todo

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 1872f60..7f71df1 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  * \r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -261,6 +261,7 @@ public class AnnotationFile
         String key = en.nextElement().toString();\r
         text.append("\t" + key + "=" + properties.get(key));\r
       }\r
+      // TODO: output alignment visualization settings here if required\r
 \r
     }\r
 \r
@@ -318,7 +319,7 @@ public class AnnotationFile
       text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
       text.append("displayText=" + sg.getDisplayText() + "\t");\r
       text.append("colourText=" + sg.getColourText() + "\t");\r
-\r
+      text.append("showUnconserved="+sg.getShowunconserved()+"\t");\r
       if (sg.textColour != java.awt.Color.black)\r
       {\r
         text.append("textCol1="\r
@@ -438,6 +439,7 @@ public class AnnotationFile
         token = st.nextToken();\r
         if (token.equalsIgnoreCase("COLOUR"))\r
         {\r
+          // TODO: use graduated colour def'n here too\r
           colourAnnotations(al, st.nextToken(), st.nextToken());\r
           continue;\r
         }\r
@@ -937,6 +939,10 @@ public class AnnotationFile
         {\r
           sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());\r
         }\r
+        else if (key.equalsIgnoreCase("showUnconserved"))\r
+        {\r
+          sg.setShowunconserved(Boolean.valueOf(value).booleanValue());\r
+        }\r
         else if (key.equalsIgnoreCase("displayText"))\r
         {\r
           sg.setDisplayText(Boolean.valueOf(value).booleanValue());\r