apply version 2.7 copyright

[jalview.git] / src / jalview / datamodel / SeqCigar.java

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index f2777f4..182ad7b 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,7 +17,9 @@
  */
 package jalview.datamodel;
 
+import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.Vector;
 
 import jalview.analysis.*;
 import jalview.util.*;
@@ -68,8 +70,8 @@ public class SeqCigar extends CigarSimple
    */
   public String getSequenceString(char GapChar)
   {
-    return (length == 0) ? "" : (String) getSequenceAndDeletions(refseq
-            .getSequenceAsString(start, end), GapChar)[0];
+    return (length == 0) ? "" : (String) getSequenceAndDeletions(
+            refseq.getSequenceAsString(start, end), GapChar)[0];
   }
 
   /**
@@ -85,18 +87,17 @@ public class SeqCigar extends CigarSimple
     {
       return null;
     }
-    Object[] edit_result = getSequenceAndDeletions(refseq
-            .getSequenceAsString(start, end), GapChar);
+    Object[] edit_result = getSequenceAndDeletions(
+            refseq.getSequenceAsString(start, end), GapChar);
     if (edit_result == null)
     {
       throw new Error(
               "Implementation Error - unexpected null from getSequenceAndDeletions");
     }
     int bounds[] = (int[]) edit_result[1];
-    seq = new Sequence(refseq.getName(), (String) edit_result[0], refseq
-            .getStart()
-            + start + bounds[0], refseq.getStart() + start
-            + ((bounds[2] == 0) ? -1 : bounds[2]));
+    seq = new Sequence(refseq.getName(), (String) edit_result[0],
+            refseq.getStart() + start + bounds[0], refseq.getStart()
+                    + start + ((bounds[2] == 0) ? -1 : bounds[2]));
     seq.setDescription(refseq.getDescription());
     int sstart = seq.getStart(), send = seq.getEnd();
     // seq.checkValidRange(); probably not needed
@@ -170,9 +171,8 @@ public class SeqCigar extends CigarSimple
       }
       else
       {
-        ds = new Sequence(seq.getName(), ungapped, seq.getStart(), seq
-                .getStart()
-                + ungapped.length() - 1);
+        ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
+                seq.getStart() + ungapped.length() - 1);
         // JBPNote: this would be consistent but may not be useful
         // seq.setDatasetSequence(ds);
       }
@@ -431,12 +431,16 @@ 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,
@@ -501,8 +505,8 @@ public class SeqCigar extends CigarSimple
             }
             else
             {
-              g_seqs[s].insert(inspos, alseqs_string[i].substring(
-                      region[0], region[1] + 1));
+              g_seqs[s].insert(inspos,
+                      alseqs_string[i].substring(region[0], region[1] + 1));
             }
           }
           shifts.addShift(region[2], insert.length); // update shift in
@@ -520,10 +524,9 @@ public class SeqCigar extends CigarSimple
     {
       int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
       SequenceI ref = alseqs[i].getRefSeq();
-      seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(), ref
-              .getStart()
-              + alseqs[i].start + bounds[0], ref.getStart()
-              + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
+      seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
+              ref.getStart() + alseqs[i].start + bounds[0], ref.getStart()
+                      + alseqs[i].start + (bounds[2] == 0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
       seqs[i].setDescription(ref.getDescription());
     }
@@ -691,4 +694,77 @@ 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;
+  }
 }