From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 24 Mar 2006 15:35:10 +0000 (+0000)
Subject: FeatureSettings bug fixed
X-Git-Tag: Root_VamJalview_2_07b+~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3cbce9e7df2da375b35afaf989a82b38328e41ae;p=jalview.git

FeatureSettings bug fixed
---

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7e2d1dd..893846c 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -472,8 +472,9 @@ public class Jalview2XML
             setting.setColour(
                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
                 );
+
             setting.setDisplay(
-                av.featuresDisplayed.contains(type)
+                av.featuresDisplayed.containsKey(type)
                 );
 
             fs.addSetting(setting);
@@ -679,12 +680,12 @@ public class Jalview2XML
             Features[] features = JSEQ[i].getFeatures();
             for (int f = 0; f < features.length; f++)
             {
-              //features[f].getBegin()
               jalview.datamodel.SequenceFeature sf
                   = new jalview.datamodel.SequenceFeature(features[f].getType(),
                   features[f].getDescription(), features[f].getStatus(),
-                  features[f].getBegin(), features[f].getEnd());
-              sf.setFeatureGroup(features[f].getFeatureGroup());
+                  features[f].getBegin(), features[f].getEnd(),
+                  features[f].getFeatureGroup());
+
               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
             }
           }
@@ -701,7 +702,8 @@ public class Jalview2XML
 
           }
         }
-        /////////////////////////////////
+
+         /////////////////////////////////
         //////////////////////////////////
         //LOAD ANNOTATIONS
         if (vamsasSet.getAnnotation() != null)
@@ -739,6 +741,7 @@ public class Jalview2XML
             }
         }
 
+
         /////////////////////////////////
         // LOAD VIEWPORT
         Viewport[] views = jms.getViewport();
@@ -805,6 +808,7 @@ public class Jalview2XML
         }
 
 
+
         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
         af.viewport.setStartRes(view.getStartRes());
@@ -889,20 +893,24 @@ public class Jalview2XML
         if(jms.getFeatureSettings()!=null)
         {
           af.viewport.featuresDisplayed = new Hashtable();
-         // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
-         // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+          String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
          {
            Setting setting = jms.getFeatureSettings().getSetting(fs);
 
            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
                new java.awt.Color(setting.getColour()));
+
+           renderOrder[fs] = setting.getType();
+
            if(setting.getDisplay())
              af.viewport.featuresDisplayed.put(
                  setting.getType(), new Integer(setting.getColour()));
          }
+         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
         }
 
+
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());