X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=fde4d90e18bbf9f5c2b1e09f3aac7850c817c9a6;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=a101fcf4db6647881971e931ac849460706b02ff;hpb=1ef53c6e1e8f030bce0933c2154a7af3773b496a;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a101fcf..fde4d90 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!
@@ -1123,15 +1102,12 @@ public class AlignViewport
 
     public void hideSelectedColumns()
     {
-      if (colSel.selected.size() < 1)
+      if (colSel.size() < 1)
         return;
 
-      while (colSel.selected.size() > 0)
-      {
-        int column = ( (Integer) colSel.selected.firstElement()).intValue();
-        colSel.hideColumns(column);
-      }
+      colSel.hideSelectedColumns();
       setSelectionGroup(null);
+
       hasHiddenColumns = true;
     }
 
@@ -1139,14 +1115,9 @@ public class AlignViewport
     public void hideColumns(int start, int end)
     {
       if(start==end)
-        end++;
-
-      for(int i=start; i<end; i++)
-      {
-        colSel.addElement(i);
-        colSel.hideColumns(i);
-      }
-
+        colSel.hideColumns(start);
+      else
+        colSel.hideColumns(start, end);
       setSelectionGroup(null);
       hasHiddenColumns = true;
     }
@@ -1168,6 +1139,19 @@ public class AlignViewport
         hasHiddenRows = false;
     }
 
+    public void showColumn(int col)
+    {
+      colSel.revealHiddenColumns(col);
+      if(colSel.getHiddenColumns()==null)
+        hasHiddenColumns = false;
+    }
+
+    public void showAllHiddenColumns()
+    {
+      colSel.revealAllHiddenColumns();
+      hasHiddenColumns = false;
+    }
+
     public void showAllHiddenSeqs()
     {
       if(alignment.getHiddenSequences().getSize()>0)
@@ -1199,22 +1183,114 @@ public class AlignViewport
       return sequences;
     }
 
+    /**
+     * This method returns the visible alignment 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 jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+    {
+      CigarArray selection=null;
+      SequenceI [] seqs= null;
+      int i, iSize;
+      int start = 0, end = 0;
+      if(selectedRegionOnly && selectionGroup!=null)
+      {
+        iSize = selectionGroup.getSize(false);
+        seqs = selectionGroup.getSequencesInOrder(alignment);
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+      }
+      else
+      {
+        iSize = alignment.getHeight();
+        seqs = alignment.getSequencesArray();
+        end = alignment.getWidth()-1;
+      }
+      SeqCigar[] selseqs = new SeqCigar[iSize];
+      for(i=0; i<iSize; i++)
+      {
+        selseqs[i] = new SeqCigar(seqs[i], start, end);
+      }
+      selection=new CigarArray(selseqs);
+      // now construct the CigarArray operations
+      if (hasHiddenColumns) {
+        Vector regions = colSel.getHiddenColumns();
+        int [] region;
+        int hideStart, hideEnd;
+        int last=start;
+        for (int j = 0; last<end & j < regions.size(); j++)
+        {
+          region = (int[]) regions.elementAt(j);
+          hideStart = region[0];
+          hideEnd = region[1];
+          // edit hidden regions to selection range
+          if(hideStart<last) {
+            if (hideEnd > last)
+            {
+              hideStart = last;
+            } else
+              continue;
+          }
 
+          if (hideStart>end)
+            break;
+
+          if (hideEnd>end)
+            hideEnd=end;
+
+          if (hideStart>hideEnd)
+            break;
+          /**
+           * form operations...
+           */
+          if (last<hideStart)
+            selection.addOperation(CigarArray.M, hideStart-last);
+          selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
+          last = hideEnd+1;
+        }
+        // Final match if necessary.
+        if (last<end)
+          selection.addOperation(CigarArray.M, end-last);
+      } else {
+        selection.addOperation(CigarArray.M, end-start);
+      }
+      return selection;
+    }
     /**
-     * This method returns the visible selected area as text, as
+     * 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
      * be returned in the result.
      * Use this for calculating trees, PCA, redundancy etc on views
      * which contain hidden columns.
      * @return String[]
      */
-    public String [] getSelectionAsString()
+    public String [] getViewAsString(boolean selectedRegionOnly)
     {
       String [] selection = null;
       SequenceI [] seqs= null;
       int i, iSize;
       int start = 0, end = 0;
-      if(selectionGroup!=null)
+      if(selectedRegionOnly && selectionGroup!=null)
       {
         iSize = selectionGroup.getSize(false);
         seqs = selectionGroup.getSequencesInOrder(alignment);
@@ -1277,8 +1353,6 @@ public class AlignViewport
         {
           selection[i] = seqs[i].getSequence(start, end);
         }
-
-    //    System.out.println(seqs[i].getName()+"\t"+ selection[i]);
       }
 
       return selection;