fix: error
This commit is contained in:
parent
650d39cff9
commit
83f11ebd67
2 changed files with 33 additions and 31 deletions
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@ -168,6 +168,7 @@ link -w -o readseq -t MPST -c 'MPS ' <20>
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#include <ctype.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "ureadseq.h"
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63
ureadseq.c
63
ureadseq.c
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@ -18,6 +18,7 @@
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#include <ctype.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#define UREADSEQ_G
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@ -123,7 +124,7 @@ Local void readline(FILE *f, char *s, long *linestart)
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}
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}
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Local void getline(struct ReadSeqVars *V)
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Local void cgetline(struct ReadSeqVars *V)
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{
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readline(V->f, V->s, &V->linestart);
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}
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@ -200,7 +201,7 @@ Local void readLoop(short margin, boolean addfirst,
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if (addfirst) addseq(V->s, V);
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do {
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getline(V);
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cgetline(V);
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V->done = feof(V->f);
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V->done |= (*endTest)(&addend, &ungetend, V);
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if (V->addit && (addend || !V->done) &&
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@ -231,7 +232,7 @@ Local void readIG(struct ReadSeqVars *V)
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while (!V->allDone) {
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do {
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getline(V);
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cgetline(V);
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for (si = V->s; *si != 0 && *si < ' '; si++)
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*si = ' '; /* drop controls */
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if (*si == 0) *V->s = 0; /* chop line to empty */
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@ -257,13 +258,13 @@ Local void readStrider(struct ReadSeqVars *V)
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{ /* ? only 1 seq/file ? */
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while (!V->allDone) {
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getline(V);
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cgetline(V);
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if (strstr(V->s, "; DNA sequence ") == V->s)
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strcpy(V->seqid, (V->s) + 16);
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else
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strcpy(V->seqid, (V->s) + 1);
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while ((!feof(V->f)) && (*V->s == ';')) {
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getline(V);
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cgetline(V);
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}
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if (feof(V->f))
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V->allDone = true;
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@ -285,17 +286,17 @@ Local void readPIR(struct ReadSeqVars *V)
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while (!V->allDone) {
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while (!(feof(V->f) || strstr(V->s, "ENTRY") ||
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strstr(V->s, "SEQUENCE")))
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getline(V);
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cgetline(V);
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strcpy(V->seqid, (V->s) + 16);
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while (!(feof(V->f) || strstr(V->s, "SEQUENCE") == V->s))
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getline(V);
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cgetline(V);
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readLoop(0, false, endPIR, V);
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if (!V->allDone) {
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while (!(
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feof(V->f) ||
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((*V->s != 0) && (strstr(V->s, "ENTRY") == V->s))))
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getline(V);
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cgetline(V);
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}
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if (feof(V->f)) V->allDone = true;
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}
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@ -314,14 +315,14 @@ Local void readGenBank(struct ReadSeqVars *V)
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while (!V->allDone) {
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strcpy(V->seqid, (V->s) + 12);
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while (!(feof(V->f) || strstr(V->s, "ORIGIN") == V->s))
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getline(V);
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cgetline(V);
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readLoop(0, false, endGB, V);
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if (!V->allDone) {
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while (!(
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feof(V->f) ||
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((*V->s != 0) && (strstr(V->s, "LOCUS") == V->s))))
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getline(V);
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cgetline(V);
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}
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if (feof(V->f)) V->allDone = true;
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}
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@ -351,11 +352,11 @@ Local void readNBRF(struct ReadSeqVars *V)
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{
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while (!V->allDone) {
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strcpy(V->seqid, (V->s) + 4);
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getline(V); /*skip title-junk line*/
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cgetline(V); /*skip title-junk line*/
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readLoop(0, false, endNBRF, V);
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if (!V->allDone) {
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while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
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getline(V);
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cgetline(V);
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}
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if (feof(V->f)) V->allDone = true;
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}
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@ -377,7 +378,7 @@ Local void readPearson(struct ReadSeqVars *V)
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if (!V->allDone) {
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while (
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!(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
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getline(V);
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cgetline(V);
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}
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if (feof(V->f)) V->allDone = true;
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}
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@ -395,7 +396,7 @@ Local void readEMBL(struct ReadSeqVars *V)
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while (!V->allDone) {
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strcpy(V->seqid, (V->s) + 5);
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do {
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getline(V);
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cgetline(V);
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} while (!(feof(V->f) | (strstr(V->s, "SQ ") == V->s)));
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readLoop(0, false, endEMBL, V);
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@ -403,7 +404,7 @@ Local void readEMBL(struct ReadSeqVars *V)
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while (
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!(feof(V->f) | ((*V->s != '\0') &
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(strstr(V->s, "ID ") == V->s))))
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getline(V);
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cgetline(V);
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}
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if (feof(V->f)) V->allDone = true;
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}
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@ -422,13 +423,13 @@ Local void readZuker(struct ReadSeqVars *V)
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/*! 1st string is Zuker's Fortran format */
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while (!V->allDone) {
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getline(V); /*s == "seqLen seqid string..."*/
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cgetline(V); /*s == "seqLen seqid string..."*/
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strcpy(V->seqid, (V->s) + 6);
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readLoop(0, false, endZuker, V);
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if (!V->allDone) {
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while (
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!(feof(V->f) | ((*V->s != '\0') & (*V->s == '('))))
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getline(V);
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cgetline(V);
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}
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if (feof(V->f)) V->allDone = true;
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}
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@ -471,7 +472,7 @@ Local void readPlain(struct ReadSeqVars *V)
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do {
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addseq(V->s, V);
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V->done = feof(V->f);
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getline(V);
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cgetline(V);
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} while (!V->done);
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if (V->choice == kListSequences) addinfo(V->seqid, V);
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V->allDone = true;
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@ -482,7 +483,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
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/*
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10nov91: Reading GCG files casued duplication of last line when
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EOF followed that line !!!
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fix: getline now sets *V->s = 0
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fix: cgetline now sets *V->s = 0
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*/
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char *si;
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@ -498,7 +499,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
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*si = 0;
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do {
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V->done = feof(V->f);
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getline(V);
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cgetline(V);
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if (!V->done) addseq((V->s), V);
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} while (!V->done);
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if (V->choice == kListSequences) addinfo(V->seqid, V);
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@ -517,7 +518,7 @@ Local void readOlsen(struct ReadSeqVars *V)
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rewind(V->f);
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V->nseq = 0;
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do {
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getline(V);
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cgetline(V);
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V->done = feof(V->f);
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if (V->done && !(*V->s))
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@ -618,7 +619,7 @@ Local void readMSF(struct ReadSeqVars *V)
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rewind(V->f);
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V->nseq = 0;
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do {
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getline(V);
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cgetline(V);
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V->done = feof(V->f);
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if (V->done && !(*V->s))
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@ -698,7 +699,7 @@ Local void readPAUPinterleaved(struct ReadSeqVars *V)
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domatch = (V->matchchar > 0);
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do {
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getline(V);
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cgetline(V);
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V->done = feof(V->f);
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if (V->done && !(*V->s))
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@ -798,7 +799,7 @@ Local void readPAUPsequential(struct ReadSeqVars *V)
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/* rewind(V->f); V->nseq= 0; << do in caller !*/
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indata = true; /* call here after we find "matrix" */
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do {
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getline(V);
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cgetline(V);
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V->done = feof(V->f);
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if (V->done && !(*V->s))
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@ -901,7 +902,7 @@ Local void readPhylipInterleaved(struct ReadSeqVars *V)
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* V->topseqlen); */
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do {
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getline(V);
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cgetline(V);
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V->done = feof(V->f);
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if (V->done && !(*V->s)) break;
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@ -953,7 +954,7 @@ Local void readPhylipSequential(struct ReadSeqVars *V)
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while (isdigit(*si)) si++;
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skipwhitespace(si);
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V->topseqlen = atol(si);
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getline(V);
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cgetline(V);
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while (!V->allDone) {
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V->seqlencount = 0;
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strncpy(V->seqid, (V->s), 10);
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@ -982,10 +983,10 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
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if (V->f == NULL)
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V->err = eFileNotFound;
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else {
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for (l = skiplines_; l > 0; l--) getline(V);
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for (l = skiplines_; l > 0; l--) cgetline(V);
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do {
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getline(V);
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cgetline(V);
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for (l = strlen(V->s); (l > 0) && (V->s[l] == ' '); l--)
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;
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} while ((l == 0) && !feof(V->f));
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@ -1036,7 +1037,7 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
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/* rewind(V->f); V->nseq= 0; ?? assume
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* it is at top ?? skiplines ... */
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while (!done) {
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getline(V);
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cgetline(V);
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tolowerstr(V->s);
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if (strstr(V->s, "matrix"))
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done = true;
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@ -1086,7 +1087,7 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
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case kFitch:
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strcpy(V->seqid, V->s);
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getline(V);
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cgetline(V);
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readFitch(V);
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break;
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@ -1095,7 +1096,7 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
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gotuw = (strstr(V->s, "..") !=
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NULL);
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if (gotuw) readUWGCG(V);
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getline(V);
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cgetline(V);
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} while (!(feof(V->f) || V->allDone));
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break;
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}
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