e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/inc/chromGraph.h src/hg/inc/chromGraph.h index ae6562d..5ae6e8e 100644 --- src/hg/inc/chromGraph.h +++ src/hg/inc/chromGraph.h @@ -1,195 +1,198 @@ /* chromGraph.h was originally generated by the autoSql program, which also * generated chromGraph.c and chromGraph.sql. This header links the database and * the RAM representation of objects. */ +/* Copyright (C) 2009 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef CHROMGRAPH_H #define CHROMGRAPH_H #ifndef TRACKDB_H #include "trackDb.h" #endif #ifndef CART_H #include "cart.h" #endif #define CHROMGRAPH_NUM_COLS 3 struct chromGraph /* A graph over a chromosome - best used for low resolution graphs */ { struct chromGraph *next; /* Next in singly linked list. */ char *chrom; /* Chromosome */ int chromStart; /* Start coordinate */ double val; /* Value at coordinate */ char *marker; /* Marker */ }; void chromGraphStaticLoad(char **row, struct chromGraph *ret); /* Load a row from chromGraph table into ret. The contents of ret will * be replaced at the next call to this function. */ struct chromGraph *chromGraphLoad(char **row); /* Load a chromGraph from row fetched with select * from chromGraph * from database. Dispose of this with chromGraphFree(). */ struct chromGraph *chromGraphLoadAll(char *fileName); /* Load all chromGraph from whitespace-separated file. * Dispose of this with chromGraphFreeList(). */ struct chromGraph *chromGraphLoadAllByChar(char *fileName, char chopper); /* Load all chromGraph from chopper separated file. * Dispose of this with chromGraphFreeList(). */ #define chromGraphLoadAllByTab(a) chromGraphLoadAllByChar(a, '\t'); /* Load all chromGraph from tab separated file. * Dispose of this with chromGraphFreeList(). */ struct chromGraph *chromGraphCommaIn(char **pS, struct chromGraph *ret); /* Create a chromGraph out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new chromGraph */ void chromGraphFree(struct chromGraph **pEl); /* Free a single dynamically allocated chromGraph such as created * with chromGraphLoad(). */ void chromGraphFreeList(struct chromGraph **pList); /* Free a list of dynamically allocated chromGraph's */ void chromGraphOutput(struct chromGraph *el, FILE *f, char sep, char lastSep); /* Print out chromGraph. Separate fields with sep. Follow last field with lastSep. */ #define chromGraphTabOut(el,f) chromGraphOutput(el,f,'\t','\n'); /* Print out chromGraph as a line in a tab-separated file. */ #define chromGraphCommaOut(el,f) chromGraphOutput(el,f,',',','); /* Print out chromGraph as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ int chromGraphCmp(const void *va, const void *vb); /* Compare to sort based on query chromStart. */ void chromGraphGetMinMax(struct chromGraph *list, double *pMin, double *pMax); /* Figure out min/max values in list. */ #define chromGraphDefaultGapToFill 25000 struct chromGraphSettings /* Settings */ { int maxGapToFill; /* Maximum gap to fill with line */ double minVal, maxVal; /* Max/min data range */ int linesAtCount; /* Number of horizontal labeling lines */ double *linesAt; /* Data values to label with horizontal line */ int minPixels; /* Minimum allowed pixels. */ int pixels; /* Actual pixels. */ int maxPixels; /* Maximum allowed pixels. */ }; void chromGraphParseMinMax(char *trackName, char *text, double *pMin, double *pMax); /* Parse out min,max from text. TrackName is just for error reporting */ void chromGraphSettingsFillFromHash(struct chromGraphSettings *cgs, struct hash *hash, char *trackName); /* Fill in settings from hash table. TrackName is just for error reporting. */ struct chromGraphSettings *chromGraphSettingsGet(char *trackName, struct sqlConnection *conn, struct trackDb *tdb, struct cart *cart); /* Get settings for chromGraph track. If you pass in all NULLs * you'll get a reasonable default. */ #define chromGraphVarNameMaxSize 512 void chromGraphVarName(char *track, char *var, char output[chromGraphVarNameMaxSize]); /* Fill in output with name of cart variable. */ void chromGraphDataRange(char *trackName, struct sqlConnection *conn, double *retMin, double *retMax); /* Get min/max values observed from metaChromGraph table */ struct slName *chromGraphListAll(struct sqlConnection *conn); /* Return list of all chrom graph tables. */ char *chromGraphBinaryFileName(char *trackName, struct sqlConnection *conn); /* Get binary file name associated with chromGraph track. Returns NULL * if no such file or track. FreeMem result when done. */ void chromGraphToBin(struct chromGraph *list, char *fileName); /* Create binary representation of chromGraph list, which should * be sorted. */ void chromGraphToBinGetMinMax(struct chromGraph *list, char *fileName, double *retMin, double *retMax); /* Create binary representation of chromGraph list, which should * be sorted. Also return min/max values seen in data*/ /* chromGraphBin interface. The general calling sequence is: * struct chromGraphBin *cgb = chromGraphBinOpen(path); * while (chromGraphBinNextChrom(cgb)) * { * char *chrom = cgb->chrom; * while (chromGraphBinNextVal(cgb)) * { * // process cgb->pos, cgb->val * } * } * chromGraphBinFree(&cgb); */ struct cgbChrom /* Info on a single chromosome in a chromGraph file */ { struct cgbChrom *next; /* Next in list. */ char *name; /* Chromosome name. */ bits64 offset; /* Offset to start of chrom in file */ }; void cgbChromFree(struct cgbChrom **pChrom); /* Free up one cgbChrom */ void cgbChromFreeList(struct cgbChrom **pList); /* Free up list of cgbChrom */ struct chromGraphBin /* A handle to binary representation to chrom graph */ { struct chromGraphBin *next; /* Next in list if any */ char *fileName; /* Name of file. */ FILE *f; /* File handle. */ boolean isSwapped; /* Need to swap? */ struct cgbChrom *chromList; /* List of chromosomes/positions */ struct hash *chromHash; /* Hash of all chromosomes/positions */ double minVal, maxVal; /* Min/max values in file */ /* Variables used when scanning through file. */ char chrom[256]; /* Current chromosome. */ bits32 chromStart; /* Current position. */ double val; /* Current value. */ }; struct chromGraphBin *chromGraphBinOpen(char *path); /* Open up a chromGraphBin file */ void chromGraphBinFree(struct chromGraphBin **pCgb); /* Close down and free up chromGraphBin. */ boolean chromGraphBinNextChrom(struct chromGraphBin *cgb); /* Fetch next chromosome, or FALSE if at end of file. */ boolean chromGraphBinNextVal(struct chromGraphBin *cgb); /* Fetch next pos/val or FALSE if at end of chromosome. */ boolean chromGraphBinSeekToChrom(struct chromGraphBin *cgb, char *chromName); /* Seek to chromosome if have data for it. Otherwise return FALSE. */ void chromGraphBinRewind(struct chromGraphBin *cgb); /* Position file pointer back to the first chromosome */ struct bed3 *chromGraphBinToBed3(char *fileName, double threshold); /* Stream through making list of all places above threshold. */ #endif /* CHROMGRAPH_H */