X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=cc2f63603ca65e00662471670e64ae927ec626ed;hb=c3d92b4b7a6cb00f9e596dbb7cd6c8508da5c252;hp=aefc233db286d963a1e691ca96703df912a40637;hpb=320c96aed11f5c396a9efd9ea83b0e35f05e21e4;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index aefc233..cc2f636 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -52,8 +52,6 @@ import java.util.Vector;
 import java.util.jar.JarEntry;
 import java.util.jar.JarInputStream;
 
-import javax.swing.JOptionPane;
-
 /**
  * DOCUMENT ME!
  * 
@@ -335,13 +333,8 @@ public class Jalview2XML_V1
           {
             cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
           }
-
-          if (cs != null)
-          {
-            cs.setThreshold(groups[i].getPidThreshold(), true);
-          }
-
         }
+        int pidThreshold = groups[i].getPidThreshold();
 
         Vector seqs = new Vector();
         int[] ids = groups[i].getSeq();
@@ -355,6 +348,7 @@ public class Jalview2XML_V1
                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
                 groups[i].getDisplayText(), groups[i].getColourText(),
                 groups[i].getStart(), groups[i].getEnd());
+        sg.getGroupColourScheme().setThreshold(pidThreshold, true);
 
         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 
@@ -373,8 +367,8 @@ public class Jalview2XML_V1
 
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+    af.viewport.getRanges().setStartSeq(view.getStartSeq());
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
     af.viewport.setColourText(view.getShowColourText());
@@ -404,20 +398,24 @@ public class Jalview2XML_V1
         cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
 
-      if (cs != null)
-      {
-        cs.setThreshold(view.getPidThreshold(), true);
-        cs.setConsensus(af.viewport.getSequenceConsensusHash());
-      }
+      // if (cs != null)
+      // {
+      // cs.setThreshold(view.getPidThreshold(), true);
+      // cs.setConsensus(af.viewport.getSequenceConsensusHash());
+      // }
     }
 
-    af.viewport.setGlobalColourScheme(cs);
+    af.viewport.getResidueShading().setThreshold(
+            view.getPidThreshold(), true);
+    af.viewport.getResidueShading().setConsensus(
+            af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);
     af.alignPanel.updateLayout();
     af.changeColour(cs);
     if (view.getConservationSelected() && cs != null)
     {
-      cs.setConservationInc(view.getConsThreshold());
+      af.viewport.getResidueShading().setConservationInc(
+              view.getConsThreshold());
     }
 
     af.viewport.setColourAppliesToAllGroups(true);
@@ -466,7 +464,7 @@ public class Jalview2XML_V1
 
           Tree tree = jms.getTree(t);
 
-          TreePanel tp = af.ShowNewickTree(
+          TreePanel tp = af.showNewickTree(
                   new jalview.io.NewickFile(tree.getNewick()),
                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
                   tree.getXpos(), tree.getYpos());