fixed plugin. It works deployed now.

README.md

@@ -8,10 +8,6 @@ Have a list of annotation names separated with a character and extract each of t
 
 ![screenshot](ui-screenshot.png)
 
-Bugs
-----
-
-Does only work from IDE. Does not work as standalone.
 
 
 Creator

src/de/mpicbg/gef/extractannotationlist/GefExtractAnnotationListOperation.java

@@ -65,29 +65,32 @@ public class GefExtractAnnotationListOperation extends DocumentOperation {
 			progressListener.setTitle(doc.getName());
 
 			Options extractionOptions = extractionOperation.getOptions(doc);
-			assert extractionOptions.setStringValue("match", "all");
-			assert extractionOptions.setStringValue("whatToExtract", "annotatedRegion");
-			assert extractionOptions.setStringValue("intersecting", "includeContained");
-			assert extractionOptions.setStringValue("concatenate", "false");
-			assert extractionOptions.setStringValue("includeIntergenicRegionsOption", "false");
-			assert extractionOptions.setStringValue("dontMatchTruncated", "false");
-			assert extractionOptions.setStringValue("extractionContextOptions.includeUpstreamBasesOption", "true");
-			assert extractionOptions.setStringValue("extractionContextOptions.numUpstreamBasesOption", "10000");
-			assert extractionOptions.setStringValue("extractionContextOptions.includeDownstreamBasesOption", "true");
-			assert extractionOptions.setStringValue("extractionContextOptions.numDownstreamBasesOption", "10000");
-			assert extractionOptions.setStringValue("annotation.0.field", "Annotation name");
-			assert extractionOptions.setStringValue("annotation.0.condition", "contains");
+			 extractionOptions.setStringValue("match", "all");
+			 extractionOptions.setStringValue("whatToExtract", "annotatedRegion");
+			 extractionOptions.setStringValue("intersecting", "includeContained");
+			 extractionOptions.setStringValue("concatenate", "false");
+			 extractionOptions.setStringValue("includeIntergenicRegionsOption", "false");
+			 extractionOptions.setStringValue("dontMatchTruncated", "false");
+			 extractionOptions.setStringValue("extractionContextOptions.includeUpstreamBasesOption", "true");
+			 extractionOptions.setStringValue("extractionContextOptions.numUpstreamBasesOption", "10000");
+			 extractionOptions.setStringValue("extractionContextOptions.includeDownstreamBasesOption", "true");
+			 extractionOptions.setStringValue("extractionContextOptions.numDownstreamBasesOption", "10000");
+			 extractionOptions.setStringValue("annotation.0.field", "Annotation name");
+			 extractionOptions.setStringValue("annotation.0.condition", "contains");
 //type
-			assert extractionOptions.setStringValue("annotation.1.field", "Annotation type");
-			assert extractionOptions.setStringValue("annotation.1.condition", "is");
-			assert extractionOptions.setStringValue("annotation.1.value", optionType);
+			 extractionOptions.setStringValue("annotation.1.field", "Annotation type");
+			 extractionOptions.setStringValue("annotation.1.condition", "is");
+			 extractionOptions.setStringValue("annotation.1.value", optionType);
 
 			for (String name : namesWanted) {
 
+				if (name.isEmpty())
+					continue;
+
 				progressListener.setMessage(name);
 				compositeProgressListener.setProgress(namesWanted.indexOf(name), namesWanted.size());
 
-				assert extractionOptions.setStringValue("annotation.0.value", name);
+				extractionOptions.setStringValue("annotation.0.value", name);
 
 				List<AnnotatedPluginDocument> resultPerOperation = null;
 				try {
@@ -97,6 +100,10 @@ public class GefExtractAnnotationListOperation extends DocumentOperation {
 //							Dialogs.showMessageDialog(e.toString());
 				}
 
+//				Dialogs.showMessageDialog(extractionOptions.getNamesAndValues(false));
+//				System.out.println(extractionOptions.getNamesAndValues(false));
+
+
 				if (resultPerOperation != null && !resultPerOperation.isEmpty()) {
 					results.addAll(resultPerOperation);
 					namesFound.add(name);