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/lib/gencodeIntron.c src/hg/lib/gencodeIntron.c deleted file mode 100644 index 34ba349..0000000 --- src/hg/lib/gencodeIntron.c +++ /dev/null @@ -1,226 +0,0 @@ -/* gencodeIntron.c was originally generated by the autoSql program, which also - * generated gencodeIntron.h and gencodeIntron.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 "gencodeIntron.h" - - -void gencodeIntronStaticLoad(char **row, struct gencodeIntron *ret) -/* Load a row from gencodeIntron 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->status = row[4]; -strcpy(ret->strand, row[5]); -ret->transcript = row[6]; -ret->geneId = row[7]; -} - -struct gencodeIntron *gencodeIntronLoad(char **row) -/* Load a gencodeIntron from row fetched with select * from gencodeIntron - * from database. Dispose of this with gencodeIntronFree(). */ -{ -struct gencodeIntron *ret; - -AllocVar(ret); -ret->chrom = cloneString(row[0]); -ret->chromStart = sqlUnsigned(row[1]); -ret->chromEnd = sqlUnsigned(row[2]); -ret->name = cloneString(row[3]); -ret->status = cloneString(row[4]); -strcpy(ret->strand, row[5]); -ret->transcript = cloneString(row[6]); -ret->geneId = cloneString(row[7]); -return ret; -} - -struct gencodeIntron *gencodeIntronLoadAll(char *fileName) -/* Load all gencodeIntron from a whitespace-separated file. - * Dispose of this with gencodeIntronFreeList(). */ -{ -struct gencodeIntron *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[8]; - -while (lineFileRow(lf, row)) - { - el = gencodeIntronLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct gencodeIntron *gencodeIntronLoadAllByChar(char *fileName, char chopper) -/* Load all gencodeIntron from a chopper separated file. - * Dispose of this with gencodeIntronFreeList(). */ -{ -struct gencodeIntron *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[8]; - -while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) - { - el = gencodeIntronLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct gencodeIntron *gencodeIntronLoadByQuery(struct sqlConnection *conn, char *query, int rowOffset) -/* Load all gencodeIntron 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 gencodeIntronFreeList(). */ -{ -struct gencodeIntron *list = NULL, *el; -struct sqlResult *sr; -char **row; - -sr = sqlGetResult(conn, query); -while ((row = sqlNextRow(sr)) != NULL) - { - el = gencodeIntronLoad(row+rowOffset); - slAddHead(&list, el); - } -slReverse(&list); -sqlFreeResult(&sr); -return list; -} - -void gencodeIntronSaveToDb(struct sqlConnection *conn, struct gencodeIntron *el, char *tableName, int updateSize) -/* Save gencodeIntron 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',%u,%u,'%s','%s','%s','%s','%s')", - tableName, el->chrom, el->chromStart, el->chromEnd, el->name, el->status, el->strand, el->transcript, el->geneId); -sqlUpdate(conn, update->string); -freeDyString(&update); -} - - -struct gencodeIntron *gencodeIntronCommaIn(char **pS, struct gencodeIntron *ret) -/* Create a gencodeIntron out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new gencodeIntron */ -{ -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->status = sqlStringComma(&s); -sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand)); -ret->transcript = sqlStringComma(&s); -ret->geneId = sqlStringComma(&s); -*pS = s; -return ret; -} - -void gencodeIntronFree(struct gencodeIntron **pEl) -/* Free a single dynamically allocated gencodeIntron such as created - * with gencodeIntronLoad(). */ -{ -struct gencodeIntron *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->chrom); -freeMem(el->name); -freeMem(el->status); -freeMem(el->transcript); -freeMem(el->geneId); -freez(pEl); -} - -void gencodeIntronFreeList(struct gencodeIntron **pList) -/* Free a list of dynamically allocated gencodeIntron's */ -{ -struct gencodeIntron *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - gencodeIntronFree(&el); - } -*pList = NULL; -} - -void gencodeIntronOutput(struct gencodeIntron *el, FILE *f, char sep, char lastSep) -/* Print out gencodeIntron. 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); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->status); -if (sep == ',') fputc('"',f); -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->transcript); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->geneId); -if (sep == ',') fputc('"',f); -fputc(lastSep,f); -} - -/* -------------------------------- End autoSql Generated Code -------------------------------- */ - -void gencodeIntronTableCreate(struct sqlConnection *conn, char *tableName, int indexSize) -/* Create a gencodeIntron table with the given name */ -{ -char *createString = -"CREATE TABLE %s (\n" -" chrom varchar(255) not null, # Chromosome\n" -" chromStart int unsigned not null, # Start position in chromosome\n" -" chromEnd int unsigned not null, # End position in chromosome\n" -" name varchar(255) not null, # Intron ID\n" -" status enum('not_tested', 'RT_positive','RT_negative','RT_wrong_junction','RT_submitted', 'RACE_validated'), # Status\n" -" strand char(1) not null, # + or -\n" -" transcript varchar(255) not null, # Transcript ID from GTF\n" -" geneId varchar(255) not null, # Gene ID from GTF\n" -" INDEX(chrom(%d),chromStart),\n" -" INDEX(chrom(%d),chromEnd)\n" -")\n"; -struct dyString *dy = newDyString(1024); -sqlDyStringPrintf(dy, createString, tableName, indexSize, indexSize, indexSize); -sqlRemakeTable(conn, tableName, dy->string); -dyStringFree(&dy); -} -