boolean for internal copies

[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 8bce1e8..393b192 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -20,8 +20,6 @@ package jalview.gui;
 \r
 import jalview.schemes.*;\r
 \r
-import jalview.gui.*;\r
-\r
 import java.io.*;\r
 \r
 import java.net.*;\r
@@ -80,7 +78,7 @@ public class Jalview2XML_V1
      *\r
      * @param file DOCUMENT ME!\r
      */\r
-    public AlignFrame LoadJalviewAlign(String file)\r
+    public AlignFrame LoadJalviewAlign(final String file)\r
     {\r
 \r
         jalview.gui.AlignFrame af = null;\r
@@ -132,39 +130,51 @@ public class Jalview2XML_V1
 \r
                     object = (JalviewModel) object.unmarshal(in);\r
 \r
-                    af = LoadFromObject(object);\r
+                    af = LoadFromObject(object, file);\r
                     entryCount++;\r
                 }\r
             }\r
             while (jarentry != null);\r
         }\r
-        catch(java.net.UnknownHostException ex)\r
+        catch (final java.net.UnknownHostException ex)\r
         {\r
           ex.printStackTrace();\r
-          System.err.println("Couldn't locate Jalview XML file : " +\r
-              ex + "\n");\r
-           JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                                    "Couldn't locate " + file,\r
-                                    "URL not found",\r
-                                    JOptionPane.WARNING_MESSAGE);\r
+          javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+          {\r
+            public void run()\r
+            {\r
 \r
+              System.err.println("Couldn't locate Jalview XML file : " +\r
+                                 ex + "\n");\r
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                                                    "Couldn't locate " + file,\r
+                                                    "URL not found",\r
+                                                    JOptionPane.WARNING_MESSAGE);\r
+            }\r
+          });\r
         }\r
         catch (Exception ex)\r
         {\r
           ex.printStackTrace();\r
-            System.err.println("Exception whilst loading jalview XML file : " +\r
-                ex + "\n");\r
-             JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
-                                      "Error loading  " + file,\r
-                                      "Error loading Jalview file",\r
-                                      JOptionPane.WARNING_MESSAGE);\r
+          System.err.println("Exception whilst loading jalview XML file : " +\r
+                             ex + "\n");\r
+          javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+          {\r
+            public void run()\r
+            {\r
 \r
+              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+                  "Error loading  " + file,\r
+                  "Error loading Jalview file",\r
+                  JOptionPane.WARNING_MESSAGE);\r
+            }\r
+          });\r
         }\r
 \r
         return af;\r
     }\r
 \r
-    AlignFrame LoadFromObject(JalviewModel object)\r
+    AlignFrame LoadFromObject(JalviewModel object, String file)\r
     {\r
         Vector seqids = new Vector();\r
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
@@ -182,7 +192,6 @@ public class Jalview2XML_V1
                     vamsasSeq[i].getSequence());\r
             jseqs[i].setStart(JSEQ[i].getStart());\r
             jseqs[i].setEnd(JSEQ[i].getEnd());\r
-            jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
             seqids.add(jseqs[i]);\r
         }\r
 \r
@@ -267,7 +276,18 @@ public class Jalview2XML_V1
         Viewport[] views = jms.getViewport();\r
         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 \r
-        AlignFrame af = new AlignFrame(al);\r
+        AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
+\r
+        af.setFileName(file, "Jalview");\r
+\r
+        for (int i = 0; i < JSEQ.length; i++)\r
+        {\r
+          af.viewport.setSequenceColour(\r
+              af.viewport.alignment.getSequenceAt(i),\r
+              new java.awt.Color(\r
+                  JSEQ[i].getColour()));\r
+        }\r
+\r
 \r
 \r
         //  af.changeColour() );\r
@@ -318,7 +338,7 @@ public class Jalview2XML_V1
                 if (groups[i].getConsThreshold() != 0)\r
                 {\r
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
-                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
+                            ResidueProperties.propHash, 3, sg.getSequences(null), 0,\r
                             sg.getWidth() - 1);\r
                     c.calculate();\r
                     c.verdict(false, 25);\r
@@ -336,41 +356,21 @@ public class Jalview2XML_V1
         af.viewport.setStartRes(view.getStartRes());\r
         af.viewport.setStartSeq(view.getStartSeq());\r
         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
-        af.viewport.showConservation = view.getShowConservation();\r
-        af.viewport.showQuality = view.getShowQuality();\r
-        af.viewport.showIdentity = view.getShowIdentity();\r
         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
-        af.abovePIDThreshold.setSelected(view.getPidSelected());\r
         af.viewport.setColourText(view.getShowColourText());\r
-        af.colourTextMenuItem.setSelected(view.getShowColourText());\r
         af.viewport.setConservationSelected(view.getConservationSelected());\r
-        af.conservationMenuItem.setSelected(view.getConservationSelected());\r
-\r
         af.viewport.setShowJVSuffix(view.getShowFullId());\r
-        af.seqLimits.setSelected(view.getShowFullId());\r
-\r
         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
                 view.getFontStyle(), view.getFontSize()));\r
         af.alignPanel.fontChanged();\r
 \r
         af.viewport.setRenderGaps(view.getRenderGaps());\r
-        af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
-\r
         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
-        af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
-\r
-\r
         af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
-\r
-        af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
-\r
-\r
         af.viewport.setShowBoxes(view.getShowBoxes());\r
-        af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
         af.viewport.setShowText(view.getShowText());\r
-        af.viewTextMenuItem.setSelected(view.getShowText());\r
 \r
         ColourSchemeI cs = null;\r
 \r
@@ -388,11 +388,10 @@ public class Jalview2XML_V1
             if(cs!=null)\r
             {\r
               cs.setThreshold(view.getPidThreshold(), true);\r
-              cs.setConsensus(af.viewport.vconsensus);\r
+              cs.setConsensus(af.viewport.hconsensus);\r
             }\r
         }\r
 \r
-        af.setColourSelected(view.getBgColour());\r
         af.viewport.setGlobalColourScheme(cs);\r
         af.viewport.setColourAppliesToAllGroups(false);\r
         af.changeColour(cs);\r
@@ -402,12 +401,8 @@ public class Jalview2XML_V1
         }\r
 \r
         af.viewport.setColourAppliesToAllGroups(true);\r
+        af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();\r
 \r
-        if (view.getShowSequenceFeatures())\r
-        {\r
-           af.viewport.showSequenceFeatures = true;\r
-           af.showSeqFeatures.setSelected(true);\r
-        }\r
 \r
         if(jms.getFeatureSettings()!=null)\r
         {\r
@@ -429,6 +424,7 @@ public class Jalview2XML_V1
          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
         }\r
 \r
+        af.setMenusFromViewport(af.viewport);\r
 \r
         Desktop.addInternalFrame(af, view.getTitle(),\r
              view.getWidth(), view.getHeight());\r