From 7c12f8eb9879172c5c437143ca5eb811a8daf5c7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Feb 2006 11:44:02 +0000
Subject: [PATCH] Features now an array

---
 src/jalview/gui/Jalview2XML.java |   32 +++++++++++++++++---------------
 1 file changed, 17 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e387967..7e2d1dd 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -195,20 +195,21 @@ public class Jalview2XML
 
             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
             {
-              Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements();
-              while(en.hasMoreElements())
+              jalview.datamodel.SequenceFeature[] sf
+                  = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+              int index = 0;
+              while(index < sf.length)
               {
                 Features features = new Features();
-                jalview.datamodel.SequenceFeature sf
-                   = (jalview.datamodel.SequenceFeature)en.nextElement();
-
-                features.setBegin(sf.getBegin());
-                features.setEnd(sf.getEnd());
-                features.setDescription(sf.getDescription());
-                features.setStatus(sf.getStatus());
-                features.setType(sf.getType());
-                features.setFeatureGroup(sf.getFeatureGroup());
+
+                features.setBegin(sf[index].getBegin());
+                features.setEnd(sf[index].getEnd());
+                features.setDescription(sf[index].getDescription());
+                features.setStatus(sf[index].getStatus());
+                features.setType(sf[index].getType());
+                features.setFeatureGroup(sf[index].getFeatureGroup());
                 jseq.addFeatures(features);
+                index ++;
               }
             }
 
@@ -458,7 +459,7 @@ public class Jalview2XML
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
 
-        if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
+        if(av.featuresDisplayed!=null)
         {
           jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
 
@@ -472,7 +473,7 @@ public class Jalview2XML
                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
                 );
             setting.setDisplay(
-                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type)
+                av.featuresDisplayed.contains(type)
                 );
 
             fs.addSetting(setting);
@@ -887,7 +888,7 @@ public class Jalview2XML
 
         if(jms.getFeatureSettings()!=null)
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector();
+          af.viewport.featuresDisplayed = new Hashtable();
          // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
          // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
@@ -897,7 +898,8 @@ public class Jalview2XML
            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
                new java.awt.Color(setting.getColour()));
            if(setting.getDisplay())
-             af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.addElement(setting.getType());
+             af.viewport.featuresDisplayed.put(
+                 setting.getType(), new Integer(setting.getColour()));
          }
         }
 
-- 
1.7.10.2