X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=95912fe7125cb13b6c667fc3a26f4fbffeecf2e6;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=f79a158487307de56bba30052129ada1d65c970b;hpb=94e3d91558ad96de545821aeb548934f8c8353a3;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index f79a158..95912fe 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -168,6 +168,14 @@ public class Jalview2XML
         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 
         jalview.datamodel.AlignmentI jal = af.viewport.alignment;
+        jalview.datamodel.AlignmentI jalhidden = null;
+
+        if(av.hasHiddenRows)
+        {
+          jalhidden = jal;
+          jal = jal.getHiddenSequences().getFullAlignment();
+        }
+
 
         SequenceSet vamsasSet = new SequenceSet();
         Sequence vamsasSeq;
@@ -176,28 +184,61 @@ public class Jalview2XML
         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 
         JSeq jseq;
+        Vector pdbfiles = null;
 
         //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());
             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
 
+            if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)
+            {
+              jalview.datamodel.DBRefEntry [] dbrefs =
+                  jal.getSequenceAt(i).getDatasetSequence().getDBRef();
+
+              for(int d=0; d<dbrefs.length; d++)
+              {
+                DBRef dbref = new DBRef();
+                dbref.setSource( dbrefs[d].getSource() );
+                dbref.setVersion( dbrefs[d].getVersion());
+                dbref.setAccessionId(dbrefs[d].getAccessionId());
+                vamsasSeq.addDBRef(dbref);
+              }
+            }
+
             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);
 
+            if (av.hasHiddenRows)
+            {
+              jseq.setHidden(jalhidden.getHiddenSequences().isHidden(
+                  jal.getSequenceAt(i)));
+
+              if(jal.getSequenceAt(i).getHiddenSequences()!=null)
+              {
+                jalview.datamodel.SequenceI [] reps =
+                    jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
+
+                for(int h=0; h<reps.length; h++)
+                {
+                  jseq.addHiddenSequences(
+                      jal.findIndex(reps[h])
+                      );
+                }
+              }
+            }
+
+
             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
             {
               jalview.datamodel.SequenceFeature[] sf
@@ -229,6 +270,39 @@ public class Jalview2XML
                 pdb.setId(entry.getId());
                 pdb.setType(entry.getType());
 
+                if(entry.getFile()!=null)
+                {
+                  if(pdbfiles==null)
+                    pdbfiles = new Vector();
+
+
+                  if(!pdbfiles.contains(entry.getId()))
+                  {
+                    pdbfiles.addElement(entry.getId());
+                    try
+                    {
+                      File file = new File(entry.getFile());
+                      if(file.exists())
+                      {
+                        byte[] data = new byte[ (int) file.length()];
+                        jout.putNextEntry(new JarEntry(entry.getId()));
+                        DataInputStream dis = new DataInputStream(new
+                            FileInputStream(file));
+                        dis.readFully(data);
+
+                        DataOutputStream dout = new DataOutputStream(jout);
+                        dout.write(data, 0, data.length);
+                        jout.closeEntry();
+                      }
+                    }
+                    catch (Exception ex)
+                    {
+                      ex.printStackTrace();
+                    }
+                  }
+                }
+
+
                 if(entry.getProperty()!=null)
                 {
                   PdbentryItem item = new PdbentryItem();
@@ -429,7 +503,7 @@ public class Jalview2XML
                 groups[i].setDisplayText(sg.getDisplayText());
                 groups[i].setColourText(sg.getColourText());
 
-                for (int s = 0; s < sg.getSize(); s++)
+                for (int s = 0; s < sg.getSize(false); s++)
                 {
                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
                     int index = seqids.indexOf(seq);
@@ -542,6 +616,18 @@ public class Jalview2XML
 
         }
 
+        if(av.hasHiddenColumns)
+        {
+          for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
+          {
+            int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
+            HiddenColumns hc = new HiddenColumns();
+            hc.setStart(region[0]);
+            hc.setEnd(region[1]);
+            view.addHiddenColumns(hc);
+          }
+        }
+
         jms.addViewport(view);
 
 
@@ -631,9 +717,7 @@ public class Jalview2XML
      */
     public AlignFrame LoadJalviewAlign(String file)
     {
-
         jalview.gui.AlignFrame af = null;
-
         try
         {
             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
@@ -662,21 +746,9 @@ 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)
+                if (jarentry != null && jarentry.getName().endsWith(".xml"))
                 {
                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
                     JalviewModel object = new JalviewModel();
@@ -685,9 +757,14 @@ public class Jalview2XML
                     unmar.setValidation(false);
                     object = (JalviewModel) unmar.unmarshal( in );
 
-                    af = LoadFromObject(object);
+                    af = LoadFromObject(object, file);
                     entryCount++;
                 }
+                else if (jarentry != null)
+                {
+                  //Some other file here.
+                  entryCount++;
+                }
             }
             while (jarentry != null);
         }
@@ -725,7 +802,53 @@ public class Jalview2XML
         return af;
     }
 
-    AlignFrame LoadFromObject(JalviewModel object)
+    String loadPDBFile(String file, String pdbId)
+    {
+      System.out.println("load file "+file);
+      try
+      {
+        JarInputStream jin = null;
+
+        if (file.startsWith("http://"))
+        {
+          jin = new JarInputStream(new URL(file).openStream());
+        }
+        else
+        {
+          jin = new JarInputStream(new FileInputStream(file));
+        }
+
+        JarEntry entry = null;
+        do
+        {
+          entry = jin.getNextJarEntry();
+        }
+        while (!entry.getName().equals(pdbId));
+
+        BufferedReader in = new BufferedReader(new InputStreamReader(jin));
+        File outFile = File.createTempFile("jalview_pdb", ".txt");
+        outFile.deleteOnExit();
+        PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+        String data;
+
+        while ( (data = in.readLine()) != null)
+        {
+          out.println(data);
+        }
+        out.close();
+        return outFile.getAbsolutePath();
+
+      }
+      catch (Exception ex)
+      {
+        ex.printStackTrace();
+      }
+
+      return null;
+    }
+
+
+    AlignFrame LoadFromObject(JalviewModel object, String file)
     {
         Vector seqids = new Vector();
         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
@@ -735,6 +858,7 @@ public class Jalview2XML
 
         //////////////////////////////////
         //LOAD SEQUENCES
+        Vector hiddenSeqs = null;
         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
         for (int i = 0; i < vamsasSeq.length; i++)
@@ -743,6 +867,12 @@ public class Jalview2XML
                     vamsasSeq[i].getSequence());
             jseqs[i].setDescription( vamsasSeq[i].getDescription() );
 
+            if(JSEQ[i].getHidden())
+            {
+              if(hiddenSeqs == null)
+                hiddenSeqs = new Vector();
+              hiddenSeqs.addElement(jseqs[i]);
+            }
             jseqs[i].setStart(JSEQ[i].getStart());
             jseqs[i].setEnd(JSEQ[i].getEnd());
             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
@@ -756,6 +886,8 @@ public class Jalview2XML
         al.setDataset(null);
         /////////////////////////////////
 
+
+        Hashtable pdbloaded = new Hashtable();
         for (int i = 0; i < vamsasSeq.length; i++)
         {
           if (JSEQ[i].getFeaturesCount() > 0)
@@ -780,13 +912,39 @@ public class Jalview2XML
               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
               entry.setId(ids[p].getId());
               entry.setType(ids[p].getType());
+              if (ids[p].getFile() != null)
+              {
+                if (!pdbloaded.containsKey(ids[p].getFile()))
+                {
+                  String tmppdb = loadPDBFile(file, ids[p].getId());
+                  entry.setFile(tmppdb);
+                  pdbloaded.put(ids[p].getId(), tmppdb);
+                }
+                else
+                  entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+              }
+
               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
             }
+          }
+          if(vamsasSeq[i].getDBRefCount()>0)
+          {
+            for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
+            {
+              jalview.datamodel.DBRefEntry entry =
+                  new jalview.datamodel.DBRefEntry(
+                      vamsasSeq[i].getDBRef(d).getSource(),
+                      vamsasSeq[i].getDBRef(d).getVersion(),
+                      vamsasSeq[i].getDBRef(d).getAccessionId()
+                      );
+              al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
+            }
 
           }
         }
 
 
+
          /////////////////////////////////
         //////////////////////////////////
         //LOAD ANNOTATIONS
@@ -915,7 +1073,7 @@ public class Jalview2XML
                 if (groups[i].getConsThreshold() != 0)
                 {
                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
-                            ResidueProperties.propHash, 3, sg.sequences, 0,
+                            ResidueProperties.propHash, 3, sg.getSequences(false), 0,
                             sg.getWidth() - 1);
                     c.calculate();
                     c.verdict(false, 25);
@@ -932,7 +1090,29 @@ public class Jalview2XML
         Viewport[] views = jms.getViewport();
         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 
+
         AlignFrame af = new AlignFrame(al);
+
+        if(hiddenSeqs!=null)
+        {
+          for(int s=0; s<JSEQ.length; s++)
+          {
+            for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
+            {
+              al.getSequenceAt(s).addHiddenSequence(
+                  al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
+                  );
+            }
+          }
+
+          for(int s=0; s<hiddenSeqs.size(); s++)
+          {
+              af.viewport.hideSequence(
+                (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));
+          }
+        }
+
+
         if(hideConsensus || hideQuality || hideConservation)
         {
           int hSize = al.getAlignmentAnnotation().length;
@@ -984,16 +1164,11 @@ public class Jalview2XML
         af.viewport.setWrapAlignment(view.getWrapAlignment());
         af.wrapMenuItem.setSelected(view.getWrapAlignment());
 
-        if (view.getWrapAlignment())
-        {
-            af.alignPanel.setWrapAlignment(view.getWrapAlignment());
-        }
-        else
-        {
-            af.annotationPanelMenuItem.setState(view.getShowAnnotation());
-            af.viewport.setShowAnnotation(view.getShowAnnotation());
-            af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
-        }
+        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());
@@ -1147,6 +1322,17 @@ public class Jalview2XML
          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
         }
 
+        if (view.getHiddenColumnsCount() > 0)
+        {
+          for (int c = 0; c < view.getHiddenColumnsCount(); c++)
+          {
+              af.viewport.hideColumns(
+                view.getHiddenColumns(c).getStart(),
+                view.getHiddenColumns(c).getEnd()+1
+                );
+          }
+        }
+
 
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());