Merge remote-tracking branch 'origin/develop' into features/JAL-2316

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 52f61b1..e751a2c 100755 (executable)
--- 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!
  * 
@@ -333,15 +331,10 @@ public class Jalview2XML_V1
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
-          }
-
-          if (cs != null)
-          {
-            cs.setThreshold(groups[i].getPidThreshold(), true);
+            cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
           }
-
         }
+        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()));
 
@@ -401,23 +395,27 @@ public class Jalview2XML_V1
       }
       else
       {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+        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);