src/hg/instinct/bioInt2/bioController.h 1.4

Index: src/hg/instinct/bioInt2/bioController.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioController.h,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/instinct/bioInt2/bioController.h	22 Mar 2009 01:07:28 -0000	1.3
+++ src/hg/instinct/bioInt2/bioController.h	23 Mar 2009 18:19:29 -0000	1.4
@@ -1,50 +1,67 @@
 /* bioController.h 
  * All rights reserved -- J. Zachary Sanborn
  */
 
 #ifndef BIOCONTROLLER_H
 #define BIOCONTROLLER_H 
 
 #include "common.h"
 #include "bioIntDb.h"
 
 
 struct analysisResult {
     struct analysisResult *next;
     char *sample;
     char *feature;
 
     double val;
     double conf;
 };
 
 struct biAnalysis {
     struct biAnalysis *next;
     char *db;
     char *tableName;
     struct slName *inputTables;
     struct hash *parameters;
 
-    struct analysisResult *(*analyze)(struct biAnalysis *ba, struct slPair *spList, 
-				     char *sample, char *gene);
+    void (*pipeline)(struct biAnalysis *ba);
+
+    struct analysisResult *(*analyze)(struct biAnalysis *ba, void *data, 
+				      char *sample, char *feature);
 }; 
 
+void analysisResultFree(struct analysisResult **pEl);
+
+void analysisResultFreeList(struct analysisResult **pList);
+
+struct hash *createHash(struct sqlConnection *biConn,
+			char *table, char *key_field, char *val_field);
 
 int findIdInTable(struct sqlConnection *biConn, char *tableName,
 		  char *idField, char *sField, char *name); 
 
+void storeAnalysisResultsInDb(struct sqlConnection *biConn, struct biAnalysis *ba,
+			      struct analysisResult *arList);
+
 void runAnalysisPipeline(struct biAnalysis *baList);
 
 /* Gene Level Analyses */
-struct analysisResult *metaGene(struct biAnalysis *ba, struct slPair *spList,
+void geneLevelPipeline(struct biAnalysis *ba);
+
+
+struct analysisResult *metaGene(struct biAnalysis *ba, void *data,
 				char *sample, char *gene); 
 
 
 /* Geneset Analyses */
+void genesetLevelPipeline(struct biAnalysis *ba);
 
+struct analysisResult *metaGeneset(struct biAnalysis *ba, void *data,
+				   char *sample, char *gene);
 
 /* Pathway Analyses */
 
 
 
 #endif /* BIOCONTROLLER_H */