39e533cc9ffcb46d9c484dc09a387a031a739391 Merge parents 1c86690 f642bab kate Mon Sep 24 16:35:53 2018 -0700 Updating from master diff --cc src/hg/inc/interact.h index 3038ff6,b682fbe..aacbf61 --- src/hg/inc/interact.h +++ src/hg/inc/interact.h @@@ -1,120 -1,125 +1,131 @@@ /* interact.h was originally generated by the autoSql program, which also * generated interact.c and interact.sql. This header links the database and * the RAM representation of objects. */ #ifndef INTERACT_H #define INTERACT_H #include "jksql.h" #define INTERACT_NUM_COLS 18 extern char *interactCommaSepFieldNames; struct interact /* Interaction between two regions */ { struct interact *next; /* Next in singly linked list. */ char *chrom; /* Chromosome (or contig, scaffold, etc.). For interchromosomal, use 2 records */ unsigned chromStart; /* Start position in chromosome of lower region. For interchromosomal, set to chromStart of this region */ unsigned chromEnd; /* End position in chromosome of upper region. For interchromosomal, set to chromEnd of this region */ char *name; /* Name of item, for display. Usually 'name1/name2' or empty */ unsigned score; /* Score from 0-1000. */ double value; /* Strength of interaction or other data value. Typically basis for score */ char *exp; /* Experiment name (metadata for filtering). Use . if not applicable */ unsigned color; /* Item color, as itemRgb in bed9. Typically based on strength or filter */ char *sourceChrom; /* Chromosome of source region (directional) or lower region. For non-directional interchromosomal, chrom of this region. */ unsigned sourceStart; /* Start position in chromosome of source/lower/this region */ unsigned sourceEnd; /* End position in chromosome of source/lower/this region */ char *sourceName; /* Identifier of source/lower/this region. Can be used as link to related table */ char *sourceStrand; /* Orientation of source/lower/this region: + or -. Use . if not applicable */ char *targetChrom; /* Chromosome of target region (directional) or upper region. For non-directional interchromosomal, chrom of other region */ unsigned targetStart; /* Start position in chromosome of target/upper/this region */ unsigned targetEnd; /* End position in chromosome of target/upper/this region */ char *targetName; /* Identifier of target/upper/this region. Can be used as link to related table */ char *targetStrand; /* Orientation of target/upper/this region: + or -. Use . if not applicable */ }; void interactStaticLoad(char **row, struct interact *ret); /* Load a row from interact table into ret. The contents of ret will * be replaced at the next call to this function. */ struct interact *interactLoadByQuery(struct sqlConnection *conn, char *query); /* Load all interact from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with interactFreeList(). */ void interactSaveToDb(struct sqlConnection *conn, struct interact *el, char *tableName, int updateSize); /* Save interact as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct interact *interactLoad(char **row); /* Load a interact from row fetched with select * from interact * from database. Dispose of this with interactFree(). */ struct interact *interactLoadAll(char *fileName); /* Load all interact from whitespace-separated file. * Dispose of this with interactFreeList(). */ struct interact *interactLoadAllByChar(char *fileName, char chopper); /* Load all interact from chopper separated file. * Dispose of this with interactFreeList(). */ #define interactLoadAllByTab(a) interactLoadAllByChar(a, '\t'); /* Load all interact from tab separated file. * Dispose of this with interactFreeList(). */ struct interact *interactCommaIn(char **pS, struct interact *ret); /* Create a interact out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new interact */ void interactFree(struct interact **pEl); /* Free a single dynamically allocated interact such as created * with interactLoad(). */ void interactFreeList(struct interact **pList); /* Free a list of dynamically allocated interact's */ void interactOutput(struct interact *el, FILE *f, char sep, char lastSep); /* Print out interact. Separate fields with sep. Follow last field with lastSep. */ #define interactTabOut(el,f) interactOutput(el,f,'\t','\n'); /* Print out interact as a line in a tab-separated file. */ #define interactCommaOut(el,f) interactOutput(el,f,',',','); /* Print out interact as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ struct asObject *interactAsObj(); /* Return asObject describing fields of barChart database table (includes bin) */ struct interact *interactLoadAndValidate(char **row); /* Load a interact from row fetched with select * from interact * from database, validating fields. Dispose of this with interactFree(). */ +struct bed *interactToBed(struct interact *inter); +/* Convert an interact to a BED12 */ + + struct interact *interactLoadAllAndValidate(char *fileName); + /* Load all interact from a whitespace-separated file. + * Dispose of this with interactFreeList(). */ + + void interactOutputCustom(struct interact *el, FILE *f, char sep, char lastSep); + /* Print out interact. Separate fields with sep. Follow last field with lastSep. + * Differs from auto-gen'ed by printing rgb color */ + + void interactFixRange(struct interact *inter); + /* Set values for chromStart/chromEnd based on source and target start/ends */ + char *interactOtherChrom(struct interact *inter); /* Get other chromosome from an interaaction. Return NULL if same chromosome */ int interactRegionCenter(int start, int end); /* Return genomic location of center of region */ +void interactRegionCenters(struct interact *inter, int *sourceCenter, int *targetCenter); +/* Return genomic position of endpoint centers */ + int interactRegionDistance(struct interact *inter); /* Return distance between region midpoints. Return -1 for other chromosome */ int interactDistanceCmp(const void *va, const void *vb); /* Compare based on distance between region midpoints */ #endif /* INTERACT_H */