X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=14bf680152cf531a5830cb72e69725f6b4ac20ac;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=cc57961160589c5068f7df08939f9a45573cb9ef;hpb=3f8dab9bfe7202a4a83a86052bcfe18f12f138a2;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index cc57961..14bf680 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -60,16 +60,14 @@ public class AlignFrame
   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)
-  {
+  public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {
 
-    viewport = new AlignViewport(al);
+    viewport = new AlignViewport(al, hiddenColumns);
 
     this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 
@@ -141,6 +139,17 @@ public class AlignFrame
 
   }
 
+
+  /**
+   * Creates a new AlignFrame object.
+   *
+   * @param al DOCUMENT ME!
+   */
+  public AlignFrame(AlignmentI al)
+  {
+    this(al, null);
+  }
+
   public AlignViewport getViewport()
   {
     return viewport;
@@ -784,7 +793,6 @@ public class AlignFrame
 
       if (newAlignment)
       {
-        System.out.println(format +" 2");
         alignment = new Alignment(sequences);
 
         if(Desktop.jalviewClipboard!=null)
@@ -795,7 +803,6 @@ public class AlignFrame
       }
       else
       {
-        System.out.println(format +" 24");
         alignment = viewport.getAlignment();
 
         //!newAlignment
@@ -2200,6 +2207,9 @@ public class AlignFrame
         return;
       }
 
+      if(viewport.alignment.getHeight()<2)
+        return;
+
       tp = new TreePanel(viewport, type, pwType);
     }
 
@@ -2288,27 +2298,28 @@ 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(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(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)
       {
@@ -2318,7 +2329,8 @@ public class AlignFrame
         {
           msa[i] = (SequenceI) seqs.elementAt(i);
         }
-      }
+      }*/
+      msa = viewport.getAlignmentView(false);
     }
     return msa;
   }
@@ -2522,7 +2534,7 @@ 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(), af);
 
@@ -2539,7 +2551,7 @@ 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(), af);