00001 /* repMask.h was originally generated by the autoSql program, which also 00002 * generated repMask.c and repMask.sql. This header links the database and the RAM 00003 * representation of objects. */ 00004 00005 #ifndef REPMASK_H 00006 #define REPMASK_H 00007 00008 struct repeatMaskOut 00009 /* Repeat Masker out format */ 00010 { 00011 struct repeatMaskOut *next; /* Next in singly linked list. */ 00012 unsigned score; /* Smith-Waterman score. */ 00013 float percDiv; /* Percentage base divergence. */ 00014 float percDel; /* Percentage deletions. */ 00015 float percInc; /* Percentage inserts. */ 00016 char *qName; /* Name of query. */ 00017 int qStart; /* Start query position. */ 00018 int qEnd; /* End query position. */ 00019 char *qLeft; /* Bases left in query. */ 00020 char strand[2]; /* Query strand (+ or C) */ 00021 char *rName; /* Repeat name */ 00022 char *rFamily; /* Repeat name */ 00023 char *rStart; /* Start position in repeat. */ 00024 unsigned rEnd; /* End position in repeat. */ 00025 char *rLeft; /* Bases left in repeat. */ 00026 }; 00027 00028 void repeatMaskOutStaticLoad(char **row, struct repeatMaskOut *ret); 00029 /* Load a row from repeatMaskOut table into ret. The contents of ret will 00030 * be replaced at the next call to this function. */ 00031 00032 struct repeatMaskOut *repeatMaskOutLoad(char **row); 00033 /* Load a repeatMaskOut from row fetched with select * from repeatMaskOut 00034 * from database. Dispose of this with repeatMaskOutFree(). */ 00035 00036 struct repeatMaskOut *repeatMaskOutCommaIn(char **pS); 00037 /* Create a repeatMaskOut out of a comma separated string. */ 00038 00039 void repeatMaskOutFree(struct repeatMaskOut **pEl); 00040 /* Free a single dynamically allocated repeatMaskOut such as created 00041 * with repeatMaskOutLoad(). */ 00042 00043 void repeatMaskOutFreeList(struct repeatMaskOut **pList); 00044 /* Free a list of dynamically allocated repeatMaskOut's */ 00045 00046 void repeatMaskOutOutput(struct repeatMaskOut *el, FILE *f, char sep, char lastSep); 00047 /* Print out repeatMaskOut. Separate fields with sep. Follow last field with lastSep. */ 00048 00049 #define repeatMaskOutTabOut(el,f) repeatMaskOutOutput(el,f,'\t','\n'); 00050 /* Print out repeatMaskOut as a line in a tab-separated file. */ 00051 00052 #define repeatMaskOutCommaOut(el,f) repeatMaskOutOutput(el,f,',',','); 00053 /* Print out repeatMaskOut as a comma separated list including final comma. */ 00054 00055 #endif /* REPMASK_H */ 00056
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