X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2e1a4e0251b169ff68777dbcd96b75fcc2984d90;hb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;hp=d4ba5eae69dad4b57ff26efb783afb33910bd380;hpb=bd56b8fb21d730b15bb759c529990d244cafbe37;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d4ba5ea..2e1a4e0 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1133,8 +1133,116 @@ public class AlignViewport
         hasHiddenRows = false;
     }
 
+    public void showAllHiddenSeqs()
+    {
+      alignment.getHiddenSequences().showAll();
+      hasHiddenRows = false;
+    }
+
     public int adjustForHiddenSeqs(int alignmentIndex)
     {
       return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
     }
+
+    /**
+     * This method returns the a new SequenceI [] with
+     * the selection sequence and start and end points adjusted
+     * @return String[]
+     */
+    public SequenceI[] getSelectionAsNewSequence()
+    {
+      SequenceI[] sequences;
+
+      if (selectionGroup == null)
+        sequences = alignment.getSequencesArray();
+      else
+        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+
+      return sequences;
+    }
+
+
+    /**
+     * This method returns the visible selected area as text, as
+     * seen on the GUI, ie if columns are hidden they will not
+     * be returned in the result.
+     * Use this for calculating trees, PCA, redundancy etc on views
+     * which contain hidden columns.
+     * @return String[]
+     */
+    public String [] getSelectionAsString()
+    {
+      String [] selection = null;
+      SequenceI [] seqs= null;
+      int i, iSize;
+      int start = 0, end = 0;
+      if(selectionGroup!=null)
+      {
+        iSize = selectionGroup.getSize(false);
+        seqs = selectionGroup.getSequencesInOrder(alignment);
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes()+1;
+      }
+      else
+      {
+        iSize = alignment.getHeight();
+        seqs = alignment.getSequencesArray();
+        end = alignment.getWidth();
+      }
+
+      selection = new String[iSize];
+
+
+      for(i=0; i<iSize; i++)
+      {
+        if (hasHiddenColumns)
+        {
+             StringBuffer visibleSeq = new StringBuffer();
+             Vector regions = colSel.getHiddenColumns();
+
+             int blockStart = start, blockEnd=end;
+             int [] region;
+             int hideStart, hideEnd;
+
+             for (int j = 0; j < regions.size(); j++)
+             {
+               region = (int[]) regions.elementAt(j);
+               hideStart = region[0];
+               hideEnd = region[1];
+
+               if(hideStart < start)
+               {
+                 continue;
+               }
+
+               blockStart = Math.min(blockStart, hideEnd+1);
+               blockEnd = Math.min(blockEnd, hideStart);
+
+               if(blockStart>blockEnd)
+               {
+                  break;
+               }
+
+
+               visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+               blockStart = hideEnd+1;
+               blockEnd = end;
+             }
+
+             if(end>blockStart)
+               visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+             selection[i] = visibleSeq.toString();
+        }
+        else
+        {
+          selection[i] = seqs[i].getSequence(start, end);
+        }
+
+    //    System.out.println(seqs[i].getName()+"\t"+ selection[i]);
+      }
+
+      return selection;
+    }
 }