00001 /* gfClientLib - stuff that both blat and pcr clients of 00002 * genoFind use. */ 00003 00004 #ifndef GFCLIENTLIB_H 00005 #define GFCLIENTLIB_H 00006 00007 void gfClientFileArray(char *fileName, char ***retFiles, int *retFileCount); 00008 /* Check if file if .2bit or .nib or .fa. If so return just that 00009 * file in a list of one. Otherwise read all file and treat file 00010 * as a list of filenames. */ 00011 00012 bioSeq *gfClientSeqList(int fileCount, char *files[], 00013 boolean isProt, boolean isTransDna, char *maskType, 00014 float minRepDivergence, boolean showStatus); 00015 /* From an array of .fa and .nib file names, create a 00016 * list of dnaSeqs, which are set up so that upper case is masked and lower case 00017 * is unmasked sequence. (This is the opposite of the input, but set so that 00018 * we can use lower case as our primary DNA sequence, which historically predates 00019 * our use of lower case masking.) Protein sequence on the other hand is 00020 * all upper case. */ 00021 00022 void gfClientUnmask(struct dnaSeq *seqList); 00023 /* Unmask all sequences. */ 00024 00025 #endif /* GFCLIENTLIB_H */ 00026
1.5.2