a program to print smith-waterman scores against a query sequence

[fastq-tools.git] / src / swsse2 / fastalib.h

diff --git a/src/swsse2/fastalib.h b/src/swsse2/fastalib.h
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+/******************************************************************
+  Copyright 2006 by Michael Farrar.  All rights reserved.
+  This program may not be sold or incorporated into a commercial product,
+  in whole or in part, without written consent of Michael Farrar.  For 
+  further information regarding permission for use or reproduction, please 
+  contact: Michael Farrar at farrar.michael@gmail.com.
+*******************************************************************/
+
+/*
+  Written by Michael Farrar, 2006.
+  Please send bug reports and/or suggestions to farrar.michael@gmail.com.
+*/
+
+#ifndef INCLUDE_FASTALIB_H
+#define INCLUDE_FASTALIB_H
+
+#include <stdio.h>
+
+#define MAX_SEQ_LENGTH (64 * 1024)
+
+typedef struct {
+    char *readBuffer;
+
+    char *seqName;
+    unsigned char *seqBuffer;
+
+    int pos;
+    int size;
+
+    FILE *fp;
+
+    int sequences;
+    int residues;
+
+    int pad;
+} FASTA_LIB;
+
+FASTA_LIB *openLib (char *file, int pad);
+void closeLib (FASTA_LIB *lib);
+
+unsigned char *nextSeq (FASTA_LIB *lib, int *length);
+
+#define seqName(LIB) (LIB->seqName)
+
+#endif /* INCLUDE_FASTALIB_H */