JAL-1499 patch from Mungo Carstairs

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
old mode 100755 (executable)
new mode 100644 (file)
index c3c86d6..977cb25
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -28,6 +28,8 @@ import jalview.datamodel.SequenceI;
 import java.io.IOException;
 import java.util.Enumeration;
 import java.util.Hashtable;
+import java.util.Map;
+import java.util.Set;
 import java.util.Vector;
 
 /**
@@ -55,7 +57,7 @@ public abstract class AlignFile extends FileParse
   /**
    * Properties to be added to generated alignment object
    */
-  protected Hashtable properties;
+  protected Hashtable<Object, Object> properties;
 
   long start;
 
@@ -130,7 +132,7 @@ 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;
@@ -173,8 +175,8 @@ public abstract class AlignFile extends FileParse
   {
     if (properties != null && properties.size() > 0)
     {
-      Enumeration keys = properties.keys();
-      Enumeration vals = properties.elements();
+      Enumeration<Object> keys = properties.keys();
+      Enumeration<Object> vals = properties.elements();
       while (keys.hasMoreElements())
       {
         al.setProperty(keys.nextElement(), vals.nextElement());
@@ -205,7 +207,7 @@ public abstract class AlignFile extends FileParse
     }
     if (properties == null)
     {
-      properties = new Hashtable();
+      properties = new Hashtable<Object, Object>();
     }
     properties.put(key, value);
   }
@@ -224,11 +226,20 @@ public abstract class AlignFile extends FileParse
    */
   protected void initData()
   {
-    seqs = new Vector();
+    seqs = new Vector<SequenceI>();
     annotations = new Vector();
   }
 
   /**
+   * Return the alignment properties (or null if none set)
+   * 
+   * @return
+   */
+  protected Set<Map.Entry<Object, Object>> getAlignmentProperties()
+  {
+    return (this.properties == null ? null : this.properties.entrySet());
+  }
+  /**
    * DOCUMENT ME!
    * 
    * @param s
@@ -236,7 +247,7 @@ 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++)
     {
@@ -296,13 +307,13 @@ 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 });