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/synMap.c src/hg/lib/synMap.c index bf1c2ac..5ca13bd 100644 --- src/hg/lib/synMap.c +++ src/hg/lib/synMap.c @@ -1,175 +1,178 @@ /* synMap.c was originally generated by the autoSql program, which also * generated synMap.h and synMap.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 "synMap.h" void synMapStaticLoad(char **row, struct synMap *ret) /* Load a row from synMap table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->chromA = row[0]; ret->chromStartA = sqlUnsigned(row[1]); ret->chromEndA = sqlUnsigned(row[2]); ret->strandA = row[3]; ret->chromB = row[4]; ret->chromStartB = sqlUnsigned(row[5]); ret->chromEndB = sqlUnsigned(row[6]); } struct synMap *synMapLoad(char **row) /* Load a synMap from row fetched with select * from synMap * from database. Dispose of this with synMapFree(). */ { struct synMap *ret; AllocVar(ret); ret->chromA = cloneString(row[0]); ret->chromStartA = sqlUnsigned(row[1]); ret->chromEndA = sqlUnsigned(row[2]); ret->strandA = cloneString(row[3]); ret->chromB = cloneString(row[4]); ret->chromStartB = sqlUnsigned(row[5]); ret->chromEndB = sqlUnsigned(row[6]); return ret; } struct synMap *synMapNoStrandLoad(char **row) /* Load a synMap from row fetched with select * from synMap * from database. Dispose of this with synMapFree(). */ { struct synMap *ret; AllocVar(ret); ret->chromA = cloneString(row[0]); ret->chromStartA = sqlUnsigned(row[1]); ret->chromEndA = sqlUnsigned(row[2]); ret->chromB = cloneString(row[3]); ret->chromStartB = sqlUnsigned(row[4]); ret->chromEndB = sqlUnsigned(row[5]); return ret; } struct synMap *synMapLoadAll(char *fileName) /* Load all synMap from a tab-separated file. * Dispose of this with synMapFreeList(). */ { struct synMap *list = NULL, *el=NULL; struct lineFile *lf = lineFileOpen(fileName, TRUE); char **row; char *words[32]; char *line = NULL; int lineSize = 1024; int wordCount = 0; int lineWCount = 0; int count =0; wordCount = lineFileChop(lf, words); if (wordCount == 0) errAbort("%s appears to be empty", fileName); lineFileClose(&lf); lf = lineFileOpen(fileName, TRUE); row = needMem(sizeof(char *) * wordCount); while (lineFileNext(lf, &line, &lineSize)) { count++; if(strstr(line, "?") == NULL) { lineWCount = chopByWhite(line, row, wordCount); if(wordCount != lineWCount) errAbort("Expecting %d words got %d at line %d\n", wordCount, lineWCount, count); if(lineWCount == 7) el = synMapLoad(row); else if(lineWCount >= 10) el = synMapNoStrandLoad(row); else errAbort("synMap::synMapLoadAll() - expecting 7 or greater than 10 fields got %d", lineWCount); slAddHead(&list, el); } } lineFileClose(&lf); slReverse(&list); return list; } struct synMap *synMapCommaIn(char **pS, struct synMap *ret) /* Create a synMap out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new synMap */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->chromA = sqlStringComma(&s); ret->chromStartA = sqlUnsignedComma(&s); ret->chromEndA = sqlUnsignedComma(&s); ret->strandA = sqlStringComma(&s); ret->chromB = sqlStringComma(&s); ret->chromStartB = sqlUnsignedComma(&s); ret->chromEndB = sqlUnsignedComma(&s); *pS = s; return ret; } void synMapFree(struct synMap **pEl) /* Free a single dynamically allocated synMap such as created * with synMapLoad(). */ { struct synMap *el; if ((el = *pEl) == NULL) return; freeMem(el->chromA); freeMem(el->strandA); freeMem(el->chromB); freez(pEl); } void synMapFreeList(struct synMap **pList) /* Free a list of dynamically allocated synMap's */ { struct synMap *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; synMapFree(&el); } *pList = NULL; } void synMapOutput(struct synMap *el, FILE *f, char sep, char lastSep) /* Print out synMap. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->chromA); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%u", el->chromStartA); fputc(sep,f); fprintf(f, "%u", el->chromEndA); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->strandA); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->chromB); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%u", el->chromStartB); fputc(sep,f); fprintf(f, "%u", el->chromEndB); fputc(lastSep,f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */