src/hg/instinct/bioInt2/bioPathway.h 1.1

Index: src/hg/instinct/bioInt2/bioPathway.h
===================================================================
RCS file: src/hg/instinct/bioInt2/bioPathway.h
diff -N src/hg/instinct/bioInt2/bioPathway.h
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/instinct/bioInt2/bioPathway.h	1 Sep 2009 05:18:02 -0000	1.1
@@ -0,0 +1,66 @@
+/* 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;
+};
+
+struct pathwayData {
+    int id;
+    struct entities *entities;
+    struct links *links;
+    
+    struct slPair *data;
+    struct hash *featureIds;
+};
+
+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 */