X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cc57961160589c5068f7df08939f9a45573cb9ef;hb=e3eb93bc131a0f088312fddde91b728dbebe40d4;hp=325a6768dc2d9b77232bacaa929fdefe3bfd181c;hpb=ef6291f17491f1c426e2cad44021c31f609e2808;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 325a676..cc57961 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -37,7 +37,6 @@ import jalview.ws.*;
 import java.awt.dnd.*;
 import org.biojava.dasobert.eventmodel.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -69,6 +68,7 @@ public class AlignFrame
    */
   public AlignFrame(AlignmentI al)
   {
+
     viewport = new AlignViewport(al);
 
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
@@ -359,16 +359,13 @@ public class AlignFrame
             JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
         if (reply == JOptionPane.YES_OPTION)
-          omitHidden = viewport.getSelectionAsString();
+          omitHidden = viewport.getViewAsString(false);
       }
 
       String output = new FormatAdapter().formatSequences(
           format,
           viewport.alignment.getSequencesArray(),
-          null);
-          //viewport.getSelectionAsNewSequence(),
-          //omitHidden) ;
-
+          omitHidden);
 
       if (output == null)
       {
@@ -400,12 +397,6 @@ public class AlignFrame
    */
   protected void outputText_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap,
-                             "Alignment output - " + e.getActionCommand(), 600,
-                             500);
-
-
     String [] omitHidden = null;
 
     if(viewport.hasHiddenColumns)
@@ -417,12 +408,20 @@ public class AlignFrame
       JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
 
       if(reply==JOptionPane.YES_OPTION)
-       omitHidden = viewport.getSelectionAsString();
+      {
+        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.getSelectionAsNewSequence(),
+        viewport.alignment.getSequencesArray(),
         omitHidden));
   }
 
@@ -480,6 +479,7 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -690,7 +690,7 @@ public class AlignFrame
 
     if (viewport.hasHiddenColumns)
     {
-      omitHidden = viewport.getSelectionAsString();
+      omitHidden = viewport.getViewAsString(true);
     }
 
     String output = new FormatAdapter().formatSequences(
@@ -768,6 +768,7 @@ 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
@@ -783,32 +784,40 @@ public class AlignFrame
 
       if (newAlignment)
       {
+        System.out.println(format +" 2");
         alignment = new Alignment(sequences);
 
         if(Desktop.jalviewClipboard!=null)
            alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );
         else
            alignment.setDataset( null );
+
       }
       else
       {
+        System.out.println(format +" 24");
         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());
 
           alignment.addSequence(newseq);
         }
+
+
         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++)
      {
@@ -1407,7 +1416,7 @@ public class AlignFrame
 
   public void showAllColumns_actionPerformed(ActionEvent e)
   {
-    viewport.getColumnSelection().revealAllHiddenColumns(viewport);
+    viewport.showAllHiddenColumns();
   }
 
   public void hideSelSequences_actionPerformed(ActionEvent e)
@@ -1423,13 +1432,14 @@ public class AlignFrame
     {
       viewport.hideSequence(seqs[i]);
     }
-    repaint();
+
+    alignPanel.repaint();
   }
 
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
-    repaint();
+    alignPanel.repaint();
   }
 
   public void hiddenMarkers_actionPerformed(ActionEvent e)
@@ -2614,11 +2624,10 @@ public class AlignFrame
 
 
 
-
 public void showTranslation_actionPerformed(ActionEvent e)
 {
   SequenceI [] selection = viewport.getSelectionAsNewSequence();
-  String [] seqstring = viewport.getSelectionAsString();
+  String [] seqstring = viewport.getViewAsString(true);
 
   int s, sSize = selection.length;
   SequenceI [] newSeq = new SequenceI[sSize];
@@ -2844,16 +2853,8 @@ public void drop(DropTargetDropEvent evt)
                                                 AppletFormatAdapter.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)), Desktop.instance);
-
-          this.paste(false);
+          String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);
+          new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);
         }
       }
       else