Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index b7e7899..e36944f 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SequenceStructureBinding;
@@ -218,6 +219,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       viewport.setColumnSelection(columnSelection);
     }
+    viewport.setScaleAboveWrapped(scaleAbove.getState());
 
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -364,18 +366,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public boolean parseFeaturesFile(String file, String type,
           boolean autoenabledisplay)
   {
-    // TODO: test if importing a features file onto an alignment which already
-    // has features with links overwrites the original links.
-
-    Hashtable featureLinks = new Hashtable();
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
-              .getAlignment(), alignPanel.seqPanel.seqCanvas
-              .getFeatureRenderer().getFeatureColours(), featureLinks,
-              true, viewport.applet.getDefaultParameter("relaxedidmatch",
-                      false));
+      Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
+              .getFeatureRenderer().getFeatureColours();
+      boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
+              "relaxedidmatch", false);
+      featuresFile = new FeaturesFile(file, type).parse(
+              viewport.getAlignment(), colours, true, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -383,10 +382,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (featuresFile)
     {
-      if (featureLinks.size() > 0)
-      {
-        alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
-      }
       if (autoenabledisplay)
       {
         viewport.setShowSequenceFeatures(true);
@@ -708,9 +703,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       // Hide everything by the current selection - this is a hack - we do the
       // invert and then hide
       // first check that there will be visible columns after the invert.
-      if ((viewport.getColumnSelection() != null
-              && viewport.getColumnSelection().getSelected() != null && viewport
-              .getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns()
               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
                       .getEndRes()))
       {
@@ -738,8 +731,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         hide = true;
         viewport.hideAllSelectedSeqs();
       }
-      else if (!(toggleCols && viewport.getColumnSelection().getSelected()
-              .size() > 0))
+      else if (!(toggleCols && viewport.hasSelectedColumns()))
       {
         viewport.showAllHiddenSeqs();
       }
@@ -747,7 +739,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (toggleCols)
     {
-      if (viewport.getColumnSelection().getSelected().size() > 0)
+      if (viewport.hasSelectedColumns())
       {
         viewport.hideSelectedColumns();
         if (!toggleSeqs)
@@ -1406,7 +1398,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return annotation;
   }
 
-  private Map<String, Object> getDisplayedFeatureCols()
+  private Map<String, FeatureColourI> getDisplayedFeatureCols()
   {
     if (alignPanel.getFeatureRenderer() != null
             && viewport.getFeaturesDisplayed() != null)
@@ -1420,15 +1412,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public String outputFeatures(boolean displayTextbox, String format)
   {
     String features;
+    FeaturesFile formatter = new FeaturesFile();
     if (format.equalsIgnoreCase("Jalview"))
     {
-      features = new FeaturesFile().printJalviewFormat(viewport
+      features = formatter.printJalviewFormat(viewport
               .getAlignment().getSequencesArray(),
               getDisplayedFeatureCols());
     }
     else
     {
-      features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
+      features = formatter.printGffFormat(viewport.getAlignment()
               .getSequencesArray(), getDisplayedFeatureCols());
     }
 
@@ -2238,7 +2231,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -2255,7 +2251,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
-    alignPanel.paintAlignment(true);
+    // JAL-2034 - should delegate to
+    // alignPanel to decide if overview needs
+    // updating.
+    alignPanel.paintAlignment(false);
     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
     viewport.sendSelection();
   }
@@ -3515,10 +3514,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
-            .getString("label.modify_identity_thereshold"));
+            .getString("label.modify_identity_threshold"));
     modifyPID.addActionListener(this);
     modifyConservation.setLabel(MessageManager
-            .getString("label.modify_conservation_thereshold"));
+            .getString("label.modify_conservation_threshold"));
     modifyConservation.addActionListener(this);
     annotationColour.setLabel(MessageManager
             .getString("action.by_annotation"));