X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=0edc57849ada3639a9322ac25e762225236ad05c;hb=21b2c08c209b0c4eb1111dab1d81e8408c245ddd;hp=c1f088b3d8965991cc5da195ad40f67ca0c562ad;hpb=e2d27f21c1655d5707adad16fe174f2c88ba7cd3;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c1f088b..0edc578 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -347,9 +347,22 @@ public class AlignFrame
     }
     else
     {
-      String output = new FormatAdapter().formatSequences(format,
-          viewport.getAlignment().
-          getSequences());
+
+      String[] omitHidden = null;
+
+      if (viewport.hasHiddenColumns)
+      {
+        System.out.println("PROMPT USER HERE");
+        omitHidden = viewport.getSelectionAsString();
+      }
+
+      String output = new FormatAdapter().formatSequences(
+          format,
+          viewport.getSelectionAsNewSequence(),
+          omitHidden) ;
+
+
+
       if (output == null)
       {
         return false;
@@ -381,12 +394,20 @@ public class AlignFrame
   protected void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
-    Desktop.addInternalFrame(cap,
-                             "Alignment output - " + e.getActionCommand(), 600,
-                             500);
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-                                              viewport.getAlignment().
-                                              getSequences()));
+
+
+    String [] omitHidden = null;
+
+    if(viewport.hasHiddenColumns)
+    {
+      System.out.println("PROMPT USER HERE");
+      omitHidden = viewport.getSelectionAsString();
+    }
+
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        viewport.getSelectionAsNewSequence(),
+        omitHidden));
   }
 
   /**
@@ -648,83 +669,32 @@ public class AlignFrame
       return;
     }
 
-    SequenceGroup sg = viewport.getSelectionGroup();
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
 
     Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
 
-    Hashtable orderedSeqs = new Hashtable();
-    SequenceI[] seqs = new SequenceI[sg.getSize(false)];
-
-    for (int i = 0; i < sg.getSize(false); i++)
-    {
-      SequenceI seq = sg.getSequenceAt(i);
-      int index = viewport.alignment.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
-    }
+    FastaFile ff = new FastaFile();
+    ff.addJVSuffix( viewport.showJVSuffix );
 
-    int index = 0, startRes, endRes;
-    char ch;
+    c.setContents(new StringSelection(ff.print(seqs)), Desktop.instance);
 
-    for (int i = 0; i < sg.getSize(false); i++)
+    Vector hiddenColumns = null;
+    if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)
     {
-      SequenceI seq = null;
-
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-
-          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++)
+      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};
   }
 
   /**
@@ -848,6 +818,18 @@ 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);
+             for(int j=region[0]; j<region[1]+1; j++)
+               af.viewport.getColumnSelection().addElement(j);
+             af.viewport.getColumnSelection().hideColumns(region[0], af.viewport);
+           }
+         }
+
 
        //>>>This is a fix for the moment, until a better solution is found!!<<<
        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
@@ -2129,10 +2111,7 @@ 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 +2128,7 @@ 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 +2379,9 @@ public class AlignFrame
       if (nf.getTree() != null)
       {
         tp = new TreePanel(viewport,
-                           viewport.getAlignment().getSequences(), nf,
                            "FromFile",
-                           title);
+                           title,
+                           nf);
 
         tp.setSize(w,h);