parsers can generate alignment properties

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index ae8e0d0..3c7e0b2 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -34,8 +34,18 @@ public abstract class AlignFile
 {
   int noSeqs = 0;
   int maxLength = 0;
+  /**
+   * Sequences to be added to form a new alignment.
+   */
   protected Vector seqs;
+  /**
+   * annotation to be added to generated alignment object
+   */
   protected Vector annotations;
+  /**
+   * Properties to be added to generated alignment object
+   */
+  protected Hashtable properties;
   long start;
   long end;
   boolean jvSuffix = true;
@@ -84,9 +94,15 @@ public abstract class AlignFile
 
     return s;
   }
-
+  /**
+   * called by AppletFormatAdapter to generate
+   * an annotated alignment, rather than bare
+   * sequences.
+   * @param al
+   */
   public void addAnnotations(Alignment al)
   {
+    addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
       al.addAnnotation(
@@ -95,7 +111,44 @@ public abstract class AlignFile
     }
 
   }
-
+  /**
+   * Add any additional information extracted
+   * from the file to the alignment properties.
+   * @note implicitly called by addAnnotations()
+   * @param al
+   */
+  public void addProperties(Alignment al)
+  {
+    if (properties!=null && properties.size()>0)
+    {
+      Enumeration keys = properties.keys();
+      Enumeration vals = properties.elements();
+      while (keys.hasMoreElements())
+      {
+        al.setProperty(keys.nextElement(), vals.nextElement());
+      }
+    }
+  }
+  protected void setAlignmentProperty(Object key, Object value)
+  {
+    if (key==null)
+    {
+      throw new Error("Implementation error: Cannot have null alignment property key.");
+    }
+    if (properties==null)
+    {
+      properties = new Hashtable();
+    }
+    properties.put(key, value);
+  }
+  protected Object getAlignmentProperty(Object key)
+  {
+    if (properties!=null && key!=null)
+    {
+      return properties.get(key);
+    }
+    return null;
+  }
   /**
    * Initialise objects to store sequence data in.
    */