X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cfbd1863b34d8728153dcb1cf772e9e3376115af;hb=0c3e6a10ea83dc9d3591e14b1e55bc98a33dede9;hp=9243e9998f39c9a2c359685b802bcf5d010f982c;hpb=008ad05ffd2964c864cdab0f18dff2fb36c82242;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9243e99..cfbd186 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -27,7 +27,6 @@ import java.awt.datatransfer.*;
 import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
-import javax.swing.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
@@ -43,15 +42,18 @@ import jalview.ws.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame
+    extends GAlignFrame implements ClipboardOwner
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
 
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_HEIGHT = 500;
-  final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
+  AlignmentPanel alignPanel;
+  AlignViewport viewport;
+
+  Vector viewports = new Vector();
+  Vector alignPanels = new Vector();
 
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
@@ -59,6 +61,7 @@ public class AlignFrame
   Stack redoList = new Stack();
   private int treeCount = 0;
 
+
   /**
    * Creates a new AlignFrame object.
    *
@@ -67,10 +70,12 @@ public class AlignFrame
   public AlignFrame(AlignmentI al)
   {
     viewport = new AlignViewport(al);
+    viewports.add(viewport);
+
 
     if(viewport.vconsensus==null)
     {
-      //Out of memory caluclating consensus.
+      //Out of memory calculating consensus.
       BLOSUM62Colour.setEnabled(false);
       PIDColour.setEnabled(false);
       conservationMenuItem.setEnabled(false);
@@ -80,12 +85,7 @@ public class AlignFrame
     }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    alignPanel.annotationPanel.adjustPanelHeight();
-    alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.
-        annotationPanel.getPreferredSize());
-    alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.
-        getPreferredSize());
-    alignPanel.setAnnotationVisible(viewport.getShowAnnotation());
+    alignPanels.add(alignPanel);
 
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
@@ -94,7 +94,23 @@ public class AlignFrame
     else if(sortby.equals("Pairwise Identity"))
       sortPairwiseMenuItem_actionPerformed(null);
 
-    getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
+    tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);
+
+    ///Dataset tab
+    /////////////////////////
+
+    if(al.getDataset()==null)
+    {
+      al.setDataset(null);
+    }
+
+    AlignViewport ds = new AlignViewport(al.getDataset(), true);
+    AlignmentPanel dap = new AlignmentPanel(this, ds);
+    tabbedPane.add("Dataset", dap);
+    viewports.add(ds);
+    alignPanels.add(dap);
+    /////////////////////////
+
 
     viewport.addPropertyChangeListener(new PropertyChangeListener()
     {
@@ -107,6 +123,7 @@ public class AlignFrame
      }
    });
 
+
 	if(Desktop.desktop!=null)
     addServiceListeners();
   }
@@ -145,6 +162,16 @@ public class AlignFrame
 
   }
 
+
+  /*
+   Added so Castor Mapping file can obtain Jalview Version
+  */
+  public String getVersion()
+  {
+    return  jalview.bin.Cache.getProperty("VERSION");
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -157,24 +184,28 @@ public class AlignFrame
     {
       BufferedReader in = new BufferedReader(new FileReader(file));
       SequenceI seq = null;
-      String line, text, token;
-      UserColourScheme ucs;
+      String line, type, desc, token;
+
       int index, start, end;
       StringTokenizer st;
-      SequenceGroup sg;
+      SequenceFeature sf;
+      FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+      int lineNo = 0;
       while ( (line = in.readLine()) != null)
       {
+        lineNo++;
         st = new StringTokenizer(line, "\t");
-        if (st.countTokens() != 6)
+        if (st.countTokens() == 2)
         {
-          System.out.println("Groups file " + file +
-                             " is invalid. Read help file.");
-          System.exit(1);
+          type = st.nextToken();
+          UserColourScheme ucs = new UserColourScheme(st.nextToken());
+          fr.setColour(type, ucs.findColour("A"));
+          continue;
         }
 
         while (st.hasMoreElements())
         {
-          text = st.nextToken();
+          desc = st.nextToken();
           token = st.nextToken();
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
@@ -189,19 +220,39 @@ public class AlignFrame
 
           start = Integer.parseInt(st.nextToken());
           end = Integer.parseInt(st.nextToken());
-          ucs = new UserColourScheme(st.nextToken());
 
           seq = viewport.alignment.getSequenceAt(index);
           start = seq.findIndex(start) - 1;
           end = seq.findIndex(end) - 1;
 
-          sg = new SequenceGroup(text, ucs, true, true, false, start, end);
-          sg.addSequence(seq, true);
+          type = st.nextToken();
+
+          if (fr.getColour(type) == null)
+          {
+            // Probably the old style groups file
+            UserColourScheme ucs = new UserColourScheme(type);
+            fr.setColour(type, ucs.findColour("A"));
+          }
+
+
+          sf = new SequenceFeature(type, desc, "", start, end);
+
+          seq.addSequenceFeature(sf);
+
+
+         // sg = new SequenceGroup(text, ucs, true, true, false, start, end);
+         // sg.addSequence(seq, false);
+
+         // viewport.alignment.addGroup(sg);
 
-          viewport.alignment.addGroup(sg);
         }
       }
 
+      viewport.showSequenceFeatures = true;
+      ((Alignment)viewport.alignment).featuresAdded = true;
+
+      alignPanel.repaint();
+
     }
     catch (Exception ex)
     {
@@ -209,6 +260,12 @@ public class AlignFrame
     }
   }
 
+  public void fetchSequence_actionPerformed(ActionEvent e)
+  {
+    new SequenceFetcher(this);
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -562,6 +619,12 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    Desktop.jalviewClipboard = null;
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -571,7 +634,6 @@ public class AlignFrame
   {
     if (viewport.getSelectionGroup() == null)
     {
-      System.out.println("null here");
       return;
     }
 
@@ -580,7 +642,7 @@ public class AlignFrame
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 
     Hashtable orderedSeqs = new Hashtable();
-    SequenceI [] seqs = new SequenceI[sg.getSize()];
+    SequenceI[] seqs = new SequenceI[sg.getSize()];
 
     for (int i = 0; i < sg.getSize(); i++)
     {
@@ -611,7 +673,6 @@ public class AlignFrame
         }
       }
 
-
       //FIND START RES
       //Returns residue following index if gap
       startRes = seq.findPosition(sg.getStartRes());
@@ -635,12 +696,21 @@ public class AlignFrame
       }
 
       seqs[i] = new Sequence(seq.getName(),
-                             seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),
+                             seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),
                              startRes,
                              endRes);
+      seqs[i].setDescription(seq.getDescription());
+      seqs[i].setDBRef(seq.getDBRef());
+      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
+      seqs[i].setDatasetSequence(seq.getDatasetSequence());
+
     }
 
-    c.setContents(new StringSelection(FastaFile.print(seqs)), null);
+    FastaFile ff = new FastaFile();
+    ff.addDBPrefix( viewport.showDBPrefix );
+    ff.addJVSuffix( viewport.showJVSuffix );
+    c.setContents(new StringSelection( ff.print(seqs)), this);
+    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
   }
 
   /**
@@ -683,14 +753,35 @@ public class AlignFrame
       }
 
       String str = (String) contents.getTransferData(DataFlavor.stringFlavor);
+      if(str.length()<1)
+        return;
 
       String format = IdentifyFile.Identify(str, "Paste");
-      SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);
+      SequenceI[] sequences;
 
+     if(Desktop.jalviewClipboard!=null)
+     {
+       // The clipboard was filled from within Jalview, we must use the sequences
+       // And dataset from the copied alignment
+       sequences = (SequenceI[])Desktop.jalviewClipboard[0];
+     }
+     else
+     {
+       sequences = new FormatAdapter().readFile(str, "Paste", format);
+     }
 
       if (newAlignment)
       {
-        AlignFrame af = new AlignFrame(new Alignment(sequences));
+
+        Alignment alignment = new Alignment(sequences);
+
+        if(Desktop.jalviewClipboard!=null)
+           alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
+        else
+           alignment.setDataset( null );
+
+
+        AlignFrame af = new AlignFrame(alignment);
         String newtitle = new String("Copied sequences");
 
         if (title.startsWith("Copied sequences"))
@@ -709,8 +800,24 @@ public class AlignFrame
       {
         //!newAlignment
         for (int i = 0; i < sequences.length; i++)
+        {
           viewport.alignment.addSequence(sequences[i]);
+          if(sequences[i].getDatasetSequence()==null)
+          {
+             ////////////////////////////
+            //Datset needs extension;
+            /////////////////////////////
+            Sequence ds = new Sequence(sequences[i].getName(),
+                                       AlignSeq.extractGaps("-. ", sequences[i].getSequence()),
+                                       sequences[i].getStart(),
+                                       sequences[i].getEnd());
+            sequences[i].setDatasetSequence(ds);
+            viewport.alignment.getDataset().addSequence(ds);
+
 
+          }
+
+        }
         viewport.setEndSeq(viewport.alignment.getHeight());
         viewport.alignment.getWidth();
         viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
@@ -1070,6 +1177,16 @@ public class AlignFrame
    if(alignPanel.overviewPanel!=null)
      alignPanel.overviewPanel.updateOverviewImage();
 
+  Provenance prov = viewport.alignment.getProvenance();
+  if(prov == null)
+   {
+     prov = new Provenance();
+     viewport.alignment.setProvenance(prov);
+   }
+
+   prov.addEntry("Me",
+       "Edited in Jalview", new java.util.Date(), "myID");
+
    alignPanel.repaint();
  }
 
@@ -1168,14 +1285,23 @@ public class AlignFrame
    *
    * @param e DOCUMENT ME!
    */
-  protected void fullSeqId_actionPerformed(ActionEvent e)
+  protected void seqLimit_actionPerformed(ActionEvent e)
   {
-    viewport.setShowFullId(fullSeqId.isSelected());
+    viewport.setShowJVSuffix(seqLimits.isSelected());
 
     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
     alignPanel.repaint();
   }
 
+  public void seqDBRef_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowDBPrefix(seqDBRef.isSelected());
+
+    alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1278,14 +1404,16 @@ public class AlignFrame
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 
     if (viewport.showSequenceFeatures &&
-        ! ( (Alignment) viewport.alignment).featuresAdded)
+        ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
     {
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.
-          alignment,
+      System.out.println("new fetcher");
+      new SequenceFeatureFetcher(viewport.
+         alignment,
           alignPanel);
-      ( (Alignment) viewport.alignment).featuresAdded = true;
     }
 
+    featureSettings.setEnabled(true);
+
     alignPanel.repaint();
   }
 
@@ -1627,8 +1755,6 @@ public class AlignFrame
     conservationMenuItem.setSelected(false);
     viewport.setConservationSelected(false);
 
-    ColourSchemeI cs = viewport.getGlobalColourScheme();
-
     changeColour(viewport.getGlobalColourScheme());
 
     modifyPID_actionPerformed(null);
@@ -1763,7 +1889,7 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,
                                    HistoryItem.SORT));
-    AlignmentSorter.sortByID(viewport.getAlignment());
+    AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);
     alignPanel.repaint();
   }
 
@@ -2242,11 +2368,11 @@ public class AlignFrame
    */
   public void BuildWebServiceMenu()
   {
-    if ( (Desktop.discoverer.services != null)
-        && (Desktop.discoverer.services.size() > 0))
+    if ( (Discoverer.services != null)
+        && (Discoverer.services.size() > 0))
     {
-      Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");
-      Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");
+      Vector msaws = (Vector) Discoverer.services.get("MsaWS");
+      Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");
       Vector wsmenu = new Vector();
       if (msaws != null)
       {
@@ -2262,8 +2388,8 @@ public class AlignFrame
             public void actionPerformed(ActionEvent e)
             {
               SequenceI[] msa = gatherSequencesForAlignment();
-              MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true);
+              new jalview.ws.MsaWSClient(sh, title, msa,
+                  false, true, viewport.getAlignment().getDataset());
 
             }
 
@@ -2279,8 +2405,8 @@ public class AlignFrame
               public void actionPerformed(ActionEvent e)
               {
                 SequenceI[] msa = gatherSequencesForAlignment();
-                MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true);
+                new jalview.ws.MsaWSClient(sh, title, msa,
+                    true, true, viewport.getAlignment().getDataset());
 
               }
 
@@ -2308,8 +2434,7 @@ public class AlignFrame
               if (msa.length == 1)
               {
                 // Single Sequence prediction
-                jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,
-                    title, msa[0]);
+                new jalview.ws.JPredClient(sh,title, msa[0]);
               }
               else
               {
@@ -2342,4 +2467,144 @@ public class AlignFrame
     // TODO: group services by location as well as function.
   }
 
+  public void vamsasStore_actionPerformed(ActionEvent e)
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty("LAST_DIRECTORY"));
+
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Export to Vamsas file");
+    chooser.setToolTipText("Export");
+
+    int value = chooser.showSaveDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
+      //vs.store(chooser.getSelectedFile().getAbsolutePath()   );
+      vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);
+    }
+  }
+
+  public void featureSettings_actionPerformed(ActionEvent e)
+  {
+    new FeatureSettings(viewport, alignPanel);
+  }
+
+
+
+public void showTranslation_actionPerformed(ActionEvent e)
+{
+
+  if(!viewport.alignment.isNucleotide())
+    return;
+
+  viewport.showTranslation(showTranslation.isSelected());
+
+  if(!viewport.alignment.isNucleotide())
+    return;
+
+  int s, sSize = viewport.alignment.getHeight();
+  SequenceI [] newSeq = new SequenceI[sSize];
+
+  int res, resSize;
+  StringBuffer protein;
+  SequenceI seq;
+  for(s=0; s<sSize; s++)
+  {
+    protein = new StringBuffer();
+    seq = (SequenceI)viewport.alignment.getSequenceAt(s);
+    resSize = seq.getLength();
+    for(res = 0; res < resSize; res+=3)
+    {
+      String codon = seq.getSequence(res, res+3);
+      codon = codon.replace('U', 'T');
+      String aa = ResidueProperties.codonTranslate(codon);
+      if(aa==null)
+        protein.append(viewport.getGapCharacter());
+      else if(aa.equals("STOP"))
+        protein.append("X");
+      else
+        protein.append( aa );
+    }
+    newSeq[s] = new Sequence(seq.getName(), protein.toString());
+  }
+
+
+  AlignmentI al = new Alignment(newSeq);
+  al.setDataset(null);
+
+
+  ////////////////////////////////
+  // Copy annotations across
+  jalview.datamodel.AlignmentAnnotation[] annotations
+      = viewport.alignment.getAlignmentAnnotation();
+  int a, aSize;
+  for (int i = 0; i < annotations.length; i++)
+  {
+
+    if (annotations[i].label.equals("Quality") ||
+        annotations[i].label.equals("Conservation") ||
+        annotations[i].label.equals("Consensus"))
+    {
+      continue;
+    }
+
+
+    aSize = viewport.alignment.getWidth()/3;
+    jalview.datamodel.Annotation [] anots =
+        new jalview.datamodel.Annotation[aSize];
+
+    for(a=0; a<viewport.alignment.getWidth(); a++)
+    {
+     if( annotations[i].annotations[a]==null
+      || annotations[i].annotations[a]==null)
+       continue;
+
+      anots[a/3] = new Annotation(
+     annotations[i].annotations[a].displayCharacter,
+     annotations[i].annotations[a].description,
+     annotations[i].annotations[a].secondaryStructure,
+     annotations[i].annotations[a].value,
+     annotations[i].annotations[a].colour);
+    }
+
+    jalview.datamodel.AlignmentAnnotation aa
+          = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
+       annotations[i].description, anots );
+     al.addAnnotation(aa);
+  }
+
+
+   // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
+    //                         NEW_WINDOW_WIDTH,
+     //                        NEW_WINDOW_HEIGHT);
+
+    AlignViewport newViewport = new AlignViewport(al);
+    AlignmentPanel ap = new AlignmentPanel(this, newViewport);
+    tabbedPane.add("Protein", ap);
+    viewports.add(newViewport);
+    alignPanels.add(ap);
+
+    ///Dataset tab
+  /////////////////////////
+
+    AlignViewport ds = new AlignViewport(al.getDataset());
+    ds.setDataset(true);
+    AlignmentPanel dap = new AlignmentPanel(this, ds);
+    tabbedPane.add("Dataset", dap);
+    viewports.add(ds);
+    alignPanels.add(dap);
+  /////////////////////////
+
+
+}
+
+public void tabSelected()
+{
+  int index = tabbedPane.getSelectedIndex();
+  viewport = (AlignViewport)viewports.elementAt(index);
+  alignPanel = (AlignmentPanel)alignPanels.elementAt(index);
+}
+
 }