X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=4af6fde9b5b06282edd98ad524a9b6d4d286e028;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=2f30e9463a994ed8c7ad9d7eaa9b6260932551dc;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 2f30e94..4af6fde 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -26,6 +26,7 @@ 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;
@@ -48,15 +49,48 @@ 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
    */
   protected float transparency = 1.0f;
 
-  protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<String, FeatureColourI>();
+  /*
+   * colour scheme for each feature type
+   */
+  protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<>();
+
+  /*
+   * visibility flag for each feature group
+   */
+  protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<>();
 
-  protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
+  /*
+   * filters for each feature type
+   */
+  protected Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
 
   protected String[] renderOrder;
 
@@ -100,6 +134,7 @@ public abstract class FeatureRendererModel
     this.renderOrder = frs.renderOrder;
     this.featureGroups = frs.featureGroups;
     this.featureColours = frs.featureColours;
+    this.featureFilters = frs.featureFilters;
     this.transparency = frs.transparency;
     this.featureOrder = frs.featureOrder;
     if (av != null && av != fr.getViewport())
@@ -156,7 +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))
@@ -192,7 +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()
   {
@@ -271,7 +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;
@@ -284,9 +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);
       }
@@ -320,7 +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++)
@@ -333,7 +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++)
     {
@@ -413,7 +452,7 @@ public abstract class FeatureRendererModel
      */
     if (minmax == null)
     {
-      minmax = new Hashtable<String, float[][]>();
+      minmax = new Hashtable<>();
     }
     synchronized (minmax)
     {
@@ -450,7 +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);
@@ -477,7 +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]);
                 }
@@ -507,7 +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]);
           }
@@ -557,20 +598,11 @@ public abstract class FeatureRendererModel
     return fc;
   }
 
-  /**
-   * Returns the configured colour for a particular feature instance. This
-   * includes calculation of 'colour by label', or of a graduated score colour,
-   * if applicable. It does not take into account feature visibility or colour
-   * transparency. Returns null for a score feature whose score value lies
-   * outside any colour threshold.
-   * 
-   * @param feature
-   * @return
-   */
+  @Override
   public Color getColour(SequenceFeature feature)
   {
     FeatureColourI fc = getFeatureStyle(feature.getType());
-    return fc.getColor(feature);
+    return getColor(feature, fc);
   }
 
   /**
@@ -582,7 +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
@@ -617,7 +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;
@@ -651,32 +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;
@@ -709,9 +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);
         }
@@ -836,7 +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())
       {
@@ -882,7 +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;
@@ -910,7 +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)
     {
@@ -931,7 +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))
@@ -966,7 +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;
@@ -986,7 +1020,7 @@ public abstract class FeatureRendererModel
   
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf))
+      if (!featureGroupNotShown(sf) && getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -995,24 +1029,28 @@ public abstract class FeatureRendererModel
   }
 
   /**
-   * Removes from the list of features any that have a feature group that is not
-   * displayed, or duplicate the location of a feature of the same type (unless
-   * 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).
+   * Removes from the list of features any whose group is not shown, or that are
+   * visible and duplicate the location of a visible feature of the same type.
+   * Should be used only for features of the same, simple, feature colour (which
+   * normally implies the same feature type). No filtering is done if
+   * transparency, or any feature filters, are in force.
    * 
    * @param features
-   * @param fc
    */
-  public void filterFeaturesForDisplay(List<SequenceFeature> features,
-          FeatureColourI fc)
+  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);
-    boolean simpleColour = fc == null || fc.isSimpleColour();
     SequenceFeature lastFeature = null;
 
     Iterator<SequenceFeature> it = features.iterator();
@@ -1031,18 +1069,119 @@ 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, FeatureMatcherSetI> getFeatureFilters()
+  {
+    return featureFilters;
+  }
+
+  @Override
+  public void setFeatureFilters(Map<String, FeatureMatcherSetI> filters)
+  {
+    featureFilters = filters;
+  }
+
+  @Override
+  public FeatureMatcherSetI getFeatureFilter(String featureType)
+  {
+    return featureFilters.get(featureType);
+  }
+
+  @Override
+  public void setFeatureFilter(String featureType, FeatureMatcherSetI filter)
+  {
+    if (filter == null || filter.isEmpty())
+    {
+      featureFilters.remove(featureType);
+    }
+    else
+    {
+      featureFilters.put(featureType, filter);
+    }
+  }
+
+  /**
+   * Answers the colour for the feature, or null if the feature is excluded by
+   * feature group visibility, by filters, or by colour threshold settings. This
+   * method does not take feature visibility into account.
+   * 
+   * @param sf
+   * @param fc
+   * @return
+   */
+  public Color getColor(SequenceFeature sf, FeatureColourI fc)
+  {
+    /*
+     * is the feature group displayed?
+     */
+    if (featureGroupNotShown(sf))
+    {
+      return null;
+    }
+
+    /*
+     * does the feature pass filters?
+     */
+    if (!featureMatchesFilters(sf))
+    {
+      return null;
+    }
+  
+    return fc.getColor(sf);
+  }
+
+  /**
+   * Answers true if there no are filters defined for the feature type, or this
+   * feature matches the filters. Answers false if the feature fails to match
+   * filters.
+   * 
+   * @param sf
+   * @return
+   */
+  protected boolean featureMatchesFilters(SequenceFeature sf)
+  {
+    FeatureMatcherSetI filter = featureFilters.get(sf.getType());
+    return filter == null ? true : filter.matches(sf);
+  }
+
+  @Override
+  public boolean isVisible(SequenceFeature feature)
+  {
+    if (feature == null)
+    {
+      return false;
+    }
+    if (getFeaturesDisplayed() == null
+            || !getFeaturesDisplayed().isVisible(feature.getType()))
+    {
+      return false;
+    }
+    if (featureGroupNotShown(feature))
+    {
+      return false;
+    }
+    FeatureColourI fc = featureColours.get(feature.getType());
+    if (fc != null && fc.isOutwithThreshold(feature))
+    {
+      return false;
+    }
+    if (!featureMatchesFilters(feature))
+    {
+      return false;
+    }
+    return true;
+  }
+
 }