X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=ffe152bc4700e1bb0e474df0ef9fb25558a47207;hb=1889827c44c51f6353fe8619e5d44b421158af23;hp=b2a1f66759e012859d2afa6395ae67058c05337d;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index b2a1f66..ffe152b 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,22 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
+import java.util.Enumeration;
 import java.util.Hashtable;
 
 import jalview.analysis.*;
@@ -429,12 +433,16 @@ public class SeqCigar extends CigarSimple
   }
 
   /**
-   * createAlignment
+   * create an alignment from the given array of cigar sequences and gap
+   * character, and marking the given segments as visible in the given
+   * columselection.
    * 
    * @param alseqs
-   *          SeqCigar[]
    * @param gapCharacter
-   *          char
+   * @param colsel
+   *          - columnSelection where hidden regions are marked
+   * @param segments
+   *          - visible regions of alignment
    * @return SequenceI[]
    */
   public static SequenceI[] createAlignmentSequences(SeqCigar[] alseqs,
@@ -688,4 +696,77 @@ public class SeqCigar extends CigarSimple
     // System.err.println("Subseqgaped\n------ktryas---dtqwrtsasll----dddptyipqqwa----slchvhryas---dtqwrtsasll--qwa----slchvh\n"+ssgapedseq+"\n"+sub_se_gp.getCigarstring());
   }
 
+  /**
+   * references to entities that this sequence cigar is associated with.
+   */
+  private Hashtable selGroups = null;
+
+  public void setGroupMembership(Object group)
+  {
+    if (selGroups == null)
+    {
+      selGroups = new Hashtable();
+    }
+    selGroups.put(group, new int[0]);
+  }
+
+  /**
+   * Test for and if present remove association to group.
+   * 
+   * @param group
+   * @return true if group was associated and it was removed
+   */
+  public boolean removeGroupMembership(Object group)
+  {
+    if (selGroups != null && selGroups.containsKey(group))
+    {
+      selGroups.remove(group);
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * forget all associations for this sequence.
+   */
+  public void clearMemberships()
+  {
+    if (selGroups != null)
+    {
+      selGroups.clear();
+    }
+    selGroups = null;
+  }
+
+  /**
+   * 
+   * @return null or array of all associated entities
+   */
+  public Object[] getAllMemberships()
+  {
+    if (selGroups == null)
+    {
+      return null;
+    }
+    Object[] mmbs = new Object[selGroups.size()];
+    Enumeration en = selGroups.keys();
+    for (int i = 0; en.hasMoreElements(); i++)
+    {
+      mmbs[i] = en.nextElement();
+    }
+    return mmbs;
+  }
+
+  /**
+   * Test for group membership
+   * 
+   * @param sgr
+   *          - a selection group or some other object that may be associated
+   *          with seqCigar
+   * @return true if sgr is associated with this seqCigar
+   */
+  public boolean isMemberOf(Object sgr)
+  {
+    return (selGroups != null) && selGroups.get(sgr) != null;
+  }
 }