1311 lines
36 KiB
C
1311 lines
36 KiB
C
/*
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Title: dialogues
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File: dialogues.c
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Purpose: Dialogues
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Last update: Thurs 31 October 1991
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Change log:
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27.11.90 SD outputOKCallback() now passes seqName in writeSeqABI() call
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28.11.90 SD put undesirables under STLOUIS compilation flag
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02.01.91 SD remerged with St Louis version
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22.07.91 LFW put in -enzyme as a command line option for STLOUIS
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17.09.91 LFW changed MRC switch to !AUTO_CLIP
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changed STLOUIS switch to OUT_SEQ
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31.10.91 SD Popup dialogue if file exists on output
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26.11.91 SD Added SCF format
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*/
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/* ---- Includes ---- */
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#include "values.h" /* IMPORT: MAXLONG */
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#include "dialogues.h"
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#include "display.h" /* IMPORT: displaySeq, unDisplaySeq */
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#include "info.h" /* IMPORT: info */
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#include "seq.h" /* IMPORT: Seq, NULLSeq */
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#include "seqRead.h" /* IMPORT: readSeq */
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#include "seqIOEdit.h" /* IMPORT: isDotNum, stripDotNum */
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#include "seqOutput.h" /* IMPORT: writeSeq */
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#include "match.h" /* IMPORT: writeSeq */
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#include <X11/Intrinsic.h>
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#include <X11/StringDefs.h>
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#include <X11/Shell.h>
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#include <X11/Xaw/AsciiText.h>
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#include <X11/Xaw/Box.h>
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#include <X11/Xaw/Label.h>
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#include <X11/Xaw/Form.h>
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#include <X11/Xaw/Toggle.h>
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#include <X11/Xaw/Dialog.h>
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/* ---- Globals ---- */
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char o_fn[200];
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char r_fn[200];
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/* ---- Statics ---- */
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static Seq currSeq = NULLSeq;
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static int indices[100]; /* array of starting indices of all of the
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matches a search for a string found */
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static int num_matches; /* total number of matches to a given
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string found in the currSeq */
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static int next_indices; /* the next indices to search for
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if the user wishes to search for
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the next occurence of string */
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/* ----- get resources -------*/
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/* allows you to get the default enzString to search for
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from the Xted file */
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typedef struct
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{ int magnif;
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String enz;
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} AppData, *AppDataPtr;
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#define XtNmagnif "magnif"
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#define XtCMagnif "Magnif"
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#define XtNenz "enz"
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#define XtCEnz "Enz"
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static XtResource resources[] = {
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{ XtNmagnif,
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XtCMagnif,
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XtRInt,
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sizeof(int),
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XtOffset(AppDataPtr, magnif),
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XtRImmediate,
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NULL
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},
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{ XtNenz,
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XtCEnz,
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XtRString,
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sizeof(String),
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XtOffset(AppDataPtr, enz),
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XtRImmediate,
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NULL
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}
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};
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void set_strand_label(Widget strandWid, Seq seq)
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{
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Cardinal nargs;
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Arg args[1];
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nargs = 0;
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if (seq->bottom) {
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XtSetArg(args[nargs], XtNlabel, "Strand: Bottom"); nargs++;
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} else {
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XtSetArg(args[nargs], XtNlabel, "Strand: Top"); nargs++;
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}
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XtSetValues(strandWid, args, nargs);
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}
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/* ---- Callbacks ---- */
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static void inputOKCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{
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Widget popupWid, nameValWid, radioGroupWid, radioGroupWid2;
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Widget seqNameWid, NorigBasesWid,strandWid;
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char *radioData, *radioData2, *fn;
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Arg args[10];
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int nargs;
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Seq oldSeq = currSeq;
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int bottom;
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char enzString[100];
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AppData app_data;
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popupWid = (Widget) client_data;
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nameValWid = XtNameToWidget(popupWid, "ioForm.nameVal");
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radioGroupWid = XtNameToWidget(popupWid, "ioForm.formatBox.plainFmt");
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radioGroupWid2 = XtNameToWidget(popupWid, "ioForm.formatBox.bottomFmt");
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seqNameWid = XtNameToWidget(XtParent(XtParent(popupWid)), "seqName");
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NorigBasesWid = XtNameToWidget(XtParent(XtParent(popupWid)), "NorigBases");
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strandWid = XtNameToWidget(XtParent(XtParent(popupWid)), "strand");
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XtGetApplicationResources(popupWid, (XtPointer) &app_data,
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resources, XtNumber(resources),
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NULL, 0);
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#ifndef AUTO_CLIP
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app_data.enz='\0';
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#endif
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/* LFW, 05.02.91, for command line option to work */
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if (strcmp(enzString,"")==0) {
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if (app_data.enz != NULL)
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strcpy(enzString,app_data.enz);
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else *enzString = '\0';
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}
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/*
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Get the name and type of the new one and read it in.
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*/
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nargs = 0;
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XtSetArg(args[nargs], XtNstring, &fn); nargs++;
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XtGetValues(nameValWid, args, nargs);
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radioData = (char *) XawToggleGetCurrent(radioGroupWid);
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radioData2 = (char *) XawToggleGetCurrent(radioGroupWid2);
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bottom = (strcmp(radioData2, "bottomFmt") == 0);
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currSeq = readSeq(fn,bottom,enzString,radioData);
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#ifdef DEF_OUT /* out_seq means default output file name
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of input_filename.seq */
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/* make a default output filename */
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sprintf(o_fn,"%s",fn);
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if (isDotNum(o_fn) != -1) stripDotNum(o_fn);
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#endif
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if (currSeq != NULLSeq)
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{ char NBasesString[10];
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XtDestroyWidget(popupWid);
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/*
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Undisplay and dispose of the old sequence.
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*/
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unDisplaySeq();
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freeSeq(oldSeq);
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/*
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Set the `file name' and `number of bases' labels.
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*/
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nargs = 0;
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XtSetArg(args[nargs], XtNlabel, fn); nargs++;
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XtSetValues(seqNameWid, args, nargs);
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nargs = 0;
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sprintf(NBasesString, "%d", getNBases(currSeq, OrigBases));
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XtSetArg(args[nargs], XtNlabel, NBasesString); nargs++;
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XtSetValues(NorigBasesWid, args, nargs);
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/* set strand label */
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set_strand_label(strandWid, currSeq);
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/* original line displaySeq(currSeq, -1, 1.0);,
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new line added by lfw: */
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displaySeq(currSeq, 1, 0.3);
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}
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else
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{ XBell(XtDisplay(popupWid), 100);
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nargs = 0;
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XtSetArg(args[nargs], XtNstring, ""); nargs++;
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XtSetValues(nameValWid, args, nargs);
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}
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}
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/********************************Check for overwriting***********************/
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#include <sys/types.h>
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#include <sys/stat.h>
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int checkOKwriteSeq(char *fn)
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/* See if file exists */
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{
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struct stat buf;
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return ( stat(fn,&buf) );
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}
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static void warningYesCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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/*
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** A yes response to the
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** warning about data not saved
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*/
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{
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int *response = (int *) client_data;
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*response = 1;
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}
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static void warningNoCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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/*
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** A No response to the
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** warning about data not saved
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*/
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{
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int *response = (int *) client_data;
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*response = 0;
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}
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static int warning(Widget parentWid, String warn_message)
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/*
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** Warn that changes have been made but contig hasn't been saved.
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*/
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{
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Widget dialog;
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Arg args[10];
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int nargs;
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int Response;
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Widget warningWid, warnFormWid;
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Position x, y;
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/*
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Position the upper left hand corner of the popup at the
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center of the parent widget.
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*/
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XtTranslateCoords(parentWid,
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(Position) 0, (Position) 0,
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&x, &y);
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nargs = 0;
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XtSetArg(args[nargs], XtNx, x); nargs++;
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XtSetArg(args[nargs], XtNy, y); nargs++;
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warningWid = XtCreatePopupShell("warning", transientShellWidgetClass,
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parentWid,
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args, nargs);
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/* Create the form */
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nargs = 0;
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warnFormWid = XtCreateManagedWidget("warnForm", formWidgetClass,
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warningWid, args, nargs);
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/* Create the form */
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nargs = 0;
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XtSetArg(args[nargs],XtNlabel,warn_message); nargs++;
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dialog = XtCreateManagedWidget("warnwid", dialogWidgetClass,
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warnFormWid, args, nargs);
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XawDialogAddButton(dialog,"Yes",warningYesCallback,(XtPointer)&Response);
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XawDialogAddButton(dialog,"No",warningNoCallback,(XtPointer)&Response);
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/* This is a modal dialogue */
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Response = -1;
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XtPopup(warningWid, XtGrabExclusive);
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while (Response==-1)
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{
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XEvent event;
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XtAppNextEvent(XtWidgetToApplicationContext(parentWid), &event);
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XtDispatchEvent(&event);
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}
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XtDestroyWidget(warningWid);
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return Response;
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}
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int check_file_is_ok(Widget w, char *fn)
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{
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if (!checkOKwriteSeq(fn)) {
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return warning(w,"File already exists\nOK to overwrite?");
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} else
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return 1;
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}
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/********************************************************************/
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static void inputCancelCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid = (Widget) client_data;
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XtDestroyWidget(popupWid);
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}
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static void outputOKCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid, nameValWid, radioGroupWid, seqNameWid;
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Widget includeHeaderWid;
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char *fn, *seqName;
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Boolean rc;
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Boolean includeHeader;
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Arg args[10];
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int nargs;
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popupWid = (Widget) client_data;
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nameValWid = XtNameToWidget(popupWid, "ioForm.nameVal");
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radioGroupWid = XtNameToWidget(popupWid, "ioForm.formatBox.plainFmt");
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includeHeaderWid = XtNameToWidget(popupWid, "ioForm.includeHeader");
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seqNameWid = XtNameToWidget(XtParent(XtParent(popupWid)), "seqName");
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nargs = 0;
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XtSetArg(args[nargs], XtNlabel, &seqName); nargs++;
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XtGetValues(seqNameWid, args, nargs);
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nargs = 0;
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XtSetArg(args[nargs], XtNstring, &fn); nargs++;
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XtGetValues(nameValWid, args, nargs);
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nargs = 0;
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XtSetArg(args[nargs], XtNstate, &includeHeader); nargs++;
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XtGetValues(includeHeaderWid, args, nargs);
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if (check_file_is_ok(w,fn)) {
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rc=writeSeq(currSeq, fn, (strlen(r_fn)==0)?seqName:r_fn,includeHeader);
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if (rc)
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{ XtDestroyWidget(popupWid);
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setDirty(currSeq, False);
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}
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else
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{ XBell(XtDisplay(popupWid), 100);
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nargs = 0;
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XtSetArg(args[nargs], XtNstring, ""); nargs++;
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XtSetValues(nameValWid, args, nargs);
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}
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} else
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XBell(XtDisplay(popupWid), 100);
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}
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static void outputCancelCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid = (Widget) client_data;
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XtDestroyWidget(popupWid);
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}
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static void checkOKCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid, parentWid;
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popupWid = (Widget) client_data;
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parentWid = XtParent(popupWid);
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XtDestroyWidget(popupWid);
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/*
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The user does want to overwrite the existing sequence.
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Mark it as clean so `inputSeq' will dispose of it.
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*/
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setDirty(currSeq, False);
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inputSeq(parentWid);
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}
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static void checkCancelCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid = (Widget) client_data;
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XtDestroyWidget(popupWid);
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}
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static void quitOKCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid = (Widget) client_data;
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XtDestroyWidget(popupWid);
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/*
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The user does not want to save the existing sequence.
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Quit the application.
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*/
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freeSeq(currSeq);
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XtDestroyApplicationContext(XtWidgetToApplicationContext(w));
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exit(0);
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}
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static void quitCancelCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid = (Widget) client_data;
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XtDestroyWidget(popupWid);
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/*
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The user does not want to quit the application.
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*/
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}
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static void searchCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
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{ Widget popupWid, nameValWid, NorigBasesWid, nextWid;
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char *astring;
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Arg args[10];
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int nargs;
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int num,i,num_bases,baseNum;
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int mag;
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char *theSeq;
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popupWid = (Widget) client_data;
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nameValWid = XtNameToWidget(popupWid, "ioForm.nameVal");
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NorigBasesWid = XtNameToWidget(XtParent(XtParent(popupWid)), "NorigBases");
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nextWid = XtNameToWidget(popupWid, "ioForm.next");
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next_indices = 0;
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num_matches = 0;
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/*
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Get the name and type of the new one and read it in.
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*/
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nargs = 0;
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XtSetArg(args[nargs], XtNstring, &astring); nargs++;
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XtGetValues(nameValWid, args, nargs);
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if (currSeq != NULLSeq)
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{
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/* astring != NULL, find the string that corresponds
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to the app_resources.astring and center the display on that string,
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change by lfw, 10/24/90 from this line to free line */
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if (astring != NULL) {
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num = 1; /* num = 1 if astring is a basenum and 0 if alpha */
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for (i = 0; i < strlen(astring); i++)
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if (!isdigit(astring[i])) {
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num = 0;
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break;
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}
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if (num==0) {
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for (i = 0; i < strlen(astring); i++)
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if (islower(astring[i])) astring[i]=toupper(astring[i]);
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}
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/* if any of the entries were alphabetic, the program
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searches for a string */
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if (num == 0) {
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num_bases = getNBases(currSeq,EdBases);
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theSeq = (char *)calloc(num_bases,sizeof(char));
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for (i = 0; i < num_bases; i++)
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theSeq[i] = getBase(currSeq, EdBases, i);
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num_matches = string_match(astring,strlen(astring),theSeq,num_bases,
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0, indices);
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if (num_matches == 0) baseNum = -5;
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else {
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baseNum = indices[0];
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next_indices++;
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}
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free(theSeq);
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}
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else {
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sscanf(astring,"%d",&baseNum) ;
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/* if (currSeq->bottom) baseNum = currSeq->NorigBases - 1 - baseNum;*/
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}
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mag = -5; /* by setting magnification to -5, the displaySeq
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routine will go and back calculate the current
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magnification */
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if (baseNum != -5) {
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displaySeq(currSeq,
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((baseNum!=NULLBaseNum) &&
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(baseNum>=0) &&
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(baseNum<getNBases(currSeq,OrigBases))
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)
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? baseNum
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: NULLBaseNum,
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mag
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);
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if (num_matches > 1) {
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nargs = 0;
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XtSetArg(args[nargs], XtNlabel, "Next?"); nargs++;
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XtSetValues(nextWid, args, nargs);
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}
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else
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XtDestroyWidget(popupWid);
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}
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else {
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nargs = 0;
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XtSetArg(args[nargs], XtNstring, "String not found"); nargs++;
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XtSetValues(nameValWid, args, nargs);
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}
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}
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}
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else
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XBell(XtDisplay(NorigBasesWid), 100);
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}
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static void searchNextCallback(Widget w,
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XtPointer client_data, XtPointer call_data)
|
|
{ Widget popupWid, nextWid;
|
|
Arg args[10];
|
|
int nargs;
|
|
int baseNum;
|
|
int mag;
|
|
|
|
popupWid = (Widget) client_data;
|
|
nextWid = XtNameToWidget(popupWid, "ioForm.next");
|
|
|
|
if (currSeq != NULLSeq)
|
|
{
|
|
mag = -5; /* by setting magnification to -5, the displaySeq
|
|
routine will go and back calculate the current
|
|
magnification */
|
|
if (next_indices < num_matches) {
|
|
baseNum = indices[next_indices];
|
|
next_indices++;
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNlabel, "Next?"); nargs++;
|
|
XtSetValues(nextWid, args, nargs);
|
|
|
|
displaySeq(currSeq,
|
|
((baseNum!=NULLBaseNum) &&
|
|
(baseNum>=0) &&
|
|
(baseNum<getNBases(currSeq,OrigBases))
|
|
)
|
|
? baseNum
|
|
: NULLBaseNum,
|
|
mag
|
|
);
|
|
}
|
|
else
|
|
XtDestroyWidget(popupWid);
|
|
}
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
/* ---- Action procedures ---- */
|
|
|
|
|
|
static void CRAction(Widget w, XEvent *event,
|
|
String *params, Cardinal *num_params)
|
|
/*
|
|
Action procedure to be called when CR is hit.
|
|
|
|
This may be called from the `ioform' directly in the case of a
|
|
`check' dialogue, or from an `ioform.nameVal' widget in the case
|
|
of an input or ouput dialogue.
|
|
We must call the `default' button callback procedure. We can
|
|
detect which is the default by looking at its borderwidth, the
|
|
default one being of size 3.
|
|
*/
|
|
{ Widget ioFormWid, okWid, cancelWid;
|
|
Arg args[10];
|
|
int nargs;
|
|
Dimension width;
|
|
|
|
ioFormWid = (strcmp("ioform", XtName(w))==0) ? w : XtParent(w);
|
|
okWid = XtNameToWidget(ioFormWid, "*OK");
|
|
cancelWid = XtNameToWidget(ioFormWid, "*Cancel");
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNborderWidth, &width); nargs++;
|
|
XtGetValues(okWid, args, nargs);
|
|
|
|
XtCallCallbacks((width==3) ? okWid : cancelWid,
|
|
XtNcallback, NULL);
|
|
}
|
|
|
|
|
|
|
|
|
|
/* ---- Internal functions ---- */
|
|
|
|
|
|
void checkInputSeq(Widget parentWid)
|
|
{ Widget checkWid, ioFormWid, ioPromptWid;
|
|
Widget okWid, cancelWid;
|
|
Arg args[10];
|
|
int nargs;
|
|
Position x, y;
|
|
Dimension width, height;
|
|
|
|
|
|
/* Add string to function bindings for our application actions */
|
|
XtActionsRec actionTable[] = { {"CRAction", CRAction} };
|
|
XtAppAddActions(XtWidgetToApplicationContext(parentWid),
|
|
actionTable, XtNumber(actionTable));
|
|
|
|
|
|
/*
|
|
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) (width / 2), (Position) (height / 2),
|
|
&x, &y);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNx, x); nargs++;
|
|
XtSetArg(args[nargs], XtNy, y); nargs++;
|
|
checkWid = XtCreatePopupShell("check", transientShellWidgetClass,
|
|
parentWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
ioFormWid = XtCreateManagedWidget("ioForm", formWidgetClass,
|
|
checkWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
ioPromptWid = XtCreateManagedWidget("ioPrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
okWid = XtCreateManagedWidget("OK", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(okWid, XtNcallback,
|
|
checkOKCallback, (XtPointer) checkWid);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, okWid); nargs++;
|
|
cancelWid = XtCreateManagedWidget("Cancel", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(cancelWid, XtNcallback,
|
|
checkCancelCallback, (XtPointer) checkWid);
|
|
|
|
|
|
/* This is a modal dialogue */
|
|
XtPopup(checkWid, XtGrabExclusive);
|
|
}
|
|
|
|
#ifdef nodef
|
|
int string_match(seq1, n1, seq2, n2, nmiss, indices)
|
|
|
|
/*
|
|
This function may be called once from initialDisplayedSeq if
|
|
the user has input a string they wish to search for in the
|
|
input sequence -- this subroutine returns *indices, the first
|
|
position at which the query sequence (app_resources.astring)
|
|
matched the input file sequence (currSeq). */
|
|
|
|
/* a modified version of match.c
|
|
finds alignments between a search sequence, seq1, and a target sequence,
|
|
seq2, with no gaps (except possibly at ends)
|
|
and at most nmiss mismatches (relative to seq1),
|
|
n1 is the length of seq1 where seq1 is assumed to start at indices 0,
|
|
n2 is the length of seq2 where seq2 is assumed to start at indices 0 */
|
|
char *seq1, *seq2;
|
|
int n1, n2, nmiss;
|
|
int *indices;
|
|
{
|
|
int i, j, d, istart, iend, i_miss, n_match;
|
|
int mtable[100][5]; /* 100 would be, now the total number
|
|
of matches the program may find between
|
|
a given input string and the sequence */
|
|
|
|
|
|
/* d = j - i is the "offset" between the two sequences */
|
|
if (n1 - n2 > nmiss) return (0);
|
|
n_match = 0;
|
|
for (d = -nmiss; d <= n2 + nmiss - n1; d++){
|
|
if (d < 0) istart = i_miss = -d;
|
|
else istart = i_miss = 0;
|
|
if (d > n2 - n1) {
|
|
iend = n2 - d;
|
|
i_miss += n1 + d - n2;
|
|
}
|
|
else iend = n1;
|
|
for (i = istart, j = d + i; i < iend; i++, j++)
|
|
if (seq1[i] != seq2[j] && ++i_miss > nmiss) goto nextd;
|
|
/* VOMIT! I want to PUKE!!!! who put this horrid goto here? */
|
|
mtable[n_match][0] = d + istart; /* indices (assuming they start at
|
|
0) of starting nucleotide in the
|
|
searched sequence */
|
|
mtable[n_match][1] = istart; /* nucleotide position in the query
|
|
sequence where match starts (assuming
|
|
query index starts with 0) */
|
|
mtable[n_match][2] = iend - istart; /* number of nucleotides in the
|
|
match */
|
|
if (mtable[n_match][2]==n1) {
|
|
indices[n_match] = mtable[n_match][0];
|
|
}
|
|
|
|
mtable[n_match][3] = i_miss; /* number of mismatches */
|
|
n_match++; /* number of matches */
|
|
if (n_match >= 100) return(n_match);
|
|
|
|
nextd:;
|
|
}
|
|
|
|
return (n_match);
|
|
/* return(0); *//*return 0 if it got to this point; that means
|
|
it must have not found an exact match, so
|
|
you want the baseNum to be 0 in that case*/
|
|
}
|
|
#endif /*nodef*/
|
|
|
|
|
|
|
|
|
|
|
|
/* ---- Exports ---- */
|
|
|
|
|
|
|
|
|
|
void inputSeq(Widget parentWid)
|
|
/*
|
|
Set up a dialogue which will read in and display a sequence.
|
|
*/
|
|
{ Widget inputWid, ioFormWid, ioPromptWid;
|
|
Widget namePromptWid, nameValWid;
|
|
Widget formatPromptWid, formatBoxWid, plainFmtWid, abiFmtWid, scfFmtWid;
|
|
Widget alfFmtWid;
|
|
Widget okWid, cancelWid;
|
|
Widget bottomFmtWid, topFmtWid;
|
|
Arg args[10];
|
|
int nargs;
|
|
Position x, y;
|
|
Dimension width, height;
|
|
|
|
|
|
/* Add string to function bindings for our application actions */
|
|
XtActionsRec actionTable[] = { {"CRAction", CRAction} };
|
|
XtAppAddActions(XtWidgetToApplicationContext(parentWid),
|
|
actionTable, XtNumber(actionTable));
|
|
|
|
|
|
/*
|
|
Check whether there is an existing sequence which
|
|
is dirty which needs saving.
|
|
*/
|
|
if (currSeq!=NULLSeq && isDirty(currSeq))
|
|
{ checkInputSeq(parentWid);
|
|
return;
|
|
}
|
|
|
|
|
|
/*
|
|
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) (width / 2), (Position) (height / 2),
|
|
&x, &y);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNx, x); nargs++;
|
|
XtSetArg(args[nargs], XtNy, y); nargs++;
|
|
inputWid = XtCreatePopupShell("input", transientShellWidgetClass,
|
|
parentWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
ioFormWid = XtCreateManagedWidget("ioForm", formWidgetClass,
|
|
inputWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
ioPromptWid = XtCreateManagedWidget("ioPrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
namePromptWid = XtCreateManagedWidget("namePrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, namePromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNeditType, XawtextEdit); nargs++;
|
|
nameValWid = XtCreateManagedWidget("nameVal", asciiTextWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, namePromptWid); nargs++;
|
|
formatPromptWid = XtCreateManagedWidget("formatPrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, namePromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, formatPromptWid); nargs++;
|
|
formatBoxWid = XtCreateManagedWidget("formatBox", boxWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
plainFmtWid = XtCreateManagedWidget("plainFmt", toggleWidgetClass,
|
|
formatBoxWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNradioGroup, plainFmtWid); nargs++;
|
|
abiFmtWid = XtCreateManagedWidget("abiFmt", toggleWidgetClass,
|
|
formatBoxWid,
|
|
args, nargs);
|
|
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNradioGroup, abiFmtWid); nargs++;
|
|
alfFmtWid = XtCreateManagedWidget("alfFmt", toggleWidgetClass,
|
|
formatBoxWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNradioGroup, abiFmtWid); nargs++;
|
|
scfFmtWid = XtCreateManagedWidget("scfFmt", toggleWidgetClass,
|
|
formatBoxWid,
|
|
args, nargs);
|
|
|
|
|
|
nargs = 0;
|
|
bottomFmtWid = XtCreateManagedWidget("bottomFmt", toggleWidgetClass,
|
|
formatBoxWid,
|
|
args, nargs);
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNradioGroup, bottomFmtWid); nargs++;
|
|
topFmtWid = XtCreateManagedWidget("topFmt", toggleWidgetClass,
|
|
formatBoxWid,
|
|
args, nargs);
|
|
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, formatPromptWid); nargs++;
|
|
okWid = XtCreateManagedWidget("OK", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(okWid, XtNcallback, inputOKCallback, (XtPointer) inputWid);
|
|
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, formatPromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, okWid); nargs++;
|
|
cancelWid = XtCreateManagedWidget("Cancel", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(cancelWid, XtNcallback,
|
|
inputCancelCallback, (XtPointer) inputWid);
|
|
|
|
|
|
/* nameVal (text) widget gets the keyboard focus */
|
|
XtSetKeyboardFocus(ioFormWid, nameValWid);
|
|
|
|
|
|
/* This is a modal dialogue */
|
|
XtPopup(inputWid, XtGrabExclusive);
|
|
}
|
|
|
|
|
|
|
|
|
|
void outputSeq(Widget parentWid, String defaultFileName)
|
|
/*
|
|
Save the current sequence using the deafult file name, if given.
|
|
*/
|
|
{ Widget outputWid, ioFormWid, ioPromptWid;
|
|
Widget namePromptWid, nameValWid;
|
|
Widget includeHeaderWid,plainFormatWid;
|
|
Widget okWid, cancelWid;
|
|
Arg args[10];
|
|
int nargs;
|
|
Position x, y;
|
|
Dimension width, height;
|
|
|
|
|
|
/* Add string to function bindings for our application actions */
|
|
XtActionsRec actionTable[] = { {"CRAction", CRAction} };
|
|
XtAppAddActions(XtWidgetToApplicationContext(parentWid),
|
|
actionTable, XtNumber(actionTable));
|
|
|
|
|
|
/* If there is no current sequence, then return */
|
|
if (currSeq==NULLSeq) return;
|
|
|
|
|
|
/*
|
|
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) (width / 2), (Position) (height / 2),
|
|
&x, &y);
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNx, x); nargs++;
|
|
XtSetArg(args[nargs], XtNy, y); nargs++;
|
|
outputWid = XtCreatePopupShell("output", transientShellWidgetClass,
|
|
parentWid,
|
|
args, nargs);
|
|
|
|
/* Create the form */
|
|
nargs = 0;
|
|
ioFormWid = XtCreateManagedWidget("ioForm", formWidgetClass,
|
|
outputWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
ioPromptWid = XtCreateManagedWidget("ioPrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
namePromptWid = XtCreateManagedWidget("namePrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, namePromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNeditType, XawtextEdit); nargs++;
|
|
XtSetArg(args[nargs], XtNstring, defaultFileName); nargs++;
|
|
nameValWid = XtCreateManagedWidget("nameVal", asciiTextWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
/* Set the insertion point after the text - dodgy method used */
|
|
XawTextSetInsertionPoint(nameValWid, MAXLONG);
|
|
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNstate, True); nargs++;
|
|
XtSetArg(args[nargs], XtNfromVert, namePromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNlabel, "Include Header"); nargs++;
|
|
includeHeaderWid = XtCreateManagedWidget("includeHeader", toggleWidgetClass,
|
|
ioFormWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNstate, False); nargs++;
|
|
XtSetArg(args[nargs], XtNfromVert, namePromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, includeHeaderWid); nargs++;
|
|
XtSetArg(args[nargs], XtNlabel, "Plain Format"); nargs++;
|
|
XtSetArg(args[nargs], XtNradioGroup, includeHeaderWid); nargs++;
|
|
plainFormatWid = XtCreateManagedWidget("plainFormat", toggleWidgetClass,
|
|
ioFormWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, includeHeaderWid); nargs++;
|
|
okWid = XtCreateManagedWidget("OK", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(okWid, XtNcallback, outputOKCallback, (XtPointer) outputWid);
|
|
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, includeHeaderWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, okWid); nargs++;
|
|
cancelWid = XtCreateManagedWidget("Cancel", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(cancelWid, XtNcallback,
|
|
outputCancelCallback, (XtPointer) outputWid);
|
|
|
|
/* nameVal (text) widget gets the keyboard focus */
|
|
XtSetKeyboardFocus(ioFormWid, nameValWid);
|
|
|
|
|
|
/* This is a modal dialogue */
|
|
XtPopup(outputWid, XtGrabExclusive);
|
|
}
|
|
|
|
|
|
|
|
|
|
void quitApplication(Widget parentWid)
|
|
/*
|
|
This function must be called to exit the application.
|
|
It ensures any current sequence is saved.
|
|
*/
|
|
{ Widget ioFormWid, ioPromptWid, quitWid;
|
|
Widget okWid, cancelWid;
|
|
Arg args[10];
|
|
int nargs;
|
|
Position x, y;
|
|
Dimension width, height;
|
|
|
|
|
|
/* Add string to function bindings for our application actions */
|
|
XtActionsRec actionTable[] = { {"CRAction", CRAction} };
|
|
XtAppAddActions(XtWidgetToApplicationContext(parentWid),
|
|
actionTable, XtNumber(actionTable));
|
|
|
|
|
|
/*
|
|
Check whether there is an existing sequence which
|
|
is dirty which needs saving.
|
|
*/
|
|
if (currSeq==NULLSeq || !isDirty(currSeq))
|
|
{ free(currSeq);
|
|
XtDestroyApplicationContext(XtWidgetToApplicationContext(parentWid));
|
|
exit(0);
|
|
}
|
|
|
|
|
|
/*
|
|
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) (width / 2), (Position) (height / 2),
|
|
&x, &y);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNx, x); nargs++;
|
|
XtSetArg(args[nargs], XtNy, y); nargs++;
|
|
quitWid = XtCreatePopupShell("quit", transientShellWidgetClass,
|
|
parentWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
ioFormWid = XtCreateManagedWidget("ioForm", formWidgetClass,
|
|
quitWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
ioPromptWid = XtCreateManagedWidget("ioPrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
okWid = XtCreateManagedWidget("OK", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(okWid, XtNcallback,
|
|
quitOKCallback, (XtPointer) quitWid);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, okWid); nargs++;
|
|
cancelWid = XtCreateManagedWidget("Cancel", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(cancelWid, XtNcallback,
|
|
quitCancelCallback, (XtPointer) quitWid);
|
|
|
|
|
|
/* This is a modal dialogue */
|
|
XtPopup(quitWid, XtGrabExclusive);
|
|
}
|
|
|
|
|
|
|
|
|
|
void initialDisplayedSeq(Widget toplevelWid,
|
|
char *format, char *fn,
|
|
int baseNum, int mag, char *astring,
|
|
char *enzyme, int bottom)
|
|
/*
|
|
This function may be called once, after the application
|
|
has been realised, to specify a sequence to be displayed
|
|
initially. If it is not called, no sequence is initially
|
|
displayed.
|
|
*/
|
|
{ Arg args[10];
|
|
int nargs;
|
|
int i;
|
|
char NBasesString[10];
|
|
char *theSeq;
|
|
AppData app_data;
|
|
char enzString[100];
|
|
|
|
|
|
int num_bases;
|
|
Widget seqNameWid = XtNameToWidget(toplevelWid, "mainForm.seqName");
|
|
Widget NorigBasesWid = XtNameToWidget(toplevelWid, "mainForm.NorigBases");
|
|
num_matches = 0;
|
|
next_indices = 0;
|
|
|
|
XtGetApplicationResources(seqNameWid, (XtPointer) &app_data,
|
|
resources, XtNumber(resources),
|
|
NULL, 0);
|
|
|
|
#ifndef AUTO_CLIP
|
|
app_data.enz='\0';
|
|
#endif
|
|
|
|
/* enzyme will already equal either the app_resources.enz or
|
|
app_data.enz, lfw 05.02.91*/
|
|
if (enzyme!=NULL)
|
|
strcpy(enzString,enzyme);
|
|
/* if (app_data.enz != NULL)
|
|
strcpy(enzString,app_data.enz);*/
|
|
else *enzString = '\0';
|
|
|
|
|
|
|
|
/* read a sequence */
|
|
currSeq = readSeq(fn,bottom,enzString,format);
|
|
|
|
if (currSeq != NULLSeq)
|
|
{
|
|
/*
|
|
Set the `file name' and `number of bases' labels.
|
|
*/
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNlabel, fn); nargs++;
|
|
XtSetValues(seqNameWid, args, nargs);
|
|
nargs = 0;
|
|
sprintf(NBasesString, "%d", getNBases(currSeq, OrigBases));
|
|
XtSetArg(args[nargs], XtNlabel, NBasesString); nargs++;
|
|
XtSetValues(NorigBasesWid, args, nargs);
|
|
|
|
/* astring != NULL, find the string that corresponds
|
|
to the app_resources.astring and center the display on that string,
|
|
change by lfw, 10/24/90 from this line to free line */
|
|
|
|
if (astring != NULL) {
|
|
num_bases = getNBases(currSeq,EdBases);
|
|
theSeq = (char *)calloc(num_bases,sizeof(char));
|
|
for (i = 0; i < num_bases; i++)
|
|
theSeq[i] = getBase(currSeq, EdBases, i);
|
|
|
|
num_matches = string_match(astring,strlen(astring),theSeq,num_bases,
|
|
0, indices);
|
|
baseNum = indices[0];
|
|
if (num_matches == 0) baseNum = 0;
|
|
|
|
free(theSeq);
|
|
}
|
|
|
|
displaySeq(currSeq,
|
|
((baseNum!=NULLBaseNum) &&
|
|
(baseNum>=0) &&
|
|
(baseNum<getNBases(currSeq,OrigBases))
|
|
)
|
|
? baseNum
|
|
: NULLBaseNum,
|
|
mag
|
|
);
|
|
}
|
|
else
|
|
XBell(XtDisplay(NorigBasesWid), 100);
|
|
|
|
}
|
|
|
|
|
|
void inputSearchString(Widget parentWid)
|
|
/*
|
|
Set up a dialogue which will read in a search for a baseNum or string
|
|
and center the display on that baseNum, added by lfw 12/04/90
|
|
*/
|
|
{ Widget searchWid, ioFormWid, ioPromptWid;
|
|
Widget nameValWid, nextWid;
|
|
Widget okWid, cancelWid;
|
|
Arg args[10];
|
|
int nargs;
|
|
Position x, y;
|
|
Dimension width, height;
|
|
|
|
|
|
/* Add string to function bindings for our application actions */
|
|
XtActionsRec actionTable[] = { {"CRAction", CRAction} };
|
|
XtAppAddActions(XtWidgetToApplicationContext(parentWid),
|
|
actionTable, XtNumber(actionTable));
|
|
|
|
/*
|
|
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) (width / 2), (Position) (height / 2),
|
|
&x, &y);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNx, x); nargs++;
|
|
XtSetArg(args[nargs], XtNy, y); nargs++;
|
|
searchWid = XtCreatePopupShell("search", transientShellWidgetClass,
|
|
parentWid,
|
|
args, nargs);
|
|
|
|
nargs = 0;
|
|
ioFormWid = XtCreateManagedWidget("ioForm", formWidgetClass,
|
|
searchWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
ioPromptWid = XtCreateManagedWidget("ioPrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
/* nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
namePromptWid = XtCreateManagedWidget("namePrompt", labelWidgetClass,
|
|
ioFormWid, args, nargs);*/
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, ioPromptWid); nargs++;
|
|
/* XtSetArg(args[nargs], XtNfromHoriz, namePromptWid); nargs++;*/
|
|
XtSetArg(args[nargs], XtNeditType, XawtextEdit); nargs++;
|
|
nameValWid = XtCreateManagedWidget("nameVal", asciiTextWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, nameValWid); nargs++;
|
|
okWid = XtCreateManagedWidget("OK", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(okWid, XtNcallback, searchCallback, (XtPointer) searchWid);
|
|
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, nameValWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, okWid); nargs++;
|
|
cancelWid = XtCreateManagedWidget("Cancel", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(cancelWid, XtNcallback,
|
|
inputCancelCallback, (XtPointer) searchWid);
|
|
|
|
|
|
|
|
nargs = 0;
|
|
XtSetArg(args[nargs], XtNfromVert, nameValWid); nargs++;
|
|
XtSetArg(args[nargs], XtNfromHoriz, cancelWid); nargs++;
|
|
nextWid = XtCreateManagedWidget("next", commandWidgetClass,
|
|
ioFormWid, args, nargs);
|
|
XtAddCallback(nextWid, XtNcallback,
|
|
searchNextCallback, (XtPointer) searchWid);
|
|
|
|
|
|
|
|
/* nameVal (text) widget gets the keyboard focus */
|
|
XtSetKeyboardFocus(ioFormWid, nameValWid);
|
|
|
|
|
|
/* This is a modal dialogue */
|
|
XtPopup(searchWid, XtGrabExclusive);
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
void information (Widget w)
|
|
/*
|
|
** Display sequence and trace information gleaned from the sequence file
|
|
*/
|
|
{
|
|
|
|
info(w, currSeq);
|
|
|
|
}
|