7bc24686024ec14d351ab208b5179ab251d7c463
tdreszer
  Fri Oct 14 16:34:15 2011 -0700
Major work on bedFilt, psl and wigMaf to make them properly composite ready.
diff --git src/hg/lib/pal.c src/hg/lib/pal.c
index 1164f71..719a00d 100644
--- src/hg/lib/pal.c
+++ src/hg/lib/pal.c
@@ -1,303 +1,303 @@
 #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"
 
 static char const rcsid[] = "$Id: pal.c,v 1.14 2009/07/06 17:43:08 braney Exp $";
 
 #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, database, &wmSpecies, &groupCnt);
+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];
 
     safef(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);
 dyStringAppend(dy, "onChange=\"");
 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];
     safef(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("<B>MAF table: </B>\n");
 cgiMakeDropListFull(hgtaCGIGeneMafTable, tables, tables, 
     count , mafTable, 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("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=POST>\n", cgiScriptName());
 cartSaveSession(cart);
 
 char *mafTable = outMafTableDrop(cart, conn);
 char *numColumns = cartUsualString(cart, hgtaCGINumColumns, "");
 
 printf("<BR><BR><B>Formatting options:</B><BR>\n");
 jsMakeTrackingCheckBox(cart, hgtaCGIGeneExons, hgtaJSGeneExons, FALSE);
 printf("Separate into exons<BR>");
 jsMakeTrackingCheckBox(cart, hgtaCGIGeneNoTrans, hgtaJSGeneNoTrans, FALSE);
 printf("Show nucleotides<BR>");
 jsMakeTrackingCheckBox(cart, hgtaCGIGeneOutBlank, hgtaJSGeneOutBlank, FALSE);
 printf("Output lines with just dashes<BR>");
 jsMakeTrackingCheckBox(cart, hgtaCGIOutTable, hgtaJSOutTable, FALSE);
 printf("Format output as table ");
 jsMakeTrackingCheckBox(cart, hgtaCGITruncHeader, hgtaJSTruncHeader, FALSE);
 printf("Truncate headers at ");
 cgiMakeTextVar(hgtaCGINumColumns, numColumns, 2);
 printf("characters (enter zero for no headers)<BR>");
 
 printf("<BR>");
 struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
 
 /* get maf parent (if any) */
 maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
 
 wigMafSpeciesTable(cart, maftdb, mafTable, database);
 
 addButtons();
 
 hPrintf("</FORM>\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);
     }
 
 cartSaveSession(cart);
 }