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/lib/fosEndPairs.c src/hg/lib/fosEndPairs.c index 5fa5d39..5757418 100644 --- src/hg/lib/fosEndPairs.c +++ src/hg/lib/fosEndPairs.c @@ -1,218 +1,221 @@ /* fosEndPairs.c was originally generated by the autoSql program, which also * generated fosEndPairs.h and fosEndPairs.sql. This module links the database and * the RAM representation of objects. */ +/* Copyright (C) 2014 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #include "common.h" #include "linefile.h" #include "dystring.h" #include "jksql.h" #include "fosEndPairs.h" struct fosEndPairs *fosEndPairsLoad(char **row) /* Load a fosEndPairs from row fetched with select * from fosEndPairs * from database. Dispose of this with fosEndPairsFree(). */ { struct fosEndPairs *ret; int sizeOne,i; char *s; AllocVar(ret); ret->lfCount = sqlUnsigned(row[8]); ret->bin = sqlSigned(row[0]); ret->chrom = cloneString(row[1]); ret->chromStart = sqlUnsigned(row[2]); ret->chromEnd = sqlUnsigned(row[3]); ret->name = cloneString(row[4]); ret->score = sqlUnsigned(row[5]); strcpy(ret->strand, row[6]); ret->pslTable = cloneString(row[7]); sqlUnsignedDynamicArray(row[9], &ret->lfStarts, &sizeOne); assert(sizeOne == ret->lfCount); sqlUnsignedDynamicArray(row[10], &ret->lfSizes, &sizeOne); assert(sizeOne == ret->lfCount); sqlStringDynamicArray(row[11], &ret->lfNames, &sizeOne); assert(sizeOne == ret->lfCount); return ret; } struct fosEndPairs *fosEndPairsLoadAll(char *fileName) /* Load all fosEndPairs from a tab-separated file. * Dispose of this with fosEndPairsFreeList(). */ { struct fosEndPairs *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[12]; while (lineFileRow(lf, row)) { el = fosEndPairsLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct fosEndPairs *fosEndPairsLoadWhere(struct sqlConnection *conn, char *table, char *where) /* Load all fosEndPairs from table that satisfy where clause. The * where clause may be NULL in which case whole table is loaded * Dispose of this with fosEndPairsFreeList(). */ { struct fosEndPairs *list = NULL, *el; struct dyString *query = dyStringNew(256); struct sqlResult *sr; char **row; sqlDyStringPrintf(query, "select * from %s", table); if (where != NULL) dyStringPrintf(query, " where %s", where); sr = sqlGetResult(conn, query->string); while ((row = sqlNextRow(sr)) != NULL) { el = fosEndPairsLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); dyStringFree(&query); return list; } struct fosEndPairs *fosEndPairsCommaIn(char **pS, struct fosEndPairs *ret) /* Create a fosEndPairs out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new fosEndPairs */ { char *s = *pS; int i; if (ret == NULL) AllocVar(ret); ret->bin = sqlSignedComma(&s); ret->chrom = sqlStringComma(&s); ret->chromStart = sqlUnsignedComma(&s); ret->chromEnd = sqlUnsignedComma(&s); ret->name = sqlStringComma(&s); ret->score = sqlUnsignedComma(&s); sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); ret->pslTable = sqlStringComma(&s); ret->lfCount = sqlUnsignedComma(&s); s = sqlEatChar(s, '{'); AllocArray(ret->lfStarts, ret->lfCount); for (i=0; ilfCount; ++i) { ret->lfStarts[i] = sqlUnsignedComma(&s); } s = sqlEatChar(s, '}'); s = sqlEatChar(s, ','); s = sqlEatChar(s, '{'); AllocArray(ret->lfSizes, ret->lfCount); for (i=0; ilfCount; ++i) { ret->lfSizes[i] = sqlUnsignedComma(&s); } s = sqlEatChar(s, '}'); s = sqlEatChar(s, ','); s = sqlEatChar(s, '{'); AllocArray(ret->lfNames, ret->lfCount); for (i=0; ilfCount; ++i) { ret->lfNames[i] = sqlStringComma(&s); } s = sqlEatChar(s, '}'); s = sqlEatChar(s, ','); *pS = s; return ret; } void fosEndPairsFree(struct fosEndPairs **pEl) /* Free a single dynamically allocated fosEndPairs such as created * with fosEndPairsLoad(). */ { struct fosEndPairs *el; if ((el = *pEl) == NULL) return; freeMem(el->chrom); freeMem(el->name); freeMem(el->pslTable); freeMem(el->lfStarts); freeMem(el->lfSizes); /* All strings in lfNames are allocated at once, so only need to free first. */ if (el->lfNames != NULL) freeMem(el->lfNames[0]); freeMem(el->lfNames); freez(pEl); } void fosEndPairsFreeList(struct fosEndPairs **pList) /* Free a list of dynamically allocated fosEndPairs's */ { struct fosEndPairs *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; fosEndPairsFree(&el); } *pList = NULL; } void fosEndPairsOutput(struct fosEndPairs *el, FILE *f, char sep, char lastSep) /* Print out fosEndPairs. Separate fields with sep. Follow last field with lastSep. */ { int i; fprintf(f, "%d", el->bin); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->chrom); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%u", el->chromStart); fputc(sep,f); fprintf(f, "%u", el->chromEnd); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->name); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%u", el->score); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->strand); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->pslTable); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%u", el->lfCount); fputc(sep,f); if (sep == ',') fputc('{',f); for (i=0; ilfCount; ++i) { fprintf(f, "%u", el->lfStarts[i]); fputc(',', f); } if (sep == ',') fputc('}',f); fputc(sep,f); if (sep == ',') fputc('{',f); for (i=0; ilfCount; ++i) { fprintf(f, "%u", el->lfSizes[i]); fputc(',', f); } if (sep == ',') fputc('}',f); fputc(sep,f); if (sep == ',') fputc('{',f); for (i=0; ilfCount; ++i) { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->lfNames[i]); if (sep == ',') fputc('"',f); fputc(',', f); } if (sep == ',') fputc('}',f); fputc(lastSep,f); }