X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=b85d5d447d320dd2d50f9e7dadece70e9fa00f12;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=b714aea53cabf9b96dea336328ca497d1ca28d14;hpb=366b11bb8e79ff5bb1a9e6c50b648c3d4101862c;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b714aea..b85d5d4 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -35,7 +35,7 @@ import jalview.jbgui.*;
 import jalview.schemes.*;
 import jalview.ws.*;
 import java.awt.dnd.*;
-
+import org.biojava.dasobert.eventmodel.*;
 
 /**
  * DOCUMENT ME!
@@ -44,7 +44,7 @@ import java.awt.dnd.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame implements ClipboardOwner, DropTargetListener
+    extends GAlignFrame implements DropTargetListener, FeatureListener
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
@@ -54,25 +54,20 @@ public class AlignFrame
   AlignmentPanel alignPanel;
   AlignViewport viewport;
 
-  Vector viewports = new Vector();
-  Vector alignPanels = new Vector();
-
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
   Stack historyList = new Stack();
   Stack redoList = new Stack();
   private int treeCount = 0;
 
-
   /**
-   * Creates a new AlignFrame object.
-   *
-   * @param al DOCUMENT ME!
+   * new alignment window with hidden columns
+   * @param al AlignmentI
+   * @param hiddenColumns ColumnSelection or null
    */
-  public AlignFrame(AlignmentI al)
-  {
-    viewport = new AlignViewport(al);
-    viewports.add(viewport);
+  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
+
+    viewport = new AlignViewport(al, hiddenColumns);
 
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
@@ -88,7 +83,6 @@ public class AlignFrame
     }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    alignPanels.add(alignPanel);
 
     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
@@ -130,11 +124,35 @@ public class AlignFrame
    });
 
 
-  if (Desktop.desktop != null)
+    if (Desktop.desktop != null)
+    {
+      addServiceListeners();
+      setGUINucleotide(al.isNucleotide());
+    }
+
+
+    if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+    {
+      wrapMenuItem.setSelected(true);
+      wrapMenuItem_actionPerformed(null);
+    }
+
+  }
+
+
+  /**
+   * Creates a new AlignFrame object.
+   *
+   * @param al DOCUMENT ME!
+   */
+  public AlignFrame(AlignmentI al)
   {
-    addServiceListeners();
-    setGUINucleotide(al.isNucleotide());
+    this(al, null);
   }
+
+  public AlignViewport getViewport()
+  {
+    return viewport;
   }
 
   /* Set up intrinsic listeners for dynamically generated GUI bits. */
@@ -168,7 +186,6 @@ public class AlignFrame
       }
       ;
     });
-
   }
 
   public void setGUINucleotide(boolean nucleotide)
@@ -186,6 +203,58 @@ public class AlignFrame
     }
   }
 
+  public void comeBackLater(FeatureEvent evt)
+  {}
+
+  public void newFeatures(FeatureEvent evt)
+  {
+    if (evt.getFeatures().length > 0)
+    {
+      alignPanel.seqPanel.seqCanvas.fr.featuresAdded();
+      alignPanel.repaint();
+      if(featureSettings!=null)
+        featureSettings.setTableData();
+    }
+  }
+
+  Hashtable progressBars;
+  public void setProgressBar(String message, long id)
+  {
+    if(progressBars == null)
+      progressBars = new Hashtable();
+
+    JPanel progressPanel;
+    GridLayout layout = (GridLayout) statusPanel.getLayout();
+    if(progressBars.get( new Long(id) )!=null)
+     {
+       progressPanel = (JPanel)progressBars.get( new Long(id) );
+       statusPanel.remove(progressPanel);
+       progressBars.remove( progressPanel );
+       progressPanel = null;
+       if(message!=null)
+         statusBar.setText(message);
+
+       layout.setRows(layout.getRows() - 1);
+     }
+    else
+    {
+      progressPanel = new JPanel(new BorderLayout(10, 5));
+
+      JProgressBar progressBar = new JProgressBar();
+      progressBar.setIndeterminate(true);
+
+      progressPanel.add(new JLabel(message), BorderLayout.WEST);
+      progressPanel.add(progressBar, BorderLayout.CENTER);
+
+      layout.setRows(layout.getRows() + 1);
+      statusPanel.add(progressPanel);
+
+      progressBars.put(new Long(id), progressPanel);
+    }
+
+    validate();
+  }
+
 
   /*
    Added so Castor Mapping file can obtain Jalview Version
@@ -195,11 +264,32 @@ public class AlignFrame
     return  jalview.bin.Cache.getProperty("VERSION");
   }
 
+  public FeatureRenderer getFeatureRenderer()
+  {
+    return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
+  }
+
 
   public void fetchSequence_actionPerformed(ActionEvent e)
   {
     new SequenceFetcher(this);
   }
+
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+    Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -208,19 +298,15 @@ public class AlignFrame
   public void saveAlignmentMenu_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-        getProperty(
-            "LAST_DIRECTORY"),
+        getProperty( "LAST_DIRECTORY"),
         new String[]
-        {
-        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-        "jar"
-    },
+        { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },
         new String[]
-        {
-        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-    }, currentFileFormat);
+        { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+        currentFileFormat,
+        false);
+
 
-    chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle("Save Alignment to file");
     chooser.setToolTipText("Save");
@@ -263,16 +349,33 @@ public class AlignFrame
             java.io.File.separatorChar) + 1);
       }
 
-      Jalview2XML.SaveAlignment(this, file, shortName);
+      new Jalview2XML().SaveAlignment(this, file, shortName);
 
       // USE Jalview2XML to save this file
       return true;
     }
     else
     {
-      String output = new FormatAdapter().formatSequences(format,
-          viewport.getAlignment().
-          getSequences());
+
+      String[] omitHidden = null;
+
+      if (viewport.hasHiddenColumns)
+      {
+        int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            "The Alignment contains hidden columns."
+            + "\nDo you want to save only the visible alignment?",
+            "Save / Omit Hidden Columns",
+            JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+        if (reply == JOptionPane.YES_OPTION)
+          omitHidden = viewport.getViewAsString(false);
+      }
+
+      String output = new FormatAdapter().formatSequences(
+          format,
+          viewport.alignment.getSequencesArray(),
+          omitHidden);
+
       if (output == null)
       {
         return false;
@@ -285,6 +388,7 @@ public class AlignFrame
 
         out.print(output);
         out.close();
+        this.setTitle(file);
         return true;
       }
       catch (Exception ex)
@@ -302,13 +406,32 @@ public class AlignFrame
    */
   protected void outputText_actionPerformed(ActionEvent e)
   {
+    String [] omitHidden = null;
+
+    if(viewport.hasHiddenColumns)
+    {
+      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          "The Alignment contains hidden columns."
+      +"\nDo you want to output only the visible alignment?",
+      "Save / Omit Hidden Columns",
+      JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+
+      if(reply==JOptionPane.YES_OPTION)
+      {
+        omitHidden = viewport.getViewAsString(false);
+      }
+    }
+
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     Desktop.addInternalFrame(cap,
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().
-                                              getSequences()));
+
+
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        viewport.alignment.getSequencesArray(),
+        omitHidden));
   }
 
   /**
@@ -360,6 +483,42 @@ public class AlignFrame
     thread.start();
   }
 
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
+    new AnnotationExporter().exportFeatures(alignPanel);
+  }
+
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
+    new AnnotationExporter().exportAnnotations(
+      alignPanel,
+      viewport.alignment.getAlignmentAnnotation()
+        );
+  }
+
+
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+    // Pick the tree file
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Load Jalview Annotations or Features File");
+    chooser.setToolTipText("Load Jalview Annotations / Features file");
+
+    int value = chooser.showOpenDialog(null);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      String choice = chooser.getSelectedFile().getPath();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(choice);
+    }
+
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -450,42 +609,8 @@ public class AlignFrame
   // used by undo and redo
   void restoreHistoryItem(HistoryItem hi)
   {
-    if (hi.getType() == HistoryItem.SORT)
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        viewport.alignment.getSequences().setElementAt(hi.getSequences()
-            .elementAt(i),
-            i);
-      }
-    }
-    else
-    {
-      for (int i = 0; i < hi.getSequences().size(); i++)
-      {
-        SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);
 
-        if (restore.getLength() == 0)
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-          viewport.alignment.getSequences().insertElementAt(restore,
-              hi.getAlignIndex(i));
-        }
-        else
-        {
-          restore.setSequence(hi.getHidden().elementAt(i).toString());
-        }
-      }
-
-      if (hi.getType() == HistoryItem.PASTE)
-      {
-        for (int i = viewport.alignment.getHeight() - 1;
-             i > (hi.getSequences().size() - 1); i--)
-        {
-          viewport.alignment.deleteSequence(i);
-        }
-      }
-    }
+    hi.restore();
 
     updateEditMenuBar();
 
@@ -513,14 +638,14 @@ public class AlignFrame
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.sequences.contains(seq))
+        if (!sg.getSequences(false).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i - 1);
 
-        if (sg.sequences.contains(temp))
+        if (sg.getSequences(false).contains(temp))
         {
           continue;
         }
@@ -535,14 +660,14 @@ public class AlignFrame
       {
         SequenceI seq = viewport.alignment.getSequenceAt(i);
 
-        if (!sg.sequences.contains(seq))
+        if (!sg.getSequences(false).contains(seq))
         {
           continue;
         }
 
         SequenceI temp = viewport.alignment.getSequenceAt(i + 1);
 
-        if (sg.sequences.contains(temp))
+        if (sg.getSequences(false).contains(temp))
         {
           continue;
         }
@@ -555,10 +680,6 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
-  public void lostOwnership(Clipboard clipboard, Transferable contents)
-  {
-    Desktop.jalviewClipboard = null;
-  }
 
 
   /**
@@ -573,79 +694,41 @@ public class AlignFrame
       return;
     }
 
-    SequenceGroup sg = viewport.getSelectionGroup();
-
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-
-    Hashtable orderedSeqs = new Hashtable();
-    SequenceI[] seqs = new SequenceI[sg.getSize()];
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    String[] omitHidden = null;
 
-    for (int i = 0; i < sg.getSize(); i++)
+    if (viewport.hasHiddenColumns)
     {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.alignment.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
+      omitHidden = viewport.getViewAsString(true);
     }
 
-    int index = 0, startRes, endRes;
-    char ch;
-
-    for (int i = 0; i < sg.getSize(); i++)
-    {
-      SequenceI seq = null;
-
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-
-          break;
-        }
-        else
-        {
-          index++;
-        }
-      }
+    String output = new FormatAdapter().formatSequences(
+        "Fasta",
+        seqs,
+        omitHidden);
 
-      //FIND START RES
-      //Returns residue following index if gap
-      startRes = seq.findPosition(sg.getStartRes());
 
-      //FIND END RES
-      //Need to find the residue preceeding index if gap
-      endRes = 0;
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+        .setContents(new StringSelection(output), Desktop.instance);
 
-      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
+    Vector hiddenColumns = null;
+    if(viewport.hasHiddenColumns)
+    {
+      hiddenColumns =new Vector();
+      int hiddenOffset = viewport.getSelectionGroup().getStartRes();
+      for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)
       {
-        ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
-        {
-          endRes++;
-        }
-      }
+        int[] region = (int[])
+            viewport.getColumnSelection().getHiddenColumns().elementAt(i);
 
-      if (endRes > 0)
-      {
-        endRes += seq.getStart() - 1;
+        hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
+                          region[1]-hiddenOffset});
       }
-
-      seqs[i] = new Sequence(seq.getName(),
-                             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());
-
     }
 
-    FastaFile ff = new FastaFile();
-    ff.addJVSuffix( viewport.showJVSuffix );
-    c.setContents(new StringSelection( ff.print(seqs)), this);
-    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
+    Desktop.jalviewClipboard = new Object[]{ seqs,
+        viewport.alignment.getDataset(),
+        hiddenColumns};
   }
 
   /**
@@ -694,6 +777,7 @@ public class AlignFrame
       String format = new IdentifyFile().Identify(str, "Paste");
       SequenceI[] sequences;
 
+
      if(Desktop.jalviewClipboard!=null)
      {
        // The clipboard was filled from within Jalview, we must use the sequences
@@ -705,69 +789,107 @@ public class AlignFrame
        sequences = new FormatAdapter().readFile(str, "Paste", format);
      }
 
+     AlignmentI alignment = null;
+
       if (newAlignment)
       {
-
-        Alignment alignment = new Alignment(sequences);
+        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"))
-        {
-          newtitle = title;
-        }
-        else
-        {
-          newtitle = newtitle.concat("- from " + title);
-        }
-
-        Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
-                                 NEW_WINDOW_HEIGHT);
       }
       else
       {
+        alignment = viewport.getAlignment();
+
         //!newAlignment
         for (int i = 0; i < sequences.length; i++)
         {
           Sequence newseq = new Sequence(sequences[i].getName(),
               sequences[i].getSequence(), sequences[i].getStart(),
               sequences[i].getEnd());
-          viewport.alignment.addSequence(newseq);
-          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());
-            newseq.setDatasetSequence(ds);
-            viewport.alignment.getDataset().addSequence(ds);
-          }
-          else
-          {
-            newseq.setDatasetSequence(sequences[i].getDatasetSequence());
-            if(sequences[i].getDatasetSequence().getAnnotation()!=null)
-            {
-              for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)
-              {
-                viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);
-              }
-            }
-          }
+
+          alignment.addSequence(newseq);
         }
-        viewport.setEndSeq(viewport.alignment.getHeight());
-        viewport.alignment.getWidth();
-        viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+
+
+        viewport.setEndSeq(alignment.getHeight());
+        alignment.getWidth();
+        viewport.firePropertyChange("alignment", null, alignment.getSequences());
       }
+
+
+
+
+
+      // Add any annotations attached to sequences
+      for (int i = 0; i < sequences.length; i++)
+     {
+       if (sequences[i].getAnnotation() != null)
+       {
+         for (int a = 0; a < sequences[i].getAnnotation().length; a++)
+         {
+           AlignmentAnnotation newAnnot =
+               new AlignmentAnnotation(
+                   sequences[i].getAnnotation()[a].label,
+                   sequences[i].getAnnotation()[a].description,
+                   sequences[i].getAnnotation()[a].annotations,
+                   sequences[i].getAnnotation()[a].graphMin,
+                   sequences[i].getAnnotation()[a].graphMax,
+                   sequences[i].getAnnotation()[a].graph);
+
+           sequences[i].getAnnotation()[a] = newAnnot;
+           newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].
+               sequenceMapping;
+           newAnnot.sequenceRef = sequences[i];
+           newAnnot.adjustForAlignment();
+           alignment.addAnnotation(newAnnot);
+           alignment.setAnnotationIndex(newAnnot, a);
+         }
+
+         alignPanel.annotationPanel.adjustPanelHeight();
+       }
+     }
+
+     if(newAlignment)
+     {
+       AlignFrame af = new AlignFrame(alignment);
+       String newtitle = new String("Copied sequences");
+
+       if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)
+         {
+           Vector hc = (Vector)Desktop.jalviewClipboard[2];
+           for(int i=0; i<hc.size(); i++)
+           {
+             int [] region = (int[]) hc.elementAt(i);
+             af.viewport.hideColumns(region[0], region[1]);
+           }
+         }
+
+
+       //>>>This is a fix for the moment, until a better solution is found!!<<<
+       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
+           alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+
+
+       if (title.startsWith("Copied sequences"))
+       {
+         newtitle = title;
+       }
+       else
+       {
+         newtitle = newtitle.concat("- from " + title);
+       }
+
+       Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,
+                                NEW_WINDOW_HEIGHT);
+
+     }
+
+
     }
     catch (Exception ex)
     {
@@ -810,7 +932,7 @@ public class AlignFrame
 
     //Jalview no longer allows deletion of residues.
     //Check here whether any residues are in selection area
-    if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
+   /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)
     {
       for (int i = 0; i < sg.sequences.size(); i++)
       {
@@ -831,14 +953,14 @@ public class AlignFrame
           j++;
         }while(j<=sg.getEndRes());
       }
-    }
+    }*/
 
 
     addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,
                                    HistoryItem.HIDE));
 
 
-    for (int i = 0; i < sg.sequences.size(); i++)
+    for (int i = 0; i < sg.getSize(false); i++)
     {
       SequenceI seq = sg.getSequenceAt(i);
       int index = viewport.getAlignment().findIndex(seq);
@@ -846,7 +968,7 @@ public class AlignFrame
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);
 
       // If the cut affects all sequences, remove highlighted columns
-      if (sg.sequences.size() == viewport.alignment.getHeight())
+      if (sg.getSize(false) == viewport.alignment.getHeight())
       {
         viewport.getColumnSelection().removeElements(sg.getStartRes(),
             sg.getEndRes() + 1);
@@ -921,11 +1043,17 @@ public class AlignFrame
    */
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
+    if(viewport.cursorMode)
+    {
+      alignPanel.seqPanel.keyboardNo1 = null;
+      alignPanel.seqPanel.keyboardNo2 = null;
+    }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
     viewport.setSelectionGroup(null);
     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
     alignPanel.idPanel.idCanvas.searchResults = null;
+    alignPanel.repaint();
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
@@ -954,6 +1082,13 @@ public class AlignFrame
     PaintRefresher.Refresh(null, viewport.alignment);
   }
 
+  public void invertColSel_actionPerformed(ActionEvent e)
+  {
+    viewport.invertColumnSelection();
+    alignPanel.repaint();
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1078,10 +1213,10 @@ public class AlignFrame
     int end = viewport.alignment.getWidth();
 
     if (viewport.getSelectionGroup() != null
-        && viewport.getSelectionGroup().sequences != null
-        && viewport.getSelectionGroup().sequences.size() > 0)
+        && viewport.getSelectionGroup().getSequences(true) != null
+        && viewport.getSelectionGroup().getSize(true) > 0)
     {
-      seqs = viewport.getSelectionGroup().sequences;
+      seqs = viewport.getSelectionGroup().getSequences(true);
       start = viewport.getSelectionGroup().getStartRes();
       end = viewport.getSelectionGroup().getEndRes()+1;
     }
@@ -1143,7 +1278,10 @@ public class AlignFrame
 
  public void alignmentChanged()
  {
-   if(viewport.vconsensus!=null)
+   if(viewport.padGaps)
+     viewport.getAlignment().padGaps();
+
+   if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)
    {
      viewport.updateConsensus();
      viewport.updateConservation();
@@ -1190,7 +1328,8 @@ public class AlignFrame
       SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);
       if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());
+        ((ClustalxColourScheme)sg.cs).resetClustalX(
+            sg.getSequences(true), sg.getWidth());
       }
       sg.recalcConservation();
     }
@@ -1205,8 +1344,11 @@ public class AlignFrame
   {
     addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,
                                    HistoryItem.HIDE));
-    if (viewport.getAlignment().padGaps())
-      alignmentChanged();
+
+    viewport.padGaps = padGapsMenuitem.isSelected();
+
+   // if (viewport.padGaps)
+    alignmentChanged();
   }
 
   /**
@@ -1271,16 +1413,55 @@ public class AlignFrame
    *
    * @param e DOCUMENT ME!
    */
-  protected void wrapMenuItem_actionPerformed(ActionEvent e)
+  public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-    viewport.setWrapAlignment(wrapMenuItem.isSelected());
-    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
     scaleAbove.setVisible(wrapMenuItem.isSelected());
     scaleLeft.setVisible(wrapMenuItem.isSelected());
     scaleRight.setVisible(wrapMenuItem.isSelected());
+    viewport.setWrapAlignment(wrapMenuItem.isSelected());
+    alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
+  }
+
+  public void showAllSeqs_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenSeqs();
+    repaint();
+  }
+
+  public void showAllColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.showAllHiddenColumns();
+  }
+
+  public void hideSelSequences_actionPerformed(ActionEvent e)
+  {
+    if(viewport.getSelectionGroup()==null)
+      return;
+
+    SequenceI [] seqs = viewport.getSelectionGroup().getSequencesInOrder(
+        viewport.alignment
+          );
+
+    for(int i=0; i<seqs.length; i++)
+    {
+      viewport.hideSequence(seqs[i]);
+    }
+
     alignPanel.repaint();
   }
 
+  public void hideSelColumns_actionPerformed(ActionEvent e)
+  {
+    viewport.hideSelectedColumns();
+    alignPanel.repaint();
+  }
+
+  public void hiddenMarkers_actionPerformed(ActionEvent e)
+  {
+    viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
+    repaint();
+  }
+
   /**
    * DOCUMENT ME!
    *
@@ -1347,22 +1528,16 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
-  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
-  {
-    if (!viewport.alignment.isNucleotide())
-    {
-      new SequenceFeatureFetcher(viewport.
-                                 alignment,
-                                 alignPanel);
-      viewport.setShowSequenceFeatures(true);
-      showSeqFeatures.setSelected(true);
-    }
-  }
-
 
+  FeatureSettings featureSettings;
   public void featureSettings_actionPerformed(ActionEvent e)
   {
-    new FeatureSettings(viewport, alignPanel);
+    if(featureSettings !=null )
+    {
+      featureSettings.close();
+      featureSettings = null;
+    }
+    featureSettings = new FeatureSettings(this);
   }
 
   /**
@@ -1545,7 +1720,7 @@ public class AlignFrame
    *
    * @param cs DOCUMENT ME!
    */
-  void changeColour(ColourSchemeI cs)
+  public void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;
 
@@ -1609,7 +1784,8 @@ public class AlignFrame
 
         if (cs instanceof ClustalxColourScheme)
         {
-          sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
+          sg.cs = new ClustalxColourScheme(
+              sg.getSequences(true), sg.getWidth());
         }
         else if (cs instanceof UserColourScheme)
         {
@@ -1633,9 +1809,10 @@ public class AlignFrame
          sg.cs.setThreshold(threshold,
                 viewport.getIgnoreGapsConsensus());
 
-          sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-              sg.getWidth()));
-        }
+         sg.cs.setConsensus(AAFrequency.calculate(
+             sg.getSequences(true), 0,
+             sg.getWidth()));
+       }
         else
           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
 
@@ -1644,7 +1821,7 @@ public class AlignFrame
         {
           Conservation c = new Conservation("Group",
                                             ResidueProperties.propHash, 3,
-                                            sg.sequences, 0,
+                                            sg.getSequences(true), 0,
                                             viewport.alignment.getWidth() - 1);
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
@@ -1883,13 +2060,10 @@ public class AlignFrame
    */
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
-    RedundancyPanel sp = new RedundancyPanel(alignPanel, this);
-    JInternalFrame frame = new JInternalFrame();
-    frame.setContentPane(sp);
-    Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,
-                             100, false);
+    new RedundancyPanel(alignPanel, this);
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -1898,7 +2072,7 @@ public class AlignFrame
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
     if ( (viewport.getSelectionGroup() == null) ||
-        (viewport.getSelectionGroup().getSize() < 2))
+        (viewport.getSelectionGroup().getSize(false) < 2))
     {
       JOptionPane.showInternalMessageDialog(this,
                                             "You must select at least 2 sequences.",
@@ -1921,8 +2095,8 @@ public class AlignFrame
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
     if ( ( (viewport.getSelectionGroup() != null) &&
-          (viewport.getSelectionGroup().getSize() < 4) &&
-          (viewport.getSelectionGroup().getSize() > 0)) ||
+          (viewport.getSelectionGroup().getSize(false) < 4) &&
+          (viewport.getSelectionGroup().getSize(false) > 0)) ||
         (viewport.getAlignment().getHeight() < 4))
     {
       JOptionPane.showInternalMessageDialog(this,
@@ -1937,6 +2111,17 @@ public class AlignFrame
      new PCAPanel(viewport);
   }
 
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+    viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    if(viewport.autoCalculateConsensus)
+    {
+      alignmentChanged();
+    }
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -1986,18 +2171,18 @@ public class AlignFrame
    */
   void NewTreePanel(String type, String pwType, String title)
   {
-    final TreePanel tp;
+    TreePanel tp;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 3))
+        (viewport.getSelectionGroup().getSize(false) > 3))
     {
       int s = 0;
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      while (s < sg.sequences.size())
+      while (s < sg.getSize(false))
       {
-        if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <
+        if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <
             sg.getEndRes())
         {
           JOptionPane.showMessageDialog(Desktop.desktop,
@@ -2012,9 +2197,7 @@ public class AlignFrame
       }
 
       title = title + " on region";
-      tp = new TreePanel(viewport,
-                         viewport.getSelectionGroup().sequences, type, pwType,
-                         sg.getStartRes(), sg.getEndRes());
+      tp = new TreePanel(viewport, type, pwType);
     }
     else
     {
@@ -2031,14 +2214,13 @@ public class AlignFrame
         return;
       }
 
-      tp = new TreePanel(viewport,
-                         viewport.getAlignment().getSequences(), type, pwType,
-                         0,
-                         viewport.alignment.getWidth());
+      if(viewport.alignment.getHeight()<2)
+        return;
+
+      tp = new TreePanel(viewport, type, pwType);
     }
 
     addTreeMenuItem(tp, title);
-    viewport.setCurrentTree(tp.getTree());
 
     Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);
   }
@@ -2123,27 +2305,28 @@ public class AlignFrame
    * or just the selected set will be submitted for multiple alignment.
    *
    */
-  private SequenceI[] gatherSequencesForAlignment()
+  private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
     // Now, check we have enough sequences
-    SequenceI[] msa = null;
+    AlignmentView msa = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 1))
+        (viewport.getSelectionGroup().getSize(false) > 1))
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
-      SequenceGroup seqs = viewport.getSelectionGroup();
+      /*SequenceGroup seqs = viewport.getSelectionGroup();
       int sz;
-      msa = new SequenceI[sz = seqs.getSize()];
+      msa = new SequenceI[sz = seqs.getSize(false)];
 
       for (int i = 0; i < sz; i++)
       {
         msa[i] = (SequenceI) seqs.getSequenceAt(i);
-      }
+      } */
+      msa = viewport.getAlignmentView(true);
     }
     else
     {
-      Vector seqs = viewport.getAlignment().getSequences();
+      /*Vector seqs = viewport.getAlignment().getSequences();
 
       if (seqs.size() > 1)
       {
@@ -2153,7 +2336,8 @@ public class AlignFrame
         {
           msa[i] = (SequenceI) seqs.elementAt(i);
         }
-      }
+      }*/
+      msa = viewport.getAlignmentView(false);
     }
     return msa;
   }
@@ -2170,19 +2354,19 @@ public class AlignFrame
     SequenceI[] msa = null;
 
     if ( (viewport.getSelectionGroup() != null) &&
-        (viewport.getSelectionGroup().getSize() > 0))
+        (viewport.getSelectionGroup().getSize(false) > 0))
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
       SequenceGroup seqs = viewport.getSelectionGroup();
 
-      if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())
+      if ( (seqs.getSize(false) == 1) || !viewport.alignment.isAligned())
       {
         seq = (SequenceI) seqs.getSequenceAt(0);
       }
       else
       {
         int sz;
-        msa = new SequenceI[sz = seqs.getSize()];
+        msa = new SequenceI[sz = seqs.getSize(false)];
 
         for (int i = 0; i < sz; i++)
         {
@@ -2286,9 +2470,9 @@ public class AlignFrame
       if (nf.getTree() != null)
       {
         tp = new TreePanel(viewport,
-                           viewport.getAlignment().getSequences(), nf,
                            "FromFile",
-                           title);
+                           title,
+                           nf);
 
         tp.setSize(w,h);
 
@@ -2347,6 +2531,7 @@ public class AlignFrame
       {
         // Add any Multiple Sequence Alignment Services
         final JMenu msawsmenu = new JMenu("Alignment");
+        final AlignFrame af = this;
         for (int i = 0, j = msaws.size(); i < j; i++)
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
@@ -2356,9 +2541,9 @@ public class AlignFrame
           {
             public void actionPerformed(ActionEvent e)
             {
-              SequenceI[] msa = gatherSequencesForAlignment();
+              AlignmentView msa = gatherSequencesForAlignment();
               new jalview.ws.MsaWSClient(sh, title, msa,
-                  false, true, viewport.getAlignment().getDataset());
+                  false, true, viewport.getAlignment().getDataset(), af);
 
             }
 
@@ -2373,9 +2558,9 @@ public class AlignFrame
             {
               public void actionPerformed(ActionEvent e)
               {
-                SequenceI[] msa = gatherSequencesForAlignment();
+                AlignmentView msa = gatherSequencesForAlignment();
                 new jalview.ws.MsaWSClient(sh, title, msa,
-                    true, true, viewport.getAlignment().getDataset());
+                    true, true, viewport.getAlignment().getDataset(), af);
 
               }
 
@@ -2458,10 +2643,12 @@ public class AlignFrame
 
 
 
-
 public void showTranslation_actionPerformed(ActionEvent e)
 {
-  int s, sSize = viewport.alignment.getHeight();
+  SequenceI [] selection = viewport.getSelectionAsNewSequence();
+  String [] seqstring = viewport.getViewAsString(true);
+
+  int s, sSize = selection.length;
   SequenceI [] newSeq = new SequenceI[sSize];
 
   int res, resSize;
@@ -2470,7 +2657,7 @@ public void showTranslation_actionPerformed(ActionEvent e)
   for(s=0; s<sSize; s++)
   {
     protein = new StringBuffer();
-    seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());
+    seq = AlignSeq.extractGaps("-. ", seqstring[s]);
     resSize = seq.length();
     resSize -= resSize%3;
 
@@ -2486,7 +2673,8 @@ public void showTranslation_actionPerformed(ActionEvent e)
       else
         protein.append( aa );
     }
-    newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());
+    newSeq[s] = new Sequence(selection[s].getName(),
+                             protein.toString());
   }
 
 
@@ -2499,42 +2687,42 @@ public void showTranslation_actionPerformed(ActionEvent e)
   jalview.datamodel.AlignmentAnnotation[] annotations
       = viewport.alignment.getAlignmentAnnotation();
   int a, aSize;
-  for (int i = 0; i < annotations.length; i++)
+  if(annotations!=null)
   {
-
-    if (annotations[i].label.equals("Quality") ||
-        annotations[i].label.equals("Conservation") ||
-        annotations[i].label.equals("Consensus"))
+    for (int i = 0; i < annotations.length; i++)
     {
-      continue;
-    }
-
+      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];
+      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;
+      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);
-    }
+        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
+      jalview.datamodel.AlignmentAnnotation aa
           = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,
-       annotations[i].description, anots );
-     al.addAnnotation(aa);
+          annotations[i].description, anots);
+      al.addAnnotation(aa);
+    }
   }
 
-
     AlignFrame af = new AlignFrame(al);
     Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),
                              NEW_WINDOW_WIDTH,
@@ -2573,92 +2761,28 @@ public void showTranslation_actionPerformed(ActionEvent e)
  *
  * @param String DOCUMENT ME!
  */
-public boolean parseGroupsFile(String file)
+public boolean parseFeaturesFile(String file, String type)
 {
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      SequenceI seq = null;
-      String line, type, desc, token;
-
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      int lineNo = 0;
-      String featureGroup = null;
-      while ( (line = in.readLine()) != null)
-      {
-        lineNo++;
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
-        {
-          type = st.nextToken();
-          if (type.equalsIgnoreCase("startgroup"))
-          {
-            featureGroup = st.nextToken();
-          }
-          else if (type.equalsIgnoreCase("endgroup"))
-          {
-            //We should check whether this is the current group,
-            //but at present theres no way of showing more than 1 group
-            st.nextToken();
-            featureGroup = null;
-          }
-          else
-          {
-            UserColourScheme ucs = new UserColourScheme(st.nextToken());
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,
-                ucs.findColour("A"));
-          }
-          continue;
-        }
-
-        while (st.hasMoreElements())
-        {
-          desc = st.nextToken();
-          token = st.nextToken();
-          if (!token.equals("ID_NOT_SPECIFIED"))
-          {
-            index = viewport.alignment.findIndex(viewport.alignment.findName(token));
-            st.nextToken();
-          }
-          else
-          {
-            index = Integer.parseInt(st.nextToken());
-          }
-
-          start = Integer.parseInt(st.nextToken());
-          end = Integer.parseInt(st.nextToken());
-
-          seq = viewport.alignment.getSequenceAt(index);
-
-          type = st.nextToken();
-
-          if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)
-          {
-            // Probably the old style groups file
-            UserColourScheme ucs = new UserColourScheme(type);
-            alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));
-          }
-
-          sf = new SequenceFeature(type, desc, "", start, end);
-          sf.setFeatureGroup(featureGroup);
-
-          seq.getDatasetSequence().addSequenceFeature(sf);
-        }
-      }
+    boolean featuresFile = false;
+    try{
+      featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),
+                                         alignPanel.seqPanel.seqCanvas.
+                                         getFeatureRenderer().featureColours,
+                                         false);
     }
-    catch (Exception ex)
+    catch(Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Error parsing groups file: " + ex);
-      return false;
     }
 
-    viewport.showSequenceFeatures = true;
-    showSeqFeatures.setSelected(true);
-    alignPanel.repaint();
-    return true;
+    if(featuresFile)
+    {
+      viewport.showSequenceFeatures = true;
+      showSeqFeatures.setSelected(true);
+      alignPanel.repaint();
+    }
+
+    return featuresFile;
 }
 
 public void dragEnter(DropTargetDragEvent evt)
@@ -2715,50 +2839,14 @@ public void drop(DropTargetDropEvent evt)
     {
       e.printStackTrace();
     }
-
     if (files != null)
     {
       try
       {
-        boolean isAnnotation = false;
 
         for (int i = 0; i < files.size(); i++)
         {
-          String file = files.get(i).toString();
-
-          isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);
-
-          if( !isAnnotation )
-          {
-            boolean isGroupsFile = parseGroupsFile(file);
-            if (!isGroupsFile)
-            {
-              String protocol = "File";
-              String format = new IdentifyFile().Identify(file, protocol);
-              SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);
-
-              FastaFile ff = new FastaFile();
-              Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-              c.setContents(new StringSelection(ff.print(sequences)), this);
-
-              this.paste(false);
-
-            }
-          }
-        }
-
-        if(isAnnotation)
-        {
-          int height = alignPanel.annotationPanel.adjustPanelHeight();
-          alignPanel.annotationScroller.setPreferredSize(
-              new Dimension(alignPanel.annotationScroller.getWidth(),
-                            height));
-
-          alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
-              alignPanel.annotationSpaceFillerHolder.getWidth(),
-              height));
-
-          alignPanel.addNotify();
+          loadJalviewDataFile(files.get(i).toString());
         }
       }
       catch (Exception ex)
@@ -2768,4 +2856,35 @@ public void drop(DropTargetDropEvent evt)
     }
 }
 
+  // This method will attempt to load a "dropped" file first by testing
+  // whether its and Annotation file, then features file. If both are
+  // false then the user may have dropped an alignment file onto this
+  // AlignFrame
+   public void loadJalviewDataFile(String file)
+  {
+    try{
+      boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.
+          alignment, file);
+
+      if (!isAnnotation)
+      {
+        boolean isGroupsFile = parseFeaturesFile(file,
+                                                AppletFormatAdapter.FILE);
+        if (!isGroupsFile)
+        {
+          String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
+          new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
+        }
+      }
+      else
+      {
+        // (isAnnotation)
+        alignPanel.adjustAnnotationHeight();
+      }
+
+    }catch(Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
 }