From 693451006944585e867137a70866d9dd40f421f2 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 2 Oct 2007 15:48:40 +0000
Subject: [PATCH] javadoc and operator for editing AlignmentAnnotation to
 remove hidden columns

---
 src/jalview/datamodel/ColumnSelection.java |   95 ++++++++++++++++++++++++++--
 1 file changed, 88 insertions(+), 7 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 4904495..73b7899 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -108,11 +108,11 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
+   * Column number at position i in selection
    *
-   * @param i DOCUMENT ME!
+   * @param i index into selected columns
    *
-   * @return DOCUMENT ME!
+   * @return column number in alignment
    */
   public int columnAt(int i)
   {
@@ -130,9 +130,9 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
+   * rightmost selected column
    *
-   * @return DOCUMENT ME!
+   * @return rightmost column in alignment that is selected
    */
   public int getMax()
   {
@@ -150,9 +150,9 @@ public class ColumnSelection
   }
 
   /**
-   * DOCUMENT ME!
+   * Leftmost column in selection
    *
-   * @return DOCUMENT ME!
+   * @return column index of leftmost column in selection
    */
   public int getMin()
   {
@@ -900,4 +900,85 @@ public class ColumnSelection
           start, end - 1};
     }
   }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
+   * @param alignmentAnnotation
+   */
+  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+  {
+    makeVisibleAnnotation(-1,-1,alignmentAnnotation);
+  }
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including sequence associated annotation).
+   * @param start remove any annotation to the right of this column
+   * @param end remove any annotation to the left of this column
+   * @param alignmentAnnotation the annotation to operate on
+   */
+  public void makeVisibleAnnotation(int start, int end, AlignmentAnnotation alignmentAnnotation)
+  {
+    if (alignmentAnnotation.annotations==null)
+    {
+      return;
+    }
+    if (start==end && end==-1)
+    {
+      start = 0;
+      end = alignmentAnnotation.annotations.length;
+    }
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      // then mangle the alignmentAnnotation annotation array
+        Vector annels = new Vector();
+        Annotation[] els = null;
+        Vector regions = getHiddenColumns();
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd,w=0;
+
+        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;
+          }
+
+          annels.addElement(els = new Annotation[blockEnd-blockStart]);
+          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
+          w+=els.length;
+          blockStart = hideEnd + 1;
+          blockEnd = end;
+        }
+
+        if (end > blockStart)
+        {
+          annels.addElement(els = new Annotation[end-blockStart]);
+          System.arraycopy(alignmentAnnotation.annotations, blockStart, els, 0, els.length);
+          w+=els.length;
+        }
+        if (w==0)
+          return;
+        Enumeration e = annels.elements();
+        alignmentAnnotation.annotations = new Annotation[w];
+        w=0;
+        while (e.hasMoreElements())
+        {
+          Annotation[] chnk = (Annotation[]) e.nextElement();
+          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w, chnk.length);
+          w+=chnk.length;
+        }
+    }
+  }
 }
-- 
1.7.10.2