X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=cc57961160589c5068f7df08939f9a45573cb9ef;hb=e3eb93bc131a0f088312fddde91b728dbebe40d4;hp=c1f088b3d8965991cc5da195ad40f67ca0c562ad;hpb=e2d27f21c1655d5707adad16fe174f2c88ba7cd3;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c1f088b..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));
@@ -347,9 +347,26 @@ public class AlignFrame
     }
     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;
@@ -380,13 +397,32 @@ 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));
   }
 
   /**
@@ -443,6 +479,7 @@ public class AlignFrame
     new AnnotationExporter().exportFeatures(alignPanel);
   }
 
+
   public void exportAnnotations_actionPerformed(ActionEvent e)
   {
     new AnnotationExporter().exportAnnotations(
@@ -648,83 +685,41 @@ public class AlignFrame
       return;
     }
 
-    SequenceGroup sg = viewport.getSelectionGroup();
-
-    Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
-
-    Hashtable orderedSeqs = new Hashtable();
-    SequenceI[] seqs = new SequenceI[sg.getSize(false)];
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    String[] omitHidden = null;
 
-    for (int i = 0; i < sg.getSize(false); 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;
+    String output = new FormatAdapter().formatSequences(
+        "Fasta",
+        seqs,
+        omitHidden);
 
-    for (int i = 0; i < sg.getSize(false); i++)
-    {
-      SequenceI seq = null;
 
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
+    Toolkit.getDefaultToolkit().getSystemClipboard()
+        .setContents(new StringSelection(output), Desktop.instance);
 
-          break;
-        }
-        else
-        {
-          index++;
-        }
-      }
-
-      //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;
-
-      for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
+    Vector hiddenColumns = null;
+    if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)
+    {
+      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;
-      }
-
-      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());
-      if(seq.getAnnotation()!=null)
-      {
-        for(int a=0; a<seq.getAnnotation().length; a++)
-          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
+        hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,
+                          region[1]-hiddenOffset});
       }
     }
 
-    FastaFile ff = new FastaFile();
-    ff.addJVSuffix( viewport.showJVSuffix );
-    c.setContents(new StringSelection( ff.print(seqs)), Desktop.instance);
-    Desktop.jalviewClipboard = new Object[]{seqs,  viewport.alignment.getDataset()};
+    Desktop.jalviewClipboard = new Object[]{ seqs,
+        viewport.alignment.getDataset(),
+        hiddenColumns};
   }
 
   /**
@@ -773,6 +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
@@ -788,32 +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++)
      {
@@ -848,6 +852,16 @@ public class AlignFrame
        AlignFrame af = new AlignFrame(alignment);
        String newtitle = new String("Copied sequences");
 
+       if(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(
@@ -1394,6 +1408,46 @@ public class AlignFrame
     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!
    *
@@ -2129,10 +2183,7 @@ public class AlignFrame
       }
 
       title = title + " on region";
-      tp = new TreePanel(viewport,
-                         viewport.getSelectionGroup().getSequences(false),
-                         type, pwType,
-                         sg.getStartRes(), sg.getEndRes());
+      tp = new TreePanel(viewport, type, pwType);
     }
     else
     {
@@ -2149,10 +2200,7 @@ public class AlignFrame
         return;
       }
 
-      tp = new TreePanel(viewport,
-                         viewport.getAlignment().getSequences(), type, pwType,
-                         0,
-                         viewport.alignment.getWidth());
+      tp = new TreePanel(viewport, type, pwType);
     }
 
     addTreeMenuItem(tp, title);
@@ -2403,9 +2451,9 @@ public class AlignFrame
       if (nf.getTree() != null)
       {
         tp = new TreePanel(viewport,
-                           viewport.getAlignment().getSequences(), nf,
                            "FromFile",
-                           title);
+                           title,
+                           nf);
 
         tp.setSize(w,h);
 
@@ -2576,10 +2624,12 @@ 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;
@@ -2588,7 +2638,7 @@ 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;
 
@@ -2604,7 +2654,8 @@ 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());
   }
 
 
@@ -2802,16 +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