X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererSettings.java;h=f594453a964eb1c320c9681e6f90457516f95c98;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=ed867f33c61fd502878ad2562a928f9c0308b4c3;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
index ed867f3..f594453 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererSettings.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,12 @@
  */
 package jalview.viewmodel.seqfeatures;
 
-import jalview.schemes.GraduatedColor;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.schemes.FeatureColour;
 
 import java.util.Arrays;
-import java.util.Hashtable;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
@@ -32,24 +34,38 @@ public class FeatureRendererSettings implements Cloneable
 {
   String[] renderOrder;
 
-  Map featureGroups;
+  /*
+   * map of {groupName, isDisplayed}
+   */
+  Map<String, Boolean> featureGroups;
 
-  Map featureColours;
+  /*
+   * map of {featureType, colourScheme}
+   */
+  Map<String, FeatureColourI> featureColours;
+
+  /*
+   * map of {featureType, filters}
+   */
+  Map<String, FeatureMatcherSetI> featureFilters;
 
   float transparency;
 
-  Map featureOrder;
+  Map<String, Float> featureOrder;
 
   public FeatureRendererSettings(String[] renderOrder,
-          Hashtable featureGroups, Hashtable featureColours,
-          float transparency, Hashtable featureOrder)
+          Map<String, Boolean> featureGroups,
+          Map<String, FeatureColourI> featureColours, float transparency,
+          Map<String, Float> featureOrder)
   {
     super();
     this.renderOrder = Arrays.copyOf(renderOrder, renderOrder.length);
-    this.featureGroups = new ConcurrentHashMap(featureGroups);
-    this.featureColours = new ConcurrentHashMap(featureColours);
+    this.featureGroups = new ConcurrentHashMap<String, Boolean>(
+            featureGroups);
+    this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
+            featureColours);
     this.transparency = transparency;
-    this.featureOrder = new ConcurrentHashMap(featureOrder);
+    this.featureOrder = new ConcurrentHashMap<String, Float>(featureOrder);
   }
 
   /**
@@ -61,9 +77,11 @@ public class FeatureRendererSettings implements Cloneable
           jalview.viewmodel.seqfeatures.FeatureRendererModel fr)
   {
     renderOrder = null;
-    featureGroups = new ConcurrentHashMap();
-    featureColours = new ConcurrentHashMap();
-    featureOrder = new ConcurrentHashMap();
+    featureGroups = new ConcurrentHashMap<String, Boolean>();
+    featureColours = new ConcurrentHashMap<String, FeatureColourI>();
+    featureFilters = new HashMap<>();
+    featureOrder = new ConcurrentHashMap<String, Float>();
+
     if (fr.renderOrder != null)
     {
       this.renderOrder = new String[fr.renderOrder.length];
@@ -72,26 +90,36 @@ public class FeatureRendererSettings implements Cloneable
     }
     if (fr.featureGroups != null)
     {
-      this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
+      this.featureGroups = new ConcurrentHashMap<String, Boolean>(
+              fr.featureGroups);
     }
     if (fr.featureColours != null)
     {
-      this.featureColours = new ConcurrentHashMap(fr.featureColours);
+      this.featureColours = new ConcurrentHashMap<String, FeatureColourI>(
+              fr.featureColours);
     }
-    Iterator en = fr.featureColours.keySet().iterator();
+    Iterator<String> en = fr.featureColours.keySet().iterator();
     while (en.hasNext())
     {
-      Object next = en.next();
-      Object val = featureColours.get(next);
-      if (val instanceof GraduatedColor)
+      String next = en.next();
+      FeatureColourI val = featureColours.get(next);
+      // if (val instanceof GraduatedColor)
+      if (val.isGraduatedColour() || val.isColourByLabel()) // why this test?
       {
-        featureColours.put(next, new GraduatedColor((GraduatedColor) val));
+        featureColours.put(next, new FeatureColour((FeatureColour) val));
       }
     }
+
+    if (fr.featureFilters != null)
+    {
+      this.featureFilters.putAll(fr.featureFilters);
+    }
+
     this.transparency = fr.transparency;
     if (fr.featureOrder != null)
     {
-      this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
+      this.featureOrder = new ConcurrentHashMap<String, Float>(
+              fr.featureOrder);
     }
   }
 }