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gentoo-full-overlay/sci-biology/readseq/files/19930201-getline.patch

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diff --git a/ureadseq.c b/ureadseq.c
index b11115d..337b16f 100644
--- a/ureadseq.c
+++ b/ureadseq.c
@@ -136,7 +136,7 @@ Local void readline(FILE *f, char *s, long *linestart)
}
}
-Local void getline(struct ReadSeqVars *V)
+Local void ghettoline(struct ReadSeqVars *V)
{
readline(V->f, V->s, &V->linestart);
}
@@ -215,7 +215,7 @@ Local void readLoop(short margin, boolean addfirst,
if (addfirst) addseq(V->s, V);
do {
- getline(V);
+ ghettoline(V);
V->done = feof(V->f);
V->done |= (*endTest)( &addend, &ungetend, V);
if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) {
@@ -246,7 +246,7 @@ Local void readIG(struct ReadSeqVars *V)
while (!V->allDone) {
do {
- getline(V);
+ ghettoline(V);
for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */
if (*si == 0) *V->s= 0; /* chop line to empty */
} while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) ));
@@ -272,13 +272,13 @@ Local void readStrider(struct ReadSeqVars *V)
{ /* ? only 1 seq/file ? */
while (!V->allDone) {
- getline(V);
+ ghettoline(V);
if (strstr(V->s,"; DNA sequence ") == V->s)
strcpy(V->seqid, (V->s)+16);
else
strcpy(V->seqid, (V->s)+1);
while ((!feof(V->f)) && (*V->s == ';')) {
- getline(V);
+ ghettoline(V);
}
if (feof(V->f)) V->allDone = true;
else readLoop(0, true, endStrider, V);
@@ -298,16 +298,16 @@ Local void readPIR(struct ReadSeqVars *V)
while (!V->allDone) {
while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) )
- getline(V);
+ ghettoline(V);
strcpy(V->seqid, (V->s)+16);
while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s))
- getline(V);
+ ghettoline(V);
readLoop(0, false, endPIR, V);
if (!V->allDone) {
while (! (feof(V->f) || ((*V->s != 0)
&& (strstr( V->s,"ENTRY") == V->s))))
- getline(V);
+ ghettoline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -327,13 +327,13 @@ Local void readGenBank(struct ReadSeqVars *V)
while (!V->allDone) {
strcpy(V->seqid, (V->s)+12);
while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s))
- getline(V);
+ ghettoline(V);
readLoop(0, false, endGB, V);
if (!V->allDone) {
while (! (feof(V->f) || ((*V->s != 0)
&& (strstr( V->s,"LOCUS") == V->s))))
- getline(V);
+ ghettoline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -364,11 +364,11 @@ Local void readNBRF(struct ReadSeqVars *V)
{
while (!V->allDone) {
strcpy(V->seqid, (V->s)+4);
- getline(V); /*skip title-junk line*/
+ ghettoline(V); /*skip title-junk line*/
readLoop(0, false, endNBRF, V);
if (!V->allDone) {
while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
- getline(V);
+ ghettoline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -390,7 +390,7 @@ Local void readPearson(struct ReadSeqVars *V)
readLoop(0, false, endPearson, V);
if (!V->allDone) {
while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
- getline(V);
+ ghettoline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -410,14 +410,14 @@ Local void readEMBL(struct ReadSeqVars *V)
while (!V->allDone) {
strcpy(V->seqid, (V->s)+5);
do {
- getline(V);
+ ghettoline(V);
} while (!(feof(V->f) | (strstr(V->s,"SQ ") == V->s)));
readLoop(0, false, endEMBL, V);
if (!V->allDone) {
while (!(feof(V->f) |
((*V->s != '\0') & (strstr(V->s,"ID ") == V->s))))
- getline(V);
+ ghettoline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -437,13 +437,13 @@ Local void readZuker(struct ReadSeqVars *V)
/*! 1st string is Zuker's Fortran format */
while (!V->allDone) {
- getline(V); /*s == "seqLen seqid string..."*/
+ ghettoline(V); /*s == "seqLen seqid string..."*/
strcpy(V->seqid, (V->s)+6);
readLoop(0, false, endZuker, V);
if (!V->allDone) {
while (!(feof(V->f) |
((*V->s != '\0') & (*V->s == '('))))
- getline(V);
+ ghettoline(V);
}
if (feof(V->f)) V->allDone = true;
}
@@ -486,7 +486,7 @@ Local void readPlain(struct ReadSeqVars *V)
do {
addseq(V->s, V);
V->done = feof(V->f);
- getline(V);
+ ghettoline(V);
} while (!V->done);
if (V->choice == kListSequences) addinfo(V->seqid, V);
V->allDone = true;
@@ -498,7 +498,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
/*
10nov91: Reading GCG files casued duplication of last line when
EOF followed that line !!!
- fix: getline now sets *V->s = 0
+ fix: ghettoline now sets *V->s = 0
*/
char *si;
@@ -512,7 +512,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
else if (si = strstr(V->seqid,"..")) *si = 0;
do {
V->done = feof(V->f);
- getline(V);
+ ghettoline(V);
if (!V->done) addseq((V->s), V);
} while (!V->done);
if (V->choice == kListSequences) addinfo(V->seqid, V);
@@ -531,7 +531,7 @@ Local void readOlsen(struct ReadSeqVars *V)
if (V->addit) V->seqlen = 0;
rewind(V->f); V->nseq= 0;
do {
- getline(V);
+ ghettoline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -614,7 +614,7 @@ Local void readMSF(struct ReadSeqVars *V)
if (V->addit) V->seqlen = 0;
rewind(V->f); V->nseq= 0;
do {
- getline(V);
+ ghettoline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -685,7 +685,7 @@ Local void readPAUPinterleaved(struct ReadSeqVars *V)
domatch= (V->matchchar > 0);
do {
- getline(V);
+ ghettoline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -766,7 +766,7 @@ Local void readPAUPsequential(struct ReadSeqVars *V)
/* rewind(V->f); V->nseq= 0; << do in caller !*/
indata= true; /* call here after we find "matrix" */
do {
- getline(V);
+ ghettoline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -851,7 +851,7 @@ Local void readPhylipInterleaved(struct ReadSeqVars *V)
/* fprintf(stderr,"Phylip-ileaf: topnseq=%d topseqlen=%d\n",V->topnseq, V->topseqlen); */
do {
- getline(V);
+ ghettoline(V);
V->done = feof(V->f);
if (V->done && !(*V->s)) break;
@@ -904,7 +904,7 @@ Local void readPhylipSequential(struct ReadSeqVars *V)
while (isdigit(*si)) si++;
skipwhitespace(si);
V->topseqlen= atol(si);
- getline(V);
+ ghettoline(V);
while (!V->allDone) {
V->seqlencount= 0;
strncpy(V->seqid, (V->s), 10);
@@ -935,10 +935,10 @@ Local void readSeqMain(
V->err = eFileNotFound;
else {
- for (l = skiplines_; l > 0; l--) getline( V);
+ for (l = skiplines_; l > 0; l--) ghettoline( V);
do {
- getline( V);
+ ghettoline( V);
for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ;
} while ((l == 0) && !feof(V->f));
@@ -963,7 +963,7 @@ Local void readSeqMain(
char *cp;
/* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */
while (!done) {
- getline( V);
+ ghettoline( V);
tolowerstr( V->s);
if (strstr( V->s, "matrix")) done= true;
if (strstr( V->s, "interleav")) interleaved= true;
@@ -995,7 +995,7 @@ Local void readSeqMain(
break;
case kFitch :
- strcpy(V->seqid, V->s); getline(V);
+ strcpy(V->seqid, V->s); ghettoline(V);
readFitch(V);
break;
@@ -1003,7 +1003,7 @@ Local void readSeqMain(
do {
gotuw = (strstr(V->s,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ ghettoline(V);
} while (!(feof(V->f) || V->allDone));
break;
}
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