JAL-1780 JAL-653 organise imports

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index af835ca..b66fb11 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,13 +22,17 @@ package jalview.io;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 /**
@@ -54,6 +58,11 @@ public abstract class AlignFile extends FileParse
   protected Vector<AlignmentAnnotation> annotations;
 
   /**
+   * SequenceGroups to be added to the alignment object
+   */
+  protected List<SequenceGroup> seqGroups;
+
+  /**
    * Properties to be added to generated alignment object
    */
   protected Hashtable properties;
@@ -165,6 +174,11 @@ public abstract class AlignFile extends FileParse
     return seqs;
   }
 
+  public List<SequenceGroup> getSeqGroups()
+  {
+    return seqGroups;
+  }
+
   /**
    * Return the Sequences in the seqs Vector as an array of Sequences
    */
@@ -174,7 +188,7 @@ public abstract class AlignFile extends FileParse
 
     for (int i = 0; i < seqs.size(); i++)
     {
-      s[i] = (SequenceI) seqs.elementAt(i);
+      s[i] = seqs.elementAt(i);
     }
 
     return s;
@@ -198,7 +212,7 @@ public abstract class AlignFile extends FileParse
        * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
        * Rna.HelixMap(pairArray);
        */
-      AlignmentAnnotation an = (AlignmentAnnotation) annotations
+      AlignmentAnnotation an = annotations
               .elementAt(i);
       an.validateRangeAndDisplay();
       al.addAnnotation(an);
@@ -206,6 +220,12 @@ public abstract class AlignFile extends FileParse
 
   }
 
+  public void addSeqGroups(AlignmentI al)
+  {
+    this.seqGroups = al.getGroups();
+
+  }
+
   /**
    * Add any additional information extracted from the file to the alignment
    * properties.
@@ -267,8 +287,9 @@ public abstract class AlignFile extends FileParse
    */
   protected void initData()
   {
-    seqs = new Vector();
-    annotations = new Vector();
+    seqs = new Vector<SequenceI>();
+    annotations = new Vector<AlignmentAnnotation>();
+    seqGroups = new ArrayList<SequenceGroup>();
     parseCalled=false;
   }
 
@@ -280,7 +301,7 @@ public abstract class AlignFile extends FileParse
    */
   protected void setSeqs(SequenceI[] s)
   {
-    seqs = new Vector();
+    seqs = new Vector<SequenceI>();
 
     for (int i = 0; i < s.length; i++)
     {
@@ -340,13 +361,13 @@ public abstract class AlignFile extends FileParse
   /**
    * vector of String[] treeName, newickString pairs
    */
-  Vector newickStrings = null;
+  Vector<String[]> newickStrings = null;
 
   protected void addNewickTree(String treeName, String newickString)
   {
     if (newickStrings == null)
     {
-      newickStrings = new Vector();
+      newickStrings = new Vector<String[]>();
     }
     newickStrings.addElement(new String[]
     { treeName, newickString });
@@ -354,11 +375,7 @@ public abstract class AlignFile extends FileParse
 
   protected int getTreeCount()
   {
-    if (newickStrings == null)
-    {
-      return 0;
-    }
-    return newickStrings.size();
+    return newickStrings == null ? 0 : newickStrings.size();
   }
 
 }