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/omicia.c src/hg/lib/omicia.c index 18f169a..a83d23b 100644 --- src/hg/lib/omicia.c +++ src/hg/lib/omicia.c @@ -1,687 +1,690 @@ /* omicia.c was originally generated by the autoSql program, which also * generated omicia.h and omicia.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 "omicia.h" void omiciaAutoStaticLoad(char **row, struct omiciaAuto *ret) /* Load a row from omiciaAuto table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->bin = sqlUnsigned(row[0]); ret->chrom = row[1]; ret->chromStart = sqlUnsigned(row[2]); ret->chromEnd = sqlUnsigned(row[3]); ret->name = row[4]; ret->score = sqlUnsigned(row[5]); safecpy(ret->strand, sizeof(ret->strand), row[6]); } struct omiciaAuto *omiciaAutoLoad(char **row) /* Load a omiciaAuto from row fetched with select * from omiciaAuto * from database. Dispose of this with omiciaAutoFree(). */ { struct omiciaAuto *ret; AllocVar(ret); ret->bin = sqlUnsigned(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]); safecpy(ret->strand, sizeof(ret->strand), row[6]); return ret; } struct omiciaAuto *omiciaAutoLoadAll(char *fileName) /* Load all omiciaAuto from a whitespace-separated file. * Dispose of this with omiciaAutoFreeList(). */ { struct omiciaAuto *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileRow(lf, row)) { el = omiciaAutoLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaAuto *omiciaAutoLoadAllByChar(char *fileName, char chopper) /* Load all omiciaAuto from a chopper separated file. * Dispose of this with omiciaAutoFreeList(). */ { struct omiciaAuto *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = omiciaAutoLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaAuto *omiciaAutoLoadByQuery(struct sqlConnection *conn, char *query) /* Load all omiciaAuto 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 omiciaAutoFreeList(). */ { struct omiciaAuto *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = omiciaAutoLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void omiciaAutoSaveToDb(struct sqlConnection *conn, struct omiciaAuto *el, char *tableName, int updateSize) /* Save omiciaAuto 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. Strings are automatically escaped to allow insertion into the database. */ { struct dyString *update = newDyString(updateSize); sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s')", tableName, el->bin, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand); sqlUpdate(conn, update->string); freeDyString(&update); } struct omiciaAuto *omiciaAutoCommaIn(char **pS, struct omiciaAuto *ret) /* Create a omiciaAuto out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaAuto */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->bin = sqlUnsignedComma(&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)); *pS = s; return ret; } void omiciaAutoFree(struct omiciaAuto **pEl) /* Free a single dynamically allocated omiciaAuto such as created * with omiciaAutoLoad(). */ { struct omiciaAuto *el; if ((el = *pEl) == NULL) return; freeMem(el->chrom); freeMem(el->name); freez(pEl); } void omiciaAutoFreeList(struct omiciaAuto **pList) /* Free a list of dynamically allocated omiciaAuto's */ { struct omiciaAuto *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; omiciaAutoFree(&el); } *pList = NULL; } void omiciaAutoOutput(struct omiciaAuto *el, FILE *f, char sep, char lastSep) /* Print out omiciaAuto. Separate fields with sep. Follow last field with lastSep. */ { fprintf(f, "%u", 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(lastSep,f); } void omiciaHandStaticLoad(char **row, struct omiciaHand *ret) /* Load a row from omiciaHand table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->bin = sqlUnsigned(row[0]); ret->chrom = row[1]; ret->chromStart = sqlUnsigned(row[2]); ret->chromEnd = sqlUnsigned(row[3]); ret->name = row[4]; ret->score = sqlUnsigned(row[5]); safecpy(ret->strand, sizeof(ret->strand), row[6]); } struct omiciaHand *omiciaHandLoad(char **row) /* Load a omiciaHand from row fetched with select * from omiciaHand * from database. Dispose of this with omiciaHandFree(). */ { struct omiciaHand *ret; AllocVar(ret); ret->bin = sqlUnsigned(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]); safecpy(ret->strand, sizeof(ret->strand), row[6]); return ret; } struct omiciaHand *omiciaHandLoadAll(char *fileName) /* Load all omiciaHand from a whitespace-separated file. * Dispose of this with omiciaHandFreeList(). */ { struct omiciaHand *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileRow(lf, row)) { el = omiciaHandLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaHand *omiciaHandLoadAllByChar(char *fileName, char chopper) /* Load all omiciaHand from a chopper separated file. * Dispose of this with omiciaHandFreeList(). */ { struct omiciaHand *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = omiciaHandLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaHand *omiciaHandLoadByQuery(struct sqlConnection *conn, char *query) /* Load all omiciaHand 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 omiciaHandFreeList(). */ { struct omiciaHand *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = omiciaHandLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void omiciaHandSaveToDb(struct sqlConnection *conn, struct omiciaHand *el, char *tableName, int updateSize) /* Save omiciaHand 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. Strings are automatically escaped to allow insertion into the database. */ { struct dyString *update = newDyString(updateSize); sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%u,%u,'%s',%u,'%s')", tableName, el->bin, el->chrom, el->chromStart, el->chromEnd, el->name, el->score, el->strand); sqlUpdate(conn, update->string); freeDyString(&update); } struct omiciaHand *omiciaHandCommaIn(char **pS, struct omiciaHand *ret) /* Create a omiciaHand out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaHand */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->bin = sqlUnsignedComma(&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)); *pS = s; return ret; } void omiciaHandFree(struct omiciaHand **pEl) /* Free a single dynamically allocated omiciaHand such as created * with omiciaHandLoad(). */ { struct omiciaHand *el; if ((el = *pEl) == NULL) return; freeMem(el->chrom); freeMem(el->name); freez(pEl); } void omiciaHandFreeList(struct omiciaHand **pList) /* Free a list of dynamically allocated omiciaHand's */ { struct omiciaHand *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; omiciaHandFree(&el); } *pList = NULL; } void omiciaHandOutput(struct omiciaHand *el, FILE *f, char sep, char lastSep) /* Print out omiciaHand. Separate fields with sep. Follow last field with lastSep. */ { fprintf(f, "%u", 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(lastSep,f); } void omiciaLinkStaticLoad(char **row, struct omiciaLink *ret) /* Load a row from omiciaLink table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->id = row[0]; ret->attrType = row[1]; ret->raKey = row[2]; ret->acc = row[3]; ret->displayVal = row[4]; } struct omiciaLink *omiciaLinkLoad(char **row) /* Load a omiciaLink from row fetched with select * from omiciaLink * from database. Dispose of this with omiciaLinkFree(). */ { struct omiciaLink *ret; AllocVar(ret); ret->id = cloneString(row[0]); ret->attrType = cloneString(row[1]); ret->raKey = cloneString(row[2]); ret->acc = cloneString(row[3]); ret->displayVal = cloneString(row[4]); return ret; } struct omiciaLink *omiciaLinkLoadAll(char *fileName) /* Load all omiciaLink from a whitespace-separated file. * Dispose of this with omiciaLinkFreeList(). */ { struct omiciaLink *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[5]; while (lineFileRow(lf, row)) { el = omiciaLinkLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaLink *omiciaLinkLoadAllByChar(char *fileName, char chopper) /* Load all omiciaLink from a chopper separated file. * Dispose of this with omiciaLinkFreeList(). */ { struct omiciaLink *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[5]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = omiciaLinkLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaLink *omiciaLinkLoadByQuery(struct sqlConnection *conn, char *query) /* Load all omiciaLink 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 omiciaLinkFreeList(). */ { struct omiciaLink *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = omiciaLinkLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void omiciaLinkSaveToDb(struct sqlConnection *conn, struct omiciaLink *el, char *tableName, int updateSize) /* Save omiciaLink 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. Strings are automatically escaped to allow insertion into the database. */ { struct dyString *update = newDyString(updateSize); sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s')", tableName, el->id, el->attrType, el->raKey, el->acc, el->displayVal); sqlUpdate(conn, update->string); freeDyString(&update); } struct omiciaLink *omiciaLinkCommaIn(char **pS, struct omiciaLink *ret) /* Create a omiciaLink out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaLink */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->id = sqlStringComma(&s); ret->attrType = sqlStringComma(&s); ret->raKey = sqlStringComma(&s); ret->acc = sqlStringComma(&s); ret->displayVal = sqlStringComma(&s); *pS = s; return ret; } void omiciaLinkFree(struct omiciaLink **pEl) /* Free a single dynamically allocated omiciaLink such as created * with omiciaLinkLoad(). */ { struct omiciaLink *el; if ((el = *pEl) == NULL) return; freeMem(el->id); freeMem(el->attrType); freeMem(el->raKey); freeMem(el->acc); freeMem(el->displayVal); freez(pEl); } void omiciaLinkFreeList(struct omiciaLink **pList) /* Free a list of dynamically allocated omiciaLink's */ { struct omiciaLink *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; omiciaLinkFree(&el); } *pList = NULL; } void omiciaLinkOutput(struct omiciaLink *el, FILE *f, char sep, char lastSep) /* Print out omiciaLink. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->id); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->attrType); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->raKey); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->acc); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->displayVal); if (sep == ',') fputc('"',f); fputc(lastSep,f); } void omiciaAttrStaticLoad(char **row, struct omiciaAttr *ret) /* Load a row from omiciaAttr table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->id = row[0]; ret->attrType = row[1]; ret->attrVal = row[2]; } struct omiciaAttr *omiciaAttrLoad(char **row) /* Load a omiciaAttr from row fetched with select * from omiciaAttr * from database. Dispose of this with omiciaAttrFree(). */ { struct omiciaAttr *ret; AllocVar(ret); ret->id = cloneString(row[0]); ret->attrType = cloneString(row[1]); ret->attrVal = cloneString(row[2]); return ret; } struct omiciaAttr *omiciaAttrLoadAll(char *fileName) /* Load all omiciaAttr from a whitespace-separated file. * Dispose of this with omiciaAttrFreeList(). */ { struct omiciaAttr *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[3]; while (lineFileRow(lf, row)) { el = omiciaAttrLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaAttr *omiciaAttrLoadAllByChar(char *fileName, char chopper) /* Load all omiciaAttr from a chopper separated file. * Dispose of this with omiciaAttrFreeList(). */ { struct omiciaAttr *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[3]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = omiciaAttrLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct omiciaAttr *omiciaAttrLoadByQuery(struct sqlConnection *conn, char *query) /* Load all omiciaAttr 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 omiciaAttrFreeList(). */ { struct omiciaAttr *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = omiciaAttrLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void omiciaAttrSaveToDb(struct sqlConnection *conn, struct omiciaAttr *el, char *tableName, int updateSize) /* Save omiciaAttr 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. Strings are automatically escaped to allow insertion into the database. */ { struct dyString *update = newDyString(updateSize); sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s')", tableName, el->id, el->attrType, el->attrVal); sqlUpdate(conn, update->string); freeDyString(&update); } struct omiciaAttr *omiciaAttrCommaIn(char **pS, struct omiciaAttr *ret) /* Create a omiciaAttr out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new omiciaAttr */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->id = sqlStringComma(&s); ret->attrType = sqlStringComma(&s); ret->attrVal = sqlStringComma(&s); *pS = s; return ret; } void omiciaAttrFree(struct omiciaAttr **pEl) /* Free a single dynamically allocated omiciaAttr such as created * with omiciaAttrLoad(). */ { struct omiciaAttr *el; if ((el = *pEl) == NULL) return; freeMem(el->id); freeMem(el->attrType); freeMem(el->attrVal); freez(pEl); } void omiciaAttrFreeList(struct omiciaAttr **pList) /* Free a list of dynamically allocated omiciaAttr's */ { struct omiciaAttr *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; omiciaAttrFree(&el); } *pList = NULL; } void omiciaAttrOutput(struct omiciaAttr *el, FILE *f, char sep, char lastSep) /* Print out omiciaAttr. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->id); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->attrType); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->attrVal); if (sep == ',') fputc('"',f); fputc(lastSep,f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */