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

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 42460dc..015b95b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -30,6 +30,7 @@ import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -54,6 +55,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
+import jalview.io.BioJsHTMLOutput;
 import jalview.io.FeaturesFile;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
@@ -115,6 +117,7 @@ import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
@@ -765,7 +768,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     setColourSelected(ColourSchemeProperty.getColourName(av
             .getGlobalColourScheme()));
 
-    showSeqFeatures.setSelected(av.showSequenceFeatures);
+    showSeqFeatures.setSelected(av.isShowSequenceFeatures());
     hiddenMarkers.setState(av.showHiddenMarkers);
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
@@ -1233,6 +1236,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     new HtmlSvgOutput(null, alignPanel);
   }
 
+  @Override
+  public void bioJSMenuItem_actionPerformed(ActionEvent e)
+  {
+    new BioJsHTMLOutput(alignPanel,
+            alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+  }
   public void createImageMap(File file, String image)
   {
     alignPanel.makePNGImageMap(file, image);
@@ -3083,7 +3092,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
             .isSelected());
-    if (viewport.getShowSequenceFeaturesHeight())
+    if (viewport.isShowSequenceFeaturesHeight())
     {
       // ensure we're actually displaying features
       viewport.setShowSequenceFeatures(true);
@@ -4188,28 +4197,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else if (viewport.getSelectionGroup() != null
             && viewport.getSelectionGroup().getSize() == 1)
     {
-      int option = JOptionPane
-              .showConfirmDialog(
-this,
-                      "More than one sequece group selection is required for this Job, click \n'Cancel' to edit your selection or 'Ok' to submit the entire sequence.",
-                      "Invalid selection",
-                      JOptionPane.OK_CANCEL_OPTION);
+      int option = JOptionPane.showConfirmDialog(this,
+              MessageManager.getString("warn.oneseq_msainput_selection"),
+              MessageManager.getString("label.invalid_selection"),
+              JOptionPane.OK_CANCEL_OPTION);
       if (option == JOptionPane.OK_OPTION)
       {
         msa = viewport.getAlignmentView(false);
       }
-
     }
     else
     {
-      /*
-       * Vector seqs = viewport.getAlignment().getSequences();
-       * 
-       * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       * 
-       * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
-       * seqs.elementAt(i); } }
-       */
       msa = viewport.getAlignmentView(false);
     }
     return msa;
@@ -4884,7 +4882,7 @@ this,
     {
       featuresFile = new FeaturesFile(file, type).parse(viewport
               .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
-              .getFeatureRenderer().featureColours, false,
+              .getFeatureRenderer().getFeatureColours(), false,
               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     } catch (Exception ex)
     {
@@ -4893,7 +4891,7 @@ this,
 
     if (featuresFile)
     {
-      viewport.showSequenceFeatures = true;
+      viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
       if (alignPanel.getSeqPanel().seqCanvas.fr != null)
       {
@@ -5832,6 +5830,15 @@ this,
             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
     alignPanel.paintAlignment(true);
   }
+
+  /**
+   * 
+   * @return alignment panels in this alignemnt frame
+   */
+  public List<AlignmentViewPanel> getAlignPanels()
+  {
+    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+  }
 }
 
 class PrintThread extends Thread