JAL-653 JAL-1780 JAL-1543 javadoc and comment about further refactoring

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 690e22a..8f5144b 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -50,16 +50,26 @@ public class FileParse
 
   public File inFile = null;
 
+  /**
+   * a viewport associated with the current file operation. May be null. May
+   * move to different object.
+   */
   private AlignViewportI viewport;
 
-  public int index = 1; // sequence counter for FileParse object created from
   /**
    * specific settings for exporting data from the current context
    */
   private AlignExportSettingI exportSettings;
 
-  // same data source
+  /**
+   * sequence counter for FileParse object created from same data source
+   */
+  public int index = 1;
 
+  /**
+   * separator for extracting specific 'frame' of a datasource for formats that
+   * support multiple records (e.g. BLC, Stockholm, etc)
+   */
   protected char suffixSeparator = '#';
 
   /**