formatting

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index ad7cdd2..4057773 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,7 +20,14 @@
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
 
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
@@ -112,7 +119,7 @@ public class Alignment implements AlignmentI
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
-    throw new Error("Alignment(CigarArray) not yet implemented");
+    throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
@@ -140,7 +147,9 @@ public class Alignment implements AlignmentI
   public SequenceI[] getSequencesArray()
   {
     if (sequences == null)
+    {
       return null;
+    }
     synchronized (sequences)
     {
       return sequences.toArray(new SequenceI[sequences.size()]);
@@ -204,7 +213,9 @@ public class Alignment implements AlignmentI
       }
     }
     if (hiddenSequences != null)
+    {
       hiddenSequences.adjustHeightSequenceAdded();
+    }
   }
 
   /**
@@ -238,7 +249,9 @@ public class Alignment implements AlignmentI
   public void finalize()
   {
     if (getDataset() != null)
+    {
       getDataset().removeAlignmentRef();
+    }
 
     dataset = null;
     sequences = null;
@@ -747,7 +760,9 @@ public class Alignment implements AlignmentI
         continue;
       }
       if (tIndex < temp.length)
+      {
         temp[tIndex++] = annotations[i];
+      }
     }
 
     if (swap)
@@ -943,6 +958,27 @@ public class Alignment implements AlignmentI
     else if (dataset == null && data != null)
     {
       dataset = data;
+      for (int i = 0; i < getHeight(); i++)
+      {
+        SequenceI currentSeq = getSequenceAt(i);
+        SequenceI dsq = currentSeq.getDatasetSequence();
+        if (dsq == null)
+        {
+          dsq = currentSeq.createDatasetSequence();
+          dataset.addSequence(dsq);
+        }
+        else
+        {
+          while (dsq.getDatasetSequence() != null)
+          {
+            dsq = dsq.getDatasetSequence();
+          }
+          if (dataset.findIndex(dsq) == -1)
+          {
+            dataset.addSequence(dsq);
+          }
+        }
+      }
     }
     dataset.addAlignmentRef();
   }
@@ -1143,7 +1179,9 @@ public class Alignment implements AlignmentI
   public void setProperty(Object key, Object value)
   {
     if (alignmentProperties == null)
+    {
       alignmentProperties = new Hashtable();
+    }
 
     alignmentProperties.put(key, value);
   }
@@ -1152,9 +1190,13 @@ public class Alignment implements AlignmentI
   public Object getProperty(Object key)
   {
     if (alignmentProperties != null)
+    {
       return alignmentProperties.get(key);
+    }
     else
+    {
       return null;
+    }
   }
 
   @Override
@@ -1176,7 +1218,9 @@ public class Alignment implements AlignmentI
   public void addCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null)
+    {
       return;
+    }
     if (codonFrameList == null)
     {
       codonFrameList = new AlignedCodonFrame[]
@@ -1210,15 +1254,21 @@ public class Alignment implements AlignmentI
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
     if (seq == null || codonFrameList == null)
+    {
       return null;
+    }
     Vector cframes = new Vector();
     for (int f = 0; f < codonFrameList.length; f++)
     {
       if (codonFrameList[f].involvesSequence(seq))
+      {
         cframes.addElement(codonFrameList[f]);
+      }
     }
     if (cframes.size() == 0)
+    {
       return null;
+    }
     AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
     cframes.copyInto(cfr);
     return cfr;
@@ -1245,7 +1295,9 @@ public class Alignment implements AlignmentI
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
     if (codons == null || codonFrameList == null)
+    {
       return false;
+    }
     boolean removed = false;
     int i = 0, iSize = codonFrameList.length;
     while (i < iSize)