00001 /***************************************************************************** 00002 * Copyright (C) 2000 Jim Kent. This source code may be freely used * 00003 * for personal, academic, and non-profit purposes. Commercial use * 00004 * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) * 00005 *****************************************************************************/ 00006 /* xenalign.h - Do cross-species DNA alignments from scratch. */ 00007 #ifndef XENALIGN_H 00008 #define XENALIGN_H 00009 00010 #ifndef NT4_H 00011 #include "nt4.h" 00012 #endif 00013 00014 int xenAlignSmall(DNA *query, int querySize, DNA *target, int targetSize, 00015 FILE *f, boolean printExtraAtEnds); 00016 /* Use dynamic programming to do small scale 00017 * (querySize * targetSize < 10,000,000) 00018 * alignment of DNA. Write results into f.*/ 00019 00020 void xenStitch(char *inName, FILE *out, int stitchMinScore, 00021 boolean compactOutput); 00022 /* Do the big old stitching run putting together contents of inName 00023 * into contigs in out. Create output in newer format. */ 00024 00025 void xenStitcher(char *inName, FILE *out, int stitchMinScore, boolean 00026 compactOutput); 00027 /* Do the big old stitching run putting together contents of inName 00028 * into contigs in out. Create output in older format. */ 00029 00030 void xenAlignBig(DNA *query, int qSize, DNA *target, int tSize, FILE *f, boolean forHtml); 00031 /* Do a big alignment - one that has to be stitched together. 00032 * Write results into f. */ 00033 00034 void xenShowAli(char *qSym, char *tSym, char *hSym, int symCount, FILE *f, 00035 int qOffset, int tOffset, char qStrand, char tStrand, int maxLineSize); 00036 /* Print alignment and HMM symbols maxLineSize bases at a time to file. */ 00037 00038 void xenAlignWorm(DNA *query, int qSize, FILE *f, boolean forHtml); 00039 /* Do alignment against worm genome. */ 00040 00041 #endif /* XENALIGN_H */
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