From bbc6f9aa881165c33675ca77489bef93d1505345 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 14:42:27 +0000
Subject: [PATCH] Place new feature on top of existing features

---
 src/jalview/appletgui/FeatureRenderer.java |   52 +++++++++++++++++-----------
 1 file changed, 31 insertions(+), 21 deletions(-)

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index b36fbfd..1061efd 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -88,14 +88,6 @@ public class FeatureRenderer
   static String lastFeatureGroupAdded;
   static String lastDescriptionAdded;
 
-  public boolean createNewFeatures(SequenceI[] sequences,
-                                   SequenceFeature[] features,
-      AlignmentPanel ap)
-  {
-    return amendFeatures(sequences, features, true, ap);
-  }
-
-
   int featureIndex = 0;
   boolean deleteFeature = false;
   Panel colourPanel;
@@ -370,8 +362,6 @@ public class FeatureRenderer
           featureGroups = new Hashtable();
         }
 
-
-
         col = colourPanel.getBackground();
         setColour(lastFeatureAdded, col);
 
@@ -383,6 +373,11 @@ public class FeatureRenderer
         }
         findAllFeatures();
 
+        String [] tro = new String[renderOrder.length];
+        tro[0] = renderOrder[renderOrder.length-1];
+        System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);
+        renderOrder = tro;
+
         return true;
       }
       else
@@ -677,21 +672,19 @@ public class FeatureRenderer
 
   public Color getColour(String featureType)
   {
-    return (Color) featureColours.get(featureType);
-  }
-
-  public void addNewFeature(String name, Color col)
-  {
-
-    setColour(name, col);
-    if (av.featuresDisplayed == null)
+    if (!featureColours.containsKey(featureType))
     {
-      av.featuresDisplayed = new Hashtable();
+      jalview.schemes.UserColourScheme ucs = new
+          jalview.schemes.UserColourScheme();
+      Color col = ucs.createColourFromName(featureType);
+      featureColours.put(featureType, col);
+      return col;
     }
-
-    av.featuresDisplayed.put(name, "NOGROUP");
+    else
+      return (Color) featureColours.get(featureType);
   }
 
+
   public void setColour(String featureType, Color col)
   {
     featureColours.put(featureType, col);
@@ -707,6 +700,23 @@ public class FeatureRenderer
       av.featuresDisplayed.clear();
     }
 
+   /* if (visibleNew)
+    {
+      if (av.featuresDisplayed != null)
+      {
+        av.featuresDisplayed.clear();
+      }
+      else
+      {
+        av.featuresDisplayed = new Hashtable();
+      }
+    }
+    if (data == null)
+    {
+      return;
+    }*/
+
+
     renderOrder = new String[data.length];
 
     if (data.length > 0)
-- 
1.7.10.2