X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=bccb877e88d0ac0718339da63e2fabd4ea033e44;hb=76b5c58c65413e8b239dbf71999f500600ef0f95;hp=af5938885ca77f8110f813021b189097022fe36d;hpb=e33cdacd2ac2836504375c538574a0f1cafec7e3;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index af59388..bccb877 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -121,6 +121,20 @@ public class AlignViewport
         setAlignment(al);
         init();
     }
+    /**
+     * Create a new AlignViewport with hidden regions
+     * @param al AlignmentI
+     * @param hiddenColumns ColumnSelection
+     */
+    public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
+      setAlignment(al);
+      if (hiddenColumns!=null) {
+        this.colSel = hiddenColumns;
+        if (hiddenColumns.getHiddenColumns() != null)
+          hasHiddenColumns = true;
+      }
+      init();
+    }
 
     void init()
     {
@@ -873,41 +887,6 @@ public class AlignViewport
         return increment;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param y DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIndex(int y)
-    {
-        int y1 = 0;
-        int starty = getStartSeq();
-        int endy = getEndSeq();
-
-        for (int i = starty; i <= endy; i++)
-        {
-            if ((i < alignment.getHeight()) &&
-                    (alignment.getSequenceAt(i) != null))
-            {
-                int y2 = y1 + getCharHeight();
-
-                if ((y >= y1) && (y <= y2))
-                {
-                    return i;
-                }
-
-                y1 = y2;
-            }
-            else
-            {
-                return -1;
-            }
-        }
-
-        return -1;
-    }
 
     /**
      * DOCUMENT ME!
@@ -1139,22 +1118,55 @@ public class AlignViewport
         colSel.hideColumns(start);
       else
         colSel.hideColumns(start, end);
-      setSelectionGroup(null);
+
       hasHiddenColumns = true;
     }
 
+    public void hideAllSelectedSeqs()
+    {
+      if (selectionGroup == null)
+        return;
+
+      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+
+      for (int i = 0; i < seqs.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seqs[i]);
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      hasHiddenRows = true;
+      setSelectionGroup(null);
+    }
+
     public void hideSequence(SequenceI seq)
     {
       if(seq!=null)
       {
         alignment.getHiddenSequences().hideSequence(seq);
         hasHiddenRows = true;
+        firePropertyChange("alignment", null, alignment.getSequences());
       }
     }
 
     public void showSequence(int index)
     {
-      alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      if(tmp.size()>0)
+      {
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
+
+        for (int t = 0; t < tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI) tmp.elementAt(t), false
+              );
+        }
+        firePropertyChange("alignment", null, alignment.getSequences());
+      }
 
       if(alignment.getHiddenSequences().getSize()<1)
         hasHiddenRows = false;
@@ -1177,11 +1189,39 @@ public class AlignViewport
     {
       if(alignment.getHiddenSequences().getSize()>0)
       {
-        alignment.getHiddenSequences().showAll();
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
+        Vector tmp = alignment.getHiddenSequences().showAll();
+        for(int t=0; t<tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI)tmp.elementAt(t), false
+              );
+        }
+        firePropertyChange("alignment", null, alignment.getSequences());
         hasHiddenRows = false;
       }
     }
 
+    public void invertColumnSelection()
+    {
+      int column;
+      for(int i=0; i<alignment.getWidth(); i++)
+      {
+        column = i;
+
+        if(colSel.contains(column))
+          colSel.removeElement(column);
+        else
+          colSel.addElement(column);
+
+      }
+
+    }
+
     public int adjustForHiddenSeqs(int alignmentIndex)
     {
       return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
@@ -1223,13 +1263,13 @@ public class AlignViewport
         iSize = selectionGroup.getSize(false);
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes()+1;
+        end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
       }
       else
       {
         iSize = alignment.getHeight();
         seqs = alignment.getSequencesArray();
-        end = alignment.getWidth();
+        end = alignment.getWidth()-1;
       }
       SeqCigar[] selseqs = new SeqCigar[iSize];
       for(i=0; i<iSize; i++)
@@ -1237,13 +1277,9 @@ public class AlignViewport
         selseqs[i] = new SeqCigar(seqs[i], start, end);
       }
       selection=new CigarArray(selseqs);
-
-      int[] hiddenregions = null;
-      char[] hr_ops = null;
+      // now construct the CigarArray operations
       if (hasHiddenColumns) {
-        Vector _hiddenregions = new Vector();
         Vector regions = colSel.getHiddenColumns();
-        int blockStart = start, blockEnd=end;
         int [] region;
         int hideStart, hideEnd;
         int last=start;
@@ -1285,7 +1321,22 @@ public class AlignViewport
       }
       return selection;
     }
-
+    /**
+     * return a compact representation of the current alignment selection to
+     * pass to an analysis function
+     * @param selectedOnly boolean true to just return the selected view
+     * @return AlignmentView
+     */
+    jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
+      // JBPNote:
+      // this is here because the AlignmentView constructor modifies the CigarArray
+      // object. Refactoring of Cigar and alignment view representation should
+      // be done to remove redundancy.
+      CigarArray aligview = getViewAsCigars(selectedOnly);
+      if (aligview!=null)
+        return new AlignmentView(aligview);
+      return null;
+    }
     /**
      * This method returns the visible alignment as text, as
      * seen on the GUI, ie if columns are hidden they will not