00001 /* aliType - some definitions for type of alignment. */ 00002 00003 #ifndef ALITYPE_H 00004 #define ALITYPE_H 00005 00006 enum gfType 00007 /* Types of sequence genoFind deals with. */ 00008 { 00009 gftDna = 0, /* DNA (genomic) */ 00010 gftRna = 1, /* RNA */ 00011 gftProt = 2, /* Protein. */ 00012 gftDnaX = 3, /* Genomic DNA translated to protein */ 00013 gftRnaX = 4, /* RNA translated to protein */ 00014 }; 00015 00016 char *gfTypeName(enum gfType type); 00017 /* Return string representing type. */ 00018 00019 enum gfType gfTypeFromName(char *name); 00020 /* Return type from string. */ 00021 00022 enum ffStringency 00023 /* How tight of a match is required. */ 00024 { 00025 ffExact = 0, /* Only an exact match will do. */ 00026 00027 ffCdna = 1, /* Near exact. Tolerate long gaps in target (genomic) */ 00028 ffTight = 2, /* Near exact. Not so tolerant of long gaps in target. */ 00029 ffLoose = 3, /* Less exact. */ 00030 }; 00031 00032 #endif /* ALITYPE_H */
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