/* dlgutil2.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: dlgutil2.c * * Author: Jonathan Kans * * Version Creation Date: 1/22/95 * * $Revision: 6.29 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #include #include #include #include #include #include #include #include #include #include #ifdef WIN_MOTIF #include #endif typedef struct datepage { DIALOG_MESSAGE_BLOCK TexT year; PopuP month; TexT day; } DatePage, PNTR DatePagePtr; extern CharPtr SaveStringFromTextAndStripNewlines (TexT t) { Char ch; size_t len; CharPtr ptr; CharPtr str; len = TextLength (t); if (len > 0) { str = MemNew (len + 1); if (str != NULL) { GetTitle (t, str, len + 1); ptr = str; ch = *ptr; while (ch != '\0') { if (ch < ' ') { *ptr = ' '; } ptr++; ch = *ptr; } TrimSpacesAroundString (str); if (StringHasNoText (str)) { str = MemFree (str); } return str; } else { return NULL; } } else { return NULL; } } static void DatePtrToDatePage (DialoG d, Pointer data) { DatePtr dp; DatePagePtr dpp; dpp = (DatePagePtr) GetObjectExtra (d); dp = (DatePtr) data; if (dpp != NULL) { DatePtrToVibrant (dp, dpp->month, dpp->day, dpp->year); } } static Pointer DatePageToDatePtr (DialoG d) { DatePtr dp; DatePagePtr dpp; dp = NULL; dpp = (DatePagePtr) GetObjectExtra (d); if (dpp != NULL) { dp = VibrantToDatePtr (dpp->month, dpp->day, dpp->year); } return (Pointer) dp; } extern DialoG CreateDateDialog (GrouP prnt, CharPtr title) { DatePagePtr dpp; GrouP f; GrouP m; GrouP p; GrouP s; p = HiddenGroup (prnt, 1, 0, NULL); SetGroupSpacing (p, 10, 10); dpp = (DatePagePtr) MemNew (sizeof (DatePage)); if (dpp) { SetObjectExtra (p, dpp, StdCleanupExtraProc); dpp->dialog = (DialoG) p; dpp->todialog = DatePtrToDatePage; dpp->fromdialog = DatePageToDatePtr; dpp->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); */ f = HiddenGroup (m, -6, 0, NULL); StaticPrompt (f, "Month", 0, popupMenuHeight, programFont, 'l'); dpp->month = PopupList (f, TRUE, NULL); InitEnumPopup (dpp->month, months_alist, NULL); SetValue (dpp->month, 1); StaticPrompt (f, "Day", 0, dialogTextHeight, programFont, 'l'); dpp->day = DialogText (f, "", 4, NULL); StaticPrompt (f, "Year", 0, dialogTextHeight, programFont, 'l'); dpp->year = DialogText (f, "", 6, NULL); } return (DialoG) p; } typedef struct featcit { DIALOG_MESSAGE_BLOCK DoC citdoc; ValNodePtr pubset; } FeatCitPage, PNTR FeatCitPagePtr; static ParData cofParFmt = {FALSE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData cofColFmt = {0, 0, 0, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}; static ParData cofeParFmt = {TRUE, FALSE, FALSE, FALSE, FALSE, 0, 0}; static ColData cofeColFmt = {0, 0, 0, 0, NULL, 'l', TRUE, FALSE, FALSE, FALSE, TRUE}; static Uint1 diamondSym [] = { 0x00, 0x10, 0x38, 0x7C, 0x38, 0x10, 0x00, 0x00 }; static void DrawCitOnFeat (DoC d, RectPtr r, Int2 item, Int2 firstLine) { Int2 lineHeight; RecT rct; if (d != NULL && r != NULL && item > 0 && firstLine == 0) { if (item == 1) return; /* citonfeattxt or citonfeathdr explanatory text */ GetItemParams (d, item, NULL, NULL, NULL, &lineHeight, NULL); rct = *r; rct.left += 1; rct.right = rct.left + 7; rct.top += (lineHeight - 7) / 2; rct.bottom = rct.top + 7; CopyBits (&rct, diamondSym); /* x = r->left + 1; y = r->top + lineHeight / 2; MoveTo (x, y); LineTo (x + 5, y); */ } } static int LIBCALLBACK CompareStrings (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1; CharPtr str2; if (ptr1 != NULL && ptr2 != NULL) { str1 = *((CharPtr PNTR) ptr1); str2 = *((CharPtr PNTR) ptr2); if (str1 != NULL && str2 != NULL) { return StringICmp (str1, str2); } else { return 0; } } else { return 0; } } static CharPtr citonfeattxt = "Press 'Edit Citations' to attach publications to this feature. \ Publications must first be added to the record. For biological \ justification, and not to credit the sequencer, create publication \ with the 'Cites a feature on the sequence' scope.\n"; static CharPtr citonfeathdr = "Press 'Edit Citations' to change publications.\n\n"; static void PubsetPtrToFeatCitPage (DialoG d, Pointer data) { Int2 count; FeatCitPagePtr fpp; Int2 i; Char label [128]; ObjMgrPtr omp; ObjMgrTypePtr omtp; ValNodePtr ppr; ValNodePtr psp; RecT r; CharPtr PNTR strs; fpp = (FeatCitPagePtr) GetObjectExtra (d); psp = (ValNodePtr) data; if (fpp != NULL) { Reset (fpp->citdoc); fpp->pubset = PubSetFree (fpp->pubset); fpp->pubset = AsnIoMemCopy (data, (AsnReadFunc) PubSetAsnRead, (AsnWriteFunc) PubSetAsnWrite); SetDocAutoAdjust (fpp->citdoc, FALSE); ObjectRect (fpp->citdoc, &r); InsetRect (&r, 4, 4); cofColFmt.pixWidth = r.right - r.left; cofColFmt.pixInset = 10; omp = ObjMgrGet (); if (omp == NULL) return; omtp = ObjMgrTypeFind (omp, OBJ_SEQFEAT_CIT, NULL, NULL); if (omtp == NULL || omtp->labelfunc == NULL) return; if (psp != NULL && psp->data.ptrvalue != NULL) { count = 0; for (ppr = psp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { count++; } if (count > 0) { strs = MemNew (sizeof (CharPtr) * (size_t) (count + 1)); if (strs != NULL) { i = 0; for (ppr = psp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { (*(omtp->labelfunc)) (ppr, label, 127, OM_LABEL_CONTENT); strs [i] = StringSave (label); i++; } HeapSort (strs, count, sizeof (CharPtr), CompareStrings); AppendText (fpp->citdoc, citonfeathdr, &cofParFmt, NULL, programFont); for (i = 0; i < count; i++) { AppendText (fpp->citdoc, strs [i], &cofParFmt, &cofColFmt, programFont); } for (i = 0; i < count; i++) { strs [i] = MemFree (strs [i]); } MemFree (strs); } else { AppendText (fpp->citdoc, citonfeattxt, &cofParFmt, NULL, programFont); } } } else { AppendText (fpp->citdoc, citonfeattxt, &cofParFmt, NULL, programFont); } SetDocShade (fpp->citdoc, DrawCitOnFeat, NULL, NULL, NULL); UpdateDocument (fpp->citdoc, 0, 0); } } static Pointer FeatCitPageToPubsetPtr (DialoG d) { FeatCitPagePtr fpp; ValNodePtr psp; psp = NULL; fpp = (FeatCitPagePtr) GetObjectExtra (d); if (fpp != NULL) { psp = AsnIoMemCopy (fpp->pubset, (AsnReadFunc) PubSetAsnRead, (AsnWriteFunc) PubSetAsnWrite); } return (Pointer) psp; } static void CleanupCitOnFeatProc (GraphiC g, VoidPtr data) { FeatCitPagePtr fpp; fpp = (FeatCitPagePtr) data; if (fpp != NULL) { PubSetFree (fpp->pubset); } MemFree (data); } static DialoG CreateCitOnFeatDialog (GrouP h, CharPtr title) { FeatCitPagePtr fpp; Int2 lineHeight; GrouP m; GrouP p; GrouP s; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); fpp = (FeatCitPagePtr) MemNew (sizeof (FeatCitPage)); if (fpp != NULL) { SetObjectExtra (p, fpp, CleanupCitOnFeatProc); fpp->dialog = (DialoG) p; fpp->todialog = PubsetPtrToFeatCitPage; fpp->fromdialog = FeatCitPageToPubsetPtr; fpp->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); */ SelectFont (programFont); lineHeight = LineHeight (); SelectFont (systemFont); cofParFmt.minHeight = lineHeight + 2; StaticPrompt (m, "Citations on Feature", 25 * stdCharWidth, 0, programFont, 'c'); fpp->citdoc = DocumentPanel (m, 25 * stdCharWidth, 5 * cofParFmt.minHeight); SetObjectExtra (fpp->citdoc, fpp, NULL); SetDocAutoAdjust (fpp->citdoc, FALSE); fpp->pubset = NULL; } return (DialoG) p; } typedef struct citlist { Uint2 entityID; Uint2 itemID; Uint2 itemtype; CharPtr label; } CitListData, PNTR CitListDataPtr; typedef struct featcitedit { FeatureFormPtr ffp; DoC allcitdoc; Int2 clickedItem; Int2 clickedRow; Int2 numitems; Int2 lineheight; Int2 index; BoolPtr chosen; ValNodePtr citlist; ValNodePtr psp; ObjMgrPtr omp; } FeatCitEdit, PNTR FeatCitEditPtr; static void CleanupFeatCitForm (GraphiC g, VoidPtr data) { FeatCitEditPtr fcep; fcep = (FeatCitEditPtr) data; if (fcep != NULL) { MemFree (fcep->chosen); } MemFree (data); } static void DrawFeatCit (DoC d, RectPtr r, Int2 item, Int2 firstLine) { FeatCitEditPtr fcep; RecT rct; fcep = (FeatCitEditPtr) GetObjectExtra (d); if (fcep != NULL && r != NULL && item > 0 && firstLine == 0) { rct = *r; rct.left += 1; rct.right = rct.left + fcep->lineheight; rct.bottom = rct.top + (rct.right - rct.left); FrameRect (&rct); if (item > 0 && item <= fcep->numitems) { if (fcep->chosen != NULL && fcep->chosen [item - 1]) { MoveTo (rct.left, rct.top); LineTo (rct.right - 1, rct.bottom - 1); MoveTo (rct.left, rct.bottom - 1); LineTo (rct.right - 1, rct.top); } } } } static void ClickFeatCit (DoC d, PoinT pt) { } static void ReleaseFeatCit (DoC d, PoinT pt) { Int2 col; FeatCitEditPtr fcep; Int2 item; RecT rct; Int2 row; fcep = (FeatCitEditPtr) GetObjectExtra (d); if (fcep != NULL && fcep->chosen != NULL) { MapDocPoint (d, pt, &item, &row, &col, &rct); rct.left += 1; rct.right = rct.left + fcep->lineheight; rct.bottom = rct.top + (rct.right - rct.left); if (row == 1 && col == 1 && item > 0 && item <= fcep->numitems && PtInRect (pt, &rct)) { if (fcep->chosen [item - 1]) { fcep->chosen [item - 1] = FALSE; } else { fcep->chosen [item - 1] = TRUE; } InsetRect (&rct, -1, -1); InvalRect (&rct); Update (); } } } static Boolean GatherAllCits (GatherContextPtr gcp) { CitListDataPtr cldp; FeatCitEditPtr fcep; Char label [128]; ObjMgrTypePtr omtp; PubdescPtr pdp; ValNodePtr sdp; SeqFeatPtr sfp; ValNodePtr vnp; if (gcp == NULL) return TRUE; fcep = (FeatCitEditPtr) gcp->userdata; if (fcep == NULL) return TRUE; label [0] = '\0'; pdp = NULL; if (gcp->thistype == OBJ_SEQDESC) { sdp = (ValNodePtr) gcp->thisitem; if (sdp == NULL || sdp->choice != Seq_descr_pub) return TRUE; pdp = sdp->data.ptrvalue; } else if (gcp->thistype == OBJ_SEQFEAT) { sfp = (SeqFeatPtr) gcp->thisitem; if (sfp == NULL || sfp->data.choice != SEQFEAT_PUB) return TRUE; pdp = sfp->data.value.ptrvalue; } else return TRUE; if (pdp == NULL) return TRUE; omtp = ObjMgrTypeFind (fcep->omp, gcp->thistype, NULL, NULL); if (omtp == NULL || omtp->labelfunc == NULL) return TRUE; (*(omtp->labelfunc)) (gcp->thisitem, label, 127, OM_LABEL_CONTENT); cldp = (CitListDataPtr) MemNew (sizeof (CitListData)); if (cldp != NULL) { vnp = ValNodeNew (fcep->citlist); if (fcep->citlist == NULL) { fcep->citlist = vnp; } if (vnp != NULL) { vnp->data.ptrvalue = cldp; cldp->entityID = gcp->entityID; cldp->itemID = gcp->itemID; cldp->itemtype = gcp->thistype; cldp->label = StringSave (label); (fcep->numitems)++; } else { MemFree (cldp); return TRUE; } } return TRUE; } static Boolean PrintCitOnFeatItem (GatherContextPtr gcp) { CharPtr PNTR rsultp; ValNodePtr sdp; SeqFeatPtr sfp; Boolean success; rsultp = (CharPtr PNTR) gcp->userdata; if (rsultp != NULL) { success = FALSE; switch (gcp->thistype) { case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; if (sdp->data.ptrvalue != NULL) { success = StdFormatPrint ((Pointer) sdp, (AsnWriteFunc) SeqDescAsnWrite, "StdSeqDesc", spop); } else { *rsultp = StringSave ("Empty Descriptor\n"); success = TRUE; } break; case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; if (sfp != NULL && (sfp->data.choice == 10 || sfp->data.value.ptrvalue != NULL)) { success = StdFormatPrint ((Pointer) sfp, (AsnWriteFunc) SeqFeatAsnWrite, "StdSeqFeat", spop); } else { *rsultp = StringSave ("Empty Feature\n"); success = TRUE; } break; default : break; } if (success) { if (spop->ptr != NULL && *((CharPtr) (spop->ptr)) != '\0') { *rsultp = spop->ptr; spop->ptr = NULL; } else { *rsultp = StringSave ("Empty Data\n"); } } else { *rsultp = StringSave ("Data Failure\n"); } } return TRUE; } static CharPtr CitOnFeatPrintProc (DoC doc, Int2 item, Pointer data) { unsigned int entityID; unsigned int itemID; unsigned int itemtype; CharPtr rsult; CharPtr str; rsult = NULL; if (data != NULL) { str = (CharPtr) data; if (sscanf (str, "%u %u %u", &entityID, &itemID, &itemtype) == 3) { GatherItem ((Uint2) entityID, (Uint2) itemID, (Uint2) itemtype, (Pointer) &rsult, PrintCitOnFeatItem); } } else { rsult = StringSave ("Null Data\n"); } return rsult; } static int LIBCALLBACK CompareCitList (VoidPtr ptr1, VoidPtr ptr2) { CitListDataPtr cldp1; CitListDataPtr cldp2; CharPtr str1; CharPtr str2; if (ptr1 != NULL && ptr2 != NULL) { cldp1 = (CitListDataPtr) ptr1; cldp2 = (CitListDataPtr) ptr2; if (cldp1 != NULL && cldp2 != NULL) { str1 = cldp1->label; str2 = cldp2->label; if (str1 != NULL && str2 != NULL) { return StringICmp (str1, str2); } else { return 0; } } else { return 0; } } else { return 0; } } static Boolean MakeMinimalCitOnFeatItem (GatherContextPtr gcp) { PubdescPtr pdp; ValNodePtr ppr; ValNodePtr sdp; SeqFeatPtr sfp; ValNodePtr vnp; ValNodePtr PNTR vnpp; vnpp = (ValNodePtr PNTR) gcp->userdata; if (vnpp != NULL) { pdp = NULL; switch (gcp->thistype) { case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; if (sdp->data.ptrvalue != NULL) { pdp = (PubdescPtr) sdp->data.ptrvalue; } break; case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; if (sfp != NULL && (sfp->data.choice == 10 || sfp->data.value.ptrvalue != NULL)) { pdp = (PubdescPtr) sfp->data.value.ptrvalue; } break; default : break; } if (pdp != NULL) { ppr = NULL; vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->choice = PUB_Equiv; vnp->data.ptrvalue = pdp->pub; ppr = MinimizePub (vnp); ValNodeFree (vnp); } vnp = ValNodeNew (*vnpp); if (*vnpp == NULL) { *vnpp = vnp; } if (vnp != NULL) { vnp->choice = PUB_Equiv; vnp->data.ptrvalue = ppr; } } } return TRUE; } static void AcceptFeatCit (ButtoN b) { Pointer data; unsigned int entityID; FeatCitEditPtr fcep; FeatureFormPtr ffp; Int2 i; unsigned int itemID; unsigned int itemtype; Int2 numItems; ValNodePtr ppr; ValNodePtr psp; CharPtr str; fcep = (FeatCitEditPtr) GetObjectExtra (b); if (fcep != NULL && fcep->chosen != NULL) { psp = NULL; ppr = NULL; GetDocParams (fcep->allcitdoc, &numItems, NULL); for (i = 1; i <= numItems; i++) { if (fcep->chosen [i - 1]) { GetItemParams (fcep->allcitdoc, i, NULL, NULL, NULL, NULL, &data); if (data != NULL) { str = (CharPtr) data; if (sscanf (str, "%u %u %u", &entityID, &itemID, &itemtype) == 3) { GatherItem ((Uint2) entityID, (Uint2) itemID, (Uint2) itemtype, (Pointer) &ppr, MakeMinimalCitOnFeatItem); } } } } ffp = (FeatureFormPtr) fcep->ffp; if (ffp != NULL) { if (ppr != NULL) { psp = ValNodeNew (NULL); if (psp != NULL) { psp->choice = 1; psp->data.ptrvalue = ppr; PointerToDialog (ffp->featcits, (Pointer) psp); } PubSetFree (psp); } else { PointerToDialog (ffp->featcits, NULL); } } } Remove (ParentWindow (b)); } static Boolean MatchMinimalCits (GatherContextPtr gcp) { FeatCitEditPtr fcep; PubdescPtr pdp; ValNodePtr ppr; ValNodePtr sdp; SeqFeatPtr sfp; ValNodePtr vnp; fcep = (FeatCitEditPtr) gcp->userdata; if (fcep != NULL) { pdp = NULL; switch (gcp->thistype) { case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; if (sdp->data.ptrvalue != NULL) { pdp = (PubdescPtr) sdp->data.ptrvalue; } break; case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; if (sfp != NULL && (sfp->data.choice == 10 || sfp->data.value.ptrvalue != NULL)) { pdp = (PubdescPtr) sfp->data.value.ptrvalue; } break; default : break; } if (pdp != NULL && fcep->psp != NULL) { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->choice = PUB_Equiv; vnp->data.ptrvalue = pdp->pub; for (ppr = fcep->psp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { if (PubLabelMatch (vnp, ppr) == 0) { fcep->chosen [fcep->index] = TRUE; } } ValNodeFree (vnp); } } } return TRUE; } static void EditFeatCitsProc (ButtoN b) { ButtoN btn; GrouP c; CitListDataPtr cldp; CitListDataPtr cldpp; Int2 count; FeatCitEditPtr fcep; FeatureFormPtr ffp; GatherScope gs; Int2 i; Int2 j; Char last [128]; CharPtr ptr; RecT r; Char str [34]; ValNodePtr vnp; WindoW w; ffp = (FeatureFormPtr) GetObjectExtra (b); if (ffp != NULL) { fcep = (FeatCitEditPtr) MemNew (sizeof (FeatCitEdit)); if (fcep != NULL) { fcep->ffp = ffp; fcep->omp = ObjMgrGet (); fcep->numitems = 0; WatchCursor (); Update (); w = MovableModalWindow (-50, -33, -10, -10, "Citations", NULL); SetObjectExtra (w, fcep, CleanupFeatCitForm); fcep->allcitdoc = DocumentPanel (w, 25 * stdCharWidth, 15 * stdLineHeight); SetObjectExtra (fcep->allcitdoc, fcep, NULL); SetDocProcs (fcep->allcitdoc, ClickFeatCit, NULL, ReleaseFeatCit, NULL); SetDocShade (fcep->allcitdoc, DrawFeatCit, NULL, NULL, NULL); c = HiddenGroup (w, 4, 0, NULL); SetGroupSpacing (c, 10, 3); btn = PushButton (c, "Accept", AcceptFeatCit); SetObjectExtra (btn, fcep, NULL); PushButton (c, "Cancel", StdCancelButtonProc); AlignObjects (ALIGN_CENTER, (HANDLE) fcep->allcitdoc, (HANDLE) c, NULL); RealizeWindow (w); SelectFont (programFont); fcep->lineheight = LineHeight (); SelectFont (systemFont); MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); MemSet ((Pointer) (gs.ignore), (int) (TRUE), (size_t) (OBJ_MAX * sizeof (Boolean))); gs.ignore [OBJ_SEQDESC] = FALSE; gs.ignore [OBJ_SEQANNOT] = FALSE; gs.ignore [OBJ_SEQFEAT] = FALSE; gs.seglevels = 1; GatherEntity (ffp->input_entityID, (Pointer) fcep, GatherAllCits, &gs); count = fcep->numitems; cldpp = (CitListDataPtr) MemNew (sizeof (CitListData) * (size_t) (count + 1)); if (cldpp != NULL) { for (i = 0, vnp = fcep->citlist; i < count && vnp != NULL; i++, vnp = vnp->next) { cldp = vnp->data.ptrvalue; if (cldp != NULL) { cldpp [i] = *cldp; cldp->label = NULL; } } fcep->citlist = ValNodeFreeData (fcep->citlist); HeapSort (cldpp, count, sizeof (CitListData), CompareCitList); last [0] = '\0'; ObjectRect (fcep->allcitdoc, &r); InsetRect (&r, 4, 4); cofeColFmt.pixWidth = r.right - r.left; cofeColFmt.pixInset = 20; fcep->numitems = 0; fcep->chosen = MemNew (sizeof (Boolean) * (size_t) (count + 1)); fcep->psp = DialogToPointer (ffp->featcits); for (i = 0, j = 0; i < count; i++) { cldp = &(cldpp [i]); if (cldp != NULL) { if (last == NULL || StringCmp (cldp->label, last) != 0) { sprintf (str, "%d %d %d", (int) cldp->entityID, (int) cldp->itemID, (int) cldp->itemtype); ptr = StringSave (str); (fcep->numitems)++; AppendItem (fcep->allcitdoc, CitOnFeatPrintProc, (Pointer) ptr, TRUE, 5, &cofeParFmt, &cofeColFmt, programFont); if (fcep->chosen != NULL) { fcep->index = j; GatherItem ((Uint2) cldp->entityID, (Uint2) cldp->itemID, (Uint2) cldp->itemtype, (Pointer) fcep, MatchMinimalCits); } j++; } StringNCpy_0 (last, cldp->label, sizeof (last)); cldpp [i].label = MemFree (cldpp [i].label); } } PubSetFree (fcep->psp); } MemFree (cldpp); Show (w); Select (w); ArrowCursor (); Update (); } } } static void ChangeGenePopupOrList (Handle gene) { FeatureFormPtr ffp; Int2 val; ffp = (FeatureFormPtr) GetObjectExtra (gene); if (ffp != NULL) { val = GetValue (ffp->gene); if (val == 1) { SafeHide (ffp->newGeneGrp); SafeHide (ffp->editGeneBtn); } else if (val == 2) { SafeHide (ffp->editGeneBtn); SafeShow (ffp->newGeneGrp); } else { SafeHide (ffp->newGeneGrp); SafeShow (ffp->editGeneBtn); } } } static void ChangeSubGroup (VoidPtr data, Int2 newval, Int2 oldval) { FeatureFormPtr ffp; ffp = (FeatureFormPtr) data; if (ffp != NULL) { if (ffp->commonPage >= 0 && ffp->commonPage <= 4) { SafeHide (ffp->commonSubGrp [ffp->commonPage]); } ffp->commonPage = newval; if (ffp->commonPage >= 0 && ffp->commonPage <= 4) { SafeShow (ffp->commonSubGrp [ffp->commonPage]); } } } typedef struct fieldpage { DIALOG_MESSAGE_BLOCK Int2 numfields; CharPtr PNTR fields; TexT PNTR values; ButtoN PNTR boxes; } FieldPage, PNTR FieldPagePtr; static Boolean ShouldBeAGBQual (Int2 qual, Boolean allowProductGBQual) { if (qual < 0) return FALSE; if (allowProductGBQual && qual == GBQUAL_product) return TRUE; if (qual == GBQUAL_citation || qual == GBQUAL_db_xref || qual == GBQUAL_evidence || qual == GBQUAL_exception || qual == GBQUAL_gene || qual == GBQUAL_label || qual == GBQUAL_map || qual == GBQUAL_note || qual == GBQUAL_partial || qual == GBQUAL_product || qual == GBQUAL_pseudo) { return FALSE; } if (Nlm_GetAppProperty ("SequinUseEMBLFeatures") == NULL) { if (qual == GBQUAL_usedin) { return FALSE; } } return TRUE; } static void GBQualPtrToFieldPage (DialoG d, Pointer data) { Char empty [4]; FieldPagePtr fpf; Int2 i; GBQualPtr list; fpf = (FieldPagePtr) GetObjectExtra (d); list = (GBQualPtr) data; if (fpf != NULL) { while (list != NULL) { if (list->qual != NULL && list->val != NULL) { for (i = 0; i < fpf->numfields; i++) { if (StringICmp (list->qual, fpf->fields [i]) == 0) { if (fpf->values [i] != NULL) { if (*(list->val) == '\0') { empty [0] = '"'; empty [1] = '"'; empty [2] = '\0'; SetTitle (fpf->values [i], empty); } else { SetTitle (fpf->values [i], list->val); } } else if (fpf->boxes [i] != NULL) { SetStatus (fpf->boxes [i], TRUE); } } } } list = list->next; } } } extern void SeqFeatPtrToFieldPage (DialoG d, SeqFeatPtr sfp); extern void SeqFeatPtrToFieldPage (DialoG d, SeqFeatPtr sfp) { /* FieldPagePtr fpf; Int2 i; fpf = (FieldPagePtr) GetObjectExtra (d); if (fpf != NULL && sfp != NULL) { for (i = 0; i < fpf->numfields; i++) { if (StringICmp ("exception", fpf->fields [i]) == 0) { if (fpf->values [i] != NULL) { if (sfp->except_text == NULL || *(sfp->except_text) == '\0') { SetTitle (fpf->values [i], ""); } else { SetTitle (fpf->values [i], sfp->except_text); } } } else if (StringICmp ("pseudo", fpf->fields [i]) == 0) { if (fpf->boxes [i] != NULL && (! GetStatus (fpf->boxes [i]))) { SetStatus (fpf->boxes [i], sfp->pseudo); } } } } */ } static Pointer FieldPageToGBQualPtr (DialoG d) { FieldPagePtr fpf; GBQualPtr gbq; GBQualPtr gbqlast; GBQualPtr head; Int2 i; head = NULL; fpf = (FieldPagePtr) GetObjectExtra (d); if (fpf != NULL) { gbq = NULL; gbqlast = NULL; for (i = 0; i < fpf->numfields; i++) { if (fpf->fields [i] == NULL || StringHasNoText (fpf->fields [i]) || (fpf->values [i] == NULL && fpf->boxes [i] ==NULL) || (fpf->values [i] != NULL && TextHasNoText (fpf->values [i]))) { } else if (fpf->boxes [i] != NULL && (! GetStatus (fpf->boxes [i]))) { } else { gbq = GBQualNew (); if (gbqlast == NULL) { head = gbq; } else { gbqlast->next = gbq; } gbqlast = gbq; if (gbq != NULL) { gbq->qual = StringSave (fpf->fields [i]); if (fpf->values [i] != NULL) { gbq->val = SaveStringFromText (fpf->values [i]); } else { gbq->val = StringSave (""); } } } } } return (Pointer) head; } static void CleanupFieldsPage (GraphiC g, VoidPtr data) { FieldPagePtr fpf; Int2 i; fpf = (FieldPagePtr) data; if (fpf != NULL) { if (fpf->fields != NULL) { for (i = 0; i < fpf->numfields; i++) { MemFree (fpf->fields [i]); } } MemFree (fpf->fields); MemFree (fpf->values); MemFree (fpf->boxes); } MemFree (data); } #define LEGAL_FEATURE 1 #define ILLEGAL_FEATURE 2 extern DialoG CreateImportFields (GrouP h, CharPtr name, SeqFeatPtr sfp, Boolean allowProductGBQual) { FieldPagePtr fpf; GrouP g; GBQualPtr gbq; Boolean hasillegal; Int2 i; Int2 index; Int2 j; Int2 max; Int2 num; GrouP p; PrompT ppt; Int2 qual; Int2 seen [ParFlat_TOTAL_GBQUAL]; SematicFeatPtr sefp; Char str [64]; Int2 wid; p = HiddenGroup (h, 1, 0, NULL); fpf = (FieldPagePtr) MemNew (sizeof (FieldPage)); if (fpf != NULL) { SetObjectExtra (p, fpf, CleanupFieldsPage); fpf->dialog = (DialoG) p; fpf->todialog = GBQualPtrToFieldPage; fpf->fromdialog = FieldPageToGBQualPtr; fpf->testdialog = NULL; gbq = NULL; if (sfp != NULL) { gbq = sfp->qual; } j = 0; hasillegal = FALSE; for (i = 0; i < ParFlat_TOTAL_GBQUAL; i++) { seen [i] = 0; } num = 0; if (name != NULL) { index = GBFeatKeyNameValid (&name, FALSE); if (index >= 0) { sefp = &(ParFlat_GBFeat [index]); for (i = 0; i < sefp->mand_num; i++) { qual = sefp->mand_qual [i]; if (qual > -1 && ShouldBeAGBQual (qual, allowProductGBQual)) { seen [qual] = LEGAL_FEATURE; } } for (i = 0; i < sefp->opt_num; i++) { qual = sefp->opt_qual [i]; if (qual > -1 && ShouldBeAGBQual (qual, allowProductGBQual)) { seen [qual] = LEGAL_FEATURE; } } } } else if (sfp != NULL && sfp->data.choice == SEQFEAT_CDREGION) { /* seen [GBQUAL_exception] = LEGAL_FEATURE; seen [GBQUAL_pseudo] = LEGAL_FEATURE; */ } while (gbq != NULL) { qual = GBQualNameValid (gbq->qual); if (qual > -1) { if (seen [qual] == 0) { seen [qual] = ILLEGAL_FEATURE; hasillegal = TRUE; } } gbq = gbq->next; } SelectFont (programFont); max = 0; for (i = 0; i < ParFlat_TOTAL_GBQUAL; i++) { if (seen [i] > 0) { num++; if (seen [i] == LEGAL_FEATURE) { StringNCpy_0 (str, ParFlat_GBQual_names [i].name, sizeof (str)); wid = StringWidth (str) + 2; } else { str [0] = '\0'; if (name != NULL) { StringCpy (str, "*"); } StringNCat (str, ParFlat_GBQual_names [i].name, sizeof (str) - 2); wid = StringWidth (str) + 2; } if (wid > max) { max = wid; } } } SelectFont (systemFont); fpf->numfields = num; fpf->fields = MemNew (sizeof (CharPtr) * (num + 1)); fpf->values = MemNew (sizeof (TexT) * (num + 1)); fpf->boxes = MemNew (sizeof (ButtoN) * (num + 1)); g = HiddenGroup (p, 2, 0, NULL); j = 0; for (i = 0; i < ParFlat_TOTAL_GBQUAL; i++) { if (seen [i] == LEGAL_FEATURE) { fpf->fields [j] = StringSave (ParFlat_GBQual_names [i].name); ppt = StaticPrompt (g, fpf->fields [j], max, dialogTextHeight, programFont, 'l'); if (ParFlat_GBQual_names [i].gbclass != Class_none) { fpf->values [j] = DialogText (g, "", 20, NULL); } else { fpf->boxes [j] = CheckBox (g, "", NULL); AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt, (HANDLE) fpf->boxes [j], NULL); } j++; } } if (hasillegal && name != NULL) { StaticPrompt (p, "Illegal Qualifiers", 0, 0, programFont, 'c'); } g = HiddenGroup (p, 2, 0, NULL); for (i = 0; i < ParFlat_TOTAL_GBQUAL; i++) { if (seen [i] == ILLEGAL_FEATURE) { fpf->fields [j] = StringSave (ParFlat_GBQual_names [i].name); str [0] = '\0'; if (name != NULL) { StringCpy (str, "*"); } StringNCat (str, fpf->fields [j], sizeof (str) - 2); ppt = StaticPrompt (g, str, max, dialogTextHeight, programFont, 'l'); if (ParFlat_GBQual_names [i].gbclass != Class_none) { fpf->values [j] = DialogText (g, "", 20, NULL); } else { fpf->boxes [j] = CheckBox (g, "", NULL); AlignObjects (ALIGN_MIDDLE, (HANDLE) ppt, (HANDLE) fpf->boxes [j], NULL); } j++; } } if (j == 0) { StaticPrompt (p, "See Attributes page to set legal qualifiers for this feature.", 0, 0, programFont, 'c'); } } return (DialoG) p; } static void ChangeCannedMessage (PopuP p) { FeatureFormPtr ffp; Int2 val; ffp = (FeatureFormPtr) GetObjectExtra (p); if (ffp == NULL) return; val = GetValue (p); switch (val) { case 1 : if (Message (MSG_YN, "Clear the explanation field?") == ANS_YES) { SetTitle (ffp->exceptText, ""); if (Message (MSG_YN, "Clear the exception flag?") == ANS_YES) { SetStatus (ffp->exception, FALSE); } } break; case 2 : SetTitle (ffp->exceptText, "RNA editing"); SetStatus (ffp->exception, TRUE); break; case 3 : SetTitle (ffp->exceptText, "reasons given in citation"); SetStatus (ffp->exception, TRUE); break; case 4 : SetTitle (ffp->exceptText, "ribosomal slippage"); SetStatus (ffp->exception, TRUE); break; case 5 : SetTitle (ffp->exceptText, "trans splicing"); SetStatus (ffp->exception, TRUE); break; case 6 : SetTitle (ffp->exceptText, "artificial frameshift"); SetStatus (ffp->exception, TRUE); default : break; } } static CharPtr crossRefWarn = "A gene mapped by cross-reference does not extend the range\n\ of the indicated gene feature. Overlap is the usual case, and\n\ it does extend the selected gene."; static CharPtr suppressWarn = "This will suppress display of a gene qualifier even though\n\ there is a gene feature that overlaps this one."; static void GeneXrefWarn (GrouP g) { Int2 val; val = GetValue (g); if (val == 2) { Message (MSG_OK, "%s", crossRefWarn); } else if (val == 3) { Message (MSG_OK, "%s", suppressWarn); } } static CharPtr commonRadioFormTabs [] = { "General", "Comment", "Citations", "Cross-Refs", NULL, NULL }; static CharPtr commonNoCitFormTabs [] = { "General", "Comment", "Cross-Refs", NULL, NULL }; extern void Nlm_LaunchGeneFeatEd (ButtoN b); extern GrouP CreateCommonFeatureGroupEx (GrouP h, FeatureFormPtr ffp, SeqFeatPtr sfp, Boolean hasGeneControl, Boolean hasCitationTab, Boolean hasGeneSuppress) { ButtoN b; GrouP c; PopuP canned; Boolean cdsQuals; GrouP f; GrouP g; Boolean hasQuals; Boolean indexerVersion; Char just; GrouP k; GrouP m; GrouP p; Int2 page; ButtoN pseudo = NULL; GrouP q; GrouP r; GrouP t; GrouP v; GrouP x; GrouP y; c = NULL; if (ffp != NULL) { hasQuals = FALSE; cdsQuals = FALSE; if (ffp->gbquals == NULL && sfp != NULL && sfp->qual != NULL) { hasQuals = TRUE; /* if (GetAppProperty ("InternalNcbiSequin") != NULL) { if (sfp->data.choice == SEQFEAT_CDREGION) { cdsQuals = TRUE; } } */ } m = HiddenGroup (h, -1, 0, NULL); SetGroupSpacing (m, 10, 10); ffp->commonPage = 0; if (cdsQuals) { } else if (hasQuals) { commonRadioFormTabs [4] = "Qualifiers"; commonNoCitFormTabs [3] = "Qualifiers"; } if (hasCitationTab) { ffp->commonRadio = CreateFolderTabs (m, commonRadioFormTabs, ffp->commonPage, 0, 0, PROGRAM_FOLDER_TAB, ChangeSubGroup, (Pointer) ffp); } else { ffp->commonRadio = CreateFolderTabs (m, commonNoCitFormTabs, ffp->commonPage, 0, 0, PROGRAM_FOLDER_TAB, ChangeSubGroup, (Pointer) ffp); } commonRadioFormTabs [4] = NULL; commonNoCitFormTabs [3] = NULL; p = HiddenGroup (m, 0, 0, NULL); c = HiddenGroup (p, -1, 0, NULL); SetGroupSpacing (c, 10, 10); f = HiddenGroup (c, -1, 0, NULL); r = HiddenGroup (f, 7, 0, NULL); StaticPrompt (r, "Flags", 0, popupMenuHeight, programFont, 'l'); ffp->partial = CheckBox (r, "Partial", NULL); indexerVersion = (Boolean) (GetAppProperty ("InternalNcbiSequin") != NULL); if (! indexerVersion) { Disable (ffp->partial); } if (ffp->pseudo == NULL) { ffp->pseudo = CheckBox (r, "Pseudo", NULL); pseudo = ffp->pseudo; /* allows pseudo control on earlier feature-specific page */ } StaticPrompt (r, "Evidence", 0, popupMenuHeight, programFont, 'l'); ffp->evidence = PopupList (r, TRUE, NULL); PopupItem (ffp->evidence, " "); PopupItem (ffp->evidence, "Experimental"); PopupItem (ffp->evidence, "Non-Experimental"); AlignObjects (ALIGN_MIDDLE, (HANDLE) ffp->partial, (HANDLE) ffp->evidence, (HANDLE) pseudo, NULL); r = HiddenGroup (f, -3, 0, NULL); ffp->exception = CheckBox (r, "Exception", NULL); StaticPrompt (r, "Explanation", 0, dialogTextHeight, programFont, 'l'); ffp->exceptText = DialogText (r, "", 12, NULL); AlignObjects (ALIGN_MIDDLE, (HANDLE) ffp->exception, (HANDLE) ffp->exceptText, NULL); if (ffp->this_subtype == FEATDEF_CDS) { StaticPrompt (r, "Standard explanation", 0, popupMenuHeight, programFont, 'l'); canned = PopupList (r, TRUE, ChangeCannedMessage); SetObjectExtra (canned, (Pointer) ffp, NULL); PopupItem (canned, " "); PopupItem (canned, "RNA editing"); PopupItem (canned, "reasons given in citation"); PopupItem (canned, "ribosomal slippage"); PopupItem (canned, "trans splicing"); PopupItem (canned, "artificial frameshift"); if (sfp != NULL && sfp->excpt) { if (StringICmp (sfp->except_text, "RNA editing") == 0) { SetValue (canned, 2); } else if (StringICmp (sfp->except_text, "reasons given in citation") == 0 || StringICmp (sfp->except_text, "reasons cited in publication") == 0) { SetValue (canned, 3); } else if (StringICmp (sfp->except_text, "ribosomal slippage") == 0) { SetValue (canned, 4); } else if (StringICmp (sfp->except_text, "ribosome slippage") == 0) { SetValue (canned, 4); } else if (StringICmp (sfp->except_text, "trans splicing") == 0) { SetValue (canned, 5); } else if (StringICmp (sfp->except_text, "trans-splicing") == 0) { SetValue (canned, 5); } else if (StringICmp (sfp->except_text, "artificial frameshift") == 0) { SetValue (canned, 6); } } else { SetValue (canned, 1); } } if (cdsQuals) { /* ffp->gbquals = CreateImportFields (c, NULL, sfp, FALSE); */ } g = NULL; k = NULL; ffp->gene = NULL; ffp->genePopup = NULL; ffp->geneList = NULL; ffp->geneNames = NULL; ffp->useGeneXref = NULL; ffp->newGeneGrp = NULL; ffp->geneSymbol = NULL; ffp->geneDesc = NULL; for (page = 0; page < 5; page++) { ffp->commonSubGrp [page] = NULL; } page = 0; if (hasGeneControl) { g = HiddenGroup (c, -2, 0, NULL); StaticPrompt (g, "Gene", 0, popupMenuHeight, programFont, 'l'); v = HiddenGroup (g, 0, 0, NULL); ffp->genePopup = PopupList (v, TRUE, (PupActnProc) ChangeGenePopupOrList); SetObjectExtra (ffp->genePopup, (Pointer) ffp, NULL); PopupItem (ffp->genePopup, " "); PopupItem (ffp->genePopup, "New:"); SetValue (ffp->genePopup, 1); Hide (ffp->genePopup); ffp->geneList = SingleList (v, 6, 3, (LstActnProc) ChangeGenePopupOrList); SetObjectExtra (ffp->geneList, (Pointer) ffp, NULL); ListItem (ffp->geneList, " "); ListItem (ffp->geneList, "New:"); SetValue (ffp->geneList, 1); Hide (ffp->geneList); k = HiddenGroup (c, 3, 0, NULL); StaticPrompt (k, "Map by", 0, stdLineHeight, programFont, 'l'); ffp->useGeneXref = HiddenGroup (k, 3, 0, GeneXrefWarn); SetObjectExtra (ffp->useGeneXref, ffp, NULL); RadioButton (ffp->useGeneXref, "Overlap"); RadioButton (ffp->useGeneXref, "Cross-reference"); RadioButton (ffp->useGeneXref, "Suppress"); SetValue (ffp->useGeneXref, 1); y = HiddenGroup (c, 0, 0, NULL); ffp->newGeneGrp = HiddenGroup (y, 2, 0, NULL); StaticPrompt (ffp->newGeneGrp, "Gene Symbol", 0, dialogTextHeight, programFont, 'l'); ffp->geneSymbol = DialogText (ffp->newGeneGrp, "", 20, NULL); StaticPrompt (ffp->newGeneGrp, "Description", 0, dialogTextHeight, programFont, 'l'); ffp->geneDesc = DialogText (ffp->newGeneGrp, "", 20, NULL); Hide (ffp->newGeneGrp); ffp->editGeneBtn = PushButton (y, "Edit Gene Feature", Nlm_LaunchGeneFeatEd); SetObjectExtra (ffp->editGeneBtn, ffp, NULL); Hide (ffp->editGeneBtn); } else if (hasGeneSuppress) { k = HiddenGroup (c, 3, 0, NULL); StaticPrompt (k, "Map by", 0, stdLineHeight, programFont, 'l'); ffp->useGeneXref = HiddenGroup (k, 3, 0, GeneXrefWarn); SetObjectExtra (ffp->useGeneXref, ffp, NULL); RadioButton (ffp->useGeneXref, "Overlap"); b = RadioButton (ffp->useGeneXref, "Cross-reference"); Disable (b); RadioButton (ffp->useGeneXref, "Suppress"); SetValue (ffp->useGeneXref, 1); y = HiddenGroup (c, 0, 0, NULL); } ffp->commonSubGrp [page] = c; page++; AlignObjects (ALIGN_CENTER, (HANDLE) f, (HANDLE) g, (HANDLE) k, (HANDLE) ffp->newGeneGrp, (HANDLE) ffp->editGeneBtn, NULL); c = HiddenGroup (p, -1, 0, NULL); SetGroupSpacing (c, 10, 10); q = HiddenGroup (c, 0, 2, NULL); StaticPrompt (q, "Comment", 25 * stdCharWidth, 0, programFont, 'c'); if (GetAppProperty ("InternalNcbiSequin") != NULL) { ffp->comment = ScrollText (q, 25, 10, programFont, TRUE, NULL); } else { ffp->comment = ScrollText (q, 25, 5, programFont, TRUE, NULL); } ffp->commonSubGrp [page] = c; Hide (ffp->commonSubGrp [page]); page++; if (hasCitationTab) { c = HiddenGroup (p, -1, 0, NULL); SetGroupSpacing (c, 10, 10); ffp->featcits = CreateCitOnFeatDialog (c, NULL); b = PushButton (c, "Edit Citations", EditFeatCitsProc); SetObjectExtra (b, ffp, NULL); ffp->commonSubGrp [page] = c; AlignObjects (ALIGN_CENTER, (HANDLE) ffp->featcits, (HANDLE) b, NULL); Hide (ffp->commonSubGrp [page]); page++; } c = HiddenGroup (p, -1, 0, NULL); SetGroupSpacing (c, 10, 10); if (GetAppProperty ("ReadOnlyDbTags") == NULL) { just = 'c'; } else { just = 'l'; StaticPrompt (c, "This page is read-only", 15 * stdCharWidth, 0, programFont, 'c'); } t = HiddenGroup (c, 2, 0, NULL); StaticPrompt (t, "Database", 7 * stdCharWidth, 0, programFont, just); StaticPrompt (t, "Object ID", 8 * stdCharWidth, 0, programFont, just); ffp->dbxrefs = CreateDbtagDialog (c, 3, -1, 7, 8); ffp->commonSubGrp [page] = c; Hide (ffp->commonSubGrp [page]); page++; c = HiddenGroup (p, -1, 0, NULL); SetGroupSpacing (c, 10, 10); x = NULL; /* z = NULL; */ if (hasQuals && ffp->gbquals == NULL) { x = HiddenGroup (c, -1, 0, NULL); /* 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'); ffp->gbquals = CreateQualsDialog (x, 5, -1, 7, 10); */ ffp->gbquals = CreateImportFields (x, NULL, sfp, FALSE); } ffp->commonSubGrp [page] = c; Hide (ffp->commonSubGrp [page]); page++; AlignObjects (ALIGN_CENTER, (HANDLE) ffp->commonRadio, (HANDLE) ffp->commonSubGrp [0], (HANDLE) ffp->commonSubGrp [1], (HANDLE) ffp->commonSubGrp [2], (HANDLE) ffp->commonSubGrp [3], (HANDLE) ffp->commonSubGrp [4], (HANDLE) ffp->gbquals, NULL); } return c; } extern GrouP CreateCommonFeatureGroup (GrouP h, FeatureFormPtr ffp, SeqFeatPtr sfp, Boolean hasGeneControl, Boolean hasCitationTab) { return CreateCommonFeatureGroupEx (h, ffp, sfp, hasGeneControl, hasCitationTab, FALSE); } static Boolean DlgutilFindBspItem (GatherContextPtr gcp) { BioseqPtr PNTR bspp; bspp = (BioseqPtr PNTR) gcp->userdata; if (bspp != NULL && gcp->thistype == OBJ_BIOSEQ) { *bspp = (BioseqPtr) gcp->thisitem; } return TRUE; } extern void SetNewFeatureDefaultInterval (FeatureFormPtr ffp) { BioseqPtr bsp; SelStructPtr sel; SeqIntPtr sip; SeqLocPtr slp; if (ffp == NULL) return; bsp = NULL; GatherItem (ffp->input_entityID, ffp->input_itemID, ffp->input_itemtype, (Pointer) (&bsp), DlgutilFindBspItem); if (bsp == NULL) return; slp = NULL; sel = ObjMgrGetSelected (); if (sel != NULL && sel->next == NULL && sel->entityID == ffp->input_entityID && sel->itemID == ffp->input_itemID && sel->itemtype == ffp->input_itemtype) { if (sel->regiontype == 1 && sel->region != NULL) { if (GetBioseqGivenSeqLoc ((SeqLocPtr) sel->region, ffp->input_entityID) == bsp) { slp = AsnIoMemCopy (sel->region, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); } } } if (slp == NULL) { slp = ValNodeNew (NULL); if (slp == NULL) return; sip = SeqIntNew (); if (sip == NULL) { slp = SeqLocFree (slp); return; } slp->choice = SEQLOC_INT; slp->data.ptrvalue = (Pointer) sip; sip->from = 0; sip->to = bsp->length - 1; sip->strand = Seq_strand_plus; sip->id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); } if (slp != NULL) { PointerToDialog (ffp->location, (Pointer) slp); SeqLocFree (slp); } } extern Boolean FileToScrollText (TexT t, CharPtr path) { FILE *fp; Int4 len; Int4 max; CharPtr str; #ifdef WIN_MAC CharPtr p; #endif #if (defined(OS_DOS) || defined (OS_NT)) CharPtr p; CharPtr q; #endif if (t != NULL && path != NULL && *path != '\0') { len = FileLength (path); #ifdef WIN_MOTIF max = INT4_MAX; #else max = (Int4) INT2_MAX; #endif if (len > 0 && len < max - 4) { str = MemNew (sizeof (char) * (len + 3)); if (str != NULL) { fp = FileOpen (path, "r"); if (fp != NULL) { FileRead (str, sizeof (char), (size_t) len, fp); #if (defined(OS_DOS) || defined (OS_NT)) p = str; q = str; while (*p) { if (*p == '\r') { p++; } else { *q = *p; p++; q++; } } *q = '\0'; #endif #ifdef WIN_MAC p = str; while (*p) { if (*p == '\r' || *p == '\n') { *p = '\015'; } p++; } #endif FileClose (fp); SetTitle (t, str); } MemFree (str); return TRUE; } } } return FALSE; } extern void ScrollTextToFile (TexT t, CharPtr path) { FILE *fp; size_t len; Int4 max; CharPtr str; #ifdef WIN_MAC CharPtr p; #endif if (t != NULL && path != NULL && *path != '\0') { len = TextLength (t); #ifdef WIN_MOTIF max = INT4_MAX; #else max = (Int4) INT2_MAX; #endif if (len > 0 && (Int4) len < max - 4) { #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) { str = MemNew (sizeof (char) * (len + 3)); if (str != NULL) { GetTitle (t, str, len + 1); #ifdef WIN_MAC p = str; while (*p) { if (*p == '\r' || *p == '\n') { *p = '\n'; } p++; } #endif FileWrite (str, sizeof (char), len, fp); MemFree (str); } FileClose (fp); } } } } extern void FileToClipboard (CharPtr path) { FILE *fp; Int4 len; Int4 max; CharPtr str; #ifdef WIN_MAC CharPtr p; #endif #if (defined(OS_DOS) || defined (OS_NT)) CharPtr p; CharPtr q; #endif if (path != NULL && *path != '\0') { len = FileLength (path); #ifdef WIN_MOTIF max = INT4_MAX; #else max = (Int4) INT2_MAX; #endif if (len > 0 && len < max - 4) { str = MemNew (sizeof (char) * (len + 3)); if (str != NULL) { fp = FileOpen (path, "r"); if (fp != NULL) { FileRead (str, sizeof (char), (size_t) len, fp); #if (defined(OS_DOS) || defined (OS_NT)) p = str; q = str; while (*p) { if (*p == '\r') { p++; } else { *q = *p; p++; q++; } } *q = '\0'; #endif #ifdef WIN_MAC p = str; while (*p) { if (*p == '\r' || *p == '\n') { *p = '\015'; } p++; } #endif FileClose (fp); Nlm_StringToClipboard (str); } MemFree (str); } } } } typedef struct textviewform { FORM_MESSAGE_BLOCK DoC doc; TexT text; } TextViewForm, PNTR TextViewFormPtr; static ParData txtParFmt = {FALSE, FALSE, FALSE, FALSE, TRUE, 0, 0}; static ColData txtColFmt = {0, 0, 80, 0, NULL, 'l', FALSE, FALSE, FALSE, FALSE, TRUE}; static void ResizeTextViewer (WindoW w) { Int2 height; RecT r; RecT s; TextViewFormPtr tfp; Int2 width; tfp = (TextViewFormPtr) GetObjectExtra (w); if (tfp != NULL) { WatchCursor (); ObjectRect (w, &r); width = r.right - r.left; height = r.bottom - r.top; if (tfp->doc != NULL) { GetPosition (tfp->doc, &s); s.right = width - s.left; s.bottom = height - s.left; SetPosition (tfp->doc, &s); AdjustPrnt (tfp->doc, &s, FALSE); txtColFmt.pixWidth = screenRect.right - screenRect.left; txtColFmt.pixInset = 8; if (Visible (tfp->doc) && AllParentsVisible (tfp->doc)) { UpdateDocument (tfp->doc, 0, 0); } } if (tfp->text != NULL) { GetPosition (tfp->text, &s); s.right = width - s.left; s.bottom = height - s.left; SetPosition (tfp->text, &s); AdjustPrnt (tfp->text, &s, FALSE); } ArrowCursor (); Update (); } } static Boolean ExportTextViewForm (ForM f, CharPtr filename) { FILE *fp; Char path [PATH_MAX]; TextViewFormPtr tfp; tfp = (TextViewFormPtr) GetObjectExtra (f); if (tfp != NULL && (tfp->doc != NULL || tfp->text != NULL)) { path [0] = '\0'; StringNCpy_0 (path, filename, sizeof (path)); 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 if (tfp->doc != NULL) { fp = FileOpen (path, "w"); if (fp != NULL) { SaveDocument (tfp->doc, fp); FileClose (fp); return TRUE; } } else if (tfp->text != NULL) { ScrollTextToFile (tfp->text, path); return TRUE; } } } return FALSE; } static void LIBCALL PrintTextViewForm (Pointer formDataPtr) { TextViewFormPtr tfp; tfp = (TextViewFormPtr) formDataPtr; if (tfp != NULL && tfp->doc != NULL) { PrintDocument (tfp->doc); } } static void TextViewFormMessage (ForM f, Int2 mssg) { TextViewFormPtr tfp; tfp = (TextViewFormPtr) GetObjectExtra (f); if (tfp != NULL) { switch (mssg) { case VIB_MSG_EXPORT : ExportTextViewForm (f, NULL); break; case VIB_MSG_CLOSE : Remove (f); break; case VIB_MSG_PRINT : PrintTextViewForm (tfp); 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 (tfp->appmessage != NULL) { tfp->appmessage (f, mssg); } break; } } } extern void LaunchGeneralTextViewer (CharPtr path, CharPtr title) { FonT fnt; Int2 pixheight; Int2 pixwidth; StdEditorProcsPtr sepp; TextViewFormPtr tfp; TextViewProcsPtr tvpp; WindoW w; #ifndef WIN_MAC MenU m; #endif tfp = (TextViewFormPtr) MemNew (sizeof (TextViewForm)); if (tfp != NULL) { w = DocumentWindow (-50, -33, -10, -10, title, StdCloseWindowProc, ResizeTextViewer); SetObjectExtra (w, tfp, StdCleanupFormProc); tfp->form = (ForM) w; tfp->exportform = ExportTextViewForm; tfp->formmessage = TextViewFormMessage; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (sepp != NULL) { SetActivate (w, sepp->activateForm); tfp->appmessage = sepp->handleMessages; } fnt = programFont; pixwidth = 35 * stdCharWidth + 17; pixheight = 20 * stdLineHeight; tvpp = (TextViewProcsPtr) GetAppProperty ("TextDisplayForm"); if (tvpp != NULL) { pixwidth = MAX (pixwidth, tvpp->minPixelWidth); pixheight = MAX (pixheight, tvpp->minPixelHeight); if (tvpp->displayFont != NULL) { fnt = tvpp->displayFont; } if (tvpp->activateForm != NULL) { SetActivate (w, tvpp->activateForm); } } #ifndef WIN_MAC m = PulldownMenu (w, "File"); FormCommandItem (m, "Export...", (BaseFormPtr) tfp, VIB_MSG_EXPORT); SeparatorItem (m); FormCommandItem (m, "Close", (BaseFormPtr) tfp, VIB_MSG_CLOSE); if (tvpp != NULL && tvpp->useScrollText) { m = PulldownMenu (w, "Edit"); FormCommandItem (m, CUT_MENU_ITEM, (BaseFormPtr) tfp, VIB_MSG_CUT); FormCommandItem (m, COPY_MENU_ITEM, (BaseFormPtr) tfp, VIB_MSG_COPY); FormCommandItem (m, PASTE_MENU_ITEM, (BaseFormPtr) tfp, VIB_MSG_PASTE); FormCommandItem (m, CLEAR_MENU_ITEM, (BaseFormPtr) tfp, VIB_MSG_DELETE); } #endif if (tvpp != NULL && tvpp->useScrollText) { tfp->text = ScrollText (w, (pixwidth + stdCharWidth - 1) / stdCharWidth, (pixheight + stdLineHeight - 1) / stdLineHeight, fnt, FALSE, NULL); SetObjectExtra (tfp->text, tfp, NULL); RealizeWindow (w); if (! FileToScrollText (tfp->text, path)) { SetTitle (tfp->text, "(Text is too large to be displayed in this control.)"); } } else { tfp->doc = DocumentPanel (w, pixwidth, pixheight); SetObjectExtra (tfp->doc, tfp, NULL); RealizeWindow (w); txtColFmt.pixWidth = screenRect.right - screenRect.left; txtColFmt.pixInset = 8; DisplayFancy (tfp->doc, path, &txtParFmt, &txtColFmt, fnt, 0); /* document.c: SaveTableItem does not strip preceeding tabs if tabCount is 0 */ } Show (w); Select (w); Update (); } } #ifndef WIN_MAC extern void CreateStdEditorFormMenus (WindoW w) { BaseFormPtr bfp; MenU m; bfp = (BaseFormPtr) GetObjectExtra (w); if (bfp != NULL) { m = PulldownMenu (w, "File"); if (bfp->importform != NULL || bfp->exportform != NULL) { if (bfp->importform != NULL) { FormCommandItem (m, "Import...", bfp, VIB_MSG_IMPORT); } if (bfp->exportform != NULL) { FormCommandItem (m, "Export...", bfp, VIB_MSG_EXPORT); } SeparatorItem (m); } FormCommandItem (m, "Close", bfp, VIB_MSG_CLOSE); m = PulldownMenu (w, "Edit"); FormCommandItem (m, CUT_MENU_ITEM, bfp, VIB_MSG_CUT); FormCommandItem (m, COPY_MENU_ITEM, bfp, VIB_MSG_COPY); FormCommandItem (m, PASTE_MENU_ITEM, bfp, VIB_MSG_PASTE); FormCommandItem (m, CLEAR_MENU_ITEM, bfp, VIB_MSG_DELETE); } } #endif static Boolean DlgutilGetLowestStackSeqEntry (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; } extern Boolean SetClosestParentIfDuplicating (BaseFormPtr bfp) { Uint2 itemID; Uint2 itemtype; StdEditorProcsPtr sepp; sepp = (StdEditorProcsPtr) GetAppProperty ("StdEditorForm"); if (bfp == NULL || sepp == NULL || (! sepp->duplicateExisting)) return FALSE; itemID = bfp->input_itemID; itemtype = bfp->input_itemtype; GatherItem (bfp->input_entityID, bfp->input_itemID, bfp->input_itemtype, (Pointer) bfp, DlgutilGetLowestStackSeqEntry); if (itemID == bfp->input_itemID && itemtype == bfp->input_itemtype) { return FALSE; } return TRUE; } /***************************************************************************** * * Bond and Point SeqLoc dialogs * *****************************************************************************/ typedef struct pointpage { DIALOG_MESSAGE_BLOCK TexT point; Int2 count; SeqEntryPtr PNTR bsptr; EnumFieldAssoc PNTR alist; PopuP strand; PopuP seqIdx; Boolean nucsOK; Boolean protsOK; Boolean showIdTags; } PointPage, PNTR PointPagePtr; typedef struct bondpage { DIALOG_MESSAGE_BLOCK DialoG pointA; DialoG pointB; } BondPage, PNTR BondPagePtr; static void FillInPointProducts (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; PointPagePtr ppp; if (sep != NULL && mydata != NULL && sep->choice == 1) { ppp = (PointPagePtr) mydata; bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp != NULL) { if ((ppp->nucsOK && ISA_na (bsp->mol)) || (ppp->protsOK && ISA_aa (bsp->mol))) { ppp->count++; ppp->bsptr [ppp->count] = sep; } } } } static ENUM_ALIST(strand_alist) {" ", Seq_strand_unknown}, /* 0 */ {"Plus", Seq_strand_plus}, /* 1 */ {"Minus", Seq_strand_minus}, /* 2 */ {"Both", Seq_strand_both}, /* 3 */ {"Reverse", Seq_strand_both_rev}, /* 4 */ {"Other", Seq_strand_other}, /* 255 */ END_ENUM_ALIST static void SeqPntPtrToPointPage (DialoG d, Pointer data) { BioseqPtr bsp; Int2 j; PointPagePtr ppp; SeqEntryPtr sep; Int2 seq; SeqPntPtr spp; Char str [16]; Uint1 strand; ppp = (PointPagePtr) GetObjectExtra (d); if (ppp == NULL) return; spp = (SeqPntPtr) data; if (spp != NULL) { sprintf (str, "%ld", (long) (spp->point + 1)); SafeSetTitle (ppp->point, str); seq = 0; strand = 0; bsp = BioseqFind (spp->id); if (bsp != NULL) { strand = spp->strand; if (strand > Seq_strand_both_rev && strand != Seq_strand_other) { strand = Seq_strand_unknown; } if (ppp->bsptr != NULL) { for (j = 1; j <= ppp->count && seq == 0; j++) { sep = ppp->bsptr [j]; if (sep != NULL && sep->choice == 1) { if (bsp == (BioseqPtr) sep->data.ptrvalue) { seq = j; } } } } } SetEnumPopup (ppp->strand, strand_alist, (UIEnum) strand); SetEnumPopup (ppp->seqIdx, ppp->alist, (UIEnum) seq); } else { SafeSetTitle (ppp->point, ""); SafeSetValue (ppp->strand, 0); SafeSetValue (ppp->seqIdx, 0); } } static Pointer PointPageToSeqPntPtr (DialoG d) { BioseqPtr bsp; PointPagePtr ppp; SeqEntryPtr sep; UIEnum seq; SeqPntPtr spp; Char str [16]; UIEnum strand; Int4 val; ppp = (PointPagePtr) GetObjectExtra (d); if (ppp == NULL) return NULL; spp = NULL; GetTitle (ppp->point, str, sizeof (str) - 1); if (StrToLong (str, &val) && val > 0) { if (GetEnumPopup (ppp->seqIdx, ppp->alist, &seq) && seq > 0 && seq <= ppp->count) { spp = SeqPntNew (); if (spp != NULL) { spp->point = val - 1; if (GetEnumPopup (ppp->strand, strand_alist, &strand)) { spp->strand = (Uint1) strand; } sep = ppp->bsptr [(Int2) seq]; if (sep != NULL && sep->choice == 1) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp != NULL) { spp->id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); } } } } } return (Pointer) spp; } static void PointEditorMessage (DialoG d, Int2 mssg) { PointPagePtr ppp; ppp = (PointPagePtr) GetObjectExtra (d); if (ppp != NULL) { if (mssg == VIB_MSG_INIT) { SeqPntPtrToPointPage (d, NULL); } else if (mssg == VIB_MSG_ENTER) { Select (ppp->point); } else if (mssg == VIB_MSG_RESET) { } } } static void CleanupPointPage (GraphiC g, VoidPtr data) { Int2 j; PointPagePtr ppp; ppp = (PointPagePtr) data; if (ppp != NULL) { MemFree (ppp->bsptr); if (ppp->alist != NULL) { for (j = 0; j <= ppp->count + 1; j++) { MemFree (ppp->alist [j].name); } } MemFree (ppp->alist); } MemFree (data); } static DialoG CreatePointEditorDialog (GrouP h, CharPtr title, SeqEntryPtr sep, Boolean nucsOK, Boolean protsOK) { BioseqPtr bsp; Int4 count; GrouP f; Int2 j; GrouP m; GrouP p; PointPagePtr ppp; CharPtr ptr; GrouP s; Boolean showIdTags; SeqIdPtr sip; Char str [128]; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); ppp = (PointPagePtr) MemNew (sizeof (PointPage)); if (ppp != NULL) { SetObjectExtra (p, ppp, CleanupPointPage); ppp->dialog = (DialoG) p; ppp->todialog = SeqPntPtrToPointPage; ppp->fromdialog = PointPageToSeqPntPtr; ppp->dialogmessage = PointEditorMessage; ppp->testdialog = NULL; ppp->importdialog = NULL; ppp->exportdialog = 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); */ ppp->nucsOK = nucsOK; ppp->protsOK = protsOK; ppp->showIdTags = FALSE; ppp->count = 0; if (sep != NULL) { count = SeqEntryCount (sep); count += 4; ppp->bsptr = MemNew (sizeof (BioseqPtr) * (size_t) count); ppp->alist = MemNew (sizeof (EnumFieldAssoc) * (size_t) count); ppp->count = 0; if (ppp->bsptr != NULL && ppp->alist != NULL) { SeqEntryExplore (sep, (Pointer) ppp, FillInPointProducts); j = 0; ppp->alist [j].name = StringSave (" "); ppp->alist [j].value = (UIEnum) 0; for (j = 1; j <= ppp->count; j++) { sep = ppp->bsptr [j]; if (sep != NULL && sep->choice == 1 && sep->data.ptrvalue != NULL) { bsp = (BioseqPtr) sep->data.ptrvalue; sip = SeqIdFindWorst (bsp->id); SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str)); ptr = StringChr (str, '|'); showIdTags = FALSE; if (ptr == NULL) { ptr = str; } else if (showIdTags) { ptr = str; } else { ptr++; } ppp->alist [j].name = StringSave (ptr); ppp->alist [j].value = (UIEnum) j; } } j = ppp->count + 1; ppp->alist [j].name = NULL; ppp->alist [j].value = (UIEnum) 0; } } else { ppp->alist = MemNew (sizeof (EnumFieldAssoc) * (size_t) 4); if (ppp->alist != NULL) { j = 0; ppp->alist [j].name = StringSave (" "); ppp->alist [j].value = (UIEnum) 0; j = 1; ppp->alist [j].name = NULL; ppp->alist [j].value = (UIEnum) 0; } } f = HiddenGroup (m, 6, 0, NULL); /*StaticPrompt (f, "Point", 0, dialogTextHeight, programFont, 'l');*/ ppp->point = DialogText (f, "", 5, NULL); if (nucsOK) { /*StaticPrompt (f, "Strand", 0, popupMenuHeight, programFont, 'c');*/ ppp->strand = PopupList (f, TRUE, NULL); InitEnumPopup (ppp->strand, strand_alist, NULL); } /*StaticPrompt (f, "SeqID", 0, popupMenuHeight, programFont, 'l');*/ ppp->seqIdx = PopupList (f, TRUE, NULL); InitEnumPopup (ppp->seqIdx, ppp->alist, NULL); } return (DialoG) p; } static void SeqLocPtrToBondPage (DialoG d, Pointer data) { BondPagePtr bpp; SeqBondPtr sbp; SeqIdPtr sip; SeqLocPtr slp; SeqPnt sqp; bpp = (BondPagePtr) GetObjectExtra (d); if (bpp == NULL) return; slp = (SeqLocPtr) data; if (slp != NULL) { if (slp->choice == SEQLOC_BOND) { sbp = (SeqBondPtr) slp->data.ptrvalue; if (sbp != NULL) { PointerToDialog (bpp->pointA, (Pointer) sbp->a); PointerToDialog (bpp->pointB, (Pointer) sbp->b); } } else { sip = SeqLocId (slp); if (sip != NULL) { sqp.strand = SeqLocStrand (slp); sqp.id = sip; sqp.point = SeqLocStart (slp); PointerToDialog (bpp->pointA, (Pointer) &sqp); sqp.point = SeqLocStop (slp); PointerToDialog (bpp->pointB, (Pointer) &sqp); } } } } static Pointer BondPageToSeqLocPtr (DialoG d) { BondPagePtr bpp; SeqBondPtr sbp; SeqLocPtr slp; bpp = (BondPagePtr) GetObjectExtra (d); if (bpp == NULL) return NULL; slp = NULL; sbp = SeqBondNew (); if (sbp != NULL) { slp = ValNodeNew (NULL); if (slp != NULL) { slp->choice = SEQLOC_BOND; slp->data.ptrvalue = (Pointer) sbp; sbp->a = DialogToPointer (bpp->pointA); sbp->b = DialogToPointer (bpp->pointB); } else { SeqBondFree (sbp); } } return (Pointer) slp; } static void BondEditorMessage (DialoG d, Int2 mssg) { BondPagePtr bpp; bpp = (BondPagePtr) GetObjectExtra (d); if (bpp != NULL) { if (mssg == VIB_MSG_INIT) { SeqLocPtrToBondPage (d, NULL); } else if (mssg == VIB_MSG_ENTER) { SendMessageToDialog (bpp->pointA, VIB_MSG_ENTER); } else if (mssg == VIB_MSG_RESET) { } } } extern DialoG CreateBondEditorDialog (GrouP h, CharPtr title, SeqEntryPtr sep); extern DialoG CreateBondEditorDialog (GrouP h, CharPtr title, SeqEntryPtr sep) { BondPagePtr bpp; GrouP f; GrouP m; GrouP p; GrouP s; p = HiddenGroup (h, 1, 0, NULL); SetGroupSpacing (p, 10, 10); bpp = (BondPagePtr) MemNew (sizeof (BondPage)); if (bpp != NULL) { SetObjectExtra (p, bpp, StdCleanupExtraProc); bpp->dialog = (DialoG) p; bpp->todialog = SeqLocPtrToBondPage; bpp->fromdialog = BondPageToSeqLocPtr; bpp->dialogmessage = BondEditorMessage; bpp->testdialog = NULL; bpp->importdialog = NULL; bpp->exportdialog = 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); */ f = HiddenGroup (m, 2, 0, NULL); StaticPrompt (f, "From", 0, popupMenuHeight, programFont, 'l'); bpp->pointA = CreatePointEditorDialog (f, NULL, sep, FALSE, TRUE); StaticPrompt (f, "(To)", 0, popupMenuHeight, programFont, 'l'); bpp->pointB = CreatePointEditorDialog (f, NULL, sep, FALSE, TRUE); } return (DialoG) p; } void GetRidOfEmptyFeatsDescStrings (Uint2 entityID, SeqEntryPtr sep) { if (entityID < 1 && sep == NULL) return; if (entityID > 0 && sep == NULL) { sep = GetTopSeqEntryForEntityID (entityID); } if (sep == NULL) return; SeqEntryExplore (sep, NULL, GetRidOfEmptyFeatsDescCallback); } extern Int2 LIBCALLBACK StdVibrantEditorMsgFunc (OMMsgStructPtr ommsp) { BaseFormPtr bfp; OMUserDataPtr omudp; omudp = (OMUserDataPtr)(ommsp->omuserdata); if (omudp == NULL) return OM_MSG_RET_ERROR; bfp = (BaseFormPtr) omudp->userdata.ptrvalue; if (bfp == NULL) return OM_MSG_RET_ERROR; switch (ommsp->message) { case OM_MSG_DEL: Remove (bfp->form); Update (); break; default : break; } return OM_MSG_RET_OK; } /* launch url section */ NLM_EXTERN void LaunchEntrezURL (CharPtr database, Int4 uid, CharPtr format) { #ifdef WIN_MOTIF NS_Window window = NULL; #endif Char url [256]; if (uid < 1 || StringHasNoText (database) || StringHasNoText (format)) return; sprintf (url, "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=%s&list_uids=%ld&dopt=%s", database, (long) uid, format); #ifdef WIN_MAC Nlm_SendURLAppleEvent (url, "MOSS", NULL); #endif #ifdef WIN_MSWIN if (! Nlm_MSWin_OpenDocument (url)) { Message (MSG_POST, "Unable to launch browser"); } #endif #ifdef WIN_MOTIF if (! NS_OpenURL (&window, url, NULL, TRUE)) { Message (MSG_POST, "Unable to launch browser"); } NS_WindowFree (window); #endif }