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 9475f00..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;
@@ -51,7 +52,7 @@ public class Alignment implements AlignmentI
 {
   private Alignment dataset;
 
-  protected List<SequenceI> sequences;
+  private List<SequenceI> sequences;
 
   protected List<SequenceGroup> groups;
 
@@ -200,6 +201,7 @@ public class Alignment implements AlignmentI
         return sequences.get(i);
       }
     }
+
     return null;
   }
 
@@ -708,18 +710,25 @@ public class Alignment implements AlignmentI
   public int getWidth()
   {
     int maxLength = -1;
-
+  
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() > maxLength)
-      {
-        maxLength = getSequenceAt(i).getLength();
-      }
+      maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
     }
-
     return maxLength;
   }
 
+  @Override
+  public int getVisibleWidth()
+  {
+    int w = getWidth();
+    if (hiddenCols != null)
+    {
+      w -= hiddenCols.getSize();
+    }
+    return w;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1605,7 +1614,10 @@ public class Alignment implements AlignmentI
     AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
             new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
     annot.hasText = false;
-    annot.setCalcId(new String(calcId));
+    if (calcId != null)
+    {
+      annot.setCalcId(new String(calcId));
+    }
     annot.autoCalculated = autoCalc;
     if (seqRef != null)
     {
@@ -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;
+  }
+
 }