src/hg/instinct/bioInt2/bioController.h 1.6

Index: src/hg/instinct/bioInt2/bioController.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioController.h,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/instinct/bioInt2/bioController.h	27 Apr 2009 06:15:48 -0000	1.5
+++ src/hg/instinct/bioInt2/bioController.h	30 Apr 2009 19:54:28 -0000	1.6
@@ -1,67 +1,81 @@
 /* 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;
 
     void (*pipeline)(struct biAnalysis *ba);
 
     struct analysisVals *(*analyze)(struct biAnalysis *ba, void *data, 
 				    int sample_id, int feature_id);
 }; 
 
-void analysisResultFree(struct analysisResult **pEl);
+void slPairHashesFree(struct slPair **pEl);
 
-void analysisResultFreeList(struct analysisResult **pList);
+void slPairHashesFreeList(struct slPair **pList);
+
+void slPairStringFree(struct slPair **pEl);
+
+void slPairStringFreeList(struct slPair **pList);
+
+struct slPair *analysisValsSamplesHashes(struct sqlConnection *biConn,
+					 struct slName *dataset);
+
+//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 */
 void geneLevelPipeline(struct biAnalysis *ba);
 
 
 struct analysisVals *metaGene(struct biAnalysis *ba, void *data,
 			      int sample_id, int feature_id);
 
 
 /* Geneset Analyses */
 void genesetLevelPipeline(struct biAnalysis *ba);
 
 struct analysisVals *metaGeneset(struct biAnalysis *ba, void *data,
 				   int sample_id, int feature_id);
 
 /* Pathway Analyses */
 
+void pathwayLevelPipeline(struct biAnalysis *ba);
 
+struct analysisVals *factorGraph(struct biAnalysis *ba, void *data,
+				 int sample_id, int feature_id);
 
 #endif /* BIOCONTROLLER_H */