X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=e6191deb0f3e5f9a26791ab7169c448f7de2e7ce;hb=237972562c84b83dbd287071cdd839d97aaf7d4b;hp=e11830985af7b108cbce2b67056cdcfd128ba6de;hpb=f3bc67915e61855d87866b4a614fe7a953813408;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index e118309..e6191de 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -48,6 +48,19 @@ import jalview.schemabinding.version2.*;
  */
 public class Jalview2XML
 {
+
+  Hashtable seqRefIds;
+
+  /**
+   * This maintains a list of viewports, the key being the
+   * seqSetId. Important to set historyItem and redoList
+   * for multiple views
+   */
+  Hashtable viewportsAdded;
+
+  String uniqueSetSuffix = "";
+
+
     // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
     public void SaveState(File statefile)
     {
@@ -112,9 +125,6 @@ public class Jalview2XML
                       AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
                           elementAt(ap);
 
-                      if (apanel.av.explodedPosition == null)
-                        apanel.av.explodedPosition = af.getBounds();
-
                       SaveState(apanel,
                                 apSize == 1 ? shortName : ap+shortName,
                                 jout, out);
@@ -146,9 +156,6 @@ public class Jalview2XML
           {
             AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
 
-            if (apanel.av.explodedPosition == null)
-              apanel.av.explodedPosition = af.getBounds();
-
             SaveState(apanel,
                       apSize==1?fileName:fileName+ap,
                       jout, out);
@@ -172,7 +179,7 @@ public class Jalview2XML
      * @param jout DOCUMENT ME!
      * @param out DOCUMENT ME!
      */
-    public void SaveState(AlignmentPanel ap,
+    public JalviewModel SaveState(AlignmentPanel ap,
                           String fileName,
                           JarOutputStream jout,
                           PrintWriter out)
@@ -208,9 +215,11 @@ public class Jalview2XML
 
         //SAVE SEQUENCES
         int id = 0;
+        jalview.datamodel.SequenceI jds;
         for (int i = 0; i < jal.getHeight(); i++)
         {
-            id = jal.getSequenceAt(i).hashCode();
+            jds = jal.getSequenceAt(i);
+            id = jds.hashCode();
 
             if(seqRefIds.get(id+"")!=null)
             {
@@ -220,14 +229,14 @@ public class Jalview2XML
             {
               vamsasSeq = new Sequence();
               vamsasSeq.setId(id + "");
-              vamsasSeq.setName(jal.getSequenceAt(i).getName());
-              vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
-              vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
+              vamsasSeq.setName(jds.getName());
+              vamsasSeq.setSequence(jds.getSequence());
+              vamsasSeq.setDescription(jds.getDescription());
 
-              if (jal.getSequenceAt(i).getDatasetSequence().getDBRef() != null)
+              if (jds.getDatasetSequence().getDBRef() != null)
               {
                 jalview.datamodel.DBRefEntry[] dbrefs =
-                    jal.getSequenceAt(i).getDatasetSequence().getDBRef();
+                    jds.getDatasetSequence().getDBRef();
 
                 for (int d = 0; d < dbrefs.length; d++)
                 {
@@ -240,20 +249,19 @@ public class Jalview2XML
               }
 
               vamsasSet.addSequence(vamsasSeq);
-              seqRefIds.put(id+"", vamsasSeq);
+              seqRefIds.put(id+"", jal.getSequenceAt(i));
             }
 
             jseq = new JSeq();
-            jseq.setStart(jal.getSequenceAt(i).getStart());
-            jseq.setEnd(jal.getSequenceAt(i).getEnd());
-            jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
+            jseq.setStart(jds.getStart());
+            jseq.setEnd(jds.getEnd());
+            jseq.setColour( av.getSequenceColour(jds).getRGB());
 
             jseq.setId(id);
 
             if (av.hasHiddenRows)
             {
-              jseq.setHidden(av.alignment.getHiddenSequences().isHidden(
-                  jal.getSequenceAt(i)));
+              jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 
               if(jal.getSequenceAt(i).getHiddenSequences()!=null)
               {
@@ -270,10 +278,10 @@ public class Jalview2XML
             }
 
 
-            if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
+            if(jds.getDatasetSequence().getSequenceFeatures()!=null)
             {
               jalview.datamodel.SequenceFeature[] sf
-                  = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
+                  = jds.getDatasetSequence().getSequenceFeatures();
               int index = 0;
               while(index < sf.length)
               {
@@ -315,9 +323,9 @@ public class Jalview2XML
               }
             }
 
-            if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
+            if(jds.getDatasetSequence().getPDBId()!=null)
             {
-              Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
+              Enumeration en = jds.getDatasetSequence().getPDBId().elements();
               while(en.hasMoreElements())
               {
                 Pdbids pdb = new Pdbids();
@@ -561,6 +569,9 @@ public class Jalview2XML
                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
                 groups[i].setDisplayText(sg.getDisplayText());
                 groups[i].setColourText(sg.getColourText());
+                groups[i].setTextCol1(sg.textColour.getRGB());
+                groups[i].setTextCol2(sg.textColour2.getRGB());
+                groups[i].setTextColThreshold(sg.thresholdTextColour);
 
                 for (int s = 0; s < sg.getSize(false); s++)
                 {
@@ -581,10 +592,22 @@ public class Jalview2XML
         view.setViewName(av.viewName);
         view.setGatheredViews(av.gatherViewsHere);
 
-        view.setXpos(av.explodedPosition.x);
-        view.setYpos(av.explodedPosition.y);
-        view.setWidth(av.explodedPosition.width);
-        view.setHeight(av.explodedPosition.height);
+
+        if (ap.av.explodedPosition != null)
+        {
+          view.setXpos(av.explodedPosition.x);
+          view.setYpos(av.explodedPosition.y);
+          view.setWidth(av.explodedPosition.width);
+          view.setHeight(av.explodedPosition.height);
+        }
+        else
+        {
+          view.setXpos(ap.alignFrame.getBounds().x);
+          view.setYpos(ap.alignFrame.getBounds().y);
+          view.setWidth(ap.alignFrame.getBounds().width);
+          view.setHeight(ap.alignFrame.getBounds().height);
+        }
+
         view.setStartRes(av.startRes);
         view.setStartSeq(av.startSeq);
 
@@ -645,13 +668,15 @@ public class Jalview2XML
         view.setShowAnnotation(av.getShowAnnotation());
         view.setShowBoxes(av.getShowBoxes());
         view.setShowColourText(av.getColourText());
-        view.setShowConservation(av.showConservation);
         view.setShowFullId(av.getShowJVSuffix());
-        view.setShowIdentity(av.showIdentity);
-        view.setShowQuality(av.showQuality);
+        view.setRightAlignIds(av.rightAlignIds);
         view.setShowSequenceFeatures(av.showSequenceFeatures);
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
+        view.setTextCol1(av.textColour.getRGB());
+        view.setTextCol2(av.textColour2.getRGB());
+        view.setTextColThreshold(av.thresholdTextColour);
+
 
         if(av.featuresDisplayed!=null)
         {
@@ -721,22 +746,29 @@ public class Jalview2XML
         object.setJalviewModelSequence(jms);
         object.getVamsasModel().addSequenceSet(vamsasSet);
 
-        try
+        if(out!=null)
         {
+          //We may not want to right the object to disk,
+          //eg we can copy the alignViewport to a new view object
+          //using save and then load
+          try
+          {
             if (!fileName.endsWith(".xml"))
             {
-                fileName = fileName + ".xml";
+              fileName = fileName + ".xml";
             }
 
             JarEntry entry = new JarEntry(fileName);
             jout.putNextEntry(entry);
 
             object.marshal(out);
-        }
-        catch (Exception ex)
-        {
+          }
+          catch (Exception ex)
+          {
             ex.printStackTrace();
+          }
         }
+        return object;
     }
 
     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
@@ -822,7 +854,6 @@ public class Jalview2XML
         return ucs;
     }
 
-    Hashtable seqRefIds;
 
     /**
      * DOCUMENT ME!
@@ -831,9 +862,13 @@ public class Jalview2XML
      */
     public AlignFrame LoadJalviewAlign(final String file)
     {
+        uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
+
         jalview.gui.AlignFrame af = null;
 
         seqRefIds = new Hashtable();
+        viewportsAdded = new Hashtable();
+
         Vector gatherToThisFrame= new Vector();
 
         try
@@ -875,7 +910,7 @@ public class Jalview2XML
                     unmar.setValidation(false);
                     object = (JalviewModel) unmar.unmarshal( in );
 
-                    af = LoadFromObject(object, file);
+                    af = LoadFromObject(object, file, true);
                     if(af.viewport.gatherViewsHere)
                     {
                       gatherToThisFrame.add(af);
@@ -989,15 +1024,16 @@ public class Jalview2XML
     }
 
 
-    AlignFrame LoadFromObject(JalviewModel object, String file)
+    AlignFrame LoadFromObject(JalviewModel object,
+                              String file,
+                              boolean loadTrees )
     {
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
         Sequence[] vamsasSeq = vamsasSet.getSequence();
 
         JalviewModelSequence jms = object.getJalviewModelSequence();
 
-        Viewport[] views = jms.getViewport();
-        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
+        Viewport view = jms.getViewport(0);
 
         //////////////////////////////////
         //LOAD SEQUENCES
@@ -1007,7 +1043,6 @@ public class Jalview2XML
 
         ArrayList tmpseqs = new ArrayList();
 
-
         boolean multipleView = false;
 
         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
@@ -1027,12 +1062,12 @@ public class Jalview2XML
             jseq.setDescription(vamsasSeq[i].getDescription());
             jseq.setStart(JSEQ[i].getStart());
             jseq.setEnd(JSEQ[i].getEnd());
-            jseq.setColor(new java.awt.Color(JSEQ[i].getColour()));
             seqRefIds.put(vamsasSeq[i].getId(), jseq);
             tmpseqs.add( jseq );
           }
 
 
+
           if (JSEQ[i].getHidden())
           {
             if (hiddenSeqs == null)
@@ -1215,8 +1250,6 @@ public class Jalview2XML
             }
         }
 
-
-        //  af.changeColour() );
         /////////////////////////
         //LOAD GROUPS
         if (jms.getJGroupCount() > 0)
@@ -1259,6 +1292,10 @@ public class Jalview2XML
                 sg.setOutlineColour(new java.awt.Color(
                         groups[i].getOutlineColour()));
 
+                sg.textColour = new java.awt.Color(groups[i].getTextCol1());
+                sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+                sg.thresholdTextColour = groups[i].getTextColThreshold();
+
                 if (groups[i].getConsThreshold() != 0)
                 {
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
@@ -1281,13 +1318,44 @@ public class Jalview2XML
                                        view.getWidth(),
                                        view.getHeight() );
 
-        af.viewport.sequenceSetID = view.getSequenceSetId();
+        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()));
+        }
+
+        //If we just load in the same jar file again, the sequenceSetId
+        //will be the same, and we end up with multiple references
+        //to the same sequenceSet. We must modify this id on load
+        //so that each load of the file gives a unique id
+        String uniqueSeqSetId =  view.getSequenceSetId()+uniqueSetSuffix;
 
         af.viewport.gatherViewsHere = view.getGatheredViews();
 
         if (view.getSequenceSetId() != null)
-          PaintRefresher.Register(af.alignPanel, view.getSequenceSetId());
+        {
+          jalview.gui.AlignViewport av =
+              (jalview.gui.AlignViewport)
+              viewportsAdded.get(uniqueSeqSetId);
+
+          af.viewport.sequenceSetID = uniqueSeqSetId;
+          if(av!=null)
+          {
 
+            af.viewport.historyList = av.historyList;
+            af.viewport.redoList = av.redoList;
+          }
+          else
+          {
+            viewportsAdded.put(uniqueSeqSetId, af.viewport);
+          }
+
+          PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+        }
         if(hiddenSeqs!=null)
         {
           for(int s=0; s<JSEQ.length; s++)
@@ -1335,45 +1403,40 @@ public class Jalview2XML
           af.alignPanel.adjustAnnotationHeight();
         }
 
-        af.viewport.viewName = view.getViewName();
+        if(view.getViewName()!=null)
+        {
+          af.viewport.viewName = view.getViewName();
+          af.setInitialTabVisible();
+        }
         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.setConservationSelected(view.getConservationSelected());
         af.viewport.setShowJVSuffix(view.getShowFullId());
-        af.seqLimits.setSelected(view.getShowFullId());
-
+        af.viewport.rightAlignIds=view.getRightAlignIds();
         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());
+
+        af.viewport.textColour = new java.awt.Color(view.getTextCol1());
+        af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
+        af.viewport.thresholdTextColour = view.getTextColThreshold();
+
 
         ColourSchemeI cs = null;
 
@@ -1481,25 +1544,28 @@ public class Jalview2XML
             if(cs!=null)
             {
               cs.setThreshold(view.getPidThreshold(), true);
-              cs.setConsensus(af.viewport.vconsensus);
+              cs.setConsensus(af.viewport.hconsensus);
             }
         }
 
-        af.setColourSelected(view.getBgColour());
+
         af.viewport.setGlobalColourScheme(cs);
         af.viewport.setColourAppliesToAllGroups(false);
-        af.changeColour(cs);
+
         if (view.getConservationSelected() && cs!=null)
         {
           cs.setConservationInc(view.getConsThreshold());
         }
 
+        af.changeColour(cs);
+
         af.viewport.setColourAppliesToAllGroups(true);
 
+
+
         if (view.getShowSequenceFeatures())
         {
            af.viewport.showSequenceFeatures = true;
-           af.showSeqFeatures.setSelected(true);
         }
 
         if(jms.getFeatureSettings()!=null)
@@ -1533,13 +1599,15 @@ public class Jalview2XML
           }
         }
 
+        af.setMenusFromViewport(af.viewport);
+
 
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());
 
         //LOAD TREES
         ///////////////////////////////////////
-        if (jms.getTreeCount() > 0)
+        if (loadTrees && jms.getTreeCount() > 0)
         {
             try
             {
@@ -1585,5 +1653,27 @@ public class Jalview2XML
 
         return af;
     }
+
+    public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
+    {
+      jalview.schemabinding.version2.JalviewModel jm
+          = SaveState(ap, null, null, null);
+
+      if (!keepSeqRefs)
+      {
+        seqRefIds.clear();
+        jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
+      }
+      else
+        uniqueSetSuffix = "";
+
+      viewportsAdded = new Hashtable();
+
+      AlignFrame af = LoadFromObject(jm, null, false);
+      af.alignPanels.clear();
+      af.closeMenuItem_actionPerformed(true);
+
+      return af.alignPanel;
+    }
 }