/* seqview.h * =========================================================================== * * 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: seqview.h * * Author: Jonathan Kans * * Version Creation Date: 4/30/95 * * $Revision: 6.35 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #ifndef _SEQVIEW_ #define _SEQVIEW_ #include #include #include #include #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /* bioseqviewdata pointer is passed to callbacks to display views */ typedef struct bioseqviewdata { BioseqPtr bsp; VieweR vwr; SegmenT pict; DoC doc; TexT text; PaneL pnl; PaneL udv; PaneL ddv; GrouP styleControlGrp; GrouP scaleControlGrp; GrouP findGeneGrp; GrouP docTxtControlGrp; GrouP baseCtgControlGrp; GrouP modeControlGrp; GrouP newGphControlGrp; GrouP pnlParentGrp; GrouP udvParentGrp; /* GrouP ddvParentGrp; */ PrompT clickMe; Boolean useScrollText; Boolean showContigJoin; Boolean launchEditors; Boolean launchSubviewers; Boolean sendSelectMessages; Boolean highlightSelections; Boolean hasTargetControl; Boolean viewWholeEntity; Boolean scaleNotCalculated; Boolean moveToOldPos; PopuP style; PopuP scale; IteM legendItem; Boolean legendOK; Int4 maxScale; Int4 minIndex; PopuP seqControl; PopuP featControl; PopuP numControl; PopuP ffModeCtrl; PopuP newGphStyle; PopuP newGphFilter; PopuP newGphScale; PopuP newGphLayout; ValNodePtr slp_list; ValNodePtr g_list; ValNodePtr anp_node; ValNodePtr ftype_list; Uint2 seq_entityID; GlobalDrawPtr gdraw_p; Boolean isGenome; Int2 expansion; Int2 itemClicked; Boolean wasDoubleClick; Boolean wasShiftKey; PoinT pnt_start; PoinT pnt_stop; Boolean old_rect_shown; FonT displayFont; ValNodePtr sentinelList; ValNodePtr entityList; /* for parts of genome record */ ValNodePtr tempResultList; /* to view results before attaching */ ForM form; } BioseqViewData, PNTR BioseqViewPtr; /* callback prototypes for implementing operations on a given page in a viewer */ typedef void (*BioseqViewProc) (BioseqViewPtr bvp); typedef void (*BioseqShowHideProc) (BioseqViewPtr bvp, Boolean show); typedef void (*BioseqExportProc) (BioseqViewPtr bvp, CharPtr filename, CharPtr dfault); typedef void (*BioseqSelectProc) (BioseqViewPtr bvp, Uint2 entityID, Uint2 itemID, Uint2 itemtype, SeqLocPtr region, Boolean select, Boolean scrollto); /* bioseqpagedata pointer array allows flexible control of pages in viewer */ typedef struct bioseqpagedata { CharPtr label; Boolean nucOK; Boolean protOK; Boolean genomeOK; Boolean needAlignment; Int4 maxLength; BioseqViewProc populate; BioseqShowHideProc show; BioseqSelectProc highlight; BioseqViewProc toClipboard; BioseqViewProc print; BioseqExportProc exprt; BioseqExportProc togif; BioseqViewProc resize; struct bioseqpagedata PNTR next; } BioseqPageData, PNTR BioseqPagePtr; /* bioseqpagedata records are available for all pre-defined report types */ extern BioseqPageData mapPageData; extern BioseqPageData sumPageData; extern BioseqPageData gphPageData; extern BioseqPageData alnPageData; extern BioseqPageData seqPageData; /* extern BioseqPageData udvPageData; extern BioseqPageData ddvPageData; */ extern BioseqPageData gbgnPageData; extern BioseqPageData gnbkPageData; extern BioseqPageData emblPageData; extern BioseqPageData ddbjPageData; extern BioseqPageData gnptPageData; extern BioseqPageData fstaPageData; extern BioseqPageData qualPageData; extern BioseqPageData asnPageData; extern BioseqPageData xmlPageData; extern BioseqPageData dskPageData; /* * The SeqViewProcsPtr may be registered with a call to SetAppProperty * e.g., SetAppProperty ("SeqDisplayForm", &viewprocs), where viewprocs * is a persistent structure filled with callback function pointers * specific for a given application. */ /* seqviewprocs is registered to allow communication to library functions */ typedef GrouP (*SeqViewControlsProc) (GrouP prnt, BaseFormPtr bfp, Int2 doctype, Int4 uid); typedef GrouP (*SeqViewFetchAlignsProc) (GrouP prnt, BaseFormPtr bfp); typedef Boolean (*SeqViewUpdateFetchCounts) (GrouP g, SeqEntryPtr sep); typedef struct seqviewprocs { Boolean hasTargetControl; Boolean hasDoneButton; Boolean hasDuplicateButton; Boolean allowScrollText; Boolean startInScrollText; Boolean launchEditors; Boolean launchSubviewers; Boolean sendSelectMessages; Boolean highlightSelections; Boolean forceSeparateViewer; Boolean keepSmartViewerVisible; Boolean cleanupObjectPtr; WndActnProc activateForm; WndActnProc closeForm; WndActnProc createMenus; GrpActnProc createToolBar; FormMessageFunc handleMessages; Int2 minPixelWidth; Int2 minPixelHeight; Int2 initNucPage; Int2 initProtPage; CharPtr initNucLabel; CharPtr initProtLabel; CharPtr initGenomeLabel; Int2 useFolderTabs; FonT displayFont; CharPtr filepath; BioseqPagePtr pageSpecs; SeqViewControlsProc makeControls; GrpActnProc updateControls; SeqViewFetchAlignsProc makeAlignBtn; SeqViewUpdateFetchCounts updateCounts; IteM alignWithChecked; /* application sets to EntrezGlobalsPtr->alignWithChecked */ Boolean alignDefault; /* application sets to EntrezGlobalsPtr->alignDefault */ Boolean lockFarComponents; } SeqViewProcs, PNTR SeqViewProcsPtr; #define REGISTER_NEW_SEQENTRY_VIEW ObjMgrProcLoad(OMPROC_VIEW,"View Bioseq Report","Bioseq Report",OBJ_BIOSEQ,0,OBJ_BIOSEQ,0,NULL,NewSeqEntryViewGenFunc,PROC_PRIORITY_DEFAULT) #define REGISTER_SMART_SEQENTRY_VIEW ObjMgrProcLoad(OMPROC_VIEW,"View Smart Bioseq Report","Bioseq Report",OBJ_BIOSEQ,0,OBJ_BIOSEQ,0,NULL,SmartSeqEntryViewGenFunc,PROC_PRIORITY_DEFAULT) extern ForM LIBCALL CreateNewSeqEntryViewForm (Int2 left, Int2 top, CharPtr title, BioseqPtr bsp, SeqViewProcsPtr svpp); /* RemoveSeqEntryViewer will hide and reuse the last window in Smart mode */ extern ForM RemoveSeqEntryViewer (ForM f); extern Int2 LIBCALLBACK NewSeqEntryViewGenFunc (Pointer data); extern Int2 LIBCALLBACK SmartSeqEntryViewGenFunc (Pointer data); extern void LIBCALL NewSaveBioseqViewFormGifItemTable (Pointer formDataPtr, CharPtr filename); extern void LIBCALL AddBioseqPageToList (BioseqPagePtr PNTR head, BioseqPagePtr bpp); extern BioseqPagePtr LIBCALL BioseqPageListFree (BioseqPagePtr bpp); extern IteM CreateLegendItem (MenU m, BaseFormPtr bfp); extern ForM MakeToolFormForBioseqView (BaseFormPtr bfp, GrpActnProc createToolBar); extern void SetBioseqViewTarget (BaseFormPtr fp, CharPtr seqId); extern BioseqViewPtr GetBioseqViewPtrFromBaseFormPtr (BaseFormPtr fp); NLM_EXTERN void Nlm_LaunchWebPage (Char *url); extern Boolean BioseqViewCanSaveFasta (ForM f, Boolean nucs, Boolean prots, Boolean onlyTarget); extern Boolean ExportBioseqViewFasta (ForM f, CharPtr filename, Boolean nucs, Boolean prots, Boolean onlyTarget); extern Boolean SeqnSeqEntrysToFasta (SeqEntryPtr sep, FILE *fp, Boolean is_na, Uint1 group_segs); /* The following functions are normally for internal use */ extern Int2 LIBCALLBACK BioseqViewMsgFunc (OMMsgStructPtr ommsp); extern Boolean InBioseqViewEntityList (Uint2 entityID, BioseqViewPtr bvp); extern void LIBCALL LaunchNewBioseqViewer (BioseqPtr bsp, Uint2 entityID, Uint2 itemID, Uint2 itemtype); extern Boolean LIBCALL IsAGenomeRecord (SeqEntryPtr sep); extern Boolean LIBCALL IsANamedAlignment (Uint2 entityID, Uint2 itemID, Uint2 itemtype); extern Boolean IsSegmentedBioseqWithoutParts (SeqEntryPtr sep); extern Boolean IsADeltaBioseq (SeqEntryPtr sep); extern Boolean LIBCALL LaunchViewerNotEditor (BioseqViewPtr bvp, SeqEntryPtr sep, Uint2 entityID, Uint2 itemID, Uint2 itemtype); extern ValNodePtr LIBCALL GetUidsForSeqEntryAligns (SeqEntryPtr sep); extern ValNodePtr LIBCALL GetIdStringsForSeqEntryAligns (SeqEntryPtr sep); extern void LIBCALL GetUidsForOneSeqAnnot (SeqAnnotPtr sap, ValNodePtr PNTR vnpp, Uint1 align_type); extern int LIBCALLBACK SortByVnpDataIntvalue (VoidPtr ptr1, VoidPtr ptr2); extern void ShowGeneList (ButtoN b); extern void EnableDisableLegendItem (BioseqViewPtr bvp, Boolean enable); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif /* ndef _SEQVIEW_ */