From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 31 Oct 2005 15:57:24 +0000 (+0000)
Subject: dbPrefix and jvsuffix added
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e378e950e3f2611dbf0dfeb2ffae60c37f7adcbe;p=jalview.git

dbPrefix and jvsuffix added
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7b394a3..1d408db 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -42,7 +42,7 @@ import jalview.ws.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame
+    extends GAlignFrame implements ClipboardOwner
 {
   /** DOCUMENT ME!! */
   public static final int NEW_WINDOW_WIDTH = 700;
@@ -103,8 +103,7 @@ public class AlignFrame
       al.setDataset(null);
     }
 
-    AlignViewport ds = new AlignViewport(al.getDataset());
-    ds.setDataset(true);
+    AlignViewport ds = new AlignViewport(al.getDataset(), true);
     AlignmentPanel dap = new AlignmentPanel(this, ds);
     tabbedPane.add("Dataset", dap);
     viewports.add(ds);
@@ -603,6 +602,12 @@ public class AlignFrame
     alignPanel.repaint();
   }
 
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    Desktop.jalviewClipboard = null;
+  }
+
+
   /**
    * DOCUMENT ME!
    *
@@ -612,7 +617,7 @@ public class AlignFrame
   {
     if (viewport.getSelectionGroup() == null)
     {
-      System.out.println("null here");
+      System.out.println("nothing selected");
       return;
     }
 
@@ -621,7 +626,7 @@ 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++)
     {
@@ -652,7 +657,6 @@ public class AlignFrame
         }
       }
 
-
       //FIND START RES
       //Returns residue following index if gap
       startRes = seq.findPosition(sg.getStartRes());
@@ -676,12 +680,20 @@ 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(new FastaFile().print(seqs)), null);
+    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
+    FastaFile ff = new FastaFile();
+    ff.addDBPrefix( viewport.showDBPrefix );
+    ff.addJVSuffix( viewport.showJVSuffix );
+    c.setContents(new StringSelection( ff.print(seqs)), this);
   }
 
   /**
@@ -728,13 +740,29 @@ public class AlignFrame
         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)
       {
+
         Alignment alignment = new Alignment(sequences);
-        alignment.setDataset( viewport.alignment.getDataset() );
+
+        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");
 
@@ -1223,14 +1251,23 @@ 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!
    *
@@ -1332,12 +1369,13 @@ public class AlignFrame
   {
     viewport.showSequenceFeatures(sequenceFeatures.isSelected());
 
-    if (viewport.showSequenceFeatures &&
-        ! ( (Alignment) viewport.alignment).featuresAdded)
+   // if (viewport.showSequenceFeatures &&
+     //   ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)
     {
-      new SequenceFeatureFetcher(viewport.
-          alignment,
-          alignPanel);
+     // System.out.println("new fetcher");
+    //  new SequenceFeatureFetcher(viewport.
+     //     alignment,
+     //     alignPanel);
     }
 
     featureSettings.setEnabled(true);
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f57e993..3ed2a7c 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -43,7 +43,8 @@ public class AlignViewport
     int endRes;
     int startSeq;
     int endSeq;
-    boolean showFullId = false;
+    boolean showDBPrefix = true;
+    boolean showJVSuffix = true;
     boolean showText = true;
     boolean showColourText = false;
     boolean showBoxes = true;
@@ -90,6 +91,13 @@ public class AlignViewport
 
     boolean isDataset = false;
 
+
+    public AlignViewport(AlignmentI al, boolean dataset)
+    {
+      isDataset = dataset;
+      setAlignment(al);
+      init();
+    }
     /**
      * Creates a new AlignViewport object.
      *
@@ -98,13 +106,18 @@ public class AlignViewport
     public AlignViewport(AlignmentI al)
     {
         setAlignment(al);
+        init();
+    }
+
+    void init()
+    {
         this.startRes = 0;
-        this.endRes = al.getWidth() - 1;
+        this.endRes = alignment.getWidth() - 1;
         this.startSeq = 0;
-        this.endSeq = al.getHeight() - 1;
+        this.endSeq = alignment.getHeight() - 1;
 
-
-      showFullId = Cache.getDefault("SHOW_FULL_ID", true);
+      showDBPrefix = Cache.getDefault("SHOW_DBPREFIX", true);
+      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
 
@@ -134,7 +147,7 @@ public class AlignViewport
 
         // We must set conservation and consensus before setting colour,
         // as Blosum and Clustal require this to be done
-        if(vconsensus==null)
+        if(vconsensus==null && !isDataset)
         {
           updateConservation();
           updateConsensus();
@@ -913,9 +926,29 @@ public class AlignViewport
      *
      * @return DOCUMENT ME!
      */
-    public boolean getShowFullId()
+    public boolean getShowJVSuffix()
+    {
+        return showJVSuffix;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setShowJVSuffix(boolean b)
+    {
+        showJVSuffix = b;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowDBPrefix()
     {
-        return showFullId;
+        return showDBPrefix;
     }
 
     /**
@@ -923,9 +956,9 @@ public class AlignViewport
      *
      * @param b DOCUMENT ME!
      */
-    public void setShowFullId(boolean b)
+    public void setShowDBPrefix(boolean b)
     {
-        showFullId = b;
+        showDBPrefix = b;
     }
 
     /**