JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 5662d0c..33699cc 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -35,6 +35,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -97,19 +98,22 @@ public class AlignViewController implements AlignViewControllerI
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
+      ColourSchemeI colours = viewport.getGlobalColourScheme();
       // set view properties for each group
       for (int g = 0; g < gps.length; g++)
       {
         // gps[g].setShowunconserved(viewport.getShowUnconserved());
         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
         viewport.getAlignment().addGroup(gps[g]);
-        Color col = new Color((int) (Math.random() * 255),
-                (int) (Math.random() * 255), (int) (Math.random() * 255));
-        col = col.brighter();
-        for (SequenceI sq : gps[g].getSequences(null))
+        if (colours != null)
         {
-          viewport.setSequenceColour(sq, col);
+          gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
         }
+        Color col = new Color((int) (Math.random() * 255),
+                (int) (Math.random() * 255), (int) (Math.random() * 255));
+        gps[g].idColour = col;
+        viewport.setUpdateStructures(true);
+        viewport.addSequenceGroup(gps[g]);
       }
       return true;
     }
@@ -349,28 +353,28 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+  public boolean parseFeaturesFile(Object file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
-    boolean featuresFile = false;
+    boolean featuresAdded = false;
+    FeatureRenderer fr = alignPanel.getFeatureRenderer();
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(
-              viewport.getAlignment().getDataset(),
-              alignPanel.getFeatureRenderer().getFeatureColours(), false,
-              relaxedIdMatching);
+      featuresAdded = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(), fr.getFeatureColours(),
+              fr.getFeatureFilters(), false, relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
     }
 
-    if (featuresFile)
+    if (featuresAdded)
     {
       avcg.refreshFeatureUI(true);
-      if (alignPanel.getFeatureRenderer() != null)
+      if (fr != null)
       {
         // update the min/max ranges where necessary
-        alignPanel.getFeatureRenderer().findAllFeatures(true);
+        fr.findAllFeatures(true);
       }
       if (avcg.getFeatureSettingsUI() != null)
       {
@@ -379,7 +383,7 @@ public class AlignViewController implements AlignViewControllerI
       alignPanel.paintAlignment(true, true);
     }
 
-    return featuresFile;
+    return featuresAdded;
 
   }