00001 /* gapCalc - Stuff to calculate complex (but linear) gap costs quickly, 00002 * and read specifications from a file. */ 00003 00004 #ifndef GAPCALC_H 00005 #define GAPCALC_H 00006 00007 00008 struct gapCalc; /* Predeclare structure. It's complex and private though, so 00009 * real declaration is in gapCalc.c. */ 00010 00011 struct gapCalc *gapCalcDefault(); 00012 /* Return default gapCalc. */ 00013 00014 struct gapCalc *gapCalcRnaDna(); 00015 /* Return gaps suitable for RNA queries vs. DNA targets */ 00016 00017 struct gapCalc *gapCalcCheap(); 00018 /* Return cheap gap costs. */ 00019 00020 struct gapCalc *gapCalcOriginal(); 00021 /* Return gap costs from original paper. */ 00022 00023 struct gapCalc *gapCalcFromFile(char *fileName); 00024 /* Return gapCalc from file. */ 00025 00026 struct gapCalc *gapCalcFromString(char *s); 00027 /* Return gapCalc from description string. */ 00028 00029 struct gapCalc *gapCalcRead(struct lineFile *lf); 00030 /* Create gapCalc from open file. */ 00031 00032 void gapCalcFree(struct gapCalc **pGapCalc); 00033 /* Free up resources associated with gapCalc. */ 00034 00035 int gapCalcCost(struct gapCalc *gapCalc, int dq, int dt); 00036 /* Figure out gap costs. */ 00037 00038 char *gapCalcSampleFileContents(); 00039 /* Return contents of a sample linear gap file. */ 00040 00041 void gapCalcTest(struct gapCalc *gapCalc); 00042 /* Print out gap cost info. */ 00043 00044 #endif /* GAPCALC_H */
1.5.2