X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=02b405ed0816b268c9f34772234458a5cbccd3a8;hb=b6c3048d27b10617873e6fd70fc73cff259de28f;hp=f772cf56f086b74f7f1e675751cdbd194eeac0c0;hpb=116f357c7b1056f7c20dd0f7ecbcb50ea50e4e72;p=jalview.git

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index f772cf5..02b405e 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -3859,7 +3859,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColourScheme(al,
+            cs = ColourSchemeProperty.getColourScheme(null, al,
                     jGroup.getColour());
           }
         }
@@ -4187,10 +4187,8 @@ public class Jalview2XML
           // TODO: verify 'associate with all views' works still
           tp.getTreeCanvas().setViewport(av); // af.viewport;
           tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
-          // FIXME: should we use safeBoolean here ?
-          tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
         }
+        tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
         if (tp == null)
         {
           warn("There was a problem recovering stored Newick tree: \n"
@@ -4973,25 +4971,27 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+                view.getBgColour());
       }
     }
 
+    /*
+     * turn off 'alignment colour applies to all groups'
+     * while restoring global colour scheme
+     */
+    viewport.setColourAppliesToAllGroups(false);
     viewport.setGlobalColourScheme(cs);
     viewport.getResidueShading().setThreshold(pidThreshold,
             view.isIgnoreGapsinConsensus());
     viewport.getResidueShading()
             .setConsensus(viewport.getSequenceConsensusHash());
-    viewport.setColourAppliesToAllGroups(false);
-
     if (safeBoolean(view.isConservationSelected()) && cs != null)
     {
       viewport.getResidueShading()
               .setConservationInc(safeInt(view.getConsThreshold()));
     }
-
     af.changeColour(cs);
-
     viewport.setColourAppliesToAllGroups(true);
 
     viewport
@@ -5067,7 +5067,8 @@ public class Jalview2XML
           float min = safeFloat(safeFloat(setting.getMin()));
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
-          FeatureColourI gc = new FeatureColour(minColour, maxColour,
+          FeatureColourI gc = new FeatureColour(maxColour, minColour,
+                  maxColour,
                   noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
@@ -5269,7 +5270,7 @@ public class Jalview2XML
     else
     {
       cs = new AnnotationColourGradient(matchedAnnotation,
-              ColourSchemeProperty.getColourScheme(al,
+              ColourSchemeProperty.getColourScheme(af.getViewport(), al,
                       viewAnnColour.getColourScheme()),
               safeInt(viewAnnColour.getAboveThreshold()));
     }
@@ -6562,7 +6563,7 @@ public class Jalview2XML
         noValueColour = maxcol;
       }
   
-      colour = new FeatureColour(mincol, maxcol, noValueColour,
+      colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
               safeFloat(colourModel.getMin()),
               safeFloat(colourModel.getMax()));
       final List<String> attributeName = colourModel.getAttributeName();