Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[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 f8a296f..6235cbe 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -36,6 +36,7 @@ import jalview.binding.Tree;
 import jalview.binding.UserColours;
 import jalview.binding.Viewport;
 import jalview.datamodel.PDBEntry;
+import jalview.io.FileFormat;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.structure.StructureSelectionManager;
@@ -51,8 +52,6 @@ import java.util.Vector;
 import java.util.jar.JarEntry;
 import java.util.jar.JarInputStream;
 
-import javax.swing.JOptionPane;
-
 /**
  * DOCUMENT ME!
  * 
@@ -155,11 +154,11 @@ public class Jalview2XML_V1
 
             System.err.println("Couldn't locate Jalview XML file : " + ex
                     + "\n");
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage("label.couldnt_locate",
                             new String[] { file }), MessageManager
                             .getString("label.url_not_found"),
-                    JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -176,12 +175,12 @@ public class Jalview2XML_V1
           public void run()
           {
 
-            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                     MessageManager.formatMessage(
                             "label.error_loading_file_params", new String[]
                             { file }), MessageManager
                             .getString("label.error_loading_jalview_file"),
-                    JOptionPane.WARNING_MESSAGE);
+                    JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -305,7 +304,7 @@ public class Jalview2XML_V1
 
     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 
-    af.setFileName(file, "Jalview");
+    af.setFileName(file, FileFormat.Jalview);
 
     for (int i = 0; i < JSEQ.length; i++)
     {
@@ -332,15 +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();
@@ -354,13 +348,14 @@ 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()));
 
         if (groups[i].getConsThreshold() != 0)
         {
-          Conservation c = new Conservation("All", 3,
-                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          Conservation c = new Conservation("All", sg.getSequences(null),
+                  0, sg.getWidth() - 1);
           c.calculate();
           c.verdict(false, 25);
           sg.cs.setConservation(c);
@@ -372,8 +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());
@@ -400,23 +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);