From affaba05818da9053e17472cedbdb99393029157 Mon Sep 17 00:00:00 2001 From: Stephan Janosch Date: Tue, 21 Nov 2017 11:04:53 +0100 Subject: [PATCH] fixed plugin. It works deployed now. --- README.md | 4 -- .../GefExtractAnnotationListOperation.java | 39 +++++++++++-------- 2 files changed, 23 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 24a8be9..0329c02 100644 --- a/README.md +++ b/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 diff --git a/src/de/mpicbg/gef/extractannotationlist/GefExtractAnnotationListOperation.java b/src/de/mpicbg/gef/extractannotationlist/GefExtractAnnotationListOperation.java index c994b5d..4546adb 100644 --- a/src/de/mpicbg/gef/extractannotationlist/GefExtractAnnotationListOperation.java +++ b/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 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); -- GitLab