add: license

LICENSE

@@ -0,0 +1,7 @@
+PUBLIC DOMAIN NOTICE:
+This software is freely available to the public for use. The author, Don Gilbert, of Readseq and the Java package 'iubio.readseq' does not place any restriction on its use or reproduction. Developers are encourged to incorporate parts in their programs. I would appreciate being cited in any work or product based on this material. This software is provided without warranty of any kind.
+
+-- Don Gilbert
+software@bio.indiana.edu, May 2001
+Bioinformatics group, Biology Department & Cntr. Genomics & Bioinformatics,
+Indiana University, Bloomington, Indiana

readseq.c

@@ -168,6 +168,7 @@ link -w -o readseq -t MPST -c 'MPS ' <20>
 
 #include <ctype.h>
 #include <stdio.h>
+#include <stdlib.h>
 #include <string.h>
 
 #include "ureadseq.h"

ureadseq.c

@@ -18,6 +18,7 @@
 
 #include <ctype.h>
 #include <stdio.h>
+#include <stdlib.h>
 #include <string.h>
 
 #define UREADSEQ_G
@@ -123,7 +124,7 @@ Local void readline(FILE *f, char *s, long *linestart)
 	}
 }
 
-Local void getline(struct ReadSeqVars *V)
+Local void cgetline(struct ReadSeqVars *V)
 {
 	readline(V->f, V->s, &V->linestart);
 }
@@ -200,7 +201,7 @@ Local void readLoop(short margin, boolean addfirst,
 
 	if (addfirst) addseq(V->s, V);
 	do {
-		getline(V);
+		cgetline(V);
 		V->done = feof(V->f);
 		V->done |= (*endTest)(&addend, &ungetend, V);
 		if (V->addit && (addend || !V->done) &&
@@ -231,7 +232,7 @@ Local void readIG(struct ReadSeqVars *V)
 
 	while (!V->allDone) {
 		do {
-			getline(V);
+			cgetline(V);
 			for (si = V->s; *si != 0 && *si < ' '; si++)
 				*si = ' ';	 /* drop controls */
 			if (*si == 0) *V->s = 0; /* chop line to empty */
@@ -257,13 +258,13 @@ Local void readStrider(struct ReadSeqVars *V)
 { /* ? only 1 seq/file ? */
 
 	while (!V->allDone) {
-		getline(V);
+		cgetline(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);
+			cgetline(V);
 		}
 		if (feof(V->f))
 			V->allDone = true;
@@ -285,17 +286,17 @@ Local void readPIR(struct ReadSeqVars *V)
 	while (!V->allDone) {
 		while (!(feof(V->f) || strstr(V->s, "ENTRY") ||
 			 strstr(V->s, "SEQUENCE")))
-			getline(V);
+			cgetline(V);
 		strcpy(V->seqid, (V->s) + 16);
 		while (!(feof(V->f) || strstr(V->s, "SEQUENCE") == V->s))
-			getline(V);
+			cgetline(V);
 		readLoop(0, false, endPIR, V);
 
 		if (!V->allDone) {
 			while (!(
 			    feof(V->f) ||
 			    ((*V->s != 0) && (strstr(V->s, "ENTRY") == V->s))))
-				getline(V);
+				cgetline(V);
 		}
 		if (feof(V->f)) V->allDone = true;
 	}
@@ -314,14 +315,14 @@ 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);
+			cgetline(V);
 		readLoop(0, false, endGB, V);
 
 		if (!V->allDone) {
 			while (!(
 			    feof(V->f) ||
 			    ((*V->s != 0) && (strstr(V->s, "LOCUS") == V->s))))
-				getline(V);
+				cgetline(V);
 		}
 		if (feof(V->f)) V->allDone = true;
 	}
@@ -351,11 +352,11 @@ Local void readNBRF(struct ReadSeqVars *V)
 {
 	while (!V->allDone) {
 		strcpy(V->seqid, (V->s) + 4);
-		getline(V); /*skip title-junk line*/
+		cgetline(V); /*skip title-junk line*/
 		readLoop(0, false, endNBRF, V);
 		if (!V->allDone) {
 			while (!(feof(V->f) || (*V->s != 0 && *V->s == '>')))
-				getline(V);
+				cgetline(V);
 		}
 		if (feof(V->f)) V->allDone = true;
 	}
@@ -377,7 +378,7 @@ Local void readPearson(struct ReadSeqVars *V)
 		if (!V->allDone) {
 			while (
 			    !(feof(V->f) || ((*V->s != 0) && (*V->s == '>'))))
-				getline(V);
+				cgetline(V);
 		}
 		if (feof(V->f)) V->allDone = true;
 	}
@@ -395,7 +396,7 @@ Local void readEMBL(struct ReadSeqVars *V)
 	while (!V->allDone) {
 		strcpy(V->seqid, (V->s) + 5);
 		do {
-			getline(V);
+			cgetline(V);
 		} while (!(feof(V->f) | (strstr(V->s, "SQ   ") == V->s)));
 
 		readLoop(0, false, endEMBL, V);
@@ -403,7 +404,7 @@ Local void readEMBL(struct ReadSeqVars *V)
 			while (
 			    !(feof(V->f) | ((*V->s != '\0') &
 					    (strstr(V->s, "ID   ") == V->s))))
-				getline(V);
+				cgetline(V);
 		}
 		if (feof(V->f)) V->allDone = true;
 	}
@@ -422,13 +423,13 @@ Local void readZuker(struct ReadSeqVars *V)
 	/*! 1st string is Zuker's Fortran format */
 
 	while (!V->allDone) {
-		getline(V); /*s == "seqLen seqid string..."*/
+		cgetline(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);
+				cgetline(V);
 		}
 		if (feof(V->f)) V->allDone = true;
 	}
@@ -471,7 +472,7 @@ Local void readPlain(struct ReadSeqVars *V)
 	do {
 		addseq(V->s, V);
 		V->done = feof(V->f);
-		getline(V);
+		cgetline(V);
 	} while (!V->done);
 	if (V->choice == kListSequences) addinfo(V->seqid, V);
 	V->allDone = true;
@@ -482,7 +483,7 @@ 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: cgetline now sets *V->s = 0
 	*/
 	char *si;
 
@@ -498,7 +499,7 @@ Local void readUWGCG(struct ReadSeqVars *V)
 		*si = 0;
 	do {
 		V->done = feof(V->f);
-		getline(V);
+		cgetline(V);
 		if (!V->done) addseq((V->s), V);
 	} while (!V->done);
 	if (V->choice == kListSequences) addinfo(V->seqid, V);
@@ -517,7 +518,7 @@ Local void readOlsen(struct ReadSeqVars *V)
 	rewind(V->f);
 	V->nseq = 0;
 	do {
-		getline(V);
+		cgetline(V);
 		V->done = feof(V->f);
 
 		if (V->done && !(*V->s))
@@ -618,7 +619,7 @@ Local void readMSF(struct ReadSeqVars *V)
 	rewind(V->f);
 	V->nseq = 0;
 	do {
-		getline(V);
+		cgetline(V);
 		V->done = feof(V->f);
 
 		if (V->done && !(*V->s))
@@ -698,7 +699,7 @@ Local void readPAUPinterleaved(struct ReadSeqVars *V)
 	domatch = (V->matchchar > 0);
 
 	do {
-		getline(V);
+		cgetline(V);
 		V->done = feof(V->f);
 
 		if (V->done && !(*V->s))
@@ -798,7 +799,7 @@ 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);
+		cgetline(V);
 		V->done = feof(V->f);
 
 		if (V->done && !(*V->s))
@@ -901,7 +902,7 @@ Local void readPhylipInterleaved(struct ReadSeqVars *V)
 	 * V->topseqlen); */
 
 	do {
-		getline(V);
+		cgetline(V);
 		V->done = feof(V->f);
 
 		if (V->done && !(*V->s)) break;
@@ -953,7 +954,7 @@ Local void readPhylipSequential(struct ReadSeqVars *V)
 	while (isdigit(*si)) si++;
 	skipwhitespace(si);
 	V->topseqlen = atol(si);
-	getline(V);
+	cgetline(V);
 	while (!V->allDone) {
 		V->seqlencount = 0;
 		strncpy(V->seqid, (V->s), 10);
@@ -982,10 +983,10 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
 	if (V->f == NULL)
 		V->err = eFileNotFound;
 	else {
-		for (l = skiplines_; l > 0; l--) getline(V);
+		for (l = skiplines_; l > 0; l--) cgetline(V);
 
 		do {
-			getline(V);
+			cgetline(V);
 			for (l = strlen(V->s); (l > 0) && (V->s[l] == ' '); l--)
 				;
 		} while ((l == 0) && !feof(V->f));
@@ -1036,7 +1037,7 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
 					/* rewind(V->f); V->nseq= 0; ?? assume
 					 * it is at top ?? skiplines ... */
 					while (!done) {
-						getline(V);
+						cgetline(V);
 						tolowerstr(V->s);
 						if (strstr(V->s, "matrix"))
 							done = true;
@@ -1086,7 +1087,7 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
 
 				case kFitch:
 					strcpy(V->seqid, V->s);
-					getline(V);
+					cgetline(V);
 					readFitch(V);
 					break;
 
@@ -1095,7 +1096,7 @@ Local void readSeqMain(struct ReadSeqVars *V, const long skiplines_,
 						gotuw = (strstr(V->s, "..") !=
 							 NULL);
 						if (gotuw) readUWGCG(V);
-						getline(V);
+						cgetline(V);
 					} while (!(feof(V->f) || V->allDone));
 					break;
 			}