X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=719cde463611d38020b7a7a977d4656e2600267c;hb=dcfba29a940c44003581f28e6da481450aa86575;hp=8bdcad46c701a9e1cd1b8a0ba28e865085853438;hpb=07108e505ff923f3b5135ffbdbb79259fe53432e;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 8bdcad4..719cde4 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -26,17 +26,18 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.util.ColorUtils;
-import jalview.util.matcher.KeyedMatcherSetI;
 
 import java.awt.Color;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
@@ -58,12 +59,12 @@ public abstract class FeatureRendererModel
 
     public final FeatureColourI featureColour;
 
-    public final KeyedMatcherSetI filter;
+    public final FeatureMatcherSetI filter;
 
     public final Boolean show;
 
     public FeatureSettingsBean(String type, FeatureColourI colour,
-            KeyedMatcherSetI theFilter, Boolean isShown)
+            FeatureMatcherSetI theFilter, Boolean isShown)
     {
       featureType = type;
       featureColour = colour;
@@ -90,7 +91,7 @@ public abstract class FeatureRendererModel
   /*
    * filters for each feature type
    */
-  protected Map<String, KeyedMatcherSetI> featureFilters = new HashMap<>();
+  protected Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 
   protected String[] renderOrder;
 
@@ -612,7 +613,7 @@ public abstract class FeatureRendererModel
    * @param type
    * @return
    */
-  protected boolean showFeatureOfType(String type)
+  public boolean showFeatureOfType(String type)
   {
     return type == null ? false : (av.getFeaturesDisplayed() == null ? true
             : av.getFeaturesDisplayed().isVisible(type));
@@ -1032,16 +1033,24 @@ public abstract class FeatureRendererModel
    * Removes from the list of features any that duplicate the location of a
    * feature of the same type. Should be used only for features of the same,
    * simple, feature colour (which normally implies the same feature type). Does
-   * not check visibility settings for feature type or feature group.
+   * not check visibility settings for feature type or feature group. No
+   * filtering is done if transparency, or any feature filters, are in force.
    * 
    * @param features
    */
   public void filterFeaturesForDisplay(List<SequenceFeature> features)
   {
-    if (features.isEmpty())
+    /*
+     * don't remove 'redundant' features if 
+     * - transparency is applied (feature count affects depth of feature colour)
+     * - filters are applied (not all features may be displayable)
+     */
+    if (features.isEmpty() || transparency != 1f
+            || !featureFilters.isEmpty())
     {
       return;
     }
+
     SequenceFeatures.sortFeatures(features, true);
     SequenceFeature lastFeature = null;
 
@@ -1068,25 +1077,25 @@ public abstract class FeatureRendererModel
   }
 
   @Override
-  public Map<String, KeyedMatcherSetI> getFeatureFilters()
+  public Map<String, FeatureMatcherSetI> getFeatureFilters()
   {
-    return new HashMap<>(featureFilters);
+    return featureFilters;
   }
 
   @Override
-  public void setFeatureFilters(Map<String, KeyedMatcherSetI> filters)
+  public void setFeatureFilters(Map<String, FeatureMatcherSetI> filters)
   {
     featureFilters = filters;
   }
 
   @Override
-  public KeyedMatcherSetI getFeatureFilter(String featureType)
+  public FeatureMatcherSetI getFeatureFilter(String featureType)
   {
     return featureFilters.get(featureType);
   }
 
   @Override
-  public void setFeatureFilter(String featureType, KeyedMatcherSetI filter)
+  public void setFeatureFilter(String featureType, FeatureMatcherSetI filter)
   {
     if (filter == null || filter.isEmpty())
     {
@@ -1100,8 +1109,8 @@ public abstract class FeatureRendererModel
 
   /**
    * Answers the colour for the feature, or null if the feature is excluded by
-   * feature type or group visibility, by filters, or by colour threshold
-   * settings
+   * feature group visibility, by filters, or by colour threshold settings. This
+   * method does not take feature visibility into account.
    * 
    * @param sf
    * @param fc
@@ -1110,14 +1119,6 @@ public abstract class FeatureRendererModel
   public Color getColor(SequenceFeature sf, FeatureColourI fc)
   {
     /*
-     * is the feature type displayed?
-     */
-    if (!showFeatureOfType(sf.getType()))
-    {
-      return null;
-    }
-
-    /*
      * is the feature group displayed?
      */
     if (featureGroupNotShown(sf))
@@ -1146,14 +1147,34 @@ public abstract class FeatureRendererModel
    */
   protected boolean featureMatchesFilters(SequenceFeature sf)
   {
-    KeyedMatcherSetI filter = featureFilters.get(sf.getType());
-    // TODO temporary fudge for Score and Label
-    return filter == null ? true
-            : filter.matches(
-                    key -> "Label".equals(key[0]) ? sf.getDescription()
-                            : ("Score".equals(key[0])
-                                    ? String.valueOf(sf.getScore())
-                                    : sf.getValueAsString(key)));
+    FeatureMatcherSetI filter = featureFilters.get(sf.getType());
+    return filter == null ? true : filter.matches(sf);
+  }
+
+  /**
+   * Answers true unless the specified group is set to hidden. Defaults to true
+   * if group visibility is not set.
+   * 
+   * @param group
+   * @return
+   */
+  public boolean isGroupVisible(String group)
+  {
+    if (!featureGroups.containsKey(group))
+    {
+      return true;
+    }
+    return featureGroups.get(group);
   }
 
+  /**
+   * Orders features in render precedence (last in order is last to render, so
+   * displayed on top of other features)
+   * 
+   * @param order
+   */
+  public void orderFeatures(Comparator<String> order)
+  {
+    Arrays.sort(renderOrder, order);
+  }
 }