Merge branch 'features/JAL-1605_html-svg-export' into develop

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

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index c68b2b1..e43c06b 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,16 +20,31 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.util.List;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Hashtable;
+import java.util.List;
 
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.util.MessageManager;
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.SwingConstants;
 
 /**
  * 
@@ -112,14 +127,16 @@ 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 +176,14 @@ 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)
@@ -206,27 +223,6 @@ public class AnnotationExporter extends JPanel
 
     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.getSeqPanel().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