X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=64d00ffef113a5396165b52f39ae19f7a55659f7;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=1ccf7e684657fc22d159b3c8ea54488f7750773f;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 1ccf7e6..64d00ff 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,488 +1,468 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
-import jalview.schemes.*;
-
-import jalview.gui.*;
-
 import java.io.*;
-
 import java.net.*;
-
 import java.util.*;
-
 import java.util.jar.*;
 
 import javax.swing.*;
 
 import org.exolab.castor.xml.*;
-
 import jalview.binding.*;
-
-
-
+import jalview.schemes.*;
+import jalview.util.jarInputStreamProvider;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class Jalview2XML_V1
 {
-   jalview.schemes.UserColourScheme GetUserColourScheme(
-        JalviewModelSequence jms, String id)
-    {
-        UserColours[] uc = jms.getUserColours();
-        UserColours colours = null;
+  boolean raiseGUI = true;
 
-        for (int i = 0; i < uc.length; i++)
-        {
-            if (uc[i].getId().equals(id))
-            {
-                colours = uc[i];
+  public Jalview2XML_V1()
+  {
 
-                break;
-            }
-        }
+  };
 
-        int csize = colours.getUserColourScheme().getColourCount();
-        java.awt.Color[] newColours = new java.awt.Color[csize];
+  public Jalview2XML_V1(boolean raiseGUI)
+  {
+    this.raiseGUI = raiseGUI;
+  };
 
-        for (int i = 0; i < csize; i++)
-        {
-            newColours[i] = new java.awt.Color(Integer.parseInt(
-                        colours.getUserColourScheme().getColour(i).getRGB(), 16));
-        }
+  jalview.schemes.UserColourScheme GetUserColourScheme(
+          JalviewModelSequence jms, String id)
+  {
+    UserColours[] uc = jms.getUserColours();
+    UserColours colours = null;
+
+    for (int i = 0; i < uc.length; i++)
+    {
+      if (uc[i].getId().equals(id))
+      {
+        colours = uc[i];
 
-        return new jalview.schemes.UserColourScheme(newColours);
+        break;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param file DOCUMENT ME!
-     */
-    public AlignFrame LoadJalviewAlign(String file)
+    int csize = colours.getUserColourScheme().getColourCount();
+    java.awt.Color[] newColours = new java.awt.Color[csize];
+
+    for (int i = 0; i < csize; i++)
     {
+      newColours[i] = new java.awt.Color(Integer.parseInt(colours
+              .getUserColourScheme().getColour(i).getRGB(), 16));
+    }
 
-        jalview.gui.AlignFrame af = null;
+    return new jalview.schemes.UserColourScheme(newColours);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param file
+   *          DOCUMENT ME!
+   */
+  public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+  {
+    final String file = jprovider.getFilename();
+    jalview.gui.AlignFrame af = null;
+
+    try
+    {
+      JarInputStream jin = null;
+      JarEntry jarentry = null;
+      int entryCount = 1;
 
-        try
+      do
+      {
+        jin = jprovider.getJarInputStream();
+
+        for (int i = 0; i < entryCount; i++)
         {
-            //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
-            URL url = null;
-
-            if (file.startsWith("http://"))
-            {
-                url = new URL(file);
-            }
-
-            JarInputStream jin = null;
-            JarEntry jarentry = null;
-            int entryCount = 1;
-
-            do
-            {
-                if (url != null)
-                {
-                    jin = new JarInputStream(url.openStream());
-                }
-                else
-                {
-                    jin = new JarInputStream(new FileInputStream(file));
-                }
-
-                for (int i = 0; i < entryCount; i++)
-                {
-                    jarentry = jin.getNextJarEntry();
-
-                  }
-
-
-                  class NoDescIDResolver implements IDResolver
-                  {
-                    public Object resolve(String idref)
-                    {
-                      System.out.println(idref+" used");
-                      return null;
-                    }
-                  }
-
-
-                if (jarentry != null)
-                {
-                    InputStreamReader in = new InputStreamReader(jin, "UTF-8");
-                    JalviewModel object = new JalviewModel();
-
-                    object = (JalviewModel) object.unmarshal(in);
-
-                    af = LoadFromObject(object);
-                    entryCount++;
-                }
-            }
-            while (jarentry != null);
+          jarentry = jin.getNextJarEntry();
         }
-        catch(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);
 
+        class NoDescIDResolver implements IDResolver
+        {
+          public Object resolve(String idref)
+          {
+            System.out.println(idref + " used");
+            return null;
+          }
         }
-        catch (Exception ex)
+
+        if (jarentry != null)
         {
-          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);
+          InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+          JalviewModel object = new JalviewModel();
 
+          object = (JalviewModel) object.unmarshal(in);
+
+          af = LoadFromObject(object, file);
+          entryCount++;
         }
+      } while (jarentry != null);
+    } catch (final java.net.UnknownHostException ex)
+    {
+      ex.printStackTrace();
+      if (raiseGUI)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
 
-        return af;
+            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)
+    {
+      System.err.println("Exception whilst loading jalview XML file : ");
+      ex.printStackTrace();
+      if (raiseGUI)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+
+            JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                    "Error loading  " + file, "Error loading Jalview file",
+                    JOptionPane.WARNING_MESSAGE);
+          }
+        });
+      }
     }
 
-    AlignFrame LoadFromObject(JalviewModel object)
-    {
-        Vector seqids = new Vector();
-        SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
-        Sequence[] vamsasSeq = vamsasSet.getSequence();
+    return af;
+  }
 
-        JalviewModelSequence jms = object.getJalviewModelSequence();
+  AlignFrame LoadFromObject(JalviewModel object, String file)
+  {
+    Vector seqids = new Vector();
+    SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+    Sequence[] vamsasSeq = vamsasSet.getSequence();
 
-        //////////////////////////////////
-        //LOAD SEQUENCES
-        jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
-        JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
-        for (int i = 0; i < vamsasSeq.length; i++)
-        {
-            jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
-                    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]);
-        }
+    JalviewModelSequence jms = object.getJalviewModelSequence();
 
-        ///SequenceFeatures are added to the DatasetSequence,
-        // so we must create the dataset before loading features
-        /////////////////////////////////
-        jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
-        al.setDataset(null);
-        /////////////////////////////////
+    // ////////////////////////////////
+    // LOAD SEQUENCES
+    jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
+    JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+    for (int i = 0; i < vamsasSeq.length; i++)
+    {
+      jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+              vamsasSeq[i].getSequence());
+      jseqs[i].setStart(JSEQ[i].getStart());
+      jseqs[i].setEnd(JSEQ[i].getEnd());
+      seqids.add(jseqs[i]);
+    }
 
-        for (int i = 0; i < vamsasSeq.length; i++)
+    // /SequenceFeatures are added to the DatasetSequence,
+    // so we must create the dataset before loading features
+    // ///////////////////////////////
+    jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+    al.setDataset(null);
+    // ///////////////////////////////
+
+    for (int i = 0; i < vamsasSeq.length; i++)
+    {
+      if (JSEQ[i].getFeaturesCount() > 0)
+      {
+        Features[] features = JSEQ[i].getFeatures();
+        for (int f = 0; f < features.length; f++)
         {
-          if (JSEQ[i].getFeaturesCount() > 0)
-          {
-            Features[] features = JSEQ[i].getFeatures();
-            for (int f = 0; f < features.length; f++)
-            {
-              jalview.datamodel.SequenceFeature sf
-                  = new jalview.datamodel.SequenceFeature(features[f].getType(),
-                  features[f].getDescription(), features[f].getStatus(),
-                  features[f].getBegin(), features[f].getEnd(),
-                  null);
-
-              al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
-            }
-          }
-          if (JSEQ[i].getPdbidsCount() > 0)
-          {
-            Pdbids[] ids = JSEQ[i].getPdbids();
-            for (int p = 0; p < ids.length; p++)
-            {
-              jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
-              entry.setId(ids[p].getId());
-              entry.setType(ids[p].getType());
-              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
-            }
+          jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+                  features[f].getType(), features[f].getDescription(),
+                  features[f].getStatus(), features[f].getBegin(),
+                  features[f].getEnd(), null);
 
-          }
+          al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
         }
-
-         /////////////////////////////////
-        //////////////////////////////////
-        //LOAD ANNOTATIONS
-        if (vamsasSet.getAnnotation() != null)
+      }
+      if (JSEQ[i].getPdbidsCount() > 0)
+      {
+        Pdbids[] ids = JSEQ[i].getPdbids();
+        for (int p = 0; p < ids.length; p++)
         {
-            Annotation[] an = vamsasSet.getAnnotation();
-
-            for (int i = 0; i < an.length; i++)
-            {
-                AnnotationElement[] ae = an[i].getAnnotationElement();
-                jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
-
-                for (int aa = 0; aa < ae.length; aa++)
-                {
-                    anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
-                            ae[aa].getDescription(),
-                            ae[aa].getSecondaryStructure().charAt(0),
-                            ae[aa].getValue());
-                }
-
-                jalview.datamodel.AlignmentAnnotation jaa = null;
-
-                if (an[i].getGraph())
-                {
-                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                            an[i].getDescription(), anot, 0, 0,
-                            jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
-                }
-                else
-                {
-                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                            an[i].getDescription(), anot);
-                }
-
-                al.addAnnotation(jaa);
-            }
+          jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+          entry.setId(ids[p].getId());
+          entry.setType(ids[p].getType());
+          al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
         }
 
+      }
+    }
 
-        /////////////////////////////////
-        // LOAD VIEWPORT
-        Viewport[] views = jms.getViewport();
-        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
-
-        AlignFrame af = new AlignFrame(al);
+    // ///////////////////////////////
+    // ////////////////////////////////
+    // LOAD ANNOTATIONS
+    if (vamsasSet.getAnnotation() != null)
+    {
+      Annotation[] an = vamsasSet.getAnnotation();
 
+      for (int i = 0; i < an.length; i++)
+      {
+        AnnotationElement[] ae = an[i].getAnnotationElement();
+        jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
+                .getWidth()];
 
-        //  af.changeColour() );
-        /////////////////////////
-        //LOAD GROUPS
-        if (jms.getJGroupCount() > 0)
+        for (int aa = 0; aa < ae.length; aa++)
         {
-            JGroup[] groups = jms.getJGroup();
-
-            for (int i = 0; i < groups.length; i++)
-            {
-                ColourSchemeI cs = null;
-
-                if (groups[i].getColour() != null)
-                {
-                    if (groups[i].getColour().startsWith("ucs"))
-                    {
-                        cs = GetUserColourScheme(jms, groups[i].getColour());
-                    }
-                    else
-                    {
-                        cs = ColourSchemeProperty.getColour(al,
-                                groups[i].getColour());
-                    }
-
-                    cs.setThreshold(groups[i].getPidThreshold(), true);
-                }
-
-                Vector seqs = new Vector();
-                int[] ids = groups[i].getSeq();
-
-                for (int s = 0; s < ids.length; s++)
-                {
-                    seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
-                            ids[s]));
-                }
-
-                jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
-                        groups[i].getName(), cs, groups[i].getDisplayBoxes(),
-                        groups[i].getDisplayText(), groups[i].getColourText(),
-                        groups[i].getStart(), groups[i].getEnd());
-
-                sg.setOutlineColour(new java.awt.Color(
-                        groups[i].getOutlineColour()));
-
-                if (groups[i].getConsThreshold() != 0)
-                {
-                    jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
-                            sg.getWidth() - 1);
-                    c.calculate();
-                    c.verdict(false, 25);
-                    sg.cs.setConservation(c);
-                }
-
-                al.addGroup(sg);
-            }
+          anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+                  ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+                  ae[aa].getSecondaryStructure().charAt(0),
+                  ae[aa].getValue());
         }
 
+        jalview.datamodel.AlignmentAnnotation jaa = null;
 
-
-        af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
-            view.getHeight());
-        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());
-
-        if (view.getWrapAlignment())
+        if (an[i].getGraph())
         {
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                  an[i].getDescription(), anot, 0, 0,
+                  jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
         }
         else
         {
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());
-            af.viewport.setShowAnnotation(view.getShowAnnotation());
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                  an[i].getDescription(), anot);
         }
 
-        af.viewport.setShowBoxes(view.getShowBoxes());
-        af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
-        af.viewport.setShowText(view.getShowText());
-        af.viewTextMenuItem.setSelected(view.getShowText());
+        al.addAnnotation(jaa);
+      }
+    }
+
+    // ///////////////////////////////
+    // LOAD VIEWPORT
+    Viewport[] views = jms.getViewport();
+    Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+
+    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() );
+    // ///////////////////////
+    // LOAD GROUPS
+    if (jms.getJGroupCount() > 0)
+    {
+      JGroup[] groups = jms.getJGroup();
+
+      for (int i = 0; i < groups.length; i++)
+      {
         ColourSchemeI cs = null;
 
-        if (view.getBgColour() != null)
+        if (groups[i].getColour() != null)
         {
-            if (view.getBgColour().startsWith("ucs"))
-            {
-                cs = GetUserColourScheme(jms, view.getBgColour());
-            }
-            else
-            {
-                cs = ColourSchemeProperty.getColour(al, view.getBgColour());
-            }
-
-            if(cs!=null)
-            {
-              cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.vconsensus);
-            }
+          if (groups[i].getColour().startsWith("ucs"))
+          {
+            cs = GetUserColourScheme(jms, groups[i].getColour());
+          }
+          else
+          {
+            cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
+          }
+
+          if (cs != null)
+          {
+            cs.setThreshold(groups[i].getPidThreshold(), true);
+          }
+
         }
 
-        af.setColourSelected(view.getBgColour());
-        af.viewport.setGlobalColourScheme(cs);
-        af.viewport.setColourAppliesToAllGroups(false);
-        af.changeColour(cs);
-        if (view.getConservationSelected() && cs!=null)
+        Vector seqs = new Vector();
+        int[] ids = groups[i].getSeq();
+
+        for (int s = 0; s < ids.length; s++)
         {
-          cs.setConservationInc(view.getConsThreshold());
+          seqs.addElement((jalview.datamodel.SequenceI) seqids
+                  .elementAt(ids[s]));
         }
 
-        af.viewport.setColourAppliesToAllGroups(true);
+        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
+                seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+                groups[i].getDisplayText(), groups[i].getColourText(),
+                groups[i].getStart(), groups[i].getEnd());
+
+        sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 
-        if (view.getShowSequenceFeatures())
+        if (groups[i].getConsThreshold() != 0)
         {
-           af.viewport.showSequenceFeatures = true;
-           af.showSeqFeatures.setSelected(true);
+          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+                  "All", ResidueProperties.propHash, 3,
+                  sg.getSequences(null), 0, sg.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, 25);
+          sg.cs.setConservation(c);
         }
 
-        if(jms.getFeatureSettings()!=null)
+        al.addGroup(sg);
+      }
+    }
+
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+            view.getHeight());
+    af.viewport.setStartRes(view.getStartRes());
+    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.setShowAnnotation(view.getShowAnnotation());
+    af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    af.viewport.setColourText(view.getShowColourText());
+    af.viewport.setConservationSelected(view.getConservationSelected());
+    af.viewport.setShowJVSuffix(view.getShowFullId());
+    af.viewport.setFont(new java.awt.Font(view.getFontName(), view
+            .getFontStyle(), view.getFontSize()));
+    af.alignPanel.fontChanged();
+
+    af.viewport.setRenderGaps(view.getRenderGaps());
+    af.viewport.setWrapAlignment(view.getWrapAlignment());
+    af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+    af.viewport.setShowAnnotation(view.getShowAnnotation());
+    af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+    af.viewport.setShowBoxes(view.getShowBoxes());
+    af.viewport.setShowText(view.getShowText());
+
+    ColourSchemeI cs = null;
+
+    if (view.getBgColour() != null)
+    {
+      if (view.getBgColour().startsWith("ucs"))
+      {
+        cs = GetUserColourScheme(jms, view.getBgColour());
+      }
+      else
+      {
+        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+      }
+
+      if (cs != null)
+      {
+        cs.setThreshold(view.getPidThreshold(), true);
+        cs.setConsensus(af.viewport.hconsensus);
+      }
+    }
+
+    af.viewport.setGlobalColourScheme(cs);
+    af.viewport.setColourAppliesToAllGroups(false);
+    af.changeColour(cs);
+    if (view.getConservationSelected() && cs != null)
+    {
+      cs.setConservationInc(view.getConsThreshold());
+    }
+
+    af.viewport.setColourAppliesToAllGroups(true);
+    af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
+
+    if (jms.getFeatureSettings() != null)
+    {
+      af.viewport.featuresDisplayed = new Hashtable();
+      String[] renderOrder = new String[jms.getFeatureSettings()
+              .getSettingCount()];
+      for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+      {
+        Setting setting = jms.getFeatureSettings().getSetting(fs);
+
+        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+                setting.getType(), new java.awt.Color(setting.getColour()));
+
+        renderOrder[fs] = setting.getType();
+
+        if (setting.getDisplay())
         {
-          af.viewport.featuresDisplayed = new Hashtable();
-          String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
-         for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
-         {
-           Setting setting = jms.getFeatureSettings().getSetting(fs);
-
-           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
-               new java.awt.Color(setting.getColour()));
-
-           renderOrder[fs] = setting.getType();
-
-           if(setting.getDisplay())
-             af.viewport.featuresDisplayed.put(
-                 setting.getType(), new Integer(setting.getColour()));
-         }
-         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+          af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+                  setting.getColour()));
         }
+      }
+      af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+    }
 
+    af.setMenusFromViewport(af.viewport);
 
-        Desktop.addInternalFrame(af, view.getTitle(),
-             view.getWidth(), view.getHeight());
+    Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+            view.getHeight());
 
-        //LOAD TREES
-        ///////////////////////////////////////
-        if (jms.getTreeCount() > 0)
+    // LOAD TREES
+    // /////////////////////////////////////
+    if (jms.getTreeCount() > 0)
+    {
+      try
+      {
+        for (int t = 0; t < jms.getTreeCount(); t++)
         {
-            try
-            {
-                for (int t = 0; t < jms.getTreeCount(); t++)
-                {
-
-                    Tree tree = jms.getTree(t);
-
-                    TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
-                                tree.getNewick()), tree.getTitle(),
-                                tree.getWidth(), tree.getHeight(),
-                                tree.getXpos(), tree.getYpos());
-
-                    tp.fitToWindow.setState(tree.getFitToWindow());
-                    tp.fitToWindow_actionPerformed(null);
-
-                    if(tree.getFontName()!=null)
-                      tp.setTreeFont(new java.awt.Font(tree.getFontName(),
-                                          tree.getFontStyle(),
-                                          tree.getFontSize()));
-                    else
-                      tp.setTreeFont(new java.awt.Font(view.getFontName(),
-                                            view.getFontStyle(),
-                                            tree.getFontSize()));
-
-                    tp.showPlaceholders(tree.getMarkUnlinked());
-                    tp.showBootstrap(tree.getShowBootstrap());
-                    tp.showDistances(tree.getShowDistances());
-
-                    tp.treeCanvas.threshold = tree.getThreshold();
-
-                    if (tree.getCurrentTree())
-                      af.viewport.setCurrentTree(tp.getTree());
-                }
-
-            }
-            catch (Exception ex)
-            {
-                ex.printStackTrace();
-            }
 
+          Tree tree = jms.getTree(t);
+
+          TreePanel tp = af.ShowNewickTree(
+                  new jalview.io.NewickFile(tree.getNewick()),
+                  tree.getTitle(), tree.getWidth(), tree.getHeight(),
+                  tree.getXpos(), tree.getYpos());
+
+          tp.fitToWindow.setState(tree.getFitToWindow());
+          tp.fitToWindow_actionPerformed(null);
+
+          if (tree.getFontName() != null)
+          {
+            tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
+                    .getFontStyle(), tree.getFontSize()));
+          }
+          else
+          {
+            tp.setTreeFont(new java.awt.Font(view.getFontName(), view
+                    .getFontStyle(), tree.getFontSize()));
+          }
+
+          tp.showPlaceholders(tree.getMarkUnlinked());
+          tp.showBootstrap(tree.getShowBootstrap());
+          tp.showDistances(tree.getShowDistances());
+
+          tp.treeCanvas.threshold = tree.getThreshold();
+
+          if (tree.getCurrentTree())
+          {
+            af.viewport.setCurrentTree(tp.getTree());
+          }
         }
 
-        return af;
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
     }
-}
 
+    return af;
+  }
+}