/usr/include/ncbi/bspview.h is in libvibrant6-dev 6.1.20120620-7.
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* ===========================================================================
*
* 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: 6.69 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#ifndef _SEQVIEW_
#define _SEQVIEW_
#include <dlogutil.h>
#include <document.h>
#include <viewer.h>
#include <glbpic.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
typedef struct seqPanelLines {
Int4 bioSeqLine; /* this line refers to bioseq line */
Int2 lineType; /* what to draw on this line (see ELineType) */
Uint4 idx; /* feature index */
Int4 row; /* index in alignment */
Boolean protProduct; /* indicates whether product sequence should be drawn */
Boolean on_the_fly; /* indicates whether translation of feature location should be drawn */
} SeqPanLine, PNTR SeqPanLinePtr;
/* 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 extraControlGrp;
GrouP newGphControlGrp;
GrouP pnlParentGrp;
PaneL seqView;
GrouP seqViewParentGrp;
PopuP newFeatControl;
PopuP newNumControl;
PopuP newGridControl;
/* for new sequence and alignment viewers */
Int4 LineHeight, LineSpace, CharHeight, CharWidth, BlocksAtLine, CharsAtLine, TotalLines, TargetRow;
Int2 SeqStartPosX; /* Draw Sequence from this x pos */
SeqAlignPtr salp;
Boolean DrawGrid, seqAlignMode;
SeqPanLinePtr PNTR SeqPanLines;
SelStructPtr sel_list;
ValNodePtr Selection;
Boolean frames[6]; /* indicates which frames should be displayed */
Boolean ShowComplement;
ValNodePtr chapter_list; /* list of chapters for SeqEd */
ValNodePtr PNTR feature_lists; /* storage for feature lists for SeqEd */
Int4 frame_for_codon_draw; /* This indicates which frame (1-6) to draw
* codons for. */
Boolean show_translation_errors; /* This indicates whether
* protein amino acids that
* do not match the sequence
* translation should be shown
* in red.
*/
Boolean on_the_fly; /* This indicates whether an on-the-fly
* translation of coding regions should
* be shown.
*/
Boolean showAlnSubstitutions; /* This indicates whether dots
* should be used to indicate
* matching characters.
*/
Int4 last_aln_row_clicked; /* This indicates the last alignment
* row clicked by the user. If this
* value is 0, no row has been selected.
* This is used for drawing the alignment
* cursor and generating the position text.
*/
GrouP udvParentGrp;
/*
GrouP ddvParentGrp;
*/
PrompT clickMe;
Boolean useScrollText;
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 ffStyleCtrl;
PopuP ffCustomBtn;
PopuP ffRifCtrl;
PopuP newGphStyle;
PopuP newGphFilter;
PopuP newGphScale;
PopuP newGphAlnScore;
PopuP newGphAlnCutoff;
ChoicE 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;
ValNodePtr bsplist;
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, Uint4 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 ftblPageData;
extern BioseqPageData fstaPageData;
extern BioseqPageData qualPageData;
extern BioseqPageData asnPageData;
extern BioseqPageData xmlPageData;
extern BioseqPageData gbseqPageData;
extern BioseqPageData dskPageData;
extern BioseqPageData asn2gphGphPageData;
extern BioseqPageData seqpnlPageData;
extern BioseqPageData seqAlnPnlPageData;
/*
* 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;
Char screenMode;
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;
typedef struct bioseqviewform {
FORM_MESSAGE_BLOCK
BioseqPagePtr bioseqNucPageList;
BioseqPagePtr bioseqProtPageList;
BioseqPagePtr currentBioseqPage;
ButtoN pubseq;
Int2 currentNucPage;
Int2 currentProtPage;
Handle nucViewControl;
Handle protViewControl;
Handle targetControl;
EnumFieldAssoc PNTR targetAlist;
Boolean usePopupForTarget;
Int4 numTargets;
Int4 targetScratchSpace;
GrouP controls;
GrpActnProc updateControls;
GrouP retrieveAlignments;
SeqViewUpdateFetchCounts updateCounts;
Boolean hasaligns;
EnumFieldAssoc PNTR workingAlist;
Int4 workingCount;
Int4 workingTargets;
BioseqViewData bvd;
Boolean cleanupObjectPtr;
WndActnProc activateForm;
ForM toolForm;
} BioseqViewForm, PNTR BioseqViewFormPtr;
#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 ForM ReplaceToolFormForBioseqView (BaseFormPtr bafp, GrpActnProc createToolBar);
typedef void (*BuildToolbarProc) PROTO((Nlm_GrouP, Pointer));
extern ForM ReplaceToolFormWithDataForBioseqView (BaseFormPtr bafp, BuildToolbarProc createToolBar, Pointer data);
extern void SetBioseqViewTarget (BaseFormPtr fp, CharPtr seqId);
extern BioseqPtr GetBioseqViewTarget (BaseFormPtr fp);
NLM_EXTERN void HideBioseqView (WindoW w);
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, Uint4 itemID, Uint2 itemtype);
extern Boolean LIBCALL IsAGenomeRecord (SeqEntryPtr sep);
extern Boolean LIBCALL IsANamedAlignment (Uint2 entityID, Uint4 itemID, Uint2 itemtype);
extern Boolean IsSegmentedBioseqWithoutParts (SeqEntryPtr sep);
extern Boolean IsADeltaBioseq (SeqEntryPtr sep);
extern Boolean LIBCALL LaunchViewerNotEditor (BioseqViewPtr bvp, SeqEntryPtr sep,
Uint2 entityID, Uint4 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);
NLM_EXTERN void RunAutoFixScript (BaseFormPtr bfp, Boolean add_object);
NLM_EXTERN void AutofixOnStartup (BaseFormPtr bfp);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif /* ndef _SEQVIEW_ */
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