533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/cgilib/genomicSuperDups.c src/hg/cgilib/genomicSuperDups.c new file mode 100644 index 0000000..ba0ce26 --- /dev/null +++ src/hg/cgilib/genomicSuperDups.c @@ -0,0 +1,286 @@ +/* genomicSuperDups.c was originally generated by the autoSql program, which also + * generated genomicSuperDups.h and genomicSuperDups.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 "genomicSuperDups.h" + + +void genomicSuperDupsStaticLoad(char **row, struct genomicSuperDups *ret) +/* Load a row from genomicSuperDups table into ret. The contents of ret will + * be replaced at the next call to this function. */ +{ + +ret->chrom = row[0]; +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = row[3]; +ret->score = sqlUnsigned(row[4]); +strcpy(ret->strand, row[5]); +ret->otherChrom = row[6]; +ret->otherStart = sqlUnsigned(row[7]); +ret->otherEnd = sqlUnsigned(row[8]); +ret->otherSize = sqlUnsigned(row[9]); +ret->uid = sqlUnsigned(row[10]); +ret->posBasesHit = sqlUnsigned(row[11]); +ret->testResult = row[12]; +ret->verdict = row[13]; +ret->chits = row[14]; +ret->ccov = row[15]; +ret->alignfile = row[16]; +ret->alignL = sqlUnsigned(row[17]); +ret->indelN = sqlUnsigned(row[18]); +ret->indelS = sqlUnsigned(row[19]); +ret->alignB = sqlUnsigned(row[20]); +ret->matchB = sqlUnsigned(row[21]); +ret->mismatchB = sqlUnsigned(row[22]); +ret->transitionsB = sqlUnsigned(row[23]); +ret->transversionsB = sqlUnsigned(row[24]); +ret->fracMatch = atof(row[25]); +ret->fracMatchIndel = atof(row[26]); +ret->jcK = atof(row[27]); +ret->k2K = atof(row[28]); +} + +struct genomicSuperDups *genomicSuperDupsLoad(char **row) +/* Load a genomicSuperDups from row fetched with select * from genomicSuperDups + * from database. Dispose of this with genomicSuperDupsFree(). */ +{ +struct genomicSuperDups *ret; + +AllocVar(ret); +ret->chrom = cloneString(row[0]); +ret->chromStart = sqlUnsigned(row[1]); +ret->chromEnd = sqlUnsigned(row[2]); +ret->name = cloneString(row[3]); +ret->score = sqlUnsigned(row[4]); +strcpy(ret->strand, row[5]); +ret->otherChrom = cloneString(row[6]); +ret->otherStart = sqlUnsigned(row[7]); +ret->otherEnd = sqlUnsigned(row[8]); +ret->otherSize = sqlUnsigned(row[9]); +ret->uid = sqlUnsigned(row[10]); +ret->posBasesHit = sqlUnsigned(row[11]); +ret->testResult = cloneString(row[12]); +ret->verdict = cloneString(row[13]); +ret->chits = cloneString(row[14]); +ret->ccov = cloneString(row[15]); +ret->alignfile = cloneString(row[16]); +ret->alignL = sqlUnsigned(row[17]); +ret->indelN = sqlUnsigned(row[18]); +ret->indelS = sqlUnsigned(row[19]); +ret->alignB = sqlUnsigned(row[20]); +ret->matchB = sqlUnsigned(row[21]); +ret->mismatchB = sqlUnsigned(row[22]); +ret->transitionsB = sqlUnsigned(row[23]); +ret->transversionsB = sqlUnsigned(row[24]); +ret->fracMatch = atof(row[25]); +ret->fracMatchIndel = atof(row[26]); +ret->jcK = atof(row[27]); +ret->k2K = atof(row[28]); +return ret; +} + +struct genomicSuperDups *genomicSuperDupsLoadAll(char *fileName) +/* Load all genomicSuperDups from a tab-separated file. + * Dispose of this with genomicSuperDupsFreeList(). */ +{ +struct genomicSuperDups *list = NULL, *el; +struct lineFile *lf = lineFileOpen(fileName, TRUE); +char *row[29]; + +while (lineFileRow(lf, row)) + { + el = genomicSuperDupsLoad(row); + slAddHead(&list, el); + } +lineFileClose(&lf); +slReverse(&list); +return list; +} + +struct genomicSuperDups *genomicSuperDupsLoadWhere(struct sqlConnection *conn, char *table, char *where) +/* Load all genomicSuperDups from table that satisfy where clause. The + * where clause may be NULL in which case whole table is loaded + * Dispose of this with genomicSuperDupsFreeList(). */ +{ +struct genomicSuperDups *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 = genomicSuperDupsLoad(row); + slAddHead(&list, el); + } +slReverse(&list); +sqlFreeResult(&sr); +dyStringFree(&query); +return list; +} + +struct genomicSuperDups *genomicSuperDupsCommaIn(char **pS, struct genomicSuperDups *ret) +/* Create a genomicSuperDups out of a comma separated string. + * This will fill in ret if non-null, otherwise will + * return a new genomicSuperDups */ +{ +char *s = *pS; + +if (ret == NULL) + AllocVar(ret); +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->otherChrom = sqlStringComma(&s); +ret->otherStart = sqlUnsignedComma(&s); +ret->otherEnd = sqlUnsignedComma(&s); +ret->otherSize = sqlUnsignedComma(&s); +ret->uid = sqlUnsignedComma(&s); +ret->posBasesHit = sqlUnsignedComma(&s); +ret->testResult = sqlStringComma(&s); +ret->verdict = sqlStringComma(&s); +ret->chits = sqlStringComma(&s); +ret->ccov = sqlStringComma(&s); +ret->alignfile = sqlStringComma(&s); +ret->alignL = sqlUnsignedComma(&s); +ret->indelN = sqlUnsignedComma(&s); +ret->indelS = sqlUnsignedComma(&s); +ret->alignB = sqlUnsignedComma(&s); +ret->matchB = sqlUnsignedComma(&s); +ret->mismatchB = sqlUnsignedComma(&s); +ret->transitionsB = sqlUnsignedComma(&s); +ret->transversionsB = sqlUnsignedComma(&s); +ret->fracMatch = sqlFloatComma(&s); +ret->fracMatchIndel = sqlFloatComma(&s); +ret->jcK = sqlFloatComma(&s); +ret->k2K = sqlFloatComma(&s); +*pS = s; +return ret; +} + +void genomicSuperDupsFree(struct genomicSuperDups **pEl) +/* Free a single dynamically allocated genomicSuperDups such as created + * with genomicSuperDupsLoad(). */ +{ +struct genomicSuperDups *el; + +if ((el = *pEl) == NULL) return; +freeMem(el->chrom); +freeMem(el->name); +freeMem(el->otherChrom); +freeMem(el->testResult); +freeMem(el->verdict); +freeMem(el->chits); +freeMem(el->ccov); +freeMem(el->alignfile); +freez(pEl); +} + +void genomicSuperDupsFreeList(struct genomicSuperDups **pList) +/* Free a list of dynamically allocated genomicSuperDups's */ +{ +struct genomicSuperDups *el, *next; + +for (el = *pList; el != NULL; el = next) + { + next = el->next; + genomicSuperDupsFree(&el); + } +*pList = NULL; +} + +void genomicSuperDupsOutput(struct genomicSuperDups *el, FILE *f, char sep, char lastSep) +/* Print out genomicSuperDups. Separate fields with sep. Follow last field with lastSep. */ +{ +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->otherChrom); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->otherStart); +fputc(sep,f); +fprintf(f, "%u", el->otherEnd); +fputc(sep,f); +fprintf(f, "%u", el->otherSize); +fputc(sep,f); +fprintf(f, "%u", el->uid); +fputc(sep,f); +fprintf(f, "%u", el->posBasesHit); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->testResult); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->verdict); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->chits); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->ccov); +if (sep == ',') fputc('"',f); +fputc(sep,f); +if (sep == ',') fputc('"',f); +fprintf(f, "%s", el->alignfile); +if (sep == ',') fputc('"',f); +fputc(sep,f); +fprintf(f, "%u", el->alignL); +fputc(sep,f); +fprintf(f, "%u", el->indelN); +fputc(sep,f); +fprintf(f, "%u", el->indelS); +fputc(sep,f); +fprintf(f, "%u", el->alignB); +fputc(sep,f); +fprintf(f, "%u", el->matchB); +fputc(sep,f); +fprintf(f, "%u", el->mismatchB); +fputc(sep,f); +fprintf(f, "%u", el->transitionsB); +fputc(sep,f); +fprintf(f, "%u", el->transversionsB); +fputc(sep,f); +fprintf(f, "%f", el->fracMatch); +fputc(sep,f); +fprintf(f, "%f", el->fracMatchIndel); +fputc(sep,f); +fprintf(f, "%f", el->jcK); +fputc(sep,f); +fprintf(f, "%f", el->k2K); +fputc(lastSep,f); +} +