From c901bd1778574b5792a7ee168bfe3e1addd3e181 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 19 May 2005 17:51:18 +0000
Subject: [PATCH] new class

---
 src/jalview/gui/Jalview2XML.java |  466 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 466 insertions(+)
 create mode 100755 src/jalview/gui/Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
new file mode 100755
index 0000000..008be21
--- /dev/null
+++ b/src/jalview/gui/Jalview2XML.java
@@ -0,0 +1,466 @@
+package jalview.gui;
+
+import java.io.*;
+import java.util.*;
+import java.util.jar.*;
+
+import jalview.binding.*;
+import jalview.schemes.*;
+import javax.swing.JInternalFrame;
+
+
+public class Jalview2XML
+{
+
+  public static void SaveState(File statefile)
+  {
+      long creation = System.currentTimeMillis();
+      JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+      try{
+        JalviewState state = new JalviewState();
+
+        Vector shortNames = new Vector();
+        for (int i = 0; i < frames.length; i++)
+        {
+          if (frames[i] instanceof AlignFrame)
+          {
+            AlignFrame af = (AlignFrame) frames[i];
+
+            String shortName = af.getTitle();
+
+            shortName = shortName.replace('/', '_');
+            shortName = shortName.replace('\\', '_');
+            String jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";
+
+            int count=1;
+            while( shortNames.contains(shortName) )
+            {
+              if(shortName.endsWith("_"+(count-1)))
+                shortName = shortName.substring(0, shortName.lastIndexOf("_"));
+
+              shortName = shortName.concat("_"+count);
+              count++;
+            }
+            shortNames.addElement(shortName);
+
+            if(!shortName.endsWith(".xml"))
+              shortName = shortName+".xml";
+
+            jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";
+
+            SaveState( af, creation, shortName, jarFile);
+            state.addFile(jarFile);
+          }
+        }
+
+        PrintWriter out = new PrintWriter(new FileWriter(statefile));
+        state.marshal(out);
+        out.close();
+      }
+      catch(Exception ex){ex.printStackTrace();}
+  }
+
+
+  public static void SaveState( AlignFrame af, long timeStamp, String fileName, String jarFile)
+  {
+
+    Vector seqids = new Vector();
+
+    AlignViewport av = af.viewport;
+
+    JalviewModel object = new JalviewModel();
+    object.setVamsasModel( new VamsasModel() );
+
+    object.setCreationDate( new java.util.Date(timeStamp) );
+
+    jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+
+    SequenceSet vamsasSet = new SequenceSet();
+    Sequence vamsasSeq;
+    JalviewModelSequence jms = new JalviewModelSequence();
+
+    vamsasSet.setGapChar(jal.getGapCharacter()+"");
+
+    JSeq jseq;
+
+
+    //SAVE SEQUENCES
+    int id = 0;
+    for(int i=0; i<jal.getHeight(); i++)
+    {
+      seqids.add(jal.getSequenceAt(i));
+
+      vamsasSeq = new Sequence( );
+      vamsasSeq.setId(id+"");
+      vamsasSeq.setName(jal.getSequenceAt(i).getName());
+      vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
+
+      jseq = new JSeq();
+      jseq.setStart(jal.getSequenceAt(i).getStart());
+      jseq.setEnd(jal.getSequenceAt(i).getEnd());
+
+      jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+
+      jseq.setId( id );
+
+      jms.addJSeq(jseq);
+      vamsasSet.addSequence(vamsasSeq);
+      id++;
+    }
+
+    //SAVE TREES
+    if(af.viewport.currentTree!=null)
+    {
+      object.getVamsasModel().addTree(af.viewport.currentTree.toString());
+    }
+
+    //SAVE ANNOTATIONS
+    if(jal.getAlignmentAnnotation()!=null)
+    {
+
+      jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();
+      for(int i=0; i<aa.length; i++)
+      {
+        if(aa[i].label.equals("Quality")
+        || aa[i].label.equals("Conservation")
+        || aa[i].label.equals("Consensus"))
+       {    continue;}
+
+        Annotation an = new Annotation();
+        an.setDescription(aa[i].description);
+        an.setGraph(aa[i].isGraph);
+        an.setLabel(aa[i].label);
+
+        AnnotationElement ae;
+
+        for(int a=0; a<aa[i].annotations.length; a++)
+        {
+          if(aa[i]==null || aa[i].annotations[a]==null)
+            continue;
+
+          ae = new AnnotationElement();
+          ae.setDescription(aa[i].annotations[a].description);
+          ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+          ae.setValue(aa[i].annotations[a].value);
+          ae.setPosition(a);
+          ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure+"");
+          an.addAnnotationElement(ae);
+        }
+
+        vamsasSet.addAnnotation(an);
+      }
+
+    }
+
+    //SAVE GROUPS
+    if(jal.getGroups()!=null)
+    {
+      JGroup [] groups = new JGroup[jal.getGroups().size()];
+      for(int i=0; i<groups.length; i++)
+      {
+        groups[i] = new JGroup();
+        jalview.datamodel.SequenceGroup sg
+            = (jalview.datamodel.SequenceGroup)jal.getGroups().elementAt(i);
+        groups[i].setStart( sg.getStartRes() );
+        groups[i].setEnd( sg.getEndRes() );
+        groups[i].setName( sg.getName());
+
+        if(sg.cs instanceof ConservationColourScheme)
+          groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);
+
+        if (sg.cs instanceof ResidueColourScheme)
+          groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());
+       else if (sg.cs instanceof ScoreColourScheme)
+         groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
+
+
+        groups[i].setColour( ColourSchemeProperty.getColourName(sg.cs) );
+        groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
+        groups[i].setDisplayBoxes(sg.getDisplayBoxes());
+        groups[i].setDisplayText(sg.getDisplayText());
+        groups[i].setColourText(sg.getColourText());
+
+        for(int s=0; s<sg.getSize(); s++)
+        {
+          jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);
+          int index = seqids.indexOf(seq);
+          groups[i].addSeq(index);
+        }
+
+      }
+
+      jms.setJGroup(groups);
+
+    }
+
+    ///////////SAVE VIEWPORT
+    Viewport view = new Viewport();
+   view.setTitle(af.getTitle());
+   view.setXpos(af.getX());
+   view.setYpos(af.getY());
+   view.setWidth(af.getWidth());
+   view.setHeight(af.getHeight());
+   view.setStartRes(av.startRes);
+   view.setStartSeq(av.startSeq);
+   view.setBgColour( ColourSchemeProperty.getColourName
+                     ( av.getGlobalColourScheme()));
+
+   ColourSchemeI cs = av.getGlobalColourScheme();
+   if(cs instanceof ConservationColourScheme)
+     view.setConsThreshold( ((ConservationColourScheme)cs).inc);
+
+   if (cs instanceof ResidueColourScheme)
+     view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
+  else if (cs instanceof ScoreColourScheme)
+     view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
+
+
+   view.setConservationSelected(av.getConservationSelected());
+   view.setPidSelected(av.getAbovePIDThreshold());
+   view.setFontName(av.font.getFontName());
+   view.setFontSize(av.font.getSize());
+   view.setFontStyle(av.font.getStyle());
+   view.setRenderGaps(av.renderGaps);
+   view.setShowAnnotation(av.getShowAnnotation());
+   view.setShowBoxes(av.getShowBoxes());
+   view.setShowColourText(av.getColourText());
+   view.setShowConservation(av.showConservation);
+   view.setShowFullId(av.getShowFullId());
+   view.setShowIdentity(av.showIdentity);
+   view.setShowQuality(av.showQuality);
+   view.setShowSequenceFeatures(av.showSequenceFeatures);
+   view.setShowText(av.getShowText());
+   view.setWrapAlignment(av.getWrapAlignment());
+
+   jms.addViewport( view );
+
+    object.setJalviewModelSequence(jms);
+    object.getVamsasModel().addSequenceSet(vamsasSet);
+
+
+    try
+    {
+    // NAME OF FILE
+     FileOutputStream fos = new FileOutputStream(jarFile);
+
+     //PUT IT IN THIS JARFILE
+     JarOutputStream jout = new JarOutputStream(fos);
+
+     //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+     ////////////////////////////////////////////////////
+     PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));
+
+     if(!fileName.endsWith(".xml"))
+              fileName = fileName+".xml";
+
+     JarEntry entry = new JarEntry(fileName);
+     jout.putNextEntry(entry);
+
+      object.marshal(out);
+      out.close();
+      fos.close();
+      jout.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  public static void LoadState(String file)
+  {
+    try{
+       JalviewState state = new JalviewState();
+       BufferedReader in = new BufferedReader(new FileReader(file));
+       state = (JalviewState)state.unmarshal(in);
+       Enumeration en = state.enumerateFile();
+       while( en.hasMoreElements() )
+       {
+         LoadJalviewAlign( en.nextElement().toString());
+       }
+    }
+    catch(Exception ex)
+    {   ex.printStackTrace(); return; }
+  }
+
+  public static void LoadJalviewAlign(String file)
+  {
+    JalviewModel object = new JalviewModel();
+    Vector seqids = new Vector();
+    try{
+      FileInputStream fis = new FileInputStream(file);
+      JarInputStream jin = new JarInputStream(fis);
+      jin.getNextJarEntry();
+      InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+      object = (JalviewModel) object.unmarshal(in);
+    }
+    catch(Exception ex)
+    {   System.out.println(ex); return; }
+
+
+     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+     Sequence [] vamsasSeq = vamsasSet.getSequence();
+
+     JalviewModelSequence jms = object.getJalviewModelSequence();
+     //////////////////////////////////
+     //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]);
+     }
+
+     /////////////////////////////////
+     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
+     /////////////////////////////////
+
+     //////////////////////////////////
+     //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()];
+         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,
+                                        0,0,1);
+          else
+            jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                                        an[i].getDescription(), anot);
+          al.addAnnotation(jaa);
+       }
+     }
+
+      /////////////////////////////////
+      // LOAD VIEWPORT
+      Viewport[] views = jms.getViewport();
+      Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+
+      AlignFrame af = new AlignFrame(al);
+    //  af.changeColour() );
+
+    /////////////////////////
+    //LOAD GROUPS
+    if (jms.getJGroupCount()>0)
+    {
+      JGroup[] groups = jms.getJGroup();
+      for (int i = 0; i < groups.length; i++)
+      {
+       ColourSchemeI cs = ColourSchemeProperty.getColour(al, groups[i].getColour() );
+       if (cs instanceof ResidueColourScheme)
+         ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+       else if (cs instanceof ScoreColourScheme)
+      ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
+
+        jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup
+                (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()));
+        int [] ids = groups[i].getSeq();
+        for(int s=0; s<ids.length; s++)
+            sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));
+
+        if(groups[i].getConsThreshold()!=0)
+        {
+          jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
+              ResidueProperties.propHash, 3,
+              sg.sequences, 0,
+              sg.getWidth() - 1);
+          c.calculate();
+          c.verdict(false, 25);
+          cs = new ConservationColourScheme(c, cs);
+          sg.cs = cs;
+        }
+
+
+        al.addGroup(sg);
+      }
+    }
+
+
+    Desktop.addInternalFrame(af, view.getTitle(), AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight());
+    af.viewport.setStartRes( view.getStartRes() );
+    af.viewport.setStartSeq( view.getStartSeq() );
+    af.viewport.setAbovePIDThreshold( view.getPidSelected() );
+    af.viewport.setColourText( view.getShowColourText() );
+    af.viewport.setConservationSelected( view.getConservationSelected());
+    af.viewport.setShowFullId( 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() );
+    if(view.getWrapAlignment())
+    {
+      af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+    }
+    else
+    {
+      af.viewport.setShowAnnotation(view.getShowAnnotation());
+      af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+    }
+
+    af.viewport.setShowBoxes( view.getShowBoxes() );
+    af.viewport.setShowText( view.getShowText() );
+
+    af.viewport.setGlobalColourScheme( ColourSchemeProperty.getColour(al, view.getBgColour()));
+    af.viewport.setColourAppliesToAllGroups(false);
+    af.changeColour( af.viewport.getGlobalColourScheme() );
+    af.viewport.setColourAppliesToAllGroups(true);
+
+    ColourSchemeI cs = af.viewport.getGlobalColourScheme();
+    if(cs instanceof ConservationColourScheme)
+      ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
+
+    if (cs instanceof ResidueColourScheme)
+      ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
+    else if (cs instanceof ScoreColourScheme)
+      ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
+
+    //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
+    if(object.getVamsasModel().getTreeCount()>0)
+    {
+      try{
+        af.ShowNewickTree(new jalview.io.NewickFile(
+            (String)object.getVamsasModel().getTree(0)), "Tree");
+      }catch(Exception ex){ex.printStackTrace();}
+
+    }
+
+  }
+}
+
+
+
-- 
1.7.10.2