JAL-3081 new method to get alignment sequence order lookup

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 93ad332..5739b7c 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -32,6 +32,7 @@ import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
@@ -717,6 +718,17 @@ public class Alignment implements AlignmentI
     return maxLength;
   }
 
+  @Override
+  public int getVisibleWidth()
+  {
+    int w = getWidth();
+    if (hiddenCols != null)
+    {
+      w -= hiddenCols.getSize();
+    }
+    return w;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1893,9 +1905,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setHiddenColumns(HiddenColumns cols)
+  public boolean setHiddenColumns(HiddenColumns cols)
   {
+    boolean changed = cols == null ? hiddenCols != null
+            : !cols.equals(hiddenCols);
     hiddenCols = cols;
+    return changed;
   }
 
   @Override
@@ -2010,4 +2025,23 @@ public class Alignment implements AlignmentI
     }
   }
 
+  /**
+   * Returns a map from sequence to position (0, 1,...) in the alignment
+   */
+  @Override
+  public Map<SequenceI, Integer> getSequencePositions()
+  {
+    Map<SequenceI, Integer> map = new HashMap<>();
+
+    synchronized (sequences)
+    {
+      int i = sequences.size();
+      for (int j = 0; j < i; j++)
+      {
+        map.put(sequences.get(j), Integer.valueOf(j));
+      }
+    }
+    return map;
+  }
+
 }