JAL-2418 source formatting

[jalview.git] / src / jalview / gui / AnnotationExporter.java

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index d688ddd..beb77ca 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
@@ -93,8 +94,8 @@ public class AnnotationExporter extends JPanel
   public void exportAnnotations(AlignmentPanel ap)
   {
     this.ap = ap;
-    annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
-            .getAlignmentAnnotation();
+    annotations = ap.av.isShowAnnotation() ? null
+            : ap.av.getAlignment().getAlignmentAnnotation();
     wholeView = true;
     startExportAnnotation();
   }
@@ -122,9 +123,9 @@ public class AnnotationExporter extends JPanel
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(features ? MessageManager
-            .getString("label.save_features_to_file") : MessageManager
-            .getString("label.save_annotation_to_file"));
+    chooser.setDialogTitle(features
+            ? MessageManager.getString("label.save_features_to_file")
+            : MessageManager.getString("label.save_annotation_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -155,20 +156,28 @@ public class AnnotationExporter extends JPanel
             .getString("label.no_features_on_alignment");
     if (features)
     {
+      Map<String, FeatureColourI> displayedFeatureColours = ap
+              .getFeatureRenderer().getDisplayedFeatureCols();
       FeaturesFile formatter = new FeaturesFile();
       SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
-      Map<String, Object> featureColours = ap.getFeatureRenderer()
+      Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
               .getDisplayedFeatureCols();
       boolean includeNonPositional = ap.av.isShowNPFeats();
       if (GFFFormat.isSelected())
       {
+        text = new FeaturesFile().printGffFormat(
+                ap.av.getAlignment().getDataset().getSequencesArray(),
+                displayedFeatureColours, true, ap.av.isShowNPFeats());
         text = formatter.printGffFormat(sequences, featureColours, true,
                 includeNonPositional);
       }
       else
       {
-        text = formatter.printJalviewFormat(sequences, featureColours,
-                true, includeNonPositional);
+        text = new FeaturesFile().printJalviewFormat(
+                ap.av.getAlignment().getDataset().getSequencesArray(),
+                displayedFeatureColours, true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
+        text = formatter.printJalviewFormat(sequences, featureColours, true,
+                includeNonPositional);
       }
     }
     else
@@ -201,23 +210,23 @@ public class AnnotationExporter extends JPanel
     {
       String text = getFileContents();
       cap.setText(text);
-      Desktop.addInternalFrame(
-              cap,
-              (features ? MessageManager.formatMessage(
-                      "label.features_for_params",
-                      new String[] { ap.alignFrame.getTitle() })
-                      : MessageManager.formatMessage(
-                              "label.annotations_for_params",
-                              new String[] { ap.alignFrame.getTitle() })),
+      Desktop.addInternalFrame(cap, (features ? MessageManager
+              .formatMessage("label.features_for_params", new String[]
+              { ap.alignFrame.getTitle() })
+              : MessageManager.formatMessage("label.annotations_for_params",
+                      new String[]
+                      { ap.alignFrame.getTitle() })),
               600, 500);
     } catch (OutOfMemoryError oom)
     {
       new OOMWarning((features ? MessageManager.formatMessage(
-              "label.generating_features_for_params",
-              new String[] { ap.alignFrame.getTitle() })
+              "label.generating_features_for_params", new String[]
+              { ap.alignFrame.getTitle() })
               : MessageManager.formatMessage(
                       "label.generating_annotations_for_params",
-                      new String[] { ap.alignFrame.getTitle() })), oom);
+                      new String[]
+                      { ap.alignFrame.getTitle() })),
+              oom);
       cap.dispose();
     }