From 825a9e8fcb05f794dc082ce84656c477cfff4918 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 31 Oct 2007 15:11:12 +0000
Subject: [PATCH] beginnings of view definition capability for annotations
 file

---
 src/jalview/io/AnnotationFile.java |   35 +++++++++++++++++++++++++++++++++--
 1 file changed, 33 insertions(+), 2 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 577b7e4..6285cf1 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -33,11 +33,42 @@ public class AnnotationFile
       "JALVIEW_ANNOTATION\n"
       + "# Created: "
       + new java.util.Date() + "\n\n");
-
+  /**
+   * convenience method for pre-2.4 feature files which have no view, hidden columns or hidden row keywords.
+   * @param annotations
+   * @param groups
+   * @param properties
+   * @return feature file as a string.
+   */
   public String printAnnotations(AlignmentAnnotation[] annotations,
                                  Vector groups,
                                  Hashtable properties)
   {
+    return printAnnotations(annotations, groups,
+            properties, null);
+
+  }
+  /**
+   * hold all the information about a particular view definition
+   * read from or written out in an annotations file.
+   */
+  public class ViewDef {
+    public String viewname;
+    public HiddenSequences hidseqs;
+    public ColumnSelection hiddencols;
+    public Vector visibleGroups;
+    public ViewDef(String viewname, HiddenSequences hidseqs,
+            ColumnSelection hiddencols)
+    {
+      this.viewname = viewname;
+      this.hidseqs = hidseqs;
+      this.hiddencols = hiddencols;
+    }
+  }
+  public String printAnnotations(AlignmentAnnotation[] annotations,
+          Vector groups,
+          Hashtable properties, ViewDef[] views)
+  {
     if (annotations != null)
     {
       boolean oneColour = true;
@@ -221,7 +252,7 @@ public class AnnotationFile
       }
 
     }
-
+    
     return text.toString();
   }
 
-- 
1.7.10.2