X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=8e12ff5c3a81e7eb49629ed6c40952ce85c4b5c3;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=2e2289c8a81838d05d95cfb06724b6fe0281b295;hpb=fd5f6d3eed59b5f6d9a7cc09e4ddeb7e78eb2f17;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2e2289c..8e12ff5 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -47,6 +47,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
+import jalview.util.ColorUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
@@ -56,8 +57,8 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Rectangle;
+import java.util.ArrayList;
 import java.util.Hashtable;
-import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JInternalFrame;
@@ -77,9 +78,9 @@ public class AlignViewport extends AlignmentViewport
 
   boolean antiAlias = false;
 
-  private Rectangle explodedGeometry;
+  private Rectangle explodedGeometry = null;
 
-  String viewName;
+  private String viewName = null;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -206,7 +207,7 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault("ANTI_ALIAS", true);
 
     viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
     setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
@@ -290,7 +291,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(this, alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -304,6 +305,7 @@ public class AlignViewport extends AlignmentViewport
     {
       residueShading.setConsensus(hconsensus);
     }
+    setColourAppliesToAllGroups(true);
   }
 
   boolean validCharWidth;
@@ -443,31 +445,6 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * returns the visible column regions of the alignment
-   * 
-   * @param selectedRegionOnly
-   *          true to just return the contigs intersecting with the selected
-   *          area
-   * @return
-   */
-  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
-  {
-    int start = 0;
-    int end = 0;
-    if (selectedRegionOnly && selectionGroup != null)
-    {
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes() + 1;
-    }
-    else
-    {
-      end = alignment.getWidth();
-    }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
-            false));
-  }
-
-  /**
    * get hash of undo and redo list for the alignment
    * 
    * @return long[] { historyList.hashCode, redoList.hashCode };
@@ -888,10 +865,9 @@ public class AlignViewport extends AlignmentViewport
     if (ap != null)
     {
       // modify GUI elements to reflect geometry change
-      Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
-              .getPreferredSize();
+      Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
       idw.width = i;
-      getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+      ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
     }
   }
 
@@ -980,19 +956,60 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
+    transferFeaturesStyles(featureSettings, false);
+  }
+
+  /**
+   * 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
+   */
+  @Override
+  public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    transferFeaturesStyles(featureSettings, true);
+  }
+
+  /**
+   * when mergeOnly is set, then group and feature visibility or feature colours
+   * are not modified for features and groups already known to the feature
+   * renderer. Feature ordering is always adjusted, and transparency is always set
+   * regardless.
+   * 
+   * @param featureSettings
+   * @param mergeOnly
+   */
+  private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
+          boolean mergeOnly)
+  {
     if (featureSettings == null)
     {
       return;
     }
-
+    
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
+    List<String> origRenderOrder = new ArrayList<>();
+    List<String> origGroups = new ArrayList<>();
+    // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+    origRenderOrder.addAll(fr.getRenderOrder());
+    origGroups.addAll(fr.getFeatureGroups());
+
     fr.findAllFeatures(true);
     List<String> renderOrder = fr.getRenderOrder();
     FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
-    displayed.clear();
+    if (!mergeOnly)
+    {
+      // only clear displayed features if we are mergeing
+      // displayed.clear();
+    }
     // TODO this clears displayed.featuresRegistered - do we care?
-
+    //
+    // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
+    // feature visibility has already been configured is not very friendly
     /*
      * set feature colour if specified by feature settings
      * set visibility of all features
@@ -1001,13 +1018,28 @@ public class AlignViewport extends AlignmentViewport
     {
       FeatureColourI preferredColour = featureSettings
               .getFeatureColour(type);
-      if (preferredColour != null)
-      {
-        fr.setColour(type, preferredColour);
-      }
-      if (featureSettings.isFeatureDisplayed(type))
+      FeatureColourI origColour = fr.getFeatureStyle(type);
+      if (!mergeOnly || (!origRenderOrder.contains(type)
+              || origColour == null
+              || (!origColour.isGraduatedColour()
+                      && origColour.getColour() != null
+                      && origColour.getColour().equals(
+                              ColorUtils.createColourFromName(type)))))
       {
-        displayed.setVisible(type);
+        // if we are merging, only update if there wasn't already a colour defined for
+        // this type
+        if (preferredColour != null)
+        {
+          fr.setColour(type, preferredColour);
+        }
+        if (featureSettings.isFeatureDisplayed(type))
+        {
+          displayed.setVisible(type);
+        }
+        else if (featureSettings.isFeatureHidden(type))
+        {
+          displayed.setHidden(type);
+        }
       }
     }
 
@@ -1016,7 +1048,12 @@ public class AlignViewport extends AlignmentViewport
      */
     for (String group : fr.getFeatureGroups())
     {
-      fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+      if (!mergeOnly || !origGroups.contains(group))
+      {
+        // when merging, display groups only if the aren't already marked as not visible
+        fr.setGroupVisibility(group,
+                featureSettings.isGroupDisplayed(group));
+      }
     }
 
     /*
@@ -1031,5 +1068,17 @@ public class AlignViewport extends AlignmentViewport
       fr.orderFeatures(featureSettings);
     }
     fr.setTransparency(featureSettings.getTransparency());
+
+    fr.notifyFeaturesChanged();
+  }
+
+  public String getViewName()
+  {
+    return viewName;
+  }
+
+  public void setViewName(String viewName)
+  {
+    this.viewName = viewName;
   }
 }