JAL-1705 first pass at applying preset feature colouring for EnsemblGene

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 06dc4c4..f754eb9 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -43,6 +43,9 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsI;
+import jalview.api.FeaturesDisplayedI;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
@@ -72,6 +75,7 @@ import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
@@ -1125,4 +1129,68 @@ public class AlignViewport extends AlignmentViewport implements
     return true;
   }
 
+  /**
+   * Applies the supplied feature settings descriptor to currently known
+   * features. This supports an 'initial configuration' of feature colouring
+   * based on a preset or user favourite. This may then be modified in the usual
+   * way using the Feature Settings dialogue.
+   * 
+   * @param featureSettings
+   */
+  public void applyFeaturesStyle(FeatureSettingsI featureSettings)
+  {
+    if (featureSettings == null)
+    {
+      return;
+    }
+
+    FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
+            .getFeatureRenderer();
+    Map<String, Object> featureColours = fr.getFeatureColours();
+    fr.findAllFeatures(true);
+    List<String> renderOrder = fr.getRenderOrder();
+    FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+    displayed.clear();
+    // TODO this clears displayed.featuresRegistered - do we care?
+
+    /*
+     * set feature colour if specified by feature settings
+     * set visibility of all features
+     */
+    for (String type : renderOrder)
+    {
+      FeatureColourI preferredColour = featureSettings
+              .getFeatureColour(type);
+      if (preferredColour != null)
+      {
+        fr.setColour(type, preferredColour);
+      }
+      if (featureSettings.isFeatureDisplayed(type))
+      {
+        displayed.setVisible(type);
+      }
+    }
+
+    /*
+     * set visibility of feature groups
+     */
+    for (String group : fr.getFeatureGroups())
+    {
+      fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+    }
+
+    /*
+     * order the features
+     */
+    if (featureSettings.optimiseOrder())
+    {
+      // TODO not supported (yet?)
+    }
+    else
+    {
+      fr.orderFeatures(featureSettings);
+    }
+    fr.setTransparency(featureSettings.getTransparency());
+  }
+
 }