X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=c58461e052b2752b5a919eecdc888aa197b993d9;hb=ef14d83cfe8ca0bb2271d50d638516cdc90c2b8b;hp=6461748ac607a1813f6f8dfbb9ec6be9cc8571e3;hpb=baa077bd19420018433d78927aad3ad139e47351;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 6461748..c58461e 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -26,11 +26,11 @@ 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;
@@ -49,6 +49,28 @@ import java.util.concurrent.ConcurrentHashMap;
 public abstract class FeatureRendererModel
         implements jalview.api.FeatureRenderer
 {
+  /*
+   * a data bean to hold one row of feature settings from the gui
+   */
+  public static class FeatureSettingsBean
+  {
+    public final String featureType;
+
+    public final FeatureColourI featureColour;
+
+    public final FeatureMatcherSetI filter;
+
+    public final Boolean show;
+
+    public FeatureSettingsBean(String type, FeatureColourI colour,
+            FeatureMatcherSetI theFilter, Boolean isShown)
+    {
+      featureType = type;
+      featureColour = colour;
+      filter = theFilter;
+      show = isShown;
+    }
+  }
 
   /*
    * global transparency for feature
@@ -68,7 +90,7 @@ 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;
 
@@ -169,7 +191,7 @@ 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 +227,7 @@ 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 +306,7 @@ 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 +319,13 @@ 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 +359,7 @@ 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 +372,7 @@ 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 +452,7 @@ public abstract class FeatureRendererModel
      */
     if (minmax == null)
     {
-      minmax = new Hashtable<String, float[][]>();
+      minmax = new Hashtable<>();
     }
     synchronized (minmax)
     {
@@ -463,7 +489,7 @@ 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);
@@ -490,7 +516,8 @@ public abstract class FeatureRendererModel
               if (mmrange != null)
               {
                 FeatureColourI fc = featureColours.get(oldRender[j]);
-                if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
+                if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+                        && !fc.isColourByAttribute())
                 {
                   fc.updateBounds(mmrange[0][0], mmrange[0][1]);
                 }
@@ -520,7 +547,8 @@ public abstract class FeatureRendererModel
         if (mmrange != null)
         {
           FeatureColourI fc = featureColours.get(newf[i]);
-          if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
+          if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+                  && !fc.isColourByAttribute())
           {
             fc.updateBounds(mmrange[0][0], mmrange[0][1]);
           }
@@ -586,7 +614,8 @@ public abstract class FeatureRendererModel
    */
   protected boolean showFeatureOfType(String type)
   {
-    return type == null ? false : av.getFeaturesDisplayed().isVisible(type);
+    return type == null ? false : (av.getFeaturesDisplayed() == null ? true
+            : av.getFeaturesDisplayed().isVisible(type));
   }
 
   @Override
@@ -621,7 +650,7 @@ public abstract class FeatureRendererModel
   {
     if (featureOrder == null)
     {
-      featureOrder = new Hashtable<String, Float>();
+      featureOrder = new Hashtable<>();
     }
     featureOrder.put(type, new Float(position));
     return position;
@@ -655,32 +684,33 @@ public abstract class FeatureRendererModel
    * Replace current ordering with new ordering
    * 
    * @param data
-   *          { String(Type), Colour(Type), Boolean(Displayed) }
+   *          an array of { Type, Colour, Filter, Boolean }
    * @return true if any visible features have been reordered, else false
    */
-  public boolean setFeaturePriority(Object[][] data)
+  public boolean setFeaturePriority(FeatureSettingsBean[] data)
   {
     return setFeaturePriority(data, true);
   }
 
   /**
-   * Sets the priority order for features, with the highest priority (displayed
-   * on top) at the start of the data array
+   * Sets the priority order for features, with the highest priority (displayed on
+   * top) at the start of the data array
    * 
    * @param data
-   *          { String(Type), Colour(Type), Boolean(Displayed) }
+   *          an array of { Type, Colour, Filter, Boolean }
    * @param visibleNew
    *          when true current featureDisplay list will be cleared
-   * @return true if any visible features have been reordered or recoloured,
-   *         else false (i.e. no need to repaint)
+   * @return true if any visible features have been reordered or recoloured, else
+   *         false (i.e. no need to repaint)
    */
-  public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
+  public boolean setFeaturePriority(FeatureSettingsBean[] data,
+          boolean visibleNew)
   {
     /*
      * 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;
@@ -713,9 +743,9 @@ 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].featureType;
+        setColour(type, data[i].featureColour);
+        if (data[i].show)
         {
           av_featuresdisplayed.setVisible(type);
         }
@@ -840,7 +870,7 @@ public abstract class FeatureRendererModel
   {
     if (featureGroups != null)
     {
-      List<String> gp = new ArrayList<String>();
+      List<String> gp = new ArrayList<>();
 
       for (String grp : featureGroups.keySet())
       {
@@ -886,7 +916,7 @@ 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;
@@ -914,7 +944,7 @@ 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)
     {
@@ -935,7 +965,7 @@ 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))
@@ -970,7 +1000,7 @@ 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;
@@ -990,7 +1020,7 @@ public abstract class FeatureRendererModel
   
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf))
+      if (!featureGroupNotShown(sf) && getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -1000,23 +1030,19 @@ public abstract class FeatureRendererModel
 
   /**
    * Removes from the list of features any that duplicate the location of a
-   * feature of the same type (unless feature is filtered out, or a graduated
-   * colour scheme or colour by label is applied). Should be used only for
-   * features of the same feature colour (which normally implies the same
-   * feature type).
+   * 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.
    * 
    * @param features
-   * @param fc
    */
-  public void filterFeaturesForDisplay(List<SequenceFeature> features,
-          FeatureColourI fc)
+  public void filterFeaturesForDisplay(List<SequenceFeature> features)
   {
     if (features.isEmpty())
     {
       return;
     }
     SequenceFeatures.sortFeatures(features, true);
-    boolean simpleColour = fc == null || fc.isSimpleColour();
     SequenceFeature lastFeature = null;
 
     Iterator<SequenceFeature> it = features.iterator();
@@ -1030,40 +1056,37 @@ public abstract class FeatureRendererModel
        * (checking type and isContactFeature as a fail-safe here, although
        * currently they are guaranteed to match in this context)
        */
-      if (simpleColour)
+      if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
+              && sf.getEnd() == lastFeature.getEnd()
+              && sf.isContactFeature() == lastFeature.isContactFeature()
+              && sf.getType().equals(lastFeature.getType()))
       {
-        if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
-                && sf.getEnd() == lastFeature.getEnd()
-                && sf.isContactFeature() == lastFeature.isContactFeature()
-                && sf.getType().equals(lastFeature.getType()))
-        {
-          it.remove();
-        }
+        it.remove();
       }
       lastFeature = sf;
     }
   }
 
   @Override
-  public Map<String, KeyedMatcherSetI> getFeatureFilters()
+  public Map<String, FeatureMatcherSetI> getFeatureFilters()
   {
     return new HashMap<>(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())
     {
@@ -1123,9 +1146,8 @@ 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));
+    FeatureMatcherSetI filter = featureFilters.get(sf.getType());
+    return filter == null ? true : filter.matches(sf);
   }
 
 }