From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 22 Aug 2005 17:02:36 +0000 (+0000)
Subject: Checks for null colour in groups
X-Git-Tag: Release_2_04~23
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b5002a21fd2bb57e6f93b59e4a8e1f93ed84415f;p=jalview.git

Checks for null colour in groups
---

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a8fb28d..ffa837d 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -294,36 +294,38 @@ public class Jalview2XML
                 groups[i].setStart(sg.getStartRes());
                 groups[i].setEnd(sg.getEndRes());
                 groups[i].setName(sg.getName());
-
-                if (sg.cs.conservationApplied())
+                if(sg.cs!=null)
                 {
-                  groups[i].setConsThreshold(sg.cs.getConservationInc());
+                  if (sg.cs.conservationApplied())
+                  {
+                    groups[i].setConsThreshold(sg.cs.getConservationInc());
 
-                  if (sg.cs instanceof jalview.schemes.UserColourScheme)
+                    if (sg.cs instanceof jalview.schemes.UserColourScheme)
+                    {
+                      groups[i].setColour(SetUserColourScheme(sg.cs,
+                          userColours,
+                          jms));
+                    }
+                    else
+                    {
+                      groups[i].setColour(ColourSchemeProperty.getColourName(sg.
+                          cs));
+                    }
+                  }
+                  else if (sg.cs instanceof jalview.schemes.UserColourScheme)
                   {
                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
-                                                            jms));
+                        jms));
                   }
                   else
                   {
-                    groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
+                    groups[i].setColour(ColourSchemeProperty.getColourName(
+                        sg.cs));
                   }
-                }
 
-               else if (sg.cs instanceof jalview.schemes.UserColourScheme)
-                {
-                    groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
-                            jms));
-                }
-                else
-                {
-                  groups[i].setColour(ColourSchemeProperty.getColourName(
-                      sg.cs));
+                  groups[i].setPidThreshold(sg.cs.getThreshold());
                 }
 
-
-                groups[i].setPidThreshold( sg.cs.getThreshold() );
-
                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
                 groups[i].setDisplayText(sg.getDisplayText());
@@ -363,16 +365,19 @@ public class Jalview2XML
 
         ColourSchemeI cs = av.getGlobalColourScheme();
 
-        if (cs.conservationApplied())
+        if(cs!=null)
         {
+          if (cs.conservationApplied())
+          {
             view.setConsThreshold(cs.getConservationInc());
-            if(cs instanceof jalview.schemes.UserColourScheme)
+            if (cs instanceof jalview.schemes.UserColourScheme)
               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
-        }
+          }
 
-        if (cs instanceof ResidueColourScheme)
-        {
-            view.setPidThreshold( cs.getThreshold() );
+          if (cs instanceof ResidueColourScheme)
+          {
+            view.setPidThreshold(cs.getThreshold());
+          }
         }
 
         view.setConservationSelected(av.getConservationSelected());
@@ -666,8 +671,7 @@ public class Jalview2XML
             }
         }
 
-        Desktop.addInternalFrame(af, view.getTitle(),
-            AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+
         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
         af.viewport.setStartRes(view.getStartRes());
@@ -724,19 +728,20 @@ public class Jalview2XML
                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
             }
 
-           cs.setThreshold(view.getPidThreshold(), true);
-
             if(cs!=null)
+            {
+              cs.setThreshold(view.getPidThreshold(), true);
               cs.setConsensus(af.viewport.vconsensus);
+            }
         }
 
         af.setColourSelected(view.getBgColour());
         af.viewport.setGlobalColourScheme(cs);
         af.viewport.setColourAppliesToAllGroups(false);
-        af.changeColour(af.viewport.getGlobalColourScheme());
-        if (view.getConservationSelected())
+        af.changeColour(cs);
+        if (view.getConservationSelected() && cs!=null)
         {
-          af.viewport.getGlobalColourScheme().setConservationInc(view.getConsThreshold());
+          cs.setConservationInc(view.getConsThreshold());
         }
 
         af.viewport.setColourAppliesToAllGroups(true);
@@ -780,12 +785,18 @@ public class Jalview2XML
                     if (tree.getCurrentTree())
                       af.viewport.setCurrentTree(tp.getTree());
                 }
+
             }
             catch (Exception ex)
             {
                 ex.printStackTrace();
             }
+
         }
+
+        Desktop.addInternalFrame(af, view.getTitle(),
+             AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+
         return af;
     }
 }