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staden-lg/src/staden/contigEditor.c

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/*
Title: contigEditor
File: contigEditor.c
Purpose: C language entry point and initialisation functions
Last update: 5 April 1993
*/
/*
*/
#define CHKPNT(W,S) \
{ XSync(XtDisplay(W),False); fprintf(stderr,"CHKPNT: %s\n",S); }
/* ---- Includes ---- */
#include <stdio.h> /* IMPORT: freopen, stdout, stderr, fprintf */
/*#include <string.h>*/
#include <X11/Intrinsic.h>
#include <X11/Shell.h>
#include <X11/StringDefs.h>
#include <X11/Xaw/Box.h>
#include <X11/Xaw/Command.h>
#include <X11/Xaw/Form.h>
#include <X11/Xaw/Label.h>
#include <X11/Xaw/Scrollbar.h>
#include <X11/Xaw/SimpleMenu.h>
#include <X11/Xaw/SmeBSB.h>
#include <X11/Xaw/SmeLine.h>
#include <X11/Xaw/Text.h>
#include <X11/Xaw/Toggle.h>
#include "Sheet.h"
#include "contigEditor.h"
#include "locks.h"
#include "main.h"
#include "select.h"
#include "tagUtils.h"
#include "edUtils.h"
#include "extend.h"
#include "undo.h"
#include "fort.h"
/* ---- Static variables ---- */
static Widget editorShellWid; /* main editor shell */
static Widget mainFormWid; /* main editor form */
static Widget buttonsWid;
static Widget exitWid; /* Leave Editor button */
static Widget undoWid; /* Undo last edit command button */
static Widget supermanWid; /* switch for Superuser class of edit commands */
static Widget revealWid; /* switch for revealing hidden cutoff information */
#ifdef nana
static Widget saveWid; /* save command button */
#endif
static Widget lockWid; /* lock button for when joining */
#ifdef nana
static Widget joinWid; /* lock button for when joining */
#endif
static Widget labelWid; /* label displaying contig name */
static Widget insertWid; /* edit mode - insertion */
static Widget replaceWid; /* edit mode - replacement */
static Widget nextWid; /* search for next problem in consensus */
static Widget disagreeFormWid; /* for displaying disagreements when joining */
static Widget dummyWid;
Widget disagreeWid;
float pcCut; /* cut off for consensus calculation */
int editorMode;
enum States {StateDown=0,StateUp} editorState = StateDown;
static int lockOffset;
/* save/lock state */
int_f save_state;
SaveStruct saveState;
DefColours defColours;
/* ---- My translation tables ---- */
static char translationTable[] =
"\
Ctrl<Btn1Down>: XawPositionSimpleMenu(edMenu) XtMenuPopup(edMenu)\n\
<Btn1Down>: StartHighlight() buttonDown()\n\
<Btn1Motion>: ExtendHighlight()\n\
<Btn1Up>: MakeSelection()\n\
<Btn2Down>(2): buttonDown() invokeTrace()\n\
<Btn2Down>: buttonDown()\n\
<Btn3Down>: ExtendHighlight()\n\
<Btn3Motion>: ExtendHighlight()\n\
<Btn3Up>: ExtendHighlight()\n\
Meta<Key>Left: MetaLeft()\n\
Meta<Key>Right: MetaRight()\n\
<Key>Right: caretRight()\n\
<Key>Left: caretLeft()\n\
<Key>Down: caretDown()\n\
<Key>Up: caretUp()\n\
<Key>Delete: deleteKey()\n\
<Key>: keyPress()";
/*
<Btn2Down>: SelectTag()\n\
Meta<Key>Up: MetaUp()\n\
*/
static XtActionsRec actionTable[] = {
{"caretRight", caretRight},
{"caretLeft", caretLeft},
{"caretDown", caretDown},
{"caretUp", caretUp},
{"deleteKey", deleteKey},
{"keyPress", keyPress},
{"buttonDown", buttonDown},
{"invokeTrace", invokeTrace},
{"StartHighlight", start_highlight},
{"ExtendHighlight", extend_highlight},
{"MakeSelection", make_selection},
{"SelectTag", select_tag},
{"MetaLeft", meta_left},
{"MetaRight", meta_right},
{"MetaUp", meta_up},
};
XtTranslations parsedTTable;
static char translationTable2[] =
"<Btn1Down>: selectRead()";
static XtActionsRec actionTable2[] = {
{"selectRead", selectRead},
};
XtTranslations parsedTTable2;
/* ---- Private Functions ---- */
static int LeaveAllowed;
static void save()
/*
** Save Changes
*/
{
EdStruct *xx = intToEdStruct(0);
saveDB(
xx,
saveState.idevr,
saveState.idevw,
saveState.idevn,
saveState.relpg,
saveState.lngthg,
saveState.lnbr,
saveState.rnbr,
saveState.maxgel
);
}
static void join()
/*
** Join request made
*/
{
joinDB(
saveState.idevr,
saveState.idevw,
saveState.idevn,
saveState.relpg,
saveState.lngthg,
saveState.lnbr,
saveState.rnbr,
saveState.maxgel,
saveState.llinol,
saveState.lnconl,
saveState.llinor,
saveState.lnconr,
saveState.ngels,
saveState.nconts,
saveState.idbsiz
);
}
static void warningYesCallback(Widget w,
XtPointer client_data, XtPointer call_data)
/*
** A yes response to the
** warning about data not saved
*/
{
Widget popupWid = (Widget) client_data;
if (editorMode == EDITMODE)
save();
else
join();
LeaveAllowed = 1;
XtDestroyWidget(popupWid);
}
static void warningNoCallback(Widget w,
XtPointer client_data, XtPointer call_data)
/*
** A No response to the
** warning about data not saved
*/
{ Widget popupWid = (Widget) client_data;
LeaveAllowed = 1;
XtDestroyWidget(popupWid);
}
static void warningCancelCallback(Widget w,
XtPointer client_data, XtPointer call_data)
/*
** A Cancel response to the
** warning about data not saved
*/
{ Widget popupWid = (Widget) client_data;
LeaveAllowed = 0;
XtDestroyWidget(popupWid);
}
static void createLabelsForBox(Widget parentWid, char *warning)
{
Arg args[10];
int nargs;
nargs = 0;
XtSetArg(args[nargs], XtNlabel, warning); nargs++;
(void) XtCreateManagedWidget("warnPrompt", labelWidgetClass,
parentWid, args, nargs);
}
static int warnNotSaved(Widget parentWid, String warning)
/*
** Warn that changes have been made but contig hasn't been saved.
*/
{ Widget warningWid, warnFormWid, warnPromptBox;
Widget yesWid, noWid, cancelWid;
Arg args[10];
int nargs;
Position x, y;
Dimension width, height;
/*
Position the upper left hand corner of the popup at the
center of the parent widget.
*/
nargs = 0;
XtSetArg(args[nargs], XtNwidth, &width); nargs++;
XtSetArg(args[nargs], XtNheight, &height); nargs++;
XtGetValues(parentWid, args, nargs);
XtTranslateCoords(parentWid,
(Position) 0, (Position) height,
&x, &y);
nargs = 0;
XtSetArg(args[nargs], XtNx, x); nargs++;
XtSetArg(args[nargs], XtNy, y); nargs++;
warningWid = XtCreatePopupShell("warning", transientShellWidgetClass,
parentWid,
args, nargs);
/* Create the form */
nargs = 0;
warnFormWid = XtCreateManagedWidget("warnForm", formWidgetClass,
warningWid, args, nargs);
nargs = 0;
warnPromptBox = XtCreateManagedWidget("warnBox", boxWidgetClass,
warnFormWid, args, nargs);
createLabelsForBox(warnPromptBox,warning);
nargs = 0;
XtSetArg(args[nargs], XtNfromVert, warnPromptBox); nargs++;
yesWid = XtCreateManagedWidget("Yes", commandWidgetClass,
warnFormWid, args, nargs);
XtAddCallback(yesWid, XtNcallback, warningYesCallback, (XtPointer) warningWid);
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, yesWid); nargs++;
XtSetArg(args[nargs], XtNfromVert, warnPromptBox); nargs++;
noWid = XtCreateManagedWidget("No", commandWidgetClass,
warnFormWid, args, nargs);
XtAddCallback(noWid, XtNcallback, warningNoCallback, (XtPointer) warningWid);
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, noWid); nargs++;
XtSetArg(args[nargs], XtNfromVert, warnPromptBox); nargs++;
cancelWid = XtCreateManagedWidget("Cancel", commandWidgetClass,
warnFormWid, args, nargs);
XtAddCallback(cancelWid, XtNcallback,
warningCancelCallback, (XtPointer) warningWid);
/* This is a modal dialogue */
LeaveAllowed = -1;
XtPopup(warningWid, XtGrabNonexclusive);
while (LeaveAllowed==-1)
{
XEvent event;
XtAppNextEvent(XtWidgetToApplicationContext(parentWid), &event);
XtDispatchEvent(&event);
}
return LeaveAllowed;
}
static void editNextCallback(Widget w, XtPointer client_data, XtPointer call_data)
/*
** Next Problem button has been pushed
*/
{
EdStruct *xx = intToEdStruct(0);
if (editorState == StateDown) return;
findNextProblem(xx);
}
static void editRevealCallback(Widget w, XtPointer client_data, XtPointer call_data)
/*
** Next Problem button has been pushed
*/
{
EdStruct *xx;
Arg args[10];
int nargs;
Boolean state;
int i;
if (editorState == StateDown) return;
nargs = 0;
XtSetArg(args[nargs], XtNstate, &state); nargs++;
XtGetValues(w, args, nargs);
for (i=0;i<editorMode;i++) {
xx = intToEdStruct(i);
xx->reveal_cutoffs=state;
redisplaySequences (xx,xx->namesWid, xx->sequencesWid, xx->displayPos, xx->displayWidth);
}
}
static void editLockCallback(Widget w, XtPointer client_data, XtPointer call_data)
/*
** Editor has been locked
*/
{
EdStruct *xx0 = intToEdStruct(0);
EdStruct *xx1 = intToEdStruct(1);
/*
int nargs;
Arg args[10];
nargs=0;
XtSetArg(args[nargs], XtNstate, &currMode); nargs++;
XtGetValues(lockWid, args, nargs);
if (currMode)
*/
lockOffset = xx1->displayPos - xx0->displayPos;
redisplaySequences (xx0,xx0->namesWid, xx0->sequencesWid, xx0->displayPos, xx0->displayWidth);
redisplaySequences (xx1,xx1->namesWid, xx1->sequencesWid, xx1->displayPos, xx1->displayWidth);
}
static void editUndoCallback(Widget w, XtPointer client_data, XtPointer call_data)
/*
** Undo last command request made
*/
{
undoLastCommand();
}
static void editExitCallback(Widget w, XtPointer client_data, XtPointer call_data)
/*
** Request made to leave the editor
*/
{
EdStruct *xx = intToEdStruct(0);
if (editorState == StateDown) return;
switch (editorMode) {
case EDITMODE:
if (editsMade(xx)) {
if (warnNotSaved(w,"Save changes?"))
{
XtPopdown(editorShellWid);
editorState = StateDown;
semaphoreRelease(activeLock);
}
} else {
XtPopdown(editorShellWid);
editorState = StateDown;
semaphoreRelease(activeLock);
}
break;
case JOINMODE: {
int overlapLength, wingeCount;
char warning[200];
countDisagreements(&overlapLength, &wingeCount);
if (overlapLength<=0) {
sprintf(warning,
"Contigs do not overlap\nPerform Join?\n");
} else {
sprintf(warning,
"Percentage Mismatch:\n %5.2f%%\nPerform Join?\n",
(float)(100*wingeCount)/(float)overlapLength);
}
if (warnNotSaved(w,warning))
{
XtPopdown(editorShellWid);
editorState = StateDown;
semaphoreRelease(activeLock);
}
break;
}
default:
XtPopdown(editorShellWid);
editorState = StateDown;
semaphoreRelease(activeLock);
}
/*
** We must shut down the search window as well
*/
if (editorState == StateDown) {
destroySearchWindow();
}
}
static void sliderScrollCallback(Widget wid,
XtPointer client_data, XtPointer call_data)
/*
** left or right mouse button has caused the
** slider to move
*/
{
EdStruct *xx = widgetToEdStruct(XtParent(wid));
int position = (int) call_data;
float topOfThumb;
int nargs;
Arg args[10];
if (editorState == StateDown) return;
nargs=0;
XtSetArg(args[nargs], XtNtopOfThumb, &topOfThumb); nargs++;
XtGetValues(wid, args, nargs);
/* Move the thumb by one screenful in the appropriate direction */
if (position>0)
incDisplayPos(xx,D_screen);
else
decDisplayPos(xx,D_screen);
}
static void leftleftCallback(Widget wid,
XtPointer client_data, XtPointer call_data)
/*
** Jump left a long way
*/
{
EdStruct *xx = widgetToEdStruct(XtParent(XtParent(wid)));
if (editorState == StateDown) return;
decDisplayPos (xx,D_halfScreen);
}
static void leftCallback(Widget wid,
XtPointer client_data, XtPointer call_data)
/*
** Jump left a short way
*/
{
EdStruct *xx = widgetToEdStruct(XtParent(XtParent(wid)));
if (editorState == StateDown) return;
decDisplayPos (xx,D_character);
}
static void rightCallback(Widget wid,
XtPointer client_data, XtPointer call_data)
/*
** Jump right a short way
*/
{
EdStruct *xx = widgetToEdStruct(XtParent(XtParent(wid)));
if (editorState == StateDown) return;
incDisplayPos (xx,D_character);
}
static void rightrightCallback(Widget wid,
XtPointer client_data, XtPointer call_data)
/*
** Jump right a long way
*/
{
EdStruct *xx = widgetToEdStruct(XtParent(XtParent(wid)));
if (editorState == StateDown) return;
incDisplayPos (xx,D_halfScreen);
}
static void sliderJumpCallback(Widget wid,
XtPointer client_data, XtPointer call_data)
/*
** Middle mouse button used to reposition scroll bar
*/
{
float percent = *((float *) call_data);
EdStruct *xx = widgetToEdStruct(XtParent(wid));
if (editorState == StateDown) return;
setDisplayPosPercent(xx,percent);
}
static void getFontDetails(int *width, int *height)
/*
** Get the font width and height
** for the contig editor window
** ASSUME a single font is used!!
*/
{
Arg args[10];
int nargs;
XFontStruct *font;
nargs = 0;
XtSetArg(args[nargs], XtNfont, &font); nargs++;
XtGetValues(labelWid, args, nargs);
*width = font->max_bounds.width;
*height = font->max_bounds.ascent + font->max_bounds.descent;
}
static void setInitialStates(int reveal_state)
/*
** Set the initial states of togglewidgets
*/
{
Arg args[10];
int nargs;
nargs = 0;
XtSetArg(args[nargs], XtNstate, False); nargs++;
XtSetValues(lockWid, args, nargs);
nargs = 0;
XtSetArg(args[nargs], XtNstate, reveal_state); nargs++;
XtSetValues(revealWid, args, nargs);
}
static void tweakGeometry1()
/*
** Some geometry tweaking must be done before widgets are realised
*/
{
EdStruct *xx;
xx = intToEdStruct(1);
if (editorMode==EDITMODE) {
XtManageChild(nextWid);
XtUnmanageChild(lockWid);
#ifdef nana
XtUnmanageChild(joinWid);
#endif
XtUnmanageChild(disagreeFormWid);
XtUnmanageChild(xx->edWid);
XawFormDoLayout(mainFormWid,True);
} else {
XtUnmanageChild(nextWid);
XtManageChild(lockWid);
#ifdef nana
XtManageChild(joinWid);
#endif
XtManageChild(disagreeFormWid);
XtManageChild(xx->edWid);
XawFormDoLayout(mainFormWid,True);
}
}
static void tweakGeometry2()
/*
** Some geometry tweaking must be done after widgets are realised
*/
{
int i;
Arg args[10];
int nargs;
EdStruct *xx;
/*
** scroll button wids
*/
for (i=0;i<editorMode;i++) {
xx = intToEdStruct(i);
nargs = 0;
XtSetArg(args[nargs], XtNwidth, xx->fontWidth*NAMELEN+10); nargs++;
XtSetValues(xx->scrollButtonsWid, args, nargs);
/*
Dimension width;
xx = intToEdStruct(i);
nargs = 0;
XtSetArg(args[nargs], XtNwidth, &width); nargs++;
XtGetValues(xx->namesWid, args, nargs);
fprintf(stderr,"width.a = %d\n",(int)width);
nargs = 0;
XtSetArg(args[nargs], XtNwidth, width); nargs++;
XtSetValues(xx->scrollButtonsWid, args, nargs);
nargs = 0;
XtSetArg(args[nargs], XtNwidth, &width); nargs++;
XtGetValues(xx->sequencesWid, args, nargs);
fprintf(stderr,"width.b = %d\n",(int)width);
nargs = 0;
XtSetArg(args[nargs], XtNwidth, width); nargs++;
XtSetValues(xx->sliderWid, args, nargs);
*/
}
}
/* ---- Exported functions ---- */
void jxedit_(
int_f *idevr, /* unit number for relationships */
int_f *idevw, /* unit number for working versions of sequences */
int_f *idevn, /* unit number for sequence names */
int_f *idevt, /* unit number for tag information */
int_f *idevc, /* unit number for comment file */
int_f *relpg, /* relative positions of gels in sequences */
int_f *lngthg, /* lengths of sequences */
int_f *lnbr, /* left neighbours */
int_f *rnbr, /* right neighbours */
int_f *maxgel, /* maximum length of gel */
int_f *idbsiz, /* size of database */
int_f *lnconl, /* left contig to join */
int_f *llinol, /* left-most gel in contig of left contig */
int_f *lnconr, /* right contig for join */
int_f *llinor, /* left-most gel in contig of right contig */
int_f *igell, /* left gel specified on entry */
int_f *igellpos,/* position in left-most gel */
int_f *igelr, /* right gel specified on entry */
int_f *igelrpos,/* position in left-most gel */
int_f *perced, /* cutoff for consensus calculation */
int_f *ngels, /* number of gels in database */
int_f *nconts, /* number of contigs in database */
int_f *idm, /* database type */
int_f *rcstate, /* reveal cutoff state */
int_f *iok /* returns 0-saved (1) | 1-saved (2) | joined (4) */
)
/*
** Interface to FORTRAN for Join editor
*/
{
EdStruct *xx[2];
int reveal_state;
int i;
semaphoreGrab(activeLock);
editorState = StateUp;
editorMode = JOINMODE;
save_state = (int_f)0;
reveal_state = (*rcstate != 0);
setInitialStates(reveal_state);
/*
** Save arguments for later use
*/
saveState.idevr = idevr;
saveState.idevw = idevw;
saveState.idevn = idevn;
saveState.idevt = idevt;
saveState.idevc = idevc;
saveState.relpg = relpg;
saveState.lngthg = lngthg;
saveState.lnbr = lnbr;
saveState.rnbr = rnbr;
saveState.maxgel = maxgel;
saveState.idbsiz = idbsiz;
saveState.llinol = llinol;
saveState.lnconl = lnconl;
saveState.llinor = llinor;
saveState.lnconr = lnconr;
saveState.perced = perced;
saveState.ngels = ngels;
saveState.nconts = nconts;
saveState.idm = idm;
pcCut = * (float *) perced;
for (i=0; i<2; i++) {
int_f *llino = (i==0)?llinol:llinor;
/*
** Set up data structures
*/
xx[i] = intToEdStruct(i);
xx[i]->reveal_cutoffs = reveal_state;
if (initialiseDB(xx[i],idevr,idevw,idevn,relpg,lngthg,lnbr,rnbr,maxgel,idbsiz,llino)) {
if (i==1) freeDB(xx[0]);
return;
}
/*
** Set up display
*/
if (createEdDisplay(xx[i],
xx[i]->namesWid,
xx[i]->sequencesWid,
(i)?*igelr:*igell,
(i)?*igelrpos:*igellpos)) {
freeDB(xx[i]);
if (i==1) freeDB(xx[0]);
return;
}
}
tweakGeometry1();
XtPopup(editorShellWid, XtGrabNone);
tweakGeometry2();
while (editorState != StateDown)
{
XEvent event;
XtAppNextEvent(XtWidgetToApplicationContext(xx[0]->edWid), &event);
XtDispatchEvent(&event);
}
for (i=0;i<2;i++) {
disown_selection(xx[i]);
freeDB(xx[i]);
cleanUpAllStacks();
}
*iok = save_state;
}
void cxedit_(
int_f *idevr, /* unit number for relationships */
int_f *idevw, /* unit number for working versions of sequences */
int_f *idevn, /* unit number for sequence names */
int_f *idevt, /* unit number for tag information */
int_f *idevc, /* unit number for comment file */
int_f *relpg, /* relative positions of gels in sequences */
int_f *lngthg, /* lengths of sequences */
int_f *lnbr, /* left neighbours */
int_f *rnbr, /* right neighbours */
int_f *maxgel, /* maximum length of gel */
int_f *idbsiz, /* size of database */
int_f *lincon, /* current contig to edit */
int_f *llino, /* left-most gel in contig */
int_f *igelno, /* gel number specified on entry */
int_f *igelpos, /* position in gel */
int_f *perced, /* cutoff for consensus calculation */
int_f *idm, /* database type */
int_f *rcstate, /* reveal cutoff state */
int_f *iok /* returns 0-saved (1) | 1-saved (2) | joined (4) */
)
/*
** Interface to FORTRAN for Contig Editor
*/
{
int reveal_state;
EdStruct *xx = intToEdStruct(0);
semaphoreGrab(activeLock);
editorState = StateUp;
editorMode = EDITMODE;
save_state = (int_f)0;
reveal_state = (*rcstate != 0);
setInitialStates(reveal_state);
/*
** Save arguments for later use
*/
saveState.idevr = idevr;
saveState.idevw = idevw;
saveState.idevn = idevn;
saveState.idevt = idevt;
saveState.idevc = idevc;
saveState.relpg = relpg;
saveState.lngthg = lngthg;
saveState.lnbr = lnbr;
saveState.rnbr = rnbr;
saveState.maxgel = maxgel;
saveState.idbsiz = idbsiz;
saveState.lincon = lincon;
saveState.llino = llino;
saveState.perced = perced;
saveState.idm = idm;
/*
** Set up data structures
*/
xx->reveal_cutoffs = reveal_state;
if (initialiseDB(xx,idevr,idevw,idevn,relpg,lngthg,lnbr,rnbr,maxgel,idbsiz,llino))
return;
/*
** Set up display
*/
pcCut = * (float *) perced;
if (createEdDisplay(xx,xx->namesWid,xx->sequencesWid,*igelno,*igelpos)) {
freeDB(xx);
return;
}
tweakGeometry1();
XtPopup(editorShellWid, XtGrabNone);
tweakGeometry2();
while (editorState != StateDown)
{
XEvent event;
XtAppNextEvent(XtWidgetToApplicationContext(xx->namesWid), &event);
XtDispatchEvent(&event);
}
disown_selection(xx);
freeDB(xx);
cleanUpAllStacks();
*iok = save_state;
}
Widget createEditWid(Widget parentWid, Widget fromVertWid, int closeToVert)
/*
** Create an form with all the trappings of an editor window
*/
{
EdStruct *xx;
Widget llWid, lWid, rWid, rrWid;
Arg args[10];
int nargs;
xx = getFreeEdStruct();
if (xx == NULL) return NULL;
getFontDetails(&xx->fontWidth,&xx->fontHeight);
/*
** create main form
*/
nargs = 0;
XtSetArg(args[nargs], XtNfromVert, fromVertWid); nargs++;
if (closeToVert) {
XtSetArg(args[nargs], XtNvertDistance, 0); nargs++;
}
xx->edWid = XtCreateManagedWidget("edForm", formWidgetClass,
parentWid, args, nargs);
/*
** Scrollers
*/
nargs = 0;
xx->scrollButtonsWid = XtCreateManagedWidget("scrollButtons", formWidgetClass,
xx->edWid, args, nargs);
nargs = 0;
llWid = XtCreateManagedWidget("leftleft", commandWidgetClass,
xx->scrollButtonsWid, args, nargs);
XtAddCallback(llWid, XtNcallback, leftleftCallback, NULL );
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, llWid); nargs++;
lWid = XtCreateManagedWidget("left", commandWidgetClass,
xx->scrollButtonsWid, args, nargs);
XtAddCallback(lWid, XtNcallback, leftCallback, NULL );
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, lWid); nargs++;
rWid = XtCreateManagedWidget("right", commandWidgetClass,
xx->scrollButtonsWid, args, nargs);
XtAddCallback(rWid, XtNcallback, rightCallback, NULL );
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, rWid); nargs++;
rrWid = XtCreateManagedWidget("rightright", commandWidgetClass,
xx->scrollButtonsWid, args, nargs);
XtAddCallback(rrWid, XtNcallback, rightrightCallback, NULL );
/*
** A Slider
*/
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, xx->scrollButtonsWid); nargs++;
XtSetArg(args[nargs], XtNhorizDistance, 0); nargs++;
XtSetArg(args[nargs], XtNorientation, XtorientHorizontal); nargs++;
XtSetArg(args[nargs], XtNheight, xx->fontHeight+4); nargs++;
XtSetArg(args[nargs], XtNwidth, xx->fontWidth*(xx->displayWidth)+8); nargs++;
xx->sliderWid = XtCreateManagedWidget("slider", scrollbarWidgetClass,
xx->edWid, args, nargs);
XtAddCallback(xx->sliderWid, XtNjumpProc, sliderJumpCallback, NULL);
XtAddCallback(xx->sliderWid, XtNscrollProc, sliderScrollCallback, NULL);
/*
** ... and a text widget or two or three
*/
nargs = 0;
XtSetArg(args[nargs], XtNfromVert, xx->sliderWid); nargs++;
XtSetArg(args[nargs], XtNvertDistance, 0); nargs++;
XtSetArg(args[nargs], XtNcolumns, NAMELEN); nargs++;
xx->namesWid = XtCreateManagedWidget("names", sheetWidgetClass,
xx->edWid, args, nargs);
XtUninstallTranslations(xx->namesWid);
/* Add string to function bindings for our application actions */
XtAppAddActions(XtWidgetToApplicationContext(xx->edWid),
actionTable2, XtNumber(actionTable2));
parsedTTable2 = XtParseTranslationTable(translationTable2);
XtUninstallTranslations(xx->namesWid);
XtAugmentTranslations(xx->namesWid,parsedTTable2);
nargs = 0;
XtSetArg(args[nargs], XtNfromVert, xx->sliderWid); nargs++;
XtSetArg(args[nargs], XtNvertDistance, 0); nargs++;
XtSetArg(args[nargs], XtNfromHoriz, xx->namesWid); nargs++;
XtSetArg(args[nargs], XtNhorizDistance, 0); nargs++;
XtSetArg(args[nargs], XtNcolumns, DEFAULT_DISPLAY_WIDTH); nargs++;
xx->sequencesWid = XtCreateManagedWidget("sequences", sheetWidgetClass,
xx->edWid, args, nargs);
/* Add string to function bindings for our application actions */
XtAppAddActions(XtWidgetToApplicationContext(xx->edWid),
actionTable, XtNumber(actionTable));
parsedTTable = XtParseTranslationTable(translationTable);
XtUninstallTranslations(xx->sequencesWid);
XtAugmentTranslations(xx->sequencesWid,parsedTTable);
/*
** Pop-up menu
*/
createEdMenu(xx->sequencesWid);
return xx->edWid;
}
Widget createDisagreeWid(Widget parentWid, Widget fromVertWid, int closeToVert)
/*
** Create a form widget with all the trappings of a
** disagreement window
*/
{
Arg args[10];
int nargs;
int fontWidth, fontHeight;
getFontDetails(&fontWidth, &fontHeight);
/*
** create main form
*/
nargs = 0;
XtSetArg(args[nargs], XtNfromVert, fromVertWid); nargs++;
if (closeToVert) {
XtSetArg(args[nargs], XtNvertDistance, 0); nargs++;
}
disagreeFormWid = XtCreateManagedWidget("disagreeForm", formWidgetClass,
parentWid, args, nargs);
nargs = 0;
XtSetArg(args[nargs], XtNrows, 1); nargs++;
XtSetArg(args[nargs], XtNcolumns, NAMELEN); nargs++;
dummyWid = XtCreateManagedWidget("dummy", sheetWidgetClass,
disagreeFormWid, args, nargs);
nargs = 0;
XtSetArg(args[nargs], XtNrows, 1); nargs++;
XtSetArg(args[nargs], XtNcolumns, DEFAULT_DISPLAY_WIDTH); nargs++;
XtSetArg(args[nargs], XtNfromHoriz, dummyWid); nargs++;
disagreeWid = XtCreateManagedWidget("disagreements", sheetWidgetClass,
disagreeFormWid, args, nargs);
XtUninstallTranslations(dummyWid);
XtUninstallTranslations(disagreeWid);
return disagreeFormWid;
}
Widget CreateEditorShell(Widget parentWid)
/*
** Create all components of the
** Contig Editor
** and
** Join Editor
*/
{
Arg args[10];
int nargs;
Widget ed1Wid;
Widget ed2Wid;
Widget dw;
/*
** Create the contig editor shell
*/
editorShellWid = XtCreatePopupShell ("Editor",
topLevelShellWidgetClass,
parentWid,
NULL, (Cardinal) 0);
mainFormWid = XtCreateManagedWidget("mainForm", formWidgetClass,
editorShellWid,
NULL, (Cardinal) 0);
/*
** The form widget holds a label
*/
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, exitWid); nargs++;
labelWid = XtCreateManagedWidget("title", labelWidgetClass,
mainFormWid, args, nargs);
/*
** Button box for contig/join editor
*/
nargs = 0;
XtSetArg(args[nargs], XtNfromHoriz, labelWid); nargs++;
buttonsWid = XtCreateManagedWidget("buttons", boxWidgetClass,
mainFormWid, args, nargs);
/*
** Toggle widgets for insert/replace edit modes
*/
nargs = 0;
insertWid = XtCreateManagedWidget("insert", toggleWidgetClass,
buttonsWid, args, nargs);
nargs = 0;
XtSetArg(args[nargs], XtNradioGroup, insertWid); nargs++;
replaceWid = XtCreateManagedWidget("replace", toggleWidgetClass,
buttonsWid, args, nargs);
/*
** Superman toggle widget (for super-duper editing)
*/
nargs = 0;
supermanWid = XtCreateManagedWidget("superman", toggleWidgetClass,
buttonsWid, args, nargs);
/*
** Reveal cutoffs
*/
nargs = 0;
revealWid = XtCreateManagedWidget("reveal", toggleWidgetClass,
buttonsWid, args, nargs);
XtAddCallback(revealWid, XtNcallback, editRevealCallback, NULL );
/*
** Undo command button
*/
nargs = 0;
undoWid = XtCreateManagedWidget("undo", commandWidgetClass,
buttonsWid, args, nargs);
XtAddCallback(undoWid, XtNcallback, editUndoCallback, NULL );
/*
** Next (problem) command button
*/
nargs = 0;
nextWid = XtCreateManagedWidget("next", commandWidgetClass,
buttonsWid, args, nargs);
XtAddCallback(nextWid, XtNcallback, editNextCallback, NULL );
#ifdef nana
/*
** Save command button
*/
nargs = 0;
saveWid = XtCreateManagedWidget("save", commandWidgetClass,
buttonsWid, args, nargs);
XtAddCallback(saveWid, XtNcallback, editSaveCallback, NULL );
#endif
/*
** Lock command button
*/
nargs = 0;
lockWid = XtCreateManagedWidget("lock", toggleWidgetClass,
buttonsWid, args, nargs);
XtAddCallback(lockWid, XtNcallback, editLockCallback, NULL );
#ifdef nana
/*
** Join command button
*/
nargs = 0;
joinWid = XtCreateManagedWidget("join", commandWidgetClass,
buttonsWid, args, nargs);
XtAddCallback(joinWid, XtNcallback, editJoinCallback, NULL );
#endif
/*
** and an exit button
*/
nargs = 0;
exitWid = XtCreateManagedWidget("exit", commandWidgetClass,
buttonsWid, args, nargs);
XtAddCallback(exitWid, XtNcallback, editExitCallback, NULL );
/*
** create editor
*/
ed1Wid = createEditWid(mainFormWid,buttonsWid,0);
dw = createDisagreeWid(mainFormWid,ed1Wid,1);
ed2Wid = createEditWid(mainFormWid,dw,1);
/*
** Create tag editor
*/
(void) createTagEditor(parentWid);
/*
** Create search diologue
*/
(void) createSearchWidget(parentWid);
return editorShellWid;
}
int editModeIsInsert()
/*
** Find out if editor is in insert mode rather than replace mode
*/
{
String currMode;
currMode = (String) XawToggleGetCurrent(insertWid);
if (currMode == NULL)
return 0;
else
return (strcmp (currMode,"insert") == 0);
}
int editModeIsSuperman()
/*
** Find out if we are entitled to use privilaged edit commands
*/
{
Boolean currMode;
int nargs;
Arg args[10];
nargs=0;
XtSetArg(args[nargs], XtNstate, &currMode); nargs++;
XtGetValues(supermanWid, args, nargs);
return currMode;
}
int inJoinMode()
/*
** Find out if the editor is in join mode
*/
{
return editorMode==JOINMODE;
}
int editorLocked()
/*
** Find out if the editor is locked (and in join mode of course)
*/
{
Boolean currMode;
int nargs;
Arg args[10];
if (inJoinMode()) {
nargs=0;
XtSetArg(args[nargs], XtNstate, &currMode); nargs++;
XtGetValues(lockWid, args, nargs);
return (currMode);
} else
return 0;
}
int editorLockedPos(int force)
/*
** Find out the locked position
*/
{
if (force) {
EdStruct *xx0 = intToEdStruct(0);
EdStruct *xx1 = intToEdStruct(1);
return xx1->displayPos - xx0->displayPos;
} else
return (lockOffset);
}
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