X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=a8fb28dfe4c1e567eb5a946dbddfedb16a328e9b;hb=95a46891288f4fc63d690cab4f56879678f54fb6;hp=44ff2ad943e9f19309353e4ef169091faa69c293;hpb=1ee8b306b296ea2724e128f66486675bdaac7a3d;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 44ff2ad..a8fb28d 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -134,6 +134,7 @@ public class Jalview2XML
         }
         catch (Exception ex)
         {
+          ex.printStackTrace();
         }
     }
 
@@ -199,38 +200,42 @@ public class Jalview2XML
         ///////////////////////////////////
         if (af.viewport.currentTree != null)
         {
-            // FIND ANY ASSOCIATED TREES
+          // FIND ANY ASSOCIATED TREES
+          // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+          if (Desktop.desktop != null)
+          {
             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
             for (int t = 0; t < frames.length; t++)
             {
-                if (frames[t] instanceof TreePanel)
-                {
-                    TreePanel tp = (TreePanel) frames[t];
+              if (frames[t] instanceof TreePanel)
+              {
+                TreePanel tp = (TreePanel) frames[t];
 
-                    if (tp.treeCanvas.av.alignment == jal)
-                    {
-                        Tree tree = new Tree();
-                        tree.setTitle(tp.getTitle());
-                        tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
-                        tree.setNewick(tp.getTree().toString());
-                        tree.setThreshold(tp.treeCanvas.threshold);
-
-                        tree.setFitToWindow(tp.fitToWindow.getState());
-                        tree.setFontSize(tp.treeCanvas.fontSize);
-                        tree.setMarkUnlinked(tp.placeholdersMenu.getState());
-                        tree.setShowBootstrap(tp.bootstrapMenu.getState());
-                        tree.setShowDistances(tp.distanceMenu.getState());
-
-                        tree.setHeight(tp.getHeight());
-                        tree.setWidth(tp.getWidth());
-                        tree.setXpos(tp.getX());
-                        tree.setYpos(tp.getY());
-
-                        jms.addTree(tree);
-                    }
+                if (tp.treeCanvas.av.alignment == jal)
+                {
+                  Tree tree = new Tree();
+                  tree.setTitle(tp.getTitle());
+                  tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
+                  tree.setNewick(tp.getTree().toString());
+                  tree.setThreshold(tp.treeCanvas.threshold);
+
+                  tree.setFitToWindow(tp.fitToWindow.getState());
+                  tree.setFontSize(tp.treeCanvas.fontSize);
+                  tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+                  tree.setShowBootstrap(tp.bootstrapMenu.getState());
+                  tree.setShowDistances(tp.distanceMenu.getState());
+
+                  tree.setHeight(tp.getHeight());
+                  tree.setWidth(tp.getWidth());
+                  tree.setXpos(tp.getX());
+                  tree.setYpos(tp.getY());
+
+                  jms.addTree(tree);
                 }
+              }
             }
+          }
         }
 
         //SAVE ANNOTATIONS
@@ -290,31 +295,35 @@ public class Jalview2XML
                 groups[i].setEnd(sg.getEndRes());
                 groups[i].setName(sg.getName());
 
-                if (sg.cs instanceof ConservationColourScheme)
+                if (sg.cs.conservationApplied())
                 {
-                    groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc);
-                }
+                  groups[i].setConsThreshold(sg.cs.getConservationInc());
 
-                if (sg.cs instanceof ResidueColourScheme)
-                {
-                    groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold());
-                }
-                else if (sg.cs instanceof ScoreColourScheme)
-                {
-                    groups[i].setPidThreshold(((ScoreColourScheme) sg.cs).getThreshold());
+                  if (sg.cs instanceof jalview.schemes.UserColourScheme)
+                  {
+                    groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+                                                            jms));
+                  }
+                  else
+                  {
+                    groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
+                  }
                 }
 
-                if (sg.cs instanceof jalview.schemes.UserColourScheme)
+               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].setColour(ColourSchemeProperty.getColourName(
+                      sg.cs));
                 }
 
+
+                groups[i].setPidThreshold( sg.cs.getThreshold() );
+
                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
                 groups[i].setDisplayText(sg.getDisplayText());
@@ -354,23 +363,21 @@ public class Jalview2XML
 
         ColourSchemeI cs = av.getGlobalColourScheme();
 
-        if (cs instanceof ConservationColourScheme)
+        if (cs.conservationApplied())
         {
-            view.setConsThreshold(((ConservationColourScheme) cs).inc);
+            view.setConsThreshold(cs.getConservationInc());
+            if(cs instanceof jalview.schemes.UserColourScheme)
+              view.setBgColour(SetUserColourScheme(cs, userColours, jms));
         }
 
         if (cs instanceof ResidueColourScheme)
         {
-            view.setPidThreshold(((ResidueColourScheme) cs).getThreshold());
-        }
-        else if (cs instanceof ScoreColourScheme)
-        {
-            view.setPidThreshold(((ScoreColourScheme) cs).getThreshold());
+            view.setPidThreshold( cs.getThreshold() );
         }
 
         view.setConservationSelected(av.getConservationSelected());
         view.setPidSelected(av.getAbovePIDThreshold());
-        view.setFontName(av.font.getFontName());
+        view.setFontName(av.font.getName());
         view.setFontSize(av.font.getSize());
         view.setFontStyle(av.font.getStyle());
         view.setRenderGaps(av.renderGaps);
@@ -518,6 +525,7 @@ public class Jalview2XML
         }
         catch (Exception ex)
         {
+          ex.printStackTrace();
             System.err.println("Exception whilst loading jalview XML file : " +
                 ex + "\n");
              JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -624,14 +632,7 @@ public class Jalview2XML
                                 groups[i].getColour());
                     }
 
-                    if (cs instanceof ResidueColourScheme)
-                    {
-                        ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
-                    }
-                    else if (cs instanceof ScoreColourScheme)
-                    {
-                        ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
-                    }
+                    cs.setThreshold(groups[i].getPidThreshold(), true);
                 }
 
                 Vector seqs = new Vector();
@@ -658,8 +659,7 @@ public class Jalview2XML
                             sg.getWidth() - 1);
                     c.calculate();
                     c.verdict(false, 25);
-                    cs = new ConservationColourScheme(c, cs);
-                    sg.cs = cs;
+                    sg.cs.setConservation(c);
                 }
 
                 al.addGroup(sg);
@@ -724,25 +724,21 @@ public class Jalview2XML
                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
             }
 
-            if (cs instanceof ConservationColourScheme)
-            {
-                ((ConservationColourScheme) cs).inc = view.getConsThreshold();
-            }
+           cs.setThreshold(view.getPidThreshold(), true);
 
-            if (cs instanceof ResidueColourScheme)
-            {
-                ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
-            }
-            else if (cs instanceof ScoreColourScheme)
-            {
-                ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
-            }
+            if(cs!=null)
+              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.viewport.getGlobalColourScheme().setConservationInc(view.getConsThreshold());
+        }
+
         af.viewport.setColourAppliesToAllGroups(true);
 
         if (view.getShowSequenceFeatures())