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/txGraph.h src/hg/inc/txGraph.h index 3547ece..efe7584 100644 --- src/hg/inc/txGraph.h +++ src/hg/inc/txGraph.h @@ -1,182 +1,185 @@ /* txGraph.h was originally generated by the autoSql program, which also * generated txGraph.c and txGraph.sql. This header links the database and * the RAM representation of objects. */ +/* Copyright (C) 2007 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef TXGRAPH_H #define TXGRAPH_H #define TXGRAPH_NUM_COLS 11 struct txGraph /* A transcription graph. Includes alt-splicing info. */ { struct txGraph *next; /* Next in singly linked list. */ char *tName; /* name of target sequence, often a chrom. */ int tStart; /* First bac touched by graph. */ int tEnd; /* Start position in first bac. */ char *name; /* Human readable name. */ char strand[3]; /* + or - strand. */ unsigned vertexCount; /* Number of vertices in graph. */ struct txVertex *vertices; /* Splice sites and soft ends. */ unsigned edgeCount; /* Number of edges in graph. */ struct txEdge *edgeList; /* Edges (introns and exons) in graph. */ int sourceCount; /* Number of sources of evidence. */ struct txSource *sources; /* Sources of evidence. */ }; struct txGraph *txGraphLoad(char **row); /* Load a txGraph from row fetched with select * from txGraph * from database. Dispose of this with txGraphFree(). */ struct txGraph *txGraphLoadAll(char *fileName); /* Load all txGraph from whitespace-separated file. * Dispose of this with txGraphFreeList(). */ struct txGraph *txGraphLoadAllByChar(char *fileName, char chopper); /* Load all txGraph from chopper separated file. * Dispose of this with txGraphFreeList(). */ #define txGraphLoadAllByTab(a) txGraphLoadAllByChar(a, '\t'); /* Load all txGraph from tab separated file. * Dispose of this with txGraphFreeList(). */ struct txGraph *txGraphCommaIn(char **pS, struct txGraph *ret); /* Create a txGraph out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new txGraph */ void txGraphFree(struct txGraph **pEl); /* Free a single dynamically allocated txGraph such as created * with txGraphLoad(). */ void txGraphFreeList(struct txGraph **pList); /* Free a list of dynamically allocated txGraph's */ void txGraphOutput(struct txGraph *el, FILE *f, char sep, char lastSep); /* Print out txGraph. Separate fields with sep. Follow last field with lastSep. */ #define txGraphTabOut(el,f) txGraphOutput(el,f,'\t','\n'); /* Print out txGraph as a line in a tab-separated file. */ #define txGraphCommaOut(el,f) txGraphOutput(el,f,',',','); /* Print out txGraph as a comma separated list including final comma. */ #define TXVERTEX_NUM_COLS 2 struct txVertex /* A vertex in a transcription graph - splice site or soft end */ { int position; /* Vertex position in genomic sequence. */ unsigned char type; /* Vertex type - ggSoftStart, ggHardStart, etc. */ }; struct txVertex *txVertexCommaIn(char **pS, struct txVertex *ret); /* Create a txVertex out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new txVertex */ void txVertexOutput(struct txVertex *el, FILE *f, char sep, char lastSep); /* Print out txVertex. Separate fields with sep. Follow last field with lastSep. */ #define txVertexTabOut(el,f) txVertexOutput(el,f,'\t','\n'); /* Print out txVertex as a line in a tab-separated file. */ #define txVertexCommaOut(el,f) txVertexOutput(el,f,',',','); /* Print out txVertex as a comma separated list including final comma. */ #define TXEDGE_NUM_COLS 5 struct txEdge /* An edge in a transcription graph - exon or intron */ { struct txEdge *next; /* Next in singly linked list. */ int startIx; /* Index of start in vertex array */ int endIx; /* Index of end in vertex array */ unsigned char type; /* Edge type */ int evCount; /* Count of evidence */ struct txEvidence *evList; /* List of evidence */ }; struct txEdge *txEdgeCommaIn(char **pS, struct txEdge *ret); /* Create a txEdge out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new txEdge */ void txEdgeFree(struct txEdge **pEl); /* Free a single dynamically allocated txEdge such as created * with txEdgeLoad(). */ void txEdgeFreeList(struct txEdge **pList); /* Free a list of dynamically allocated txEdge's */ void txEdgeOutput(struct txEdge *el, FILE *f, char sep, char lastSep); /* Print out txEdge. Separate fields with sep. Follow last field with lastSep. */ #define txEdgeTabOut(el,f) txEdgeOutput(el,f,'\t','\n'); /* Print out txEdge as a line in a tab-separated file. */ #define txEdgeCommaOut(el,f) txEdgeOutput(el,f,',',','); /* Print out txEdge as a comma separated list including final comma. */ #define TXEVIDENCE_NUM_COLS 3 struct txEvidence /* Information on evidence for an edge. */ { struct txEvidence *next; /* Next in singly linked list. */ int sourceId; /* Id (index) in sources list */ int start; /* Start position */ int end; /* End position */ }; struct txEvidence *txEvidenceCommaIn(char **pS, struct txEvidence *ret); /* Create a txEvidence out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new txEvidence */ void txEvidenceFree(struct txEvidence **pEl); /* Free a single dynamically allocated txEvidence such as created * with txEvidenceLoad(). */ void txEvidenceFreeList(struct txEvidence **pList); /* Free a list of dynamically allocated txEvidence's */ void txEvidenceOutput(struct txEvidence *el, FILE *f, char sep, char lastSep); /* Print out txEvidence. Separate fields with sep. Follow last field with lastSep. */ #define txEvidenceTabOut(el,f) txEvidenceOutput(el,f,'\t','\n'); /* Print out txEvidence as a line in a tab-separated file. */ #define txEvidenceCommaOut(el,f) txEvidenceOutput(el,f,',',','); /* Print out txEvidence as a comma separated list including final comma. */ #define TXSOURCE_NUM_COLS 2 struct txSource /* Source of evidence in graph. */ { char *type; /* Type: refSeq, mrna, est, etc. */ char *accession; /* GenBank accession. With type forms a key */ }; struct txSource *txSourceCommaIn(char **pS, struct txSource *ret); /* Create a txSource out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new txSource */ void txSourceFreeInternals(struct txSource *array, int count); /* Free internals of a simple type txSource (one not put on a list). */ void txSourceOutput(struct txSource *el, FILE *f, char sep, char lastSep); /* Print out txSource. Separate fields with sep. Follow last field with lastSep. */ #define txSourceTabOut(el,f) txSourceOutput(el,f,'\t','\n'); /* Print out txSource as a line in a tab-separated file. */ #define txSourceCommaOut(el,f) txSourceOutput(el,f,',',','); /* Print out txSource as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* TXGRAPH_H */