JAL-1482 feature renderer and manipulation code refactored to renderer and abstract...

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 1e87a93..61c5ee1 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -112,14 +112,16 @@ public class AnnotationExporter extends JPanel
         if (GFFFormat.isSelected())
         {
           text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
-                  .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
+                  .getDataset().getSequencesArray(), ap
+                  .getFeatureRenderer().getDisplayedFeatureCols(), true,
+                  ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
         }
         else
         {
           text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
-                  .getDataset().getSequencesArray(),
-                  getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
+                  .getDataset().getSequencesArray(), ap
+                  .getFeatureRenderer().getDisplayedFeatureCols(), true,
+                  ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
         }
       }
       else
@@ -159,14 +161,14 @@ public class AnnotationExporter extends JPanel
       if (GFFFormat.isSelected())
       {
         text = new FeaturesFile().printGFFFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(),
-                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+                .getDataset().getSequencesArray(), ap.getFeatureRenderer()
+                .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
       else
       {
         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
-                .getDataset().getSequencesArray(),
-                getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
+                .getDataset().getSequencesArray(), ap.getFeatureRenderer()
+                .getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
       }
     }
     else if (!features)
@@ -186,38 +188,27 @@ public class AnnotationExporter extends JPanel
     try
     {
       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()})), 600, 500);
+      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()}) : MessageManager.formatMessage("label.generating_annotations_for_params", new String[]{ap.alignFrame.getTitle()}))
-              , oom);
+      new OOMWarning((features ? MessageManager.formatMessage(
+              "label.generating_features_for_params", new String[]
+              { ap.alignFrame.getTitle() }) : MessageManager.formatMessage(
+              "label.generating_annotations_for_params", new String[]
+              { ap.alignFrame.getTitle() })), oom);
       cap.dispose();
     }
 
     close_actionPerformed(null);
   }
 
-  private Hashtable getDisplayedFeatureCols()
-  {
-    Hashtable fcols = new Hashtable();
-    if (ap.av.featuresDisplayed == null)
-    {
-      return fcols;
-    }
-    Enumeration en = ap.av.featuresDisplayed.keys();
-    FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
-                                                                     // higher
-                                                                     // level
-                                                                     // method ?
-    while (en.hasMoreElements())
-    {
-      Object col = en.nextElement();
-      fcols.put(col, fr.featureColours.get(col));
-    }
-    return fcols;
-  }
-
   public void close_actionPerformed(ActionEvent e)
   {
     try