->appmessage = sepp->handleMessages; } g = HiddenGroup (w, -1, 0, NULL); vfp->data = CreateVisStrDialog (g, NULL, subtype); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdAcceptFormButtonProc); SetObjectExtra (b, vfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); } return (ForM) w; } static CharPtr citInCommentMsg = "This comment looks like it has citation references in [#] form.\n\ You should put comments about references in the REMARK section by\n\ double clicking on the reference and launching its editor.\n\ Continue saving this comment?"; static void VisStrDescFormActnProc (ForM f) { OMProcControl ompc; CharPtr str; Boolean suspicious; VisStrFormPtr vfp; vfp = (VisStrFormPtr) GetObjectExtra (f); if (vfp != NULL) { str = DialogToPointer (vfp->data); if (str == NULL || StringHasNoText (str)) { MemSet ((Pointer) &ompc, 0, sizeof (OMProcControl)); ompc.do_not_reload_from_cache = TRUE; ompc.input_entityID = vfp->input_entityID; ompc.input_itemID = vfp->input_itemID; ompc.input_itemtype = vfp->input_itemtype; if (! DetachDataForProc (&ompc, FALSE)) { Message (MSG_ERROR, "DetachDataForProc failed"); } GetRidOfEmptyFeatsDescStrings (vfp->input_entityID, NULL); ObjMgrSetDirtyFlag (vfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, vfp->input_entityID, vfp->input_itemID, vfp->input_itemtype); MemFree (str); return; } suspicious = FALSE; if (vfp->subtype == Seq_descr_comment) { suspicious = SerialNumberInString (str); } MemFree (str); if (suspicious) { if (Message (MSG_OKC, "%s", citInCommentMsg) == ANS_CANCEL) { Remove (f); return; } } if (DescFormReplaceWithoutUpdateProc (f)) { GetRidOfEmptyFeatsDescStrings (vfp->input_entityID, NULL); if (GetAppProperty ("InternalNcbiSequin") != NULL) { ExtendGeneFeatIfOnMRNA (vfp->input_entityID, NULL); } ObjMgrSetDirtyFlag (vfp->input_entityID, TRUE); ObjMgrSendMsg (OM_MSG_UPDATE, vfp->input_entityID, vfp->input_itemID, vfp->input_itemtype); } } } extern Int2 LIBCALLBACK VisStrGenFunc (Pointer data) { OMProcControlPtr ompcp; OMUserDataPtr omudp; ObjMgrProcPtr proc; ValNodePtr sdp; Uint2 subtype; VisStrFormPtr vfp; WindoW w; ompcp = (OMProcControlPtr) data; sdp = NULL; subtype = 0; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; proc = ompcp->proc; switch (ompcp->input_itemtype) { case OBJ_SEQDESC : sdp = (ValNodePtr) ompcp->input_data; if (sdp != NULL && (sdp->choice != Seq_descr_title && sdp->choice != Seq_descr_comment && sdp->choice != Seq_descr_name && sdp->choice != Seq_descr_region)) { return OM_MSG_RET_ERROR; } subtype = sdp->choice; break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { vfp = (VisStrFormPtr) omudp->userdata.ptrvalue; if (vfp != NULL) { Select (vfp->form); } return OM_MSG_RET_DONE; } if (sdp == NULL) { subtype = proc->subinputtype; } if (subtype == Seq_descr_title) { w = (WindoW) CreateVisStrForm (-50, -33, "Title", subtype, VisStrDescFormActnProc); } else if (subtype == Seq_descr_comment) { w = (WindoW) CreateVisStrForm (-50, -33, "Comment", subtype, VisStrDescFormActnProc); } else if (subtype == Seq_descr_name) { w = (WindoW) CreateVisStrForm (-50, -33, "Name", subtype, VisStrDescFormActnProc); } else if (subtype == Seq_descr_region) { w = (WindoW) CreateVisStrForm (-50, -33, "Region", subtype, VisStrDescFormActnProc); } else { return OM_MSG_RET_ERROR; } vfp = (VisStrFormPtr) GetObjectExtra (w); if (vfp != NULL) { vfp->input_entityID = ompcp->input_entityID; vfp->input_itemID = ompcp->input_itemID; vfp->input_itemtype = ompcp->input_itemtype; vfp->this_itemtype = OBJ_SEQDESC; vfp->this_subtype = subtype; vfp->procid = ompcp->proc->procid; vfp->proctype = ompcp->proc->proctype; vfp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, vfp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) vfp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToDialog (vfp->data, VIB_MSG_INIT); if (sdp != NULL) { PointerToDialog (vfp->data, (Pointer) sdp->data.ptrvalue); SetClosestParentIfDuplicating ((BaseFormPtr) vfp); } } Show (w); Select (w); return OM_MSG_RET_DONE; } typedef struct dateform { DESCRIPTOR_FORM_BLOCK } DateForm, PNTR DateFormPtr; static void DateFormMessage (ForM f, Int2 mssg) { DateFormPtr dfp; dfp = (DateFormPtr) GetObjectExtra (f); if (dfp != NULL) { switch (mssg) { case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_CUT : StdCutTextProc (NULL); break; case VIB_MSG_COPY : StdCopyTextProc (NULL); break; case VIB_MSG_PASTE : StdPasteTextProc (NULL); break; case VIB_MSG_DELETE : StdDeleteTextProc (NULL); break; default : if (dfp->appmessage != NULL) { dfp->appmessage (f, mssg); } break; } } } extern ForM CreateDateForm (Int2 left, Int2 top, CharPtr title, FormActnFunc actproc) { ButtoN b; GrouP c; DateFormPtr dfp; GrouP g; StdEditorProcsPtr sepp; WindoW w; w = NULL; dfp = (DateFormPtr) MemNew (sizeof (DateForm)); if (dfp != NULL) { w = FixedWindow (left, top, -10, -10, title, StdCloseWindowProc); SetObjectExtra (w, dfp, StdDescFormCleanupProc); dfp->form = (ForM) w; dfp->actproc = actproc; dfp->formmessage = DateFormMessage; #ifndef WIN_MAC CreateStdEditorFormMenus (w); #endif sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); dfp->appmessage = sepp->handleMessages; } g = HiddenGroup (w, -1, 0, NULL); dfp->data = CreateDateDialog (g, NULL); c = HiddenGroup (w, 2, 0, NULL); b = PushButton (c, "Accept", StdAcceptFormButtonProc); SetObjectExtra (b, dfp, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) g, (HANDLE) c, NULL); RealizeWindow (w); } return (ForM) w; } extern Int2 LIBCALLBACK DateGenFunc (Pointer data) { DateFormPtr dfp; Uint2 itemtype; OMProcControlPtr ompcp; OMUserDataPtr omudp; ObjMgrProcPtr proc; ValNodePtr sdp; CharPtr title; Uint2 subtype; WindoW w; ompcp = (OMProcControlPtr) data; sdp = NULL; itemtype = 0; subtype = 0; if (ompcp == NULL || ompcp->proc == NULL) return OM_MSG_RET_ERROR; title = "Date"; proc = ompcp->proc; switch (ompcp->input_itemtype) { case OBJ_SEQDESC : sdp = (ValNodePtr) ompcp->input_data; if (sdp != NULL && (sdp->choice != Seq_descr_create_date && sdp->choice != Seq_descr_update_date)) { return OM_MSG_RET_ERROR; } itemtype = OBJ_SEQDESC; subtype = sdp->choice; break; case OBJ_BIOSEQ : break; case OBJ_BIOSEQSET : break; case 0 : break; default : return OM_MSG_RET_ERROR; } omudp = ItemAlreadyHasEditor (ompcp->input_entityID, ompcp->input_itemID, ompcp->input_itemtype, ompcp->proc->procid); if (omudp != NULL) { dfp = (DateFormPtr) omudp->userdata.ptrvalue; if (dfp != NULL) { Select (dfp->form); } return OM_MSG_RET_DONE; } if (sdp != NULL) { if (sdp->choice == Seq_descr_create_date) { title = "Create Date"; } else { title = "Update Date"; } } else { itemtype = proc->inputtype; subtype = proc->subinputtype; if (itemtype == OBJ_SEQDESC && subtype == Seq_descr_create_date) { title = "Create Date"; } else if (itemtype == OBJ_SEQDESC && subtype == Seq_descr_update_date) { title = "Update Date"; } else { return OM_MSG_RET_ERROR; } } w = (WindoW) CreateDateForm (-50, -33, title, StdDescFormActnProc); dfp = (DateFormPtr) GetObjectExtra (w); if (dfp != NULL) { dfp->input_entityID = ompcp->input_entityID; dfp->input_itemID = ompcp->input_itemID; dfp->input_itemtype = ompcp->input_itemtype; dfp->this_itemtype = itemtype; dfp->this_subtype = subtype; dfp->procid = ompcp->proc->procid; dfp->proctype = ompcp->proc->proctype; dfp->userkey = OMGetNextUserKey (); omudp = ObjMgrAddUserData (ompcp->input_entityID, ompcp->proc->procid, OMPROC_EDIT, dfp->userkey); if (omudp != NULL) { omudp->userdata.ptrvalue = (Pointer) dfp; omudp->messagefunc = StdVibrantEditorMsgFunc; } SendMessageToDialog (dfp->data, VIB_MSG_INIT); if (sdp != NULL) { PointerToDialog (dfp->data, (Pointer) sdp->data.ptrvalue); SetClosestParentIfDuplicating ((BaseFormPtr) dfp); } } Show (w); Select (w); return OM_MSG_RET_DONE; }