258 lines
7.9 KiB
C
258 lines
7.9 KiB
C
#include <X11/Intrinsic.h>
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#include "tagUtils.h"
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#include "fort.h"
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#ifndef _edUtils_h
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#define _edUtils_h
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/*
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** constant definitions
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*/
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#define MAX_DISPLAY_WIDTH 200
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#define DEFAULT_DISPLAY_WIDTH 80
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#define DB_NAMELEN 16 /* size of records in AR file */
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#define DB_GELNOLEN 5
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#define NAMELEN (DB_NAMELEN + DB_GELNOLEN + 1)
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#define BASES 6
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/*
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** Useful distances
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** (treat as symbolic rather than actual distances)
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*/
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#define D_screen 80
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#define D_halfScreen 40
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#define D_character 1
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/*
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** Flags for the internal database
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*/
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/* for whole database */
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#define DB_ACCESS (1L<<0)
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#define DB_DATA_TYPE (1L<<1)
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#define DB_STORAGE (1L<<2)
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#define DB_ACCESS_READONLY (0L)
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#define DB_ACCESS_UPDATE (DB_ACCESS)
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#define DB_DATA_TYPE_DNA (0L)
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#define DB_DATA_TYPE_PROTEIN (DB_DATA_TYPE)
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#define DB_STORAGE_DISK (0L)
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#define DB_STORAGE_INTERNAL (DB_STORAGE)
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#define DB_DELAYED_READ (0L)
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/* for each sequence */
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#define DB_FLAG_NONE (0L)
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#define DB_FLAG_IN_MEMORY (1L<<0)
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#define DB_FLAG_SEQ_MODIFIED (1L<<1)
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#define DB_FLAG_REL_MODIFIED (1L<<2)
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#define DB_FLAG_TAG_MODIFIED (1L<<3)
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#define DB_FLAG_SELECTED (1L<<4)
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#define DB_FLAG_TAG_IN_MEMORY (1L<<5)
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#define DB_FLAG_SEQ_IN_MEMORY (1L<<0)
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#define DB_FLAG_NAME_IN_MEMORY (1L<<6)
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/*
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** type definitions
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*/
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typedef struct {
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int relPos;
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int length;
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int number;
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int complemented;
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char *name;
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char *sequence;
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long flags;
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tagStruct *tagList;
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} DBStruct, *DBptr;
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/* REMEMBER TO: update structure initialisation in edUtils.c */
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typedef struct {
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int oldMax;
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long DB_flags;
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int DB_gelCount;
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int DB_contigNum;
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int *DBlist;
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int *DBorder;
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DBStruct *DB;
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int displayPos ;
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int displayWidth;
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int displayHeight;
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int cursorPos;
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int cursorSeq;
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int rulerDisplayed;
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int consensusDisplayed;
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int fontWidth;
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int fontHeight;
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Widget edWid;
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Widget namesWid;
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Widget sequencesWid;
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Widget scrollButtonsWid;
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Widget sliderWid;
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char displayedConsensus[ MAX_DISPLAY_WIDTH ];
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int select_made;
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int select_seq;
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int select_start_pos;
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int select_end_pos;
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tagStruct *select_tag;
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int reveal_cutoffs;
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int showDifferences;
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} EdStruct, *EdStructPtr;
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/* REMEMBER TO: update structure initialisation in edUtils.c */
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/*
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** Useful macros concerning internal database
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*/
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#define DBgetRelPos(X,A) ((X)->DB[(A)].relPos)
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#define DBgetLength(X,A) ((X)->DB[(A)].length)
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#define DBgetNumber(X,A) ((X)->DB[(A)].number)
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#define DBgetComp(X,A) ((X)->DB[(A)].complemented)
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#define DBgetFlags(X,A) ((X)->DB[(A)].flags)
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extern char *DBgetSeq();
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extern tagStruct *DBgetTags();
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extern char *DBgetName();
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/****************/
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#define DB_RelPos(X,A) ((X)->DB[(A)].relPos)
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#define DB_Length(X,A) ((X)->DB[(A)].length)
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#define DB_Number(X,A) ((X)->DB[(A)].number)
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#define DB_Comp(X,A) ((X)->DB[(A)].complemented)
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#define DB_Name(X,A) ((X)->DB[(A)].name)
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#define DB_Seq(X,A) ((X)->DB[(A)].sequence)
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#define DB_Flags(X,A) ((X)->DB[(A)].flags)
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#define DB_Tags(X,A) ((X)->DB[(A)].tagList)
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/****************/
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#define COMPLEMENTED -1
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#define BOTH_STRANDS 0
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#define UNCOMPLEMENTED 1
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#define DBgetGelName(xx,i) ( &( DBgetName(xx,i) )[DB_GELNOLEN+1] )
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#define DBsetRelPos(X,A,B) (X)->DB[(A)].relPos = (B)
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#define DBsetLength(X,A,B) (X)->DB[(A)].length = (B)
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#define DBsetNumber(X,A,B) (X)->DB[(A)].number = (B)
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#define DBsetComp(X,A,B) (X)->DB[(A)].complemented = (B)
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#define DBsetName(X,A,B) (X)->DB[(A)].name = (B)
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#define DBsetSeq(X,A,B) (X)->DB[(A)].sequence = (B)
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#define DBsetFlags(X,A,B) (X)->DB[(A)].flags = (B)
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#define DBsetTags(X,A,B) (X)->DB[(A)].tagList = (B)
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/*
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** Useful macros
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*/
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#define normalisePos(X,S,P,L) \
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( (DBgetComp((X),(S))==UNCOMPLEMENTED) ? (P) : (DBgetLength((X),(S)) - (P) - (L) + 2) )
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/*
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** External definitions
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*/
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extern int initialiseDB(
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EdStruct *xx,
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int_f *idevr, /* unit number for relationships */
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int_f *idevw, /* unit number for working versions of sequences */
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int_f *idevn, /* unit number for sequence names */
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int_f *relpg, /* relative positions of gels in sequences */
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int_f *lngthg, /* lengths of sequences */
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int_f *lnbr, /* left neighbours */
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int_f *rnbr, /* right neighbours */
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int_f *maxgel, /* maximum length of gel */
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int_f *idbsiz, /* size of database */
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int_f *llino /* left-most gel in contig */
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);
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extern void saveDB(
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EdStruct *xx,
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int_f *idevr, /* unit number for relationships */
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int_f *idevw, /* unit number for working versions of sequences */
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int_f *idevn, /* unit number for sequence names */
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int_f *relpg, /* relative positions of gels in sequences */
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int_f *lngthg, /* lengths of sequences */
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int_f *lnbr, /* left neighbours */
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int_f *rnbr, /* right neighbours */
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int_f *maxgel /* maximum length of gel */
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);
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extern void joinDB(
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int_f *idevr, /* unit number for relationships */
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int_f *idevw, /* unit number for working versions of sequences */
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int_f *idevn, /* unit number for sequence names */
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int_f *relpg, /* relative positions of gels in sequences */
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int_f *lngthg, /* lengths of sequences */
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int_f *lnbr, /* left neighbours */
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int_f *rnbr, /* right neighbours */
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int_f *maxgel, /* maximum length of gel */
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int_f *llinol,
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int_f *lnconl,
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int_f *llinor,
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int_f *lnconr,
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int_f *ngels,
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int_f *nconts,
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int_f *idbsiz
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);
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extern void freeDB(EdStruct *xx);
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extern void countDisagreements(int *overlapLength, int *wingeCount);
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extern int createEdDisplay(EdStruct *xx,Widget namesWid, Widget sequencesWid,int seq,int pos);
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extern void incDisplayPos(EdStruct *xx, int distance);
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extern void decDisplayPos(EdStruct *xx, int distance);
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extern void setDisplayPos(EdStruct *xx, int pos);
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extern void setDisplayPosPercent(EdStruct *xx, float percent);
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extern int posToIndex(EdStruct *xx, int pos);
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extern void undoLastCommand();
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extern void saveDatabase(EdStruct *xx);
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extern void caretRight(Widget, XEvent *, String *, Cardinal *);
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extern void caretLeft(Widget, XEvent *, String *, Cardinal *);
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extern void caretDown(Widget, XEvent *, String *, Cardinal *);
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extern void caretUp(Widget, XEvent *, String *, Cardinal *);
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extern void deleteKey(Widget, XEvent *, String *, Cardinal *);
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extern void keyPress(Widget, XEvent *, String *, Cardinal *);
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extern void buttonDown(Widget, XEvent *, String *, Cardinal *);
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extern void invokeTrace(Widget, XEvent *, String *, Cardinal *);
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extern void selectRead(Widget, XEvent *, String *, Cardinal *);
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extern EdStructPtr intToEdStruct(int i);
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extern EdStructPtr widgetToEdStruct(Widget w);
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extern EdStructPtr getFreeEdStruct();
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extern void DBgetSequence(EdStruct *xx, int seq, int pos, int width, char *str);
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/*
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** get part of a sequence from its `pos' base for `width' bases
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** Bases number from 0?
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*/
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extern int *sequencesInRegion(EdStruct *xx,int pos, int width);
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/*
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** Return a pointer to list of sequences in region of contig
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*/
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extern int *sequencesOnScreen(EdStruct *xx,int pos, int width);
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/*
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** Return a pointer to list of sequences on screen
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*/
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extern int positionInContig(EdStruct *xx, int seq, int pos);
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/*
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** returns relative position in a sequence as an
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** absolute position in the contig
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*/
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extern void DBcalcConsensus (EdStruct *xx,int pos, int width, char *str, int strand);
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/*
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** calculate the consensus for position `pos' in contig,
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** for `width' characters. Take into accound readings on `strand' only:
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**
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*/
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extern void redisplaySequences (EdStruct *xx, Widget namesWid, Widget sequencesWid, int pos, int width);
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/*
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** Redisplay the whole sequence display
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*/
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extern void redisplayWithCursor(EdStruct *xx);
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/*
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** Redisplay screen, ensuring cursor display
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*/
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void calculateConsensusLength(EdStruct *xx);
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/*
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** Calculate dynamic consensus length
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*/
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#endif /* _edUtils_h */
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