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/trackTable.c src/hg/lib/trackTable.c deleted file mode 100644 index f0174c8..0000000 --- src/hg/lib/trackTable.c +++ /dev/null @@ -1,409 +0,0 @@ -/* trackTable.c was originally generated by the autoSql program, which also - * generated trackTable.h and trackTable.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 "jksql.h" -#include "trackTable.h" -#include "hdb.h" - - -void trackTableStaticLoad(char **row, struct trackTable *ret) -/* Load a row from trackTable table into ret. The contents of ret will - * be replaced at the next call to this function. */ -{ - -ret->mapName = row[0]; -ret->tableName = row[1]; -ret->shortLabel = row[2]; -ret->longLabel = row[3]; -ret->visibility = sqlUnsigned(row[4]); -ret->colorR = sqlUnsigned(row[5]); -ret->colorG = sqlUnsigned(row[6]); -ret->colorB = sqlUnsigned(row[7]); -ret->altColorR = sqlUnsigned(row[8]); -ret->altColorG = sqlUnsigned(row[9]); -ret->altColorB = sqlUnsigned(row[10]); -ret->useScore = sqlUnsigned(row[11]); -ret->isSplit = sqlUnsigned(row[12]); -ret->private = sqlUnsigned(row[13]); -} - -struct trackTable *trackTableLoad(char **row) -/* Load a trackTable from row fetched with select * from trackTable - * from database. Dispose of this with trackTableFree(). */ -{ -struct trackTable *ret; - -AllocVar(ret); -ret->mapName = cloneString(row[0]); -ret->tableName = cloneString(row[1]); -ret->shortLabel = cloneString(row[2]); -ret->longLabel = cloneString(row[3]); -ret->visibility = sqlUnsigned(row[4]); -ret->colorR = sqlUnsigned(row[5]); -ret->colorG = sqlUnsigned(row[6]); -ret->colorB = sqlUnsigned(row[7]); -ret->altColorR = sqlUnsigned(row[8]); -ret->altColorG = sqlUnsigned(row[9]); -ret->altColorB = sqlUnsigned(row[10]); -ret->useScore = sqlUnsigned(row[11]); -ret->isSplit = sqlUnsigned(row[12]); -ret->private = sqlUnsigned(row[13]); -return ret; -} - -struct trackTable *trackTableLoadAll(char *fileName) -/* Load all trackTable from a tab-separated file. - * Dispose of this with trackTableFreeList(). */ -{ -struct trackTable *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[15]; - -while (lineFileRow(lf, row)) - { - el = trackTableLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct trackTable *trackTableCommaIn(char **pS, struct trackTable *ret) -/* Create a trackTable out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new trackTable */ -{ -char *s = *pS; - -if (ret == NULL) - AllocVar(ret); -ret->mapName = sqlStringComma(&s); -ret->tableName = sqlStringComma(&s); -ret->shortLabel = sqlStringComma(&s); -ret->longLabel = sqlStringComma(&s); -ret->visibility = sqlUnsignedComma(&s); -ret->colorR = sqlUnsignedComma(&s); -ret->colorG = sqlUnsignedComma(&s); -ret->colorB = sqlUnsignedComma(&s); -ret->altColorR = sqlUnsignedComma(&s); -ret->altColorG = sqlUnsignedComma(&s); -ret->altColorB = sqlUnsignedComma(&s); -ret->useScore = sqlUnsignedComma(&s); -ret->isSplit = sqlUnsignedComma(&s); -ret->private = sqlUnsignedComma(&s); -*pS = s; -return ret; -} - -void trackTableFree(struct trackTable **pEl) -/* Free a single dynamically allocated trackTable such as created - * with trackTableLoad(). */ -{ -struct trackTable *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->mapName); -freeMem(el->tableName); -freeMem(el->shortLabel); -freeMem(el->longLabel); -freez(pEl); -} - -void trackTableFreeList(struct trackTable **pList) -/* Free a list of dynamically allocated trackTable's */ -{ -struct trackTable *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - trackTableFree(&el); - } -*pList = NULL; -} - -void trackTableOutput(struct trackTable *el, FILE *f, char sep, char lastSep) -/* Print out trackTable. Separate fields with sep. Follow last field with lastSep. */ -{ -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->mapName); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->tableName); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->shortLabel); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->longLabel); -if (sep == ',') fputc('"',f); -fputc(sep,f); -fprintf(f, "%u", el->visibility); -fputc(sep,f); -fprintf(f, "%u", el->colorR); -fputc(sep,f); -fprintf(f, "%u", el->colorG); -fputc(sep,f); -fprintf(f, "%u", el->colorB); -fputc(sep,f); -fprintf(f, "%u", el->altColorR); -fputc(sep,f); -fprintf(f, "%u", el->altColorG); -fputc(sep,f); -fprintf(f, "%u", el->altColorB); -fputc(sep,f); -fprintf(f, "%u", el->useScore); -fputc(sep,f); -fprintf(f, "%u", el->isSplit); -fputc(sep,f); -fprintf(f, "%u", el->private); -fputc(sep,f); -} - -/* ---------------- End of AutoSQL generated code. ------------------ */ - -static struct trackTable builtIns[] = -{ - { - NULL, - "hgEst", /* mapName */ - "est", /* tableName */ - "Human ESTs", /* shortLabel */ - "Human ESTs", /* longLabel */ - 0, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgMrna", /* mapName */ - "mrna", /* tableName */ - "Full MGC mRNAs", /* shortLabel */ - "Full Length MGC mRNAs", /* longLabel */ - 2, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "BACends", /* mapName */ - "bacEnds", /* tableName */ - "BAC ends", /* shortLabel */ - "BAC end pairs", /* longLabel */ - 0, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgEst", /* mapName */ - "est", /* tableName */ - "Human ESTs", /* shortLabel */ - "Human ESTs", /* longLabel */ - 0, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 1, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgIntronEst", /* mapName */ - "intronEst", /* tableName */ - "Spliced ESTs", /* shortLabel */ - "Human ESTs That Have Been Spliced", /* longLabel */ - 1, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 1, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgMrna", /* mapName */ - "mrna", /* tableName */ - "Sequenced mRNAs", /* shortLabel */ - "Sequenced mRNAs from Genbank", /* longLabel */ - 2, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 1, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgRepeat", /* mapName */ - "rmsk", /* tableName */ - "RepeatMasker", /* shortLabel */ - "Repeating Elements by RepeatMasker", /* longLabel */ - 1, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 1, /* useScore */ - 1, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgBlatMouse", /* mapName */ - "blatMouse", /* tableName */ - "Mouse Blat", /* shortLabel */ - "Mouse Translated Blat Alignments", /* longLabel */ - 0, /* visibility */ - 100,50,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 1, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgContig", /* mapName */ - "ctgPos", /* tableName */ - "Chromosome Band", /* shortLabel */ - "Chromosome Bands Localized by FISH Mapping Clones", /* longLabel */ - 1, /* visibility */ - 150,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgCytoBands", /* mapName */ - "cytoBand", /* tableName */ - "Chromosome Band", /* shortLabel */ - "Chromosome Bands Localized by FISH Mapping Clones", /* longLabel */ - 1, /* visibility */ - 0,0,0, /* color */ - 150,50,50, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgExoFish", /* mapName */ - "exoFish", /* tableName */ - "Exofish ecores", /* shortLabel */ - "Exofish Tetraodon/Human Conserved Regions (ecores)", /* longLabel */ - 1, /* visibility */ - 153,21,153, /* color */ - 0,0,255, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgGcPercent", /* mapName */ - "gcPercent", /* tableName */ - "GC Percent", /* shortLabel */ - "Percentage GC in 20,000 Base Windows", /* longLabel */ - 0, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgMusTest1", /* mapName */ - "musTest1", /* tableName */ - "Mouse Test 40", /* shortLabel */ - "Mouse Translated Blat Alignments Score > 40", /* longLabel */ - 0, /* visibility */ - 0,0,0, /* color */ - 0,0,0, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 1, /* private */ - }, - { - NULL, - "hgRefGene", /* mapName */ - "refGene", /* tableName */ - "RefSeq Genes", /* shortLabel */ - "GenBank RefSeq Genes", /* longLabel */ - 2, /* visibility */ - 20,20,170, /* color */ - 137,137,212, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgRnaGene", /* mapName */ - "rnaGene", /* tableName */ - "RNA Genes", /* shortLabel */ - "Non-coding RNA Genes (dark) and Pseudogenes (light)", /* longLabel */ - 2, /* visibility */ - 170,80,130, /* color */ - 230,180,130, /* altColor */ - 0, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, - { - NULL, - "hgStsMarker", /* mapName */ - "stsMarker", /* tableName */ - "STS Markers", /* shortLabel */ - "STS Markers on Genetic (blue), FISH (green) and Radiation Hybrid (black) Maps", /* longLabel */ - 1, /* visibility */ - 0,0,0, /* color */ - 128,128,255, /* altColor */ - 1, /* useScore */ - 0, /* isSplit */ - 0, /* private */ - }, -}; - -struct trackTable *hGetTracks(char *db) -/* Get track table for specified database. */ -{ -struct trackTable *ttList = NULL, *tt; -int i; -char table[256]; - -for (i=0; i<ArraySize(builtIns); ++i) - { - tt = builtIns+i; - if (tt->isSplit) - safef(table, sizeof(table), "chr22_%s", tt->tableName); - else - safef(table, sizeof(table), "%s", tt->tableName); - if (hTableExists(db, table)) - { - slAddHead(&ttList, tt); - } - } -slReverse(&ttList); -return ttList; -} -