Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@457 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/DataSourceGenerationException.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.dataSources;
 
+import org.broadinstitute.sting.utils.StingException;
+
 /**
  * User: aaron
  * Date: Mar 26, 2009
@@ -18,7 +20,12 @@ package org.broadinstitute.sting.gatk.dataSources;
  * This exception is throw when we're unable to generate a data source,
  * most likely due to an incomplete input source list
  */
-public class DataSourceGenerationException extends Exception {
-    
+public class DataSourceGenerationException extends StingException {
+    public DataSourceGenerationException(String message) {
+        super(message);
+    }
    
+    public DataSourceGenerationException(String message, Throwable throwable) {
+        super(message, throwable);
+    }
 }

java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceLoadException.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
 
+import org.broadinstitute.sting.utils.StingException;
+
 /**
  *
  * User: aaron
@@ -26,7 +28,7 @@ package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
  * <p/>
  * Generate this on a simple data source load exception
  */
-public class SimpleDataSourceLoadException extends Exception {
+public class SimpleDataSourceLoadException extends StingException {
     public SimpleDataSourceLoadException(String msg) {
         super(msg);
     }

java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SimpleDataSourceSplitException.java

@@ -1,5 +1,7 @@
 package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
 
+import org.broadinstitute.sting.utils.StingException;
+
 /**
  *
  * User: aaron
@@ -26,7 +28,7 @@ package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
  * <p/>
  * A descriptions should go here. Blame aaron if it's missing.
  */
-public class SimpleDataSourceSplitException extends Exception {
+public class SimpleDataSourceSplitException extends StingException {
     public SimpleDataSourceSplitException(String msg) {
         super(msg);
     }

java/src/org/broadinstitute/sting/utils/StingException.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting;
+package org.broadinstitute.sting.utils;
 
 /**
  *
@@ -31,5 +31,9 @@ public class StingException extends Exception {
     public StingException(String msg) {
         super(msg);
     }
+
+    public StingException(String message, Throwable throwable) {
+        super(message, throwable);
+    }
 }