diff --git a/belvu.c b/belvu.c
index 30ab956b32b6755ee174ccca555d5845bb70f0f1..3558dd8bd57beaa018729564b523b0ba6e2e58c6 100644
--- a/belvu.c
+++ b/belvu.c
@@ -249,7 +249,7 @@
* HISTORY:
* Last edited: May 28 11:43 2008 (edgrif)
* Created: Aug 03 1994 (Erik.Sonnhammer@cgb.ki.se)
- * CVS info: $Id: belvu.c,v 1.1 2009-11-03 18:28:23 edgrif Exp $
+ * CVS info: $Id: belvu.c,v 1.2 2010-08-31 15:30:55 gb10 Exp $
*/
@@ -291,8 +291,6 @@
#include <wh/graph.h>
#include <wh/gex.h>
#include <wh/key.h>
-#define BELVU /* Fix horrible include mess in dotter_.h */
-#include <wh/dotter_.h>
#include <wh/menu.h>
diff --git a/blxdotter.c b/blxdotter.c
index 5bd47cbc5e051f8ed64deab0a7d429a858142b70..1da2249afd43fbc037f297b7dfaa5cc5287dc75e 100644
--- a/blxdotter.c
+++ b/blxdotter.c
@@ -1004,21 +1004,16 @@ gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **erro
return FALSE;
}
- /* Get the match sequence. Blixem uses g_malloc consistently now to allocate
- * strings but unfortunately dotter will free this string with messfree, so
- * we need to copy the result into a string allocated with messalloc. */
+ /* Get the match sequence. */
GError *tmpError = NULL;
- char *dotterSSeqTemp = getDotterSSeq(blxWindow, &tmpError);
- if (!dotterSSeqTemp)
+ char *dotterSSeq = getDotterSSeq(blxWindow, &tmpError);
+
+ if (!dotterSSeq)
{
g_propagate_error(error, tmpError);
return FALSE;
}
- char *dotterSSeq = messalloc(strlen(dotterSSeqTemp) + 1);
- strcpy(dotterSSeq, dotterSSeqTemp);
- g_free(dotterSSeqTemp);
-
/* Get the coords */
int dotterStart = UNSET_INT, dotterEnd = UNSET_INT, dotterZoom = 0;
if (!getDotterRange(blxWindow, dotterSSeq, FALSE, &dotterStart, &dotterEnd, &dotterZoom, &tmpError))
@@ -1031,30 +1026,25 @@ gboolean callDotter(GtkWidget *blxWindow, const gboolean hspsOnly, GError **erro
const BlxStrand strand = bc->seqType == BLXSEQ_DNA ? mspGetRefStrand(firstMsp) : blxWindowGetActiveStrand(blxWindow);
const int frame = mspGetRefFrame(firstMsp, bc->seqType);
- char *querySeqSegmentTemp = getSequenceSegment(bc,
- bc->refSeq,
- dotterStart,
- dotterEnd,
- strand,
- BLXSEQ_DNA, /* calculated dotter coords are always in terms of DNA seq */
- frame,
- FALSE, /* input coords are always left-to-right, even if display reversed */
- bc->displayRev, /* whether to reverse */
- bc->displayRev, /* whether to allow rev strands to be complemented */
- FALSE, /* don't allow translation to a peptide seq */
- &tmpError);
-
- if (!querySeqSegmentTemp)
+ char *querySeqSegment = getSequenceSegment(bc,
+ bc->refSeq,
+ dotterStart,
+ dotterEnd,
+ strand,
+ BLXSEQ_DNA, /* calculated dotter coords are always in terms of DNA seq */
+ frame,
+ FALSE, /* input coords are always left-to-right, even if display reversed */
+ bc->displayRev, /* whether to reverse */
+ bc->displayRev, /* whether to allow rev strands to be complemented */
+ FALSE, /* don't allow translation to a peptide seq */
+ &tmpError);
+
+ if (!querySeqSegment)
{
g_propagate_error(error, tmpError);
return FALSE;
}
- /* Again, dotter will free this with messfree, so we need to pass a string allocated with messalloc */
- char *querySeqSegment = messalloc(strlen(querySeqSegmentTemp) + 1);
- strcpy(querySeqSegment, querySeqSegmentTemp);
- g_free(querySeqSegmentTemp);
-
/* Get the match sequence name (chopping off the letters before the colon, if there is one). */
const char *dotterSName = strchr(mspGetSName(firstMsp), ':');
if (dotterSName)
diff --git a/dotter.c b/dotter.c
index 0657c408019963bcbc8124bc3015a25bab69fd48..ddd5c67427122a72ad45404c3a970e7713f68b9c 100644
--- a/dotter.c
+++ b/dotter.c
@@ -29,7 +29,7 @@
* * Mar 17 16:24 1999 (edgrif): Fixed bug which crashed xace when a
* negative alignment length was given.
* Created: Wed Mar 17 16:23:21 1999 (edgrif)
- * CVS info: $Id: dotter.c,v 1.11 2010-08-24 12:27:59 gb10 Exp $
+ * CVS info: $Id: dotter.c,v 1.12 2010-08-31 15:30:55 gb10 Exp $
*-------------------------------------------------------------------
*/
@@ -247,6 +247,7 @@ static int gArrayGetLen(GArray *array);
#define drawBlastHSPlinefStr "Draw Blast HSPs (colour = f(score))"
#define togglePixelmapStr "Pixelmap"
+
static void dotterRampChange(BOOL isDrag);
static MENU dotterMenu ;
static MENUOPT mainMenu[] = {
@@ -532,7 +533,7 @@ void dotter (char type,
{
int i;
- messalloccheck();
+// messalloccheck();
/* Reset global statics */
resfac = PixelmapON = 1;
@@ -552,7 +553,7 @@ void dotter (char type,
blastx = 1;
resfac = 3;
abetsize = 20; break;
- default: fatal("Invalid sequence type passed to Dotter: %c", type);
+ default: g_error("Invalid sequence type passed to Dotter: %c", type);
}
/* Option parsing */
@@ -597,18 +598,18 @@ void dotter (char type,
handle = handleCreate();
banner = (char *)handleAlloc(0, handle, 1000);
- qname = messalloc(strlen(queryname)+1); strcpy(qname, queryname);
+ qname = g_malloc(strlen(queryname)+1); strcpy(qname, queryname);
qseq = queryseq;
qoffset = qoff;
- sname = messalloc(strlen(subjectname)+1); strcpy(sname, subjectname);
+ sname = g_malloc(strlen(subjectname)+1); strcpy(sname, subjectname);
sseq = subjectseq;
soffset = soff;
MSPlist = MSPs;
MSPoffset = MSPoff;
- if (!(qlen = strlen(qseq))) fatal("queryseq is empty");
- if (!(slen = strlen(sseq))) fatal("subjectseq is empty");
+ if (!(qlen = strlen(qseq))) g_error("queryseq is empty");
+ if (!(slen = strlen(sseq))) g_error("subjectseq is empty");
for (i = 0; i < qlen; i++) qseq[i] = freeupper(qseq[i]);
for (i = 0; i < slen; i++) sseq[i] = freeupper(sseq[i]);
@@ -652,7 +653,7 @@ void dotter (char type,
if (savefile)
{
if (!(saveFil = fopen (savefile, "wb")))
- fatal("Failed to open %s", savefile);
+ g_error("Failed to open %s", savefile);
}
@@ -682,17 +683,17 @@ void dotter (char type,
if (qlen4 % 4)
qlen4 += 4-(qlen4 % 4);
if (qlen/resfac > qlen4*zoom)
- fatal("qlen/resfac > qlen4*zoom (%d > %d (%d*%d))",
+ g_error("qlen/resfac > qlen4*zoom (%d > %d (%d*%d))",
qlen/resfac, qlen4*zoom, qlen4, zoom);
slen4 = (int)ceil((double)slen/zoom);
if (slen4 % 4)
slen4 += 4-(slen4 % 4);
if (slen > slen4*zoom)
- fatal("slen > slen4*zoom (%d > %d (%d*%d))", slen, slen4, zoom, slen4*zoom);
+ g_error("slen > slen4*zoom (%d > %d (%d*%d))", slen, slen4, zoom, slen4*zoom);
datalen = slen4*qlen4;
- data = (UCHAR *)messalloc(datalen);
+ data = (UCHAR *)g_malloc(datalen);
}
if (savefile)
@@ -835,21 +836,6 @@ static void setMenuCheckmarks(void)
}
-void fatal(char *format, ...)
-{
- va_list ap;
-
- printf("\nFATAL ERROR: ");
-
- va_start(ap, format);
- vprintf(format, ap);
- va_end(ap);
-
- printf("\n");
- exit(1);
-}
-
-
static void Help(void)
{
graphMessage (messprintf("\
@@ -976,12 +962,12 @@ static void loadPlot(char *loadfile)
format;
if (!(fil = fopen (loadfile, "rb")))
- fatal("Failed to open %s", loadfile);
+ g_error("Failed to open %s", loadfile);
- if ((fread(&format, 1, 1, fil)) != 1) fatal("reading file %s", loadfile);
- if ((fread(&zoom, 1, 4, fil)) != 4) fatal("reading file %s", loadfile);
- if ((fread(&qlen4, 1, 4, fil)) != 4) fatal("reading file %s", loadfile);
- if ((fread(&slen4, 1, 4, fil)) != 4) fatal("reading file %s", loadfile);
+ if ((fread(&format, 1, 1, fil)) != 1) g_error("reading file %s", loadfile);
+ if ((fread(&zoom, 1, 4, fil)) != 4) g_error("reading file %s", loadfile);
+ if ((fread(&qlen4, 1, 4, fil)) != 4) g_error("reading file %s", loadfile);
+ if ((fread(&slen4, 1, 4, fil)) != 4) g_error("reading file %s", loadfile);
#ifdef ALPHA
reversebytes(&zoom, 4);
reversebytes(&qlen4, 4);
@@ -996,19 +982,19 @@ static void loadPlot(char *loadfile)
}
else if (format == 2)
{
- if ((fread(&pixelFac, 1, 4, fil)) != 4) fatal("reading file %s", loadfile);
- if ((fread(&win, 1, 4, fil)) != 4) fatal("reading file %s", loadfile);
- if ((fread(&MNlen, 1, 4, fil)) != 4) fatal("reading file %s", loadfile);
+ if ((fread(&pixelFac, 1, 4, fil)) != 4) g_error("reading file %s", loadfile);
+ if ((fread(&win, 1, 4, fil)) != 4) g_error("reading file %s", loadfile);
+ if ((fread(&MNlen, 1, 4, fil)) != 4) g_error("reading file %s", loadfile);
#ifdef ALPHA
reversebytes(&pixelFac, 4);
reversebytes(&win, 4);
reversebytes(&MNlen, 4);
#endif
- if ((fread(&MATRIX_NAME, 1, MNlen, fil)) != MNlen) fatal("reading file %s", loadfile);
+ if ((fread(&MATRIX_NAME, 1, MNlen, fil)) != MNlen) g_error("reading file %s", loadfile);
MATRIX_NAME[MNlen] = 0;
for (i = 0; i < 24; i++)
for (j = 0; j < 24; j++) {
- if ((fread(&mtx, 1, 4, fil)) != 4) fatal("reading file %s", loadfile);
+ if ((fread(&mtx, 1, 4, fil)) != 4) g_error("reading file %s", loadfile);
#ifdef ALPHA
reversebytes(&mtx, 4);
#endif
@@ -1017,21 +1003,21 @@ static void loadPlot(char *loadfile)
dotstart = MNlen + 2329;
}
else
- fatal("Unknown dotter file format version: %d", format);
+ g_error("Unknown dotter file format version: %d", format);
fseek(fil, 0, SEEK_END);
n = ftell(fil);
if (n-dotstart != qlen4*slen4)
- fatal("Wrong number of pixels in %s: %d. Expected %d * %-d = %d\n",
+ g_error("Wrong number of pixels in %s: %d. Expected %d * %-d = %d\n",
loadfile, n, qlen4, slen4, qlen4*slen4);
datalen = slen4*qlen4;
- data = (UCHAR *)messalloc(datalen);
+ data = (UCHAR *)g_malloc(datalen);
fseek(fil, dotstart, SEEK_SET);
if ((n = fread(data, 1, qlen4*slen4, fil)) != qlen4*slen4)
- fatal("Read wrong number of pixels from %s: %d. Expected %d * %-d = %d\n",
+ g_error("Read wrong number of pixels from %s: %d. Expected %d * %-d = %d\n",
loadfile, n, qlen4, slen4, qlen4*slen4);
fclose(fil);
@@ -1260,7 +1246,7 @@ static void calcWindow(void)
dotpos = qlen4*dotposs + dotposq;
if (dotpos < 0 || dotpos >= datalen) {
- messerror ( "Pixel out of bounds (%d) in blastx: %d\n",
+ g_critical ( "Pixel out of bounds (%d) in blastx: %d\n",
datalen-1, dotpos);
}
else {
@@ -1321,7 +1307,7 @@ static void calcWindow(void)
dotpos = qlen4*dotposs + dotposq;
if (dotpos < 0 || dotpos > datalen-1) {
- messerror ( "Pixel out of bounds (%d) in blastp/blastn-forw: %d\n",
+ g_critical ( "Pixel out of bounds (%d) in blastp/blastn-forw: %d\n",
datalen-1, dotpos);
}
else {
@@ -1392,7 +1378,7 @@ static void calcWindow(void)
dotpos = qlen4*dotposs + dotposq;
if (dotpos < 0 || dotpos >= datalen) {
- messerror ( "Pixel out of bounds (%d) in blastn-rev: %d\n",
+ g_critical ( "Pixel out of bounds (%d) in blastn-rev: %d\n",
datalen-1, dotpos);
}
else {
@@ -1419,10 +1405,10 @@ static void calcWindow(void)
dotposCopy = qlen4*q + s;
if (dotpos < 0 || dotpos >= datalen)
- messerror ( "Source pixel out of bounds (%d) in mirrorCopy: %d\n",
+ g_critical ( "Source pixel out of bounds (%d) in mirrorCopy: %d\n",
datalen-1, dotpos);
if (dotposCopy < 0 || dotposCopy >= datalen)
- messerror ( "Destination pixel out of bounds (%d) in mirrorCopy: %d\n",
+ g_critical ( "Destination pixel out of bounds (%d) in mirrorCopy: %d\n",
datalen-1, dotposCopy);
data[dotposCopy] = data[dotpos];
}
@@ -1430,7 +1416,7 @@ static void calcWindow(void)
}
handleDestroy(calcHandle);
- messalloccheck();
+// messalloccheck();
pixelmap_done = 1;
}
@@ -2474,8 +2460,8 @@ static void graphPixelLine(int strength, int sx, int sy, int ex, int ey)
dotpos = qlen4*(y) + x;
if (dotpos < 0 || dotpos > datalen-1) {
- messout("Pixel out of bounds (0-%d) in graphPixelLine: %d."
- "Crash imminent.", datalen-1, dotpos);
+ g_critical("Pixel out of bounds (0-%d) in graphPixelLine: %d."
+ "Crash imminent.", datalen-1, dotpos);
}
else
{
@@ -2645,7 +2631,7 @@ static void drawBlastHSPs(void)
graphPixelLine(strength, sx, sy, ex, ey);
}
else {
- messout("Unknown BlastMode = bug -> contact Erik");
+ g_critical("Unknown BlastMode = bug -> contact Sanger");
}
}
}
@@ -3180,14 +3166,14 @@ static void initAlignment(void)
{
/* static int warned=0;
- if (!warned) messout("The residue colours of the Aligment tool have been corrupted by Jean."
+ if (!warned) g_critical("The residue colours of the Aligment tool have been corrupted by Jean."
" Send complaints to mieg@kaa.crbm.cnrs-mop.fr");
warned=1;*/
}
if (!CrosshairON)
{
- messout("Turn on the crosshair !");
+ g_critical("Turn on the crosshair !");
return;
}
@@ -3482,7 +3468,7 @@ int findCommand (char *command, char **retp)
/* Don't use csh - fails if the path is not set in .cshrc * /
if (access(csh, X_OK)) {
- messout("Could not find %s", csh);
+ g_critical("Could not find %s", csh);
return 0;
}
if (!(pipe = (FILE *)popen(messprintf("%s -cf \"which %s\"", csh, command), "r"))) {
@@ -3504,7 +3490,7 @@ int findCommand (char *command, char **retp)
return 0;
*/
- path = messalloc(strlen(getenv("PATH"))+1);
+ path = g_malloc(strlen(getenv("PATH"))+1);
/* Don't free 'path' since it changes later on - never mind,
we're only calling it once */
@@ -3575,7 +3561,7 @@ static void callDotter(int dotterZoom, int xstart, int ystart, int xend, int yen
if (!dotterBinary) {
printf("Looking for Dotter ...\n");
if (!findCommand("dotter", &(dotterBinary))) {
- messout("Failed to zoom in - %s. "
+ g_critical("Failed to zoom in - %s. "
"($PATH=%s)", dotterBinary, getenv("PATH"));
dotterBinary = 0;
return;
@@ -3758,18 +3744,18 @@ static void initWindow(char *winsize)
if (!winsize || freeupper(*winsize) == 'K') {
if (win < 3) {
- messout("Karlin/Altschul estimate of window size = %d ignored. Using 10 instead.\n", win);
+ g_critical("Karlin/Altschul estimate of window size = %d ignored. Using 10 instead.\n", win);
win = 10;
}
if (win > 50) {
- messout("Karlin/Altschul estimate of window size = %d ignored. Using 50 instead.\n", win);
+ g_critical("Karlin/Altschul estimate of window size = %d ignored. Using 50 instead.\n", win);
win = 50;
}
return;
}
if (!atoi(winsize))
- fatal("Bad window size specification: %s", winsize);
+ g_error("Bad window size specification: %s", winsize);
win = atoi(winsize);
}
@@ -3811,17 +3797,17 @@ static void dotterDestroy(void)
}
}
- /* Free stuff messalloc'ed in calling routine (usually blixem or dotterMain) */
- messfree(qseq);
- messfree(sseq);
+ /* Free stuff g_malloc'ed in calling routine (usually blixem or dotterMain) */
+ g_free(qseq);
+ g_free(sseq);
/* Don't free MSP's since that will screw blixem up !!! */
if (graphActivate(dotterGraph))
graphClear();
- messfree(data);
- messfree(HSPpixels);
+ g_free(data);
+ g_free(HSPpixels);
if (graphActivate(alnGraph))
{
@@ -4053,7 +4039,7 @@ static void dotterRedraw(void)
if (!HSPpixels)
{
int i;
- HSPpixels = (UCHAR *)messalloc(datalen);
+ HSPpixels = (UCHAR *)g_malloc(datalen);
for (i=0; i < datalen; i++)
HSPpixels[i] = 0;
}
@@ -4065,7 +4051,7 @@ static void dotterRedraw(void)
if (HSPgaps && !gapwarned)
{
graphRedraw();
- messout("Note: gapped HSPs are shown ungapped in Dotter.");
+ g_critical("Note: gapped HSPs are shown ungapped in Dotter.");
gapwarned = 1;
}
}
@@ -4106,7 +4092,7 @@ static void readmtx(int MATRIX[24][24], char *mtxfile)
if (!(fil = fopen(mtxfile, "r")) &&
!(fil = fopen(messprintf("%s/%s", getenv("BLASTMAT"), mtxfile), "r")))
- fatal("Failed to open score matrix file %s - not found in ./ or $BLASTMAT/.", mtxfile);
+ g_error("Failed to open score matrix file %s - not found in ./ or $BLASTMAT/.", mtxfile);
/* Ignore header ... */
while (!feof(fil) && *line == '#')
@@ -4116,14 +4102,16 @@ static void readmtx(int MATRIX[24][24], char *mtxfile)
for (row = 0; row < 24; row++)
{
if (!(fgets(line, 1024, fil)))
- fatal("Wrong number of rows in matrix file: %d (should be 24).", row);
+ g_error("Wrong number of rows in matrix file: %d (should be 24).", row);
p = strtok(line, " \t\n");
for (col = 0; col < 24; col++)
{
while (*p == '*' || isalpha((int) *p))
p = strtok(NULL, " \t\n");
- if (!p) fatal("Error on row %d in matrix file.", row);
+
+ if (!p)
+ g_error("Error on row %d in matrix file.", row);
MATRIX[row][col] = atoi(p);
diff --git a/dotter.h b/dotter.h
index 6fb7a936b5381dfc4943e850f5c2c02ef55a2ce6..577449c2c95fa425479a2f712f53f88ed1c276b1 100644
--- a/dotter.h
+++ b/dotter.h
@@ -28,13 +28,13 @@
*
* dotter(type, 0, 0, qseq, 0, 0, sseq, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
*
- * NOTE: qseq and sseq must be messalloc'ed in the calling routine.
- * They are messfree'd by Dotter.
+ * NOTE: qseq and sseq must be g_malloc'ed in the calling routine.
+ * They are g_free'd by Dotter.
*
* HISTORY:
* Last edited: Nov 14 09:19 2007 (edgrif)
* Created: Thu Aug 26 17:16:19 1999 (fw)
- * CVS info: $Id: dotter.h,v 1.5 2010-08-24 12:27:59 gb10 Exp $
+ * CVS info: $Id: dotter.h,v 1.6 2010-08-31 15:30:55 gb10 Exp $
*-------------------------------------------------------------------
*/
#ifndef DEF_DOTTER_H
@@ -55,7 +55,7 @@ void dotter(
Name of Horizontal sequence */
char *queryseq, /* Mandatory, NULL terminated string
- Horisontal sequence - messfree'd by Dotter */
+ Horisontal sequence - g_free'd by Dotter */
int qoff, /* Optional, may be NULL
Coordinate offset of horisontal sequence */
@@ -64,7 +64,7 @@ void dotter(
Name of vertical sequence */
char *subjectseq, /* Mandatory, NULL terminated string
- vertical sequence - messfree'd by Dotter */
+ vertical sequence - g_free'd by Dotter */
int soff, /* Optional, may be NULL
Coordinate offset of horisontal sequence */
diff --git a/dotterKarlin.c b/dotterKarlin.c
index b367138f8f204e210fdcf86a6c4d03872d4edc1a..bb5c2c05ce894bdfbda4bf66ba9365d5afc3fcf1 100644
--- a/dotterKarlin.c
+++ b/dotterKarlin.c
@@ -1,5 +1,5 @@
/* Last edited: Oct 26 10:45 2003 (edgrif) */
-/* $Id: dotterKarlin.c,v 1.1 2009-11-03 18:28:23 edgrif Exp $ */
+/* $Id: dotterKarlin.c,v 1.2 2010-08-31 15:30:55 gb10 Exp $ */
/*
-------------------------------------------------------------
@@ -37,8 +37,6 @@
#include "gex.h"
#include "dotter_.h"
-#define NA 24 /* Not A residue */
-
#define MAXIT 20 /* Maximum number of iterations used in calculating K */
/* For greater accuracy, set SUMLIMIT to 0.00001 */
@@ -214,31 +212,31 @@ See: Karlin, S. & Altschul, S.F. "Methods for Assessing the Statistical
/* Check that scores and their associated probabilities are valid */
if (low >= 0.) {
- messout("Karlin-Altschul statistics error: There must be at least one negative score in the substitution matrix.");
+ g_critical("Karlin-Altschul statistics error: There must be at least one negative score in the substitution matrix.");
return -1.0;
}
for (i=range=high-low; i > -low && pr[i] == 0.0; --i);
if (i <= -low) {
- messout("Karlin-Altschul statistics error: A positive score is impossible in the context of the scoring scheme, the residue composition of the query sequence, and the residue composition assumed for the database.");
+ g_critical("Karlin-Altschul statistics error: A positive score is impossible in the context of the scoring scheme, the residue composition of the query sequence, and the residue composition assumed for the database.");
return -1.0;
}
for (sum=i=0; i<=range; sum += pr[i++])
if (pr[i] < 0.) {
- messout("Karlin-Altschul statistics error: Negative probabilities for scores are disallowed.");
+ g_critical("Karlin-Altschul statistics error: Negative probabilities for scores are disallowed.");
return -1.0;
}
if (sum<0.99995 || sum>1.00005)
printf("Score probabilities sum to %.5lf and will be normalized to 1.", sum);
- p = (double *)messalloc(sizeof(*p) * (range+1));
+ p = (double *)g_malloc(sizeof(*p) * (range+1));
for (Sum=low,i=0; i<=range; ++i)
Sum += i*(p[i]=pr[i]/sum);
if (Sum >= 0.) {
- messout("Karlin/Altschul statistics failed due to non-negative expected score: %#0.3lg", Sum);
+ g_critical("Karlin/Altschul statistics failed due to non-negative expected score: %#0.3lg", Sum);
return Sum;
}
@@ -280,7 +278,7 @@ See: Karlin, S. & Altschul, S.F. "Methods for Assessing the Statistical
}
Sum = 0.;
lo = hi = 0;
- P = (double *)messalloc(MAXIT* (range+1) * sizeof(*P));
+ P = (double *)g_malloc(MAXIT* (range+1) * sizeof(*P));
*P = sum = oldsum = oldsum2 = 1.;
for (j=0; j<MAXIT && sum > SUMLIMIT; oldsum = sum, Sum += sum /= ++j) {
first = last = range;
@@ -307,12 +305,12 @@ See: Karlin, S. & Altschul, S.F. "Methods for Assessing the Statistical
ratio = oldsum / oldsum2;
if (ratio >= (1.0 - SUMLIMIT*0.001))
{
- messerror ("Value calculated for K was too high due to insufficient iterations. "
+ g_critical ("Value calculated for K was too high due to insufficient iterations. "
"Fudging it.") ;
*K = 0.1 ;
goto OKExit ;
/* was:
- fatal("Value calculated for K was too high due to insufficient iterations. "
+ g_error("Value calculated for K was too high due to insufficient iterations. "
"Alternatively, the expected average score is insufficiently negative.") ;
*/
}
@@ -331,8 +329,8 @@ See: Karlin, S. & Altschul, S.F. "Methods for Assessing the Statistical
OKExit:
- messfree(p);
- messfree(P);
+ g_free(p);
+ g_free(P);
return 0; /* Parameters calculated successfully */
}
@@ -353,10 +351,10 @@ int winsizeFromlambdak(int mtx[24][24], int *tob, int abetsize, char *qseq, char
qij, exp_MSP_score, sum;
- n1 = (int *)messalloc((abetsize+4)*sizeof(int));
- n2 = (int *)messalloc((abetsize+4)*sizeof(int));
- fq1 = (double *)messalloc((abetsize+4)*sizeof(double));
- fq2 = (double *)messalloc((abetsize+4)*sizeof(double));
+ n1 = (int *)g_malloc((abetsize+4)*sizeof(int));
+ n2 = (int *)g_malloc((abetsize+4)*sizeof(int));
+ fq1 = (double *)g_malloc((abetsize+4)*sizeof(double));
+ fq2 = (double *)g_malloc((abetsize+4)*sizeof(double));
/* Find high and lows score in score matrix */
@@ -400,7 +398,7 @@ int winsizeFromlambdak(int mtx[24][24], int *tob, int abetsize, char *qseq, char
/* Calculate probability of each score */
range = highs - lows;
- prob = (double *)messalloc(sizeof(double)*(range+1));
+ prob = (double *)g_malloc(sizeof(double)*(range+1));
for (i = 0; i <= range; ++i) prob[i] = 0.0;
for (i = 0; i < abetsize; ++i)
@@ -413,7 +411,7 @@ int winsizeFromlambdak(int mtx[24][24], int *tob, int abetsize, char *qseq, char
if ((*exp_res_score = karlin(lows, highs, prob, Lambda, &K, &H)))
{
- messout("Setting ad hoc values to winsize=%d and expected score=%.3f", 25, *exp_res_score);
+ g_critical("Setting ad hoc values to winsize=%d and expected score=%.3f", 25, *exp_res_score);
return 25;
}
@@ -444,11 +442,11 @@ int winsizeFromlambdak(int mtx[24][24], int *tob, int abetsize, char *qseq, char
*exp_res_score, retval);
- messfree(prob);
- messfree(n1);
- messfree(n2);
- messfree(fq1);
- messfree(fq2);
+ g_free(prob);
+ g_free(n1);
+ g_free(n2);
+ g_free(fq1);
+ g_free(fq2);
return retval;
}
diff --git a/dotterMain.c b/dotterMain.c
index 9e49c7478d66f0beece804d57cc0c59a9d3dea23..05feec759c10597bf0075ae9333ccf6d99372136 100644
--- a/dotterMain.c
+++ b/dotterMain.c
@@ -26,7 +26,7 @@
* HISTORY:
* Last edited: Aug 26 15:42 2009 (edgrif)
* Created: Thu Aug 26 17:17:30 1999 (fw)
- * CVS info: $Id: dotterMain.c,v 1.11 2010-08-24 12:27:59 gb10 Exp $
+ * CVS info: $Id: dotterMain.c,v 1.12 2010-08-31 15:30:55 gb10 Exp $
*-------------------------------------------------------------------
*/
@@ -37,7 +37,8 @@
#include <wh/gex.h>
#include <SeqTools/utilities.h>
#include <SeqTools/blixem_.h>
-#include <wh/dotter_.h>
+#include <SeqTools/dotter_.h>
+#include <SeqTools/utilities.h>
#define UNSET_INT -1
@@ -122,7 +123,7 @@ static char *stringUnprotect(char **textp, char *target)
if (!target)
{
- target = messalloc(count+1);
+ target = g_malloc(count+1);
goto redo;
}
@@ -141,20 +142,20 @@ static void addBreakline (MSP **MSPlist, char *name, char *desc, int pos, char s
*cp;
if (!*MSPlist) {
- *MSPlist = (MSP *)messalloc(sizeof(MSP));
+ *MSPlist = (MSP *)g_malloc(sizeof(MSP));
msp = *MSPlist;
}
else {
msp = *MSPlist;
while(msp->next) msp = msp->next;
- msp->next = (MSP *)messalloc(sizeof(MSP));
+ msp->next = (MSP *)g_malloc(sizeof(MSP));
msp = msp->next;
}
- msp->qname = messalloc(strlen(name)+1);
+ msp->qname = g_malloc(strlen(name)+1);
strcpy(msp->qname, name);
- msp->desc = messalloc(strlen(desc)+1);
+ msp->desc = g_malloc(strlen(desc)+1);
strcpy(msp->desc, desc);
if ((cp = (char *)strchr(msp->desc, ' ')))
*cp = 0;
@@ -227,7 +228,7 @@ static char* getUsageText()
#endif
;
- usage = messalloc(strlen(usageText) + strlen(dotterVersion) + strlen(cc_date) + 20);
+ usage = g_malloc(strlen(usageText) + strlen(dotterVersion) + strlen(cc_date) + 20);
sprintf(usage, "%s%s, compiled %s\n", usageText, dotterVersion, cc_date);
return usage;
@@ -236,6 +237,11 @@ static char* getUsageText()
int main(int argc, char **argv)
{
+ /* Set the message handlers */
+ g_log_set_default_handler(defaultMessageHandler, NULL);
+ g_log_set_handler(NULL, G_LOG_LEVEL_ERROR | G_LOG_LEVEL_CRITICAL, popupMessageHandler, NULL);
+
+
DotterOptions options = {0, 0, 0, UNSET_INT, UNSET_INT, 0, 0, 1, 0, 0, 0.0, NULL, NULL, NULL, NULL, NULL, NULL, NULL};
char
@@ -270,24 +276,24 @@ int main(int argc, char **argv)
switch (optc)
{
case 'b':
- options.savefile = messalloc(strlen(optarg)+1);
+ options.savefile = g_malloc(strlen(optarg)+1);
strcpy(options.savefile, optarg); break;
case 'c': opts[1] = 'C'; break;
case 'D': opts[0] = ' '; break;
case 'f':
- options.FSfilename = messalloc(strlen(optarg)+1);
+ options.FSfilename = g_malloc(strlen(optarg)+1);
strcpy(options.FSfilename, optarg); break;
case 'F':
options.seqInSFS = 1;
- options.FSfilename = messalloc(strlen(optarg)+1);
+ options.FSfilename = g_malloc(strlen(optarg)+1);
strcpy(options.FSfilename, optarg); break;
case 'H': opts[2] = 'H'; break;
case 'i': options.install = 0; break;
case 'l':
- options.loadfile = messalloc(strlen(optarg)+1);
+ options.loadfile = g_malloc(strlen(optarg)+1);
strcpy(options.loadfile, optarg); break;
case 'M':
- options.mtxfile = messalloc(strlen(optarg)+1);
+ options.mtxfile = g_malloc(strlen(optarg)+1);
strcpy(options.mtxfile, optarg); break;
case 'm': options.memoryLimit = atof(optarg); break;
case 'p': options.pixelFacset = atoi(optarg); break;
@@ -297,19 +303,19 @@ int main(int argc, char **argv)
case 's': options.soffset = atoi(optarg); break;
case 'S':
options.selfcall = 1;
- options.qname = messalloc(strlen(argv[optind])+1); strcpy(options.qname, argv[optind]);
+ options.qname = g_malloc(strlen(argv[optind])+1); strcpy(options.qname, argv[optind]);
options.qlen = atoi(argv[optind+1]);
- options.sname = messalloc(strlen(argv[optind+2])+1); strcpy(options.sname, argv[optind+2]);
+ options.sname = g_malloc(strlen(argv[optind+2])+1); strcpy(options.sname, argv[optind+2]);
options.slen = atoi(argv[optind+3]);
- dotterBinary = messalloc(strlen(argv[optind+4])+1);
+ dotterBinary = g_malloc(strlen(argv[optind+4])+1);
strcpy(dotterBinary, argv[optind+4]);
break;
case 'W':
- options.winsize = messalloc(strlen(optarg)+1);
+ options.winsize = g_malloc(strlen(optarg)+1);
strcpy(options.winsize, optarg); break;
case 'w': opts[1] = 'W'; break;
case 'z': options.dotterZoom = atoi(optarg); break;
- default : fatal("Illegal option");
+ default : g_error("Illegal option");
}
}
@@ -327,7 +333,7 @@ int main(int argc, char **argv)
for (i = optind+2; i < argc; i++)
len += strlen(argv[i])+1;
- Xoptions = messalloc(len+1);
+ Xoptions = g_malloc(len+1);
for (i = optind+2; i < argc; i++) {
strcat(Xoptions, argv[i]);
@@ -337,20 +343,20 @@ int main(int argc, char **argv)
if (options.selfcall) /* Dotter calling dotter */
{
- qseq = (char *)messalloc(options.qlen+1);
- sseq = (char *)messalloc(options.slen+1);
+ qseq = (char *)g_malloc(options.qlen+1);
+ sseq = (char *)g_malloc(options.slen+1);
int l = fread(qseq, 1, options.qlen, stdin);
if (l != options.qlen)
{
- fatal("Only read %d chars to qseq, expected %d", l, options.qlen);
+ g_error("Only read %d chars to qseq, expected %d", l, options.qlen);
}
qseq[options.qlen] = 0;
l = fread(sseq, 1, options.slen, stdin);
if (l != options.slen)
{
- fatal("Only read %d chars to sseq, expected %d", l, options.slen);
+ g_error("Only read %d chars to sseq, expected %d", l, options.slen);
}
sseq[options.slen] = 0;
@@ -365,12 +371,12 @@ int main(int argc, char **argv)
if (!MSPlist)
{
- MSPlist = (MSP *)messalloc(sizeof(MSP));
+ MSPlist = (MSP *)g_malloc(sizeof(MSP));
msp = MSPlist;
}
else
{
- msp->next = (MSP *)messalloc(sizeof(MSP));
+ msp->next = (MSP *)g_malloc(sizeof(MSP));
msp = msp->next;
}
@@ -420,7 +426,7 @@ int main(int argc, char **argv)
qfilename = argv[optind];
fseek(qfile, 0, SEEK_END);
options.qlen = ftell(qfile);
- qseq = (char *)messalloc(options.qlen+1);
+ qseq = (char *)g_malloc(options.qlen+1);
fseek(qfile, 0, SEEK_SET);
if ((cp = (char *)strrchr(argv[optind], '/')))
@@ -440,7 +446,7 @@ int main(int argc, char **argv)
sfilename = argv[optind+1];
fseek(sfile, 0, SEEK_END);
options.slen = ftell(sfile);
- sseq = (char *)messalloc(options.slen+1);
+ sseq = (char *)g_malloc(options.slen+1);
fseek(sfile, 0, SEEK_SET);
if ((cp = (char *)strrchr(argv[optind]+1, '/')))
@@ -474,8 +480,8 @@ int main(int argc, char **argv)
cq++;
if (++l == 1)
{
- options.qname = messalloc(strlen(cq)+1); strNamecpy(options.qname, cq);
- firstdesc = messalloc(strlen(cq)+1);
+ options.qname = g_malloc(strlen(cq)+1); strNamecpy(options.qname, cq);
+ firstdesc = g_malloc(strlen(cq)+1);
strcpy(firstdesc, cq);
}
else
@@ -489,7 +495,7 @@ int main(int argc, char **argv)
addBreakline (&MSPlist, qfilename, firstdesc, 0, '1');
/* change sequence name to filename */
- options.qname = messalloc(strlen(qfilename)+1); strcpy(options.qname, qfilename);
+ options.qname = g_malloc(strlen(qfilename)+1); strcpy(options.qname, qfilename);
}
addBreakline (&MSPlist, qfilename, cq, count, '1');
@@ -521,8 +527,8 @@ int main(int argc, char **argv)
if ((cq = (char *)strchr(line, '>'))) {
cq++;
if (++l == 1) {
- options.sname = messalloc(strlen(cq)+1); strNamecpy(options.sname, cq);
- firstdesc = messalloc(strlen(cq)+1);
+ options.sname = g_malloc(strlen(cq)+1); strNamecpy(options.sname, cq);
+ firstdesc = g_malloc(strlen(cq)+1);
strcpy(firstdesc, cq);
}
else {
@@ -535,7 +541,7 @@ int main(int argc, char **argv)
addBreakline (&MSPlist, sfilename, firstdesc, 0, '2');
/* change sequence name to filename */
- options.sname = messalloc(strlen(sfilename)+1); strcpy(options.sname, sfilename);
+ options.sname = g_malloc(strlen(sfilename)+1); strcpy(options.sname, sfilename);
}
addBreakline (&MSPlist, sfilename, cq, count, '2');
}
@@ -591,19 +597,22 @@ int main(int argc, char **argv)
printf("\nDetected sequence types: DNA vs. Protein\n");
type = 'X';
}
- else fatal("Illegal sequence types: Protein vs. DNA - turn arguments around!\n\n%s", usage);
-
+ else
+ {
+ g_error("Illegal sequence types: Protein vs. DNA - turn arguments around!\n\n%s", usage);
+ }
+
if (options.revcompq)
{
if (type != 'X')
{
- fatal("Revcomp'ing horizontal_sequence only needed in DNA vs. Protein");
+ g_error("Revcomp'ing horizontal_sequence only needed in DNA vs. Protein");
}
else
{
- cc = messalloc(options.qlen+1);
+ cc = g_malloc(options.qlen+1);
revComplement(cc, qseq);
- messfree(qseq);
+ g_free(qseq);
qseq = cc;
}
}
diff --git a/dotter_.h b/dotter_.h
index e031712c394b4fde0ae00a5ef888b51419bfee8e..aacf5fed71d351200717c29b7ec826ae575d6a71 100644
--- a/dotter_.h
+++ b/dotter_.h
@@ -26,7 +26,7 @@
* HISTORY:
* Last edited: Sep 15 08:36 2006 (edgrif)
* Created: Thu Aug 26 17:17:58 1999 (fw)
- * CVS info: $Id: dotter_.h,v 1.3 2010-05-19 10:27:32 gb10 Exp $
+ * CVS info: $Id: dotter_.h,v 1.4 2010-08-31 15:30:55 gb10 Exp $
*-------------------------------------------------------------------
*/
@@ -35,39 +35,18 @@
#include <SeqTools/dotter.h>
-#define AAID_MIN 1 /* Smallest letter value in binary alphabet */
-#define AAID_MAX 24 /* Maximum letter value in binary alphabet */
-#define AAID_CNT 24 /* Number of letters in alphabet */
-#define AAID_NAR (AAID_MAX+1)
-#define AAID_IGNORE (AAID_MAX+3)
+#define NR 23 /* Not A residue */
+#define NA 24 /* Not A residue */
-#define NA 24 /* Not A residue */
-#define EL (NA+1) /* End of Line */
-#define ES (NA+2) /* End of Sequence */
-#define IC AAID_IGNORE /* Ignore this Character */
-
-#define UNKNOWN_AA_CHR 'X'
-#define STOP_AA_CHR '*'
-#define GAP_AA_CHR '-'
-
-#define NR 23 /* Not A residue */
#if !defined(NAMESIZE)
#define NAMESIZE 10
#endif
-char *translate(char *seq, char **code);
extern char *stdcode1[]; /* 1-letter amino acid translation code */
int winsizeFromlambdak(int mtx[24][24], int *tob, int abetsize, char *qseq, char *sseq,
double *exp_res_score, double *Lambda);
-#if !defined BELVU
-/* Horrifically the headers for belvu, dotter and blixem all include each other for
- * inappropriate reasons..there should some common headers/.o files and all would be
- * well.... */
-void fatal(char *format, ...);
-#endif
-
void argvAdd(int *argc, char ***argv, char *s);