X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=227cb49626a64eceaafe3cf3b0d286c84d12575f;hb=ea49c8f1b0d681ec87547fc4055eb35a1165aee3;hp=993b4020f6033d52c5314106be287b632402f31e;hpb=e49f51b882c6d3e6dbcc9e377e21c18b91fbbd5a;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 993b402..227cb49 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -18,10 +18,11 @@
  */
 package jalview.gui;
 
-import jalview.io.*;
 
 import jalview.schemes.*;
 
+import jalview.gui.*;
+
 import java.io.*;
 
 import java.net.*;
@@ -32,7 +33,11 @@ import java.util.jar.*;
 
 import javax.swing.*;
 
-import jalview.binding.*;
+import org.exolab.castor.xml.*;
+
+import jalview.schemabinding.version2.*;
+
+
 
 
 /**
@@ -44,7 +49,7 @@ import jalview.binding.*;
 public class Jalview2XML
 {
     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
-    public static void SaveState(File statefile)
+    public void SaveState(File statefile)
     {
         long creation = System.currentTimeMillis();
         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -116,7 +121,7 @@ public class Jalview2XML
     }
 
     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
-    public static void SaveAlignment(AlignFrame af, String jarFile,
+    public void SaveAlignment(AlignFrame af, String jarFile,
         String fileName)
     {
         try
@@ -148,7 +153,7 @@ public class Jalview2XML
      * @param jout DOCUMENT ME!
      * @param out DOCUMENT ME!
      */
-    public static void SaveState(AlignFrame af, long timeStamp,
+    public void SaveState(AlignFrame af, long timeStamp,
         String fileName, JarOutputStream jout, PrintWriter out)
     {
         Vector seqids = new Vector();
@@ -157,7 +162,7 @@ public class Jalview2XML
         AlignViewport av = af.viewport;
 
         JalviewModel object = new JalviewModel();
-        object.setVamsasModel(new jalview.binding.VamsasModel());
+        object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
         object.setCreationDate(new java.util.Date(timeStamp));
         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
@@ -195,19 +200,21 @@ public class Jalview2XML
 
             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
             {
-              Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements();
-              while(en.hasMoreElements())
+              jalview.datamodel.SequenceFeature[] sf
+                  = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+              int index = 0;
+              while(index < sf.length)
               {
                 Features features = new Features();
-                jalview.datamodel.SequenceFeature sf
-                   = (jalview.datamodel.SequenceFeature)en.nextElement();
-
-                features.setBegin(sf.getBegin());
-                features.setEnd(sf.getEnd());
-                features.setDescription(sf.getDescription());
-                features.setStatus(sf.getStatus());
-                features.setType(sf.getType());
+
+                features.setBegin(sf[index].getBegin());
+                features.setEnd(sf[index].getEnd());
+                features.setDescription(sf[index].getDescription());
+                features.setStatus(sf[index].getStatus());
+                features.setType(sf[index].getType());
+                features.setFeatureGroup(sf[index].getFeatureGroup());
                 jseq.addFeatures(features);
+                index ++;
               }
             }
 
@@ -309,11 +316,28 @@ public class Jalview2XML
 
                 Annotation an = new Annotation();
                 an.setDescription(aa[i].description);
+
+                if(aa[i].sequenceRef!=null)
+                 {
+                   an.setSequenceRef(aa[i].sequenceRef.getName());
+                 }
+
                 if(aa[i].graph>0)
                 {
                   an.setGraph(true);
                   an.setGraphType(aa[i].graph);
+                  if(aa[i].getThreshold()!=null)
+                  {
+                    ThresholdLine line = new ThresholdLine();
+                    line.setLabel(aa[i].getThreshold().label);
+                    line.setValue(aa[i].getThreshold().value);
+                    line.setColour(aa[i].getThreshold().colour.getRGB());
+                    an.setThresholdLine(line);
+                  }
                 }
+                else
+                  an.setGraph(false);
+
                 an.setLabel(aa[i].label);
 
                 AnnotationElement ae;
@@ -371,6 +395,12 @@ public class Jalview2XML
                           cs));
                     }
                   }
+                  else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+                  {
+                    groups[i].setColour(
+                        ColourSchemeProperty.getColourName(
+                      ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
+                  }
                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
                   {
                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
@@ -417,6 +447,26 @@ public class Jalview2XML
             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
                     userColours, jms));
         }
+        else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+        {
+           jalview.schemes.AnnotationColourGradient acg
+              = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
+
+            AnnotationColours ac = new AnnotationColours();
+            ac.setAboveThreshold(acg.getAboveThreshold());
+            ac.setThreshold(acg.getAnnotationThreshold());
+            ac.setAnnotation(acg.getAnnotation());
+            if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+              ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+                    userColours, jms));
+            else
+              ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+
+            ac.setMaxColour(acg.getMaxColour().getRGB());
+            ac.setMinColour(acg.getMinColour().getRGB());
+            view.setAnnotationColours(ac);
+            view.setBgColour("AnnotationColourGradient");
+        }
         else
         {
             view.setBgColour(ColourSchemeProperty.getColourName(
@@ -457,21 +507,23 @@ public class Jalview2XML
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
 
-        if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
+        if(av.featuresDisplayed!=null)
         {
-          jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+          jalview.schemabinding.version2.FeatureSettings fs
+              = new jalview.schemabinding.version2.FeatureSettings();
 
-          Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
-          while (e.hasMoreElements())
+          String [] renderOrder =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+          for(int ro=0; ro<renderOrder.length; ro++)
           {
-            String type = e.nextElement().toString();
             Setting setting = new Setting();
-            setting.setType(type);
+            setting.setType(renderOrder[ro]);
             setting.setColour(
-                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
                 );
+
             setting.setDisplay(
-                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type)
+                av.featuresDisplayed.containsKey(renderOrder[ro])
                 );
 
             fs.addSetting(setting);
@@ -505,7 +557,7 @@ public class Jalview2XML
         }
     }
 
-    static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+    String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
         Vector userColours, JalviewModelSequence jms)
     {
         String id = null;
@@ -516,12 +568,12 @@ public class Jalview2XML
             userColours.add(ucs);
 
             java.awt.Color[] colours = ucs.getColours();
-            jalview.binding.UserColours uc = new jalview.binding.UserColours();
-            jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
+            jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
+            jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 
             for (int i = 0; i < colours.length; i++)
             {
-                jalview.binding.Colour col = new jalview.binding.Colour();
+                jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
                 jbucs.addColour(col);
             }
@@ -535,7 +587,7 @@ public class Jalview2XML
         return id;
     }
 
-    static jalview.schemes.UserColourScheme GetUserColourScheme(
+   jalview.schemes.UserColourScheme GetUserColourScheme(
         JalviewModelSequence jms, String id)
     {
         UserColours[] uc = jms.getUserColours();
@@ -568,9 +620,9 @@ public class Jalview2XML
      *
      * @param file DOCUMENT ME!
      */
-    public static AlignFrame LoadJalviewAlign(String file)
+    public AlignFrame LoadJalviewAlign(String file)
     {
-        JalviewModel object = new JalviewModel();
+
         jalview.gui.AlignFrame af = null;
 
         try
@@ -601,12 +653,29 @@ public class Jalview2XML
                 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");
-                    object = (JalviewModel) object.unmarshal(in);
+                    JalviewModel object = new JalviewModel();
+
+                    Unmarshaller unmar = new Unmarshaller(object);
+                    unmar.setValidation(false);
+                    object = (JalviewModel) unmar.unmarshal( in );
+
                     af = LoadFromObject(object);
                     entryCount++;
                 }
@@ -626,6 +695,14 @@ public class Jalview2XML
         }
         catch (Exception ex)
         {
+          //Is Version 1 Jar file?
+          af =  new Jalview2XML_V1().LoadJalviewAlign(file);
+
+          if(af!=null)
+          {
+            System.out.println("Successfully loaded archive file");
+            return af;
+          }
           ex.printStackTrace();
             System.err.println("Exception whilst loading jalview XML file : " +
                 ex + "\n");
@@ -639,7 +716,7 @@ public class Jalview2XML
         return af;
     }
 
-    static AlignFrame LoadFromObject(JalviewModel object)
+    AlignFrame LoadFromObject(JalviewModel object)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -677,11 +754,12 @@ public class Jalview2XML
             Features[] features = JSEQ[i].getFeatures();
             for (int f = 0; f < features.length; f++)
             {
-              //features[f].getBegin()
               jalview.datamodel.SequenceFeature sf
                   = new jalview.datamodel.SequenceFeature(features[f].getType(),
                   features[f].getDescription(), features[f].getStatus(),
-                  features[f].getBegin(), features[f].getEnd());
+                  features[f].getBegin(), features[f].getEnd(),
+                  features[f].getFeatureGroup());
+
               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
             }
           }
@@ -698,7 +776,8 @@ public class Jalview2XML
 
           }
         }
-        /////////////////////////////////
+
+         /////////////////////////////////
         //////////////////////////////////
         //LOAD ANNOTATIONS
         if (vamsasSet.getAnnotation() != null)
@@ -714,7 +793,7 @@ public class Jalview2XML
                 {
                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
                             ae[aa].getDescription(),
-                            ae[aa].getSecondaryStructure().charAt(0),
+                            ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
                             ae[aa].getValue());
                 }
 
@@ -722,9 +801,20 @@ public class Jalview2XML
 
                 if (an[i].getGraph())
                 {
-                    jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
-                            an[i].getDescription(), anot, 0, 0,
-                            an[i].getGraphType());
+                  jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+                      an[i].getDescription(), anot, 0, 0,
+                      an[i].getGraphType());
+
+                  if (an[i].getThresholdLine() != null)
+                  {
+                    jaa.setThreshold(new jalview.datamodel.GraphLine(
+                                  an[i].getThresholdLine().getValue(),
+                                  an[i].getThresholdLine().getLabel(),
+                                new java.awt.Color(an[i].getThresholdLine().getColour()))
+                             );
+
+                  }
+
                 }
                 else
                 {
@@ -732,10 +822,19 @@ public class Jalview2XML
                             an[i].getDescription(), anot);
                 }
 
+                if(an[i].getSequenceRef()!=null)
+                {
+                  jaa.createSequenceMapping(
+                      al.findName(an[i].getSequenceRef()), 1
+                      );
+                  al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+                }
+
                 al.addAnnotation(jaa);
             }
         }
 
+
         /////////////////////////////////
         // LOAD VIEWPORT
         Viewport[] views = jms.getViewport();
@@ -767,7 +866,8 @@ public class Jalview2XML
                                 groups[i].getColour());
                     }
 
-                    cs.setThreshold(groups[i].getPidThreshold(), true);
+                    if(cs!=null)
+                      cs.setThreshold(groups[i].getPidThreshold(), true);
                 }
 
                 Vector seqs = new Vector();
@@ -802,6 +902,7 @@ public class Jalview2XML
         }
 
 
+
         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
         af.viewport.setStartRes(view.getStartRes());
@@ -854,6 +955,96 @@ public class Jalview2XML
             {
                 cs = GetUserColourScheme(jms, view.getBgColour());
             }
+            else if(view.getBgColour().startsWith("Annotation"))
+            {
+              //int find annotation
+              for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+              {
+                if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
+                    equals(view.getAnnotationColours().getAnnotation()))
+                {
+                  if (af.viewport.alignment.getAlignmentAnnotation()[i].
+                      getThreshold() == null)
+                  {
+                    af.viewport.alignment.getAlignmentAnnotation()[i].
+                        setThreshold(
+                            new jalview.datamodel.GraphLine(
+                                view.getAnnotationColours().getThreshold(),
+                                "Threshold", java.awt.Color.black)
+
+                        );
+                  }
+
+
+                  if (view.getAnnotationColours().getColourScheme().equals(
+                      "None"))
+                  {
+                    cs = new AnnotationColourGradient(
+                        af.viewport.alignment.getAlignmentAnnotation()[i],
+                        new java.awt.Color(view.getAnnotationColours().
+                                           getMinColour()),
+                        new java.awt.Color(view.getAnnotationColours().
+                                           getMaxColour()),
+                        view.getAnnotationColours().getAboveThreshold());
+                  }
+                  else if (view.getAnnotationColours().getColourScheme().
+                           startsWith("ucs"))
+                  {
+                     cs = new AnnotationColourGradient(
+                         af.viewport.alignment.getAlignmentAnnotation()[i],
+                         GetUserColourScheme(jms, view.getAnnotationColours().
+                                                        getColourScheme()),
+                         view.getAnnotationColours().getAboveThreshold()
+                         );
+                   }
+                   else
+                   {
+                     cs = new AnnotationColourGradient(
+                         af.viewport.alignment.getAlignmentAnnotation()[i],
+                         ColourSchemeProperty.getColour(al,
+                         view.getAnnotationColours().getColourScheme()),
+                         view.getAnnotationColours().getAboveThreshold()
+                         );
+                   }
+
+                  // Also use these settings for all the groups
+                  if (al.getGroups() != null)
+                    for (int g = 0; g < al.getGroups().size(); g++)
+                    {
+                      jalview.datamodel.SequenceGroup sg
+                          = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
+
+                      if(sg.cs == null)
+                        continue;
+
+
+                  /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
+                      {
+                        sg.cs = new AnnotationColourGradient(
+                            af.viewport.alignment.getAlignmentAnnotation()[i],
+                            new java.awt.Color(view.getAnnotationColours().
+                                               getMinColour()),
+                            new java.awt.Color(view.getAnnotationColours().
+                                               getMaxColour()),
+                            view.getAnnotationColours().getAboveThreshold());
+                      }
+                      else*/
+                      {
+                        sg.cs = new AnnotationColourGradient(
+                            af.viewport.alignment.getAlignmentAnnotation()[i],
+                            sg.cs,
+                            view.getAnnotationColours().getAboveThreshold()
+                            );
+                      }
+
+                    }
+
+
+                  break;
+                }
+
+              }
+            }
             else
             {
                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
@@ -879,27 +1070,31 @@ public class Jalview2XML
 
         if (view.getShowSequenceFeatures())
         {
-           af.featureSettings.setEnabled(true);
            af.viewport.showSequenceFeatures = true;
-           af.sequenceFeatures.setSelected(true);
+           af.showSeqFeatures.setSelected(true);
         }
 
         if(jms.getFeatureSettings()!=null)
         {
-          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector();
-         // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
-         // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+          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.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.addElement(setting.getType());
+             af.viewport.featuresDisplayed.put(
+                 setting.getType(), new Integer(setting.getColour()));
          }
+         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
         }
 
+
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());
 
@@ -952,3 +1147,4 @@ public class Jalview2XML
         return af;
     }
 }
+