Commit affaba05 authored by janosch's avatar janosch

fixed plugin. It works deployed now.

parent 87c826ed
...@@ -8,10 +8,6 @@ Have a list of annotation names separated with a character and extract each of t ...@@ -8,10 +8,6 @@ Have a list of annotation names separated with a character and extract each of t
![screenshot](ui-screenshot.png) ![screenshot](ui-screenshot.png)
Bugs
----
Does only work from IDE. Does not work as standalone.
Creator Creator
......
...@@ -65,29 +65,32 @@ public class GefExtractAnnotationListOperation extends DocumentOperation { ...@@ -65,29 +65,32 @@ public class GefExtractAnnotationListOperation extends DocumentOperation {
progressListener.setTitle(doc.getName()); progressListener.setTitle(doc.getName());
Options extractionOptions = extractionOperation.getOptions(doc); Options extractionOptions = extractionOperation.getOptions(doc);
assert extractionOptions.setStringValue("match", "all"); extractionOptions.setStringValue("match", "all");
assert extractionOptions.setStringValue("whatToExtract", "annotatedRegion"); extractionOptions.setStringValue("whatToExtract", "annotatedRegion");
assert extractionOptions.setStringValue("intersecting", "includeContained"); extractionOptions.setStringValue("intersecting", "includeContained");
assert extractionOptions.setStringValue("concatenate", "false"); extractionOptions.setStringValue("concatenate", "false");
assert extractionOptions.setStringValue("includeIntergenicRegionsOption", "false"); extractionOptions.setStringValue("includeIntergenicRegionsOption", "false");
assert extractionOptions.setStringValue("dontMatchTruncated", "false"); extractionOptions.setStringValue("dontMatchTruncated", "false");
assert extractionOptions.setStringValue("extractionContextOptions.includeUpstreamBasesOption", "true"); extractionOptions.setStringValue("extractionContextOptions.includeUpstreamBasesOption", "true");
assert extractionOptions.setStringValue("extractionContextOptions.numUpstreamBasesOption", "10000"); extractionOptions.setStringValue("extractionContextOptions.numUpstreamBasesOption", "10000");
assert extractionOptions.setStringValue("extractionContextOptions.includeDownstreamBasesOption", "true"); extractionOptions.setStringValue("extractionContextOptions.includeDownstreamBasesOption", "true");
assert extractionOptions.setStringValue("extractionContextOptions.numDownstreamBasesOption", "10000"); extractionOptions.setStringValue("extractionContextOptions.numDownstreamBasesOption", "10000");
assert extractionOptions.setStringValue("annotation.0.field", "Annotation name"); extractionOptions.setStringValue("annotation.0.field", "Annotation name");
assert extractionOptions.setStringValue("annotation.0.condition", "contains"); extractionOptions.setStringValue("annotation.0.condition", "contains");
//type //type
assert extractionOptions.setStringValue("annotation.1.field", "Annotation type"); extractionOptions.setStringValue("annotation.1.field", "Annotation type");
assert extractionOptions.setStringValue("annotation.1.condition", "is"); extractionOptions.setStringValue("annotation.1.condition", "is");
assert extractionOptions.setStringValue("annotation.1.value", optionType); extractionOptions.setStringValue("annotation.1.value", optionType);
for (String name : namesWanted) { for (String name : namesWanted) {
if (name.isEmpty())
continue;
progressListener.setMessage(name); progressListener.setMessage(name);
compositeProgressListener.setProgress(namesWanted.indexOf(name), namesWanted.size()); compositeProgressListener.setProgress(namesWanted.indexOf(name), namesWanted.size());
assert extractionOptions.setStringValue("annotation.0.value", name); extractionOptions.setStringValue("annotation.0.value", name);
List<AnnotatedPluginDocument> resultPerOperation = null; List<AnnotatedPluginDocument> resultPerOperation = null;
try { try {
...@@ -97,6 +100,10 @@ public class GefExtractAnnotationListOperation extends DocumentOperation { ...@@ -97,6 +100,10 @@ public class GefExtractAnnotationListOperation extends DocumentOperation {
// Dialogs.showMessageDialog(e.toString()); // Dialogs.showMessageDialog(e.toString());
} }
// Dialogs.showMessageDialog(extractionOptions.getNamesAndValues(false));
// System.out.println(extractionOptions.getNamesAndValues(false));
if (resultPerOperation != null && !resultPerOperation.isEmpty()) { if (resultPerOperation != null && !resultPerOperation.isEmpty()) {
results.addAll(resultPerOperation); results.addAll(resultPerOperation);
namesFound.add(name); namesFound.add(name);
......
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