X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=1f2cbb1708024243be75be38434d2a4cf228e8d0;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=d652da2a5aec05c6abeda173a8c290f6019d2211;hpb=15ade8926ea520ead84b0dd75c6a3aaac7368bc5;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d652da2..1f2cbb1 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
@@ -210,9 +251,34 @@ public class Jalview2XML
                 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());
+                features.setScore(sf[index].getScore());
+                if(sf[index].links!=null)
+                {
+                  for(int l=0; l<sf[index].links.size(); l++)
+                  {
+                    OtherData keyValue = new OtherData();
+                    keyValue.setKey("LINK_"+l);
+                    keyValue.setValue(sf[index].links.elementAt(l).toString());
+                    features.addOtherData(keyValue);
+                  }
+                }
+                if(sf[index].otherDetails!=null)
+                {
+                  String key;
+                  Enumeration keys = sf[index].otherDetails.keys();
+                  while(keys.hasMoreElements())
+                  {
+                    key = keys.nextElement().toString();
+                    OtherData keyValue = new OtherData();
+                    keyValue.setKey( key );
+                    keyValue.setValue(
+                        sf[index].otherDetails.get(key).toString());
+                    features.addOtherData(keyValue);
+                  }
+                }
+
                 jseq.addFeatures(features);
                 index ++;
               }
@@ -230,6 +296,39 @@ 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();
@@ -307,19 +406,31 @@ public class Jalview2XML
 
             for (int i = 0; i < aa.length; i++)
             {
+                Annotation an = new Annotation();
+
                 if (aa[i].label.equals("Quality") ||
                         aa[i].label.equals("Conservation") ||
                         aa[i].label.equals("Consensus"))
                 {
+                    an.setLabel(aa[i].label);
+                    an.setGraph(true);
+                    vamsasSet.addAnnotation(an);
                     continue;
                 }
 
-                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);
+                  an.setGraphGroup(aa[i].graphGroup);
                   if(aa[i].getThreshold()!=null)
                   {
                     ThresholdLine line = new ThresholdLine();
@@ -350,6 +461,10 @@ public class Jalview2XML
                     ae.setPosition(a);
                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
                         "");
+
+                    if(aa[i].annotations[a].colour!=java.awt.Color.black)
+                      ae.setColour(aa[i].annotations[a].colour.getRGB());
+
                     an.addAnnotationElement(ae);
                 }
 
@@ -414,7 +529,7 @@ 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);
@@ -508,6 +623,8 @@ public class Jalview2XML
 
           String [] renderOrder =
               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+
+          Vector settingsAdded = new Vector();
           for(int ro=0; ro<renderOrder.length; ro++)
           {
             Setting setting = new Setting();
@@ -521,12 +638,46 @@ public class Jalview2XML
                 );
 
             fs.addSetting(setting);
+            settingsAdded.addElement(renderOrder[ro]);
+          }
 
+          //Make sure we save none displayed feature settings
+          Enumeration en =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+          while(en.hasMoreElements())
+          {
+            String key = en.nextElement().toString();
+            if(settingsAdded.contains(key))
+              continue;
+
+            Setting setting = new Setting();
+            setting.setType(key);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+                );
+
+            setting.setDisplay(false);
+
+            fs.addSetting(setting);
+            settingsAdded.addElement(key);
           }
+
           jms.setFeatureSettings(fs);
 
         }
 
+        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);
 
 
@@ -616,9 +767,7 @@ public class Jalview2XML
      */
     public AlignFrame LoadJalviewAlign(String file)
     {
-
         jalview.gui.AlignFrame af = null;
-
         try
         {
             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
@@ -647,21 +796,9 @@ 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();
@@ -670,14 +807,22 @@ 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);
         }
         catch(java.net.UnknownHostException ex)
         {
+          if (Desktop.instance != null)
+            Desktop.instance.stopLoading();
+
           ex.printStackTrace();
           System.err.println("Couldn't locate Jalview XML file : " +
               ex + "\n");
@@ -689,12 +834,15 @@ public class Jalview2XML
         }
         catch (Exception ex)
         {
+          if (Desktop.instance != null)
+            Desktop.instance.stopLoading();
+
           //Is Version 1 Jar file?
           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 
           if(af!=null)
           {
-            System.out.println("Successfuly loaded archive file");
+            System.out.println("Successfully loaded archive file");
             return af;
           }
           ex.printStackTrace();
@@ -710,7 +858,53 @@ 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);
@@ -720,6 +914,7 @@ 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++)
@@ -728,6 +923,12 @@ 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()));
@@ -741,6 +942,8 @@ public class Jalview2XML
         al.setDataset(null);
         /////////////////////////////////
 
+
+        Hashtable pdbloaded = new Hashtable();
         for (int i = 0; i < vamsasSeq.length; i++)
         {
           if (JSEQ[i].getFeaturesCount() > 0)
@@ -754,6 +957,17 @@ public class Jalview2XML
                   features[f].getBegin(), features[f].getEnd(),
                   features[f].getFeatureGroup());
 
+              sf.setScore(features[f].getScore());
+              for(int od=0; od<features[f].getOtherDataCount(); od++)
+              {
+                OtherData keyValue = features[f].getOtherData(od);
+                if(keyValue.getKey().startsWith("LINK"))
+                  sf.addLink(keyValue.getValue());
+                else
+                  sf.setValue(keyValue.getKey(), keyValue.getValue());
+
+              }
+
               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
             }
           }
@@ -765,21 +979,68 @@ 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
+        boolean hideQuality = true,
+            hideConservation = true,
+            hideConsensus = true;
+
         if (vamsasSet.getAnnotation() != null)
         {
             Annotation[] an = vamsasSet.getAnnotation();
 
             for (int i = 0; i < an.length; i++)
             {
+               if (an[i].getLabel().equals("Quality"))
+                {
+                 hideQuality = false;
+                 continue;
+                }
+               else if(an[i].getLabel().equals("Conservation"))
+               {
+                 hideConservation = false;
+                 continue;
+               }
+               else if(an[i].getLabel().equals("Consensus"))
+               {
+                 hideConsensus = false;
+                 continue;
+               }
+
                 AnnotationElement[] ae = an[i].getAnnotationElement();
                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
 
@@ -789,6 +1050,7 @@ public class Jalview2XML
                             ae[aa].getDescription(),
                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
                             ae[aa].getValue());
+                    anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
                 }
 
                 jalview.datamodel.AlignmentAnnotation jaa = null;
@@ -799,6 +1061,8 @@ public class Jalview2XML
                       an[i].getDescription(), anot, 0, 0,
                       an[i].getGraphType());
 
+                  jaa.graphGroup = an[i].getGraphGroup();
+
                   if (an[i].getThresholdLine() != null)
                   {
                     jaa.setThreshold(new jalview.datamodel.GraphLine(
@@ -816,19 +1080,19 @@ 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();
-        Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
-
-        AlignFrame af = new AlignFrame(al);
-
-
         //  af.changeColour() );
         /////////////////////////
         //LOAD GROUPS
@@ -876,7 +1140,7 @@ 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);
@@ -888,6 +1152,56 @@ public class Jalview2XML
         }
 
 
+        /////////////////////////////////
+        // LOAD VIEWPORT
+        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;
+          for (int h = 0; h < hSize; h++)
+          {
+            if (
+                (hideConsensus &&
+                 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
+                ||
+                (hideQuality &&
+                 al.getAlignmentAnnotation()[h].label.equals("Quality"))
+                ||
+                (hideConservation &&
+                 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
+            {
+              al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
+              hSize--;
+              h--;
+            }
+          }
+          af.alignPanel.adjustAnnotationHeight();
+        }
 
         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
@@ -917,16 +1231,11 @@ 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());
@@ -1080,6 +1389,17 @@ 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());