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/pal.c src/hg/cgilib/pal.c
new file mode 100644
index 0000000..527e7b7
--- /dev/null
+++ src/hg/cgilib/pal.c
@@ -0,0 +1,305 @@
+/* Copyright (C) 2014 The Regents of the University of California
+ * See README in this or parent directory for licensing information. */
+
+#include "common.h"
+#include "hash.h"
+#include "cart.h"
+#include "genePred.h"
+#include "genePredReader.h"
+#include "mafGene.h"
+#include "trackDb.h"
+#include "hdb.h"
+#include "hgMaf.h"
+#include "jsHelper.h"
+#include "hPrint.h"
+#include "hdb.h"
+
+
+#define hgtaCGIGeneMafTable "hgta_mafGeneMafTable"
+#define hgtaJSGeneMafTable "mafGeneMafTable"
+#define hgtaCGIGeneExons "hgta_mafGeneExons"
+#define hgtaJSGeneExons "mafGeneExons"
+#define hgtaCGIGeneNoTrans "hgta_mafGeneNoTrans"
+#define hgtaJSGeneNoTrans "mafGeneNoTrans"
+#define hgtaCGIGeneOutBlank "hgta_mafGeneOutBlank"
+#define hgtaJSGeneOutBlank "mafGeneOutBlank"
+#define hgtaCGIOutTable "hgta_mafOutTable"
+#define hgtaJSOutTable "mafOutTable"
+#define hgtaCGINumColumns "hgta_mafNumColumns"
+#define hgtaJSNumColumns "mafNumColumns"
+#define hgtaCGITruncHeader "hgta_mafTruncHeader"
+#define hgtaJSTruncHeader "mafTruncHeader"
+
+static char *curVars[] = {
+ hgtaCGIGeneMafTable, hgtaCGIGeneExons,
+ hgtaCGIGeneNoTrans, hgtaCGIGeneOutBlank,
+ hgtaCGIOutTable, hgtaCGINumColumns,
+ hgtaCGITruncHeader,
+ };
+
+int palOutPredList(struct sqlConnection *conn, struct cart *cart,
+ struct genePred *list)
+/* output a list of genePreds in pal format */
+{
+if (list == NULL)
+ return 0;
+
+char *mafTable = cartString(cart, hgtaCGIGeneMafTable);
+char *database = sqlGetDatabase(conn);
+struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
+struct wigMafSpecies *wmSpecies;
+int groupCnt;
+
+/* get maf parent (if any) */
+maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
+
+/* this queries the state of the getSpecies dialog */
+wigMafGetSpecies(cart, maftdb, maftdb->track, database, &wmSpecies, &groupCnt);
+
+/* since the species selection dialog doesn't list
+ * the reference species, we just automatically include
+ * it */
+struct slName *includeList = slNameNew(database);
+
+/* now make a list of all species that are on */
+for(; wmSpecies; wmSpecies = wmSpecies->next)
+ {
+ if (wmSpecies->on)
+ {
+ struct slName *newName = slNameNew(wmSpecies->name);
+ slAddHead(&includeList, newName);
+ }
+ }
+slReverse(&includeList);
+
+boolean inExons = cartUsualBoolean(cart, hgtaCGIGeneExons , FALSE);
+boolean noTrans = cartUsualBoolean(cart, hgtaCGIGeneNoTrans, FALSE);
+boolean outBlank = cartUsualBoolean(cart, hgtaCGIGeneOutBlank, FALSE);
+boolean outTable = cartUsualBoolean(cart, hgtaCGIOutTable, FALSE);
+boolean truncHeader = cartUsualBoolean(cart, hgtaCGITruncHeader, FALSE);
+int numCols = cartUsualInt(cart, hgtaCGINumColumns, 20);
+unsigned options = 0;
+
+if (inExons) options |= MAFGENE_EXONS;
+if (noTrans) options |= MAFGENE_NOTRANS;
+if (outBlank) options |= MAFGENE_OUTBLANK;
+if (outTable) options |= MAFGENE_OUTTABLE;
+
+if (!truncHeader)
+ numCols = -1;
+
+/* send out the alignments */
+int outCount = 0;
+for( ; list ; list = list->next)
+ {
+ if (list->cdsStart != list->cdsEnd)
+ {
+ outCount++;
+ mafGeneOutPred(stdout, list, database, mafTable,
+ includeList, options, numCols);
+ }
+ }
+
+slNameFreeList(&includeList);
+return outCount;
+}
+
+int palOutPredsInBeds(struct sqlConnection *conn, struct cart *cart,
+ struct bed *beds, char *table )
+/* output the alignments whose names and coords match a bed*/
+{
+struct genePred *list = NULL;
+
+for(; beds; beds = beds->next)
+ {
+ char where[10 * 1024];
+
+ sqlSafefFrag(where, sizeof where,
+ "name = '%s' and chrom='%s' and txEnd > %d and txStart <= %d",
+ beds->name, beds->chrom, beds->chromStart, beds->chromEnd);
+
+ struct genePredReader *reader = genePredReaderQuery( conn, table, where);
+ struct genePred *pred;
+ while ((pred = genePredReaderNext(reader)) != NULL)
+ slAddHead(&list, pred);
+
+ genePredReaderFree(&reader);
+ }
+
+int outCount = 0;
+if (list != NULL)
+ {
+ slReverse(&list);
+ outCount = palOutPredList( conn, cart, list);
+ genePredFreeList(&list);
+ }
+
+return outCount;
+}
+
+static char *onChangeEnd(struct dyString **pDy)
+/* Finish up javascript onChange command. */
+{
+dyStringAppend(*pDy, "document.hiddenForm.submit();");
+return dyStringCannibalize(pDy);
+}
+
+static struct dyString *onChangeStart()
+/* Start up a javascript onChange command */
+{
+struct dyString *dy = dyStringNew(1024);
+jsDropDownCarryOver(dy, hgtaCGIGeneMafTable);
+jsTrackedVarCarryOver(dy, hgtaCGIGeneExons, hgtaJSGeneExons);
+jsTrackedVarCarryOver(dy, hgtaCGIGeneNoTrans, hgtaJSGeneNoTrans);
+jsTrackedVarCarryOver(dy, hgtaCGIGeneOutBlank, hgtaJSGeneOutBlank);
+jsTrackedVarCarryOver(dy, hgtaCGIOutTable, hgtaJSOutTable);
+jsTrackedVarCarryOver(dy, hgtaCGITruncHeader, hgtaJSTruncHeader);
+jsTextCarryOver(dy, hgtaCGINumColumns);
+return dy;
+}
+
+static char *onChangeGenome()
+/* Get group-changing javascript. */
+{
+struct dyString *dy = onChangeStart();
+return onChangeEnd(&dy);
+}
+
+static char * getConservationTrackName( struct sqlConnection *conn)
+{
+struct slName *dbList = hTrackDbList();
+struct slName *dbl = dbList;
+char *ret = NULL;
+
+for(; dbl; dbl = dbl->next)
+ {
+ char query[512];
+ sqlSafef(query, sizeof query,
+ "select tableName from %s where shortLabel='Conservation'", dbl->name);
+
+ struct sqlResult *sr = sqlGetResult(conn, query);
+ char **row;
+ struct slName *tableList = NULL;
+ while ((row = sqlNextRow(sr)) != NULL)
+ {
+ struct slName *name = newSlName(row[0]);
+ slAddHead(&tableList, name);
+ }
+ sqlFreeResult(&sr);
+
+ struct slName *l = tableList;
+
+ for(; l; l = l->next)
+ if (sqlTableExists(conn, l->name))
+ ret = cloneString(l->name);
+
+ slFreeList(&tableList);
+
+ if (ret != NULL)
+ break;
+ }
+slFreeList(&dbList);
+
+return ret;
+}
+
+static char * outMafTableDrop(struct cart *cart, struct sqlConnection *conn)
+{
+struct slName *list = hTrackTablesOfType(conn, "wigMaf%%");
+int count = slCount(list);
+
+if (count == 0)
+ errAbort("There are no multiple alignments available for this genome.");
+
+char **tables = needMem(sizeof(char *) * count);
+char **tb = tables;
+char *mafTable = cartOptionalString(cart, hgtaCGIGeneMafTable);
+
+if (mafTable != NULL)
+ {
+ struct slName *l = list;
+ for(; l; l=l->next)
+ if (sameString(l->name, mafTable))
+ break;
+
+ /* didn't find mafTable in list, reset it */
+ if (l == NULL)
+ mafTable = NULL;
+ }
+
+if (mafTable == NULL)
+ {
+ if ((mafTable = getConservationTrackName(conn)) == NULL)
+ mafTable = list->name;
+
+ cartSetString(cart, hgtaCGIGeneMafTable, mafTable);
+ }
+
+for(; list; list = list->next)
+ *tb++ = list->name;
+
+printf("MAF table: \n");
+cgiMakeDropListFull(hgtaCGIGeneMafTable, tables, tables,
+ count , mafTable, "change", onChangeGenome());
+
+return mafTable;
+}
+
+void palOptions(struct cart *cart,
+ struct sqlConnection *conn, void (*addButtons)(),
+ char *extraVar)
+/* output the options dialog (select MAF file, output options */
+{
+char *database = sqlGetDatabase(conn);
+
+hPrintf("\n");
+
+/* Hidden form - for benefit of javascript. */
+ {
+ static char *saveVars[32];
+ int varCount = ArraySize(curVars);
+
+ assert(varCount < (sizeof saveVars / sizeof(char *)));
+ memcpy(saveVars, curVars, varCount * sizeof(saveVars[0]));
+ if (extraVar != NULL)
+ {
+ assert(varCount + 1 < (sizeof saveVars / sizeof(char *)));
+ saveVars[varCount] = extraVar;
+ varCount++;
+ }
+ jsCreateHiddenForm(cart, cgiScriptName(), saveVars, varCount);
+ }
+
+}