src/hg/instinct/bioInt2/bioPathway.h 1.2

Index: src/hg/instinct/bioInt2/bioPathway.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/instinct/bioInt2/bioPathway.h,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/instinct/bioInt2/bioPathway.h	1 Sep 2009 05:18:02 -0000	1.1
+++ src/hg/instinct/bioInt2/bioPathway.h	5 Sep 2009 01:12:01 -0000	1.2
@@ -1,66 +1,73 @@
 /* bioPathway.h 
  * All rights reserved -- J. Zachary Sanborn & Steve Benz
  */
 
 #ifndef BIOPATHWAY_H
 #define BIOPATHWAY_H 
 
 extern char *fgDir;
 extern char *tmpDir;
 
 /* pathway-level analysis functions */
 struct links {
     struct links *next;
     char *parent_name;
     char *child_name;
     char *link_type;
 };
 
 struct entities {
     struct entities *next;
     int id;
     char *type;
     char *name;
 };
 
+// more compact way to pass around em parameters
+struct emParams {
+	double mRNA[3][3];
+	double genome[3][3];
+};
+
 struct pathwayData {
     int id;
     struct entities *entities;
     struct links *links;
     
     struct slPair *data;
     struct hash *featureIds;
+	struct emParams *emParameters;
 };
 
 struct analysisVals *readAnalysisValsFromFile(char *filename, 
 					      struct entities *enList, int sample_id);
 
 boolean writePathwayFile(char *filename, struct pathwayData *pd);
 
 boolean prepFactorGraph(struct biAnalysis *ba, void *data);
 
 void entitiesFree(struct entities **pEl);
 
 void entitiesFreeList(struct entities **pList);
 
 void linksFree(struct links **pEl);
 
 /* Free a list of dynamically allocated link's */
 void linksFreeList(struct links **pList);
 
 void pathwayDataFree(struct pathwayData **pEl);
 
 void slPairPathwayFree(struct slPair **pEl);
 
 void slPairPathwayFreeList(struct slPair **pList);
 
 void storePathwayValsInDb(struct sqlConnection *biConn, char *tableName,
 			  struct pathwayVals *pvList);
 
 struct slPair *getPathways(struct sqlConnection *biConn);
 
 boolean writeEvidenceFile(char *filenamePrefix, struct pathwayData *pd);
 
 struct pathwayVals *convertToPathwayVals(struct analysisVals *avList, int pathway_id);
 
 #endif /* BIOPATHWAY_H */