src/hg/instinct/bioInt2/bioController.c 1.13

Index: src/hg/instinct/bioInt2/bioController.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioController.c,v
retrieving revision 1.12
retrieving revision 1.13
diff -b -B -U 4 -r1.12 -r1.13
--- src/hg/instinct/bioInt2/bioController.c	23 Jul 2009 19:49:33 -0000	1.12
+++ src/hg/instinct/bioInt2/bioController.c	1 Sep 2009 05:18:01 -0000	1.13
@@ -180,8 +180,10 @@
 else if (sameString(am->name, "metaGeneset"))
     modulePrefix = "mg";
 else if (sameString(am->name, "factorGraph"))
     modulePrefix = "fg";
+else if (sameString(am->name, "factorGraphEM"))
+    modulePrefix = "fgEM";
 
 dyStringPrintf(dy, "%s", modulePrefix);
 for (sl = slList; sl; sl = sl->next)
     dyStringPrintf(dy, "_%s", sl->name);
@@ -292,8 +294,10 @@
 else if (sameString(am->type, "set"))
     ba->pipeline = genesetLevelPipeline;
 else if (sameString(am->type, "pathway"))
     ba->pipeline = pathwayLevelPipeline;
+else if (sameString(am->type, "pathwayEM"))
+    ba->pipeline = pathwayLevelPipelineUsingEM;
 else
     ba->pipeline = NULL;
 
 /* Set analysis algorithm by module name*/
@@ -302,8 +306,10 @@
 else if (sameString(am->name, "metaGeneset"))
     ba->analyze = metaGeneset;
 else if (sameString(am->name, "factorGraph"))
     ba->analyze = factorGraph;
+else if (sameString(am->name, "factorGraphEM"))
+    ba->analyze = factorGraphUsingEM;
 else
     ba->analyze = NULL;
 }
 
@@ -387,8 +393,11 @@
 
 /* Pathway Factor Graph module */
 storeAnalysisModule(biConn, "factorGraph", "pathway");
 
+/* Pathway Factor Graph module */
+storeAnalysisModule(biConn, "factorGraphEM", "pathwayEM");
+
 /* Set up more modules below, similar to above */
 }
 
 void createStandardPipeline(struct sqlConnection *biConn, int cohort_id)
@@ -441,8 +450,20 @@
 struct analyses *fg = createAnalyses(biConn, cohort_id, am, input_tables, params);
 analysesFree(&fg);
 analysisModulesFree(&am);
 hashFree(&params);
+
+/* Set factor graph analysis modules */
+am = analysisModulesMatching(biConn, "name", "factorGraphEM");
+if (!am)
+    errAbort("No analysis module named factorGraphEM");
+
+params = hashNew(0);
+hashAdd(params, "fxn", cloneString("factorGraphDAIUsingEM"));
+struct analyses *fgEM = createAnalyses(biConn, cohort_id, am, input_tables, params);
+analysesFree(&fgEM);
+analysisModulesFree(&am);
+hashFree(&params);
 }
 
 
 void prepareDatabase(struct sqlConnection *biConn)