JAL-2069 spike updated with latest (FeatureTypeSettings)

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index c2f5bb7..4797675 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -49,6 +49,17 @@ import java.util.concurrent.ConcurrentHashMap;
 public abstract class FeatureRendererModel
         implements jalview.api.FeatureRenderer
 {
+  /*
+   * column indices of fields in Feature Settings table
+   * todo: transfer valuers as data beans instead of Object[][]
+   */
+  public static final int TYPE_COLUMN = 0;
+
+  public static final int COLOUR_COLUMN = 1;
+
+  public static final int FILTER_COLUMN = 2;
+
+  public static final int SHOW_COLUMN = 3;
 
   /*
    * global transparency for feature
@@ -169,7 +180,7 @@ public abstract class FeatureRendererModel
     {
       av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
     }
-    List<String> nft = new ArrayList<String>();
+    List<String> nft = new ArrayList<>();
     for (String featureType : featureTypes)
     {
       if (!fdi.isRegistered(featureType))
@@ -205,7 +216,7 @@ public abstract class FeatureRendererModel
     renderOrder = neworder;
   }
 
-  protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+  protected Map<String, float[][]> minmax = new Hashtable<>();
 
   public Map<String, float[][]> getMinMax()
   {
@@ -284,7 +295,7 @@ public abstract class FeatureRendererModel
      * include features at the position provided their feature type is 
      * displayed, and feature group is null or marked for display
      */
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
     if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
     {
       return result;
@@ -297,9 +308,13 @@ public abstract class FeatureRendererModel
     List<SequenceFeature> features = sequence.findFeatures(column, column,
             visibleTypes);
 
+    /*
+     * include features unless their feature group is not displayed, or
+     * they are hidden (have no colour) based on a filter or colour threshold
+     */
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf))
+      if (!featureGroupNotShown(sf) && getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -333,7 +348,7 @@ public abstract class FeatureRendererModel
     }
     FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
 
-    Set<String> oldfeatures = new HashSet<String>();
+    Set<String> oldfeatures = new HashSet<>();
     if (renderOrder != null)
     {
       for (int i = 0; i < renderOrder.length; i++)
@@ -346,7 +361,7 @@ public abstract class FeatureRendererModel
     }
 
     AlignmentI alignment = av.getAlignment();
-    List<String> allfeatures = new ArrayList<String>();
+    List<String> allfeatures = new ArrayList<>();
 
     for (int i = 0; i < alignment.getHeight(); i++)
     {
@@ -426,7 +441,7 @@ public abstract class FeatureRendererModel
      */
     if (minmax == null)
     {
-      minmax = new Hashtable<String, float[][]>();
+      minmax = new Hashtable<>();
     }
     synchronized (minmax)
     {
@@ -463,7 +478,7 @@ public abstract class FeatureRendererModel
    */
   private void updateRenderOrder(List<String> allFeatures)
   {
-    List<String> allfeatures = new ArrayList<String>(allFeatures);
+    List<String> allfeatures = new ArrayList<>(allFeatures);
     String[] oldRender = renderOrder;
     renderOrder = new String[allfeatures.size()];
     boolean initOrders = (featureOrder == null);
@@ -624,7 +639,7 @@ public abstract class FeatureRendererModel
   {
     if (featureOrder == null)
     {
-      featureOrder = new Hashtable<String, Float>();
+      featureOrder = new Hashtable<>();
     }
     featureOrder.put(type, new Float(position));
     return position;
@@ -683,7 +698,7 @@ public abstract class FeatureRendererModel
      * note visible feature ordering and colours before update
      */
     List<String> visibleFeatures = getDisplayedFeatureTypes();
-    Map<String, FeatureColourI> visibleColours = new HashMap<String, FeatureColourI>(
+    Map<String, FeatureColourI> visibleColours = new HashMap<>(
             getFeatureColours());
 
     FeaturesDisplayedI av_featuresdisplayed = null;
@@ -716,9 +731,9 @@ public abstract class FeatureRendererModel
     {
       for (int i = 0; i < data.length; i++)
       {
-        String type = data[i][0].toString();
-        setColour(type, (FeatureColourI) data[i][1]);
-        if (((Boolean) data[i][2]).booleanValue())
+        String type = data[i][TYPE_COLUMN].toString();
+        setColour(type, (FeatureColourI) data[i][COLOUR_COLUMN]);
+        if (((Boolean) data[i][SHOW_COLUMN]).booleanValue())
         {
           av_featuresdisplayed.setVisible(type);
         }
@@ -843,7 +858,7 @@ public abstract class FeatureRendererModel
   {
     if (featureGroups != null)
     {
-      List<String> gp = new ArrayList<String>();
+      List<String> gp = new ArrayList<>();
 
       for (String grp : featureGroups.keySet())
       {
@@ -889,7 +904,7 @@ public abstract class FeatureRendererModel
   @Override
   public Map<String, FeatureColourI> getDisplayedFeatureCols()
   {
-    Map<String, FeatureColourI> fcols = new Hashtable<String, FeatureColourI>();
+    Map<String, FeatureColourI> fcols = new Hashtable<>();
     if (getViewport().getFeaturesDisplayed() == null)
     {
       return fcols;
@@ -917,7 +932,7 @@ public abstract class FeatureRendererModel
   public List<String> getDisplayedFeatureTypes()
   {
     List<String> typ = getRenderOrder();
-    List<String> displayed = new ArrayList<String>();
+    List<String> displayed = new ArrayList<>();
     FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
     if (feature_disp != null)
     {
@@ -938,7 +953,7 @@ public abstract class FeatureRendererModel
   @Override
   public List<String> getDisplayedFeatureGroups()
   {
-    List<String> _gps = new ArrayList<String>();
+    List<String> _gps = new ArrayList<>();
     for (String gp : getFeatureGroups())
     {
       if (checkGroupVisibility(gp, false))
@@ -973,7 +988,7 @@ public abstract class FeatureRendererModel
   public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
           int resNo)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
     if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
     {
       return result;
@@ -993,7 +1008,7 @@ public abstract class FeatureRendererModel
   
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf))
+      if (!featureGroupNotShown(sf) && getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -1120,8 +1135,13 @@ public abstract class FeatureRendererModel
   protected boolean featureMatchesFilters(SequenceFeature sf)
   {
     KeyedMatcherSetI filter = featureFilters.get(sf.getType());
-    return filter == null ? true : filter.matches(key -> sf
-            .getValueAsString(key));
+    // 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)));
   }
 
 }