00001 /***************************************************************************** 00002 * Copyright (C) 2002 Ryan Weber. This source code may be freely used * 00003 * for personal, academic, and non-profit purposes. Commercial use * 00004 * permitted only by explicit agreement with Ryan Weber (weber@cse.ucsc.edu) * 00005 *****************************************************************************/ 00006 /* jointalign.h - routines for printing a joint alignment in html. */ 00007 00008 #ifndef JOINTALIGN_H 00009 #define JOINTALIGN_H 00010 00011 void htmlPrintJointAlignment( char *seq1, char *seq2, int columnNum, 00012 int start, int end, char *strand ); 00013 /* Print sequences 1 and 2 (assumed to be a joint alignment), 00014 * formatted for html output. Coordinates are printed based on 00015 * the start and end positions and oriented according to the 00016 * strand the sequences are on (+ or -).*/ 00017 00018 boolean ucaseMatch( char a, char b ); 00019 /* Case insensitive character matching */ 00020 00021 void validateSeqs( char *seq1, char *seq2 ); 00022 /*Make sure sequences are the same length*/ 00023 00024 void htmlPrintJointAlignmentLine( char *seq1, char *seq2, int start, int end); 00025 /* Prints one line of the joint alignment between seq1 and seq2, 00026 * from seq[start] to seq[end-1].*/ 00027 00028 00029 #endif /* JOINTALIGN */ 00030
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