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 #ifndef MATOFF_H 00007 #define MATOFF_H 00008 00009 /* Convert between mrnaAli and ffAli representations of an alignment. */ 00010 00011 struct mrnaAli *ffToMa(struct ffAli *ffLeft, 00012 struct dnaSeq *mrnaSeq, char *mrnaAcc, 00013 struct dnaSeq *genoSeq, char *genoAcc, 00014 boolean isRc, boolean isEst); 00015 /* Convert ffAli structure to mrnaAli. */ 00016 00017 struct ffAli *maToFf(struct mrnaAli *ma, DNA *needle, DNA *haystack); 00018 /* Convert from database to internal representation of alignment. */ 00019 00020 #endif /* MATOFF_H */ 00021
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