X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=b34786472757897c1fcc920118dbfdd0a3d12b22;hb=a575ad65d52a25cbaf25a9a3995bdd981aa50611;hp=428789f871ed2e2b81b2c000eb979806d47d1197;hpb=d69ea8f1997771890b44e4b332a7ca84fe6f0893;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 428789f..b347864 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -80,7 +80,7 @@ public class Jalview2XML_V1
      *
      * @param file DOCUMENT ME!
      */
-    public AlignFrame LoadJalviewAlign(String file)
+    public AlignFrame LoadJalviewAlign(final String file)
     {
 
         jalview.gui.AlignFrame af = null;
@@ -132,39 +132,51 @@ public class Jalview2XML_V1
 
                     object = (JalviewModel) object.unmarshal(in);
 
-                    af = LoadFromObject(object);
+                    af = LoadFromObject(object, file);
                     entryCount++;
                 }
             }
             while (jarentry != null);
         }
-        catch(java.net.UnknownHostException ex)
+        catch (final java.net.UnknownHostException ex)
         {
           ex.printStackTrace();
-          System.err.println("Couldn't locate Jalview XML file : " +
-              ex + "\n");
-           JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                    "Couldn't locate " + file,
-                                    "URL not found",
-                                    JOptionPane.WARNING_MESSAGE);
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
 
+              System.err.println("Couldn't locate Jalview XML file : " +
+                                 ex + "\n");
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                                    "Couldn't locate " + file,
+                                                    "URL not found",
+                                                    JOptionPane.WARNING_MESSAGE);
+            }
+          });
         }
         catch (Exception ex)
         {
           ex.printStackTrace();
-            System.err.println("Exception whilst loading jalview XML file : " +
-                ex + "\n");
-             JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                      "Error loading  " + file,
-                                      "Error loading Jalview file",
-                                      JOptionPane.WARNING_MESSAGE);
+          System.err.println("Exception whilst loading jalview XML file : " +
+                             ex + "\n");
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
 
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  "Error loading  " + file,
+                  "Error loading Jalview file",
+                  JOptionPane.WARNING_MESSAGE);
+            }
+          });
         }
 
         return af;
     }
 
-    AlignFrame LoadFromObject(JalviewModel object)
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -182,7 +194,6 @@ public class Jalview2XML_V1
                     vamsasSeq[i].getSequence());
             jseqs[i].setStart(JSEQ[i].getStart());
             jseqs[i].setEnd(JSEQ[i].getEnd());
-            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
             seqids.add(jseqs[i]);
         }
 
@@ -269,6 +280,17 @@ public class Jalview2XML_V1
 
         AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 
+        af.setFileName(file, "Jalview");
+
+        for (int i = 0; i < JSEQ.length; i++)
+        {
+          af.viewport.setSequenceColour(
+              af.viewport.alignment.getSequenceAt(i),
+              new java.awt.Color(
+                  JSEQ[i].getColour()));
+        }
+
+
 
         //  af.changeColour() );
         /////////////////////////
@@ -336,41 +358,21 @@ public class Jalview2XML_V1
         af.viewport.setStartRes(view.getStartRes());
         af.viewport.setStartSeq(view.getStartSeq());
         af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.viewport.showConservation = view.getShowConservation();
-        af.viewport.showQuality = view.getShowQuality();
-        af.viewport.showIdentity = view.getShowIdentity();
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
-        af.abovePIDThreshold.setSelected(view.getPidSelected());
         af.viewport.setColourText(view.getShowColourText());
-        af.colourTextMenuItem.setSelected(view.getShowColourText());
         af.viewport.setConservationSelected(view.getConservationSelected());
-        af.conservationMenuItem.setSelected(view.getConservationSelected());
-
         af.viewport.setShowJVSuffix(view.getShowFullId());
-        af.seqLimits.setSelected(view.getShowFullId());
-
         af.viewport.setFont(new java.awt.Font(view.getFontName(),
                 view.getFontStyle(), view.getFontSize()));
         af.alignPanel.fontChanged();
 
         af.viewport.setRenderGaps(view.getRenderGaps());
-        af.renderGapsMenuItem.setSelected(view.getRenderGaps());
-
         af.viewport.setWrapAlignment(view.getWrapAlignment());
-        af.wrapMenuItem.setSelected(view.getWrapAlignment());
-
-
         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-
-        af.annotationPanelMenuItem.setState(view.getShowAnnotation());
         af.viewport.setShowAnnotation(view.getShowAnnotation());
         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-
-
         af.viewport.setShowBoxes(view.getShowBoxes());
-        af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
         af.viewport.setShowText(view.getShowText());
-        af.viewTextMenuItem.setSelected(view.getShowText());
 
         ColourSchemeI cs = null;
 
@@ -392,7 +394,6 @@ public class Jalview2XML_V1
             }
         }
 
-        af.setColourSelected(view.getBgColour());
         af.viewport.setGlobalColourScheme(cs);
         af.viewport.setColourAppliesToAllGroups(false);
         af.changeColour(cs);
@@ -402,12 +403,8 @@ public class Jalview2XML_V1
         }
 
         af.viewport.setColourAppliesToAllGroups(true);
+        af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 
-        if (view.getShowSequenceFeatures())
-        {
-           af.viewport.showSequenceFeatures = true;
-           af.showSeqFeatures.setSelected(true);
-        }
 
         if(jms.getFeatureSettings()!=null)
         {
@@ -429,6 +426,7 @@ public class Jalview2XML_V1
          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
         }
 
+        af.setMenusFromViewport(af.viewport);
 
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());