X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=8706ad5d3154443552e74ecfb840bfbfef1e0058;hb=8edebdd9789b2d93fb8f9db24b8be2c1e6317690;hp=62503a0397b9a869cf9b7466cde2364f366ae36e;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 62503a0..8706ad5 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -34,6 +34,8 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
+import jalview.util.Comparison;
+import jalview.util.Format;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
@@ -88,8 +90,8 @@ public class AnnotationFile
   }
 
   /**
-   * convenience method for pre-2.9 annotation files which have no view, hidden
-   * columns or hidden row keywords.
+   * convenience method for pre-2.8.3 annotation files which have no view,
+   * hidden columns or hidden row keywords.
    * 
    * @param annotations
    * @param list
@@ -278,8 +280,8 @@ public class AnnotationFile
             graphLine.append("\t");
             graphLine.append(row.getThreshold().label);
             graphLine.append("\t");
-            graphLine.append(jalview.util.Format.getHexString(row
-                    .getThreshold().colour));
+            graphLine
+                    .append(Format.getHexString(row.getThreshold().colour));
             graphLine.append(newline);
           }
 
@@ -310,7 +312,7 @@ public class AnnotationFile
                 && j < row.annotations.length; j++)
         {
           if (refSeq != null
-                  && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+                  && Comparison.isGap(refSeq.getCharAt(j)))
           {
             continue;
           }
@@ -377,7 +379,7 @@ public class AnnotationFile
             {
               text.append(comma
                       + "["
-                      + jalview.util.Format
+                      + Format
                               .getHexString(row.annotations[j].colour)
                       + "]");
               comma = ",";
@@ -398,7 +400,7 @@ public class AnnotationFile
           colours.append("COLOUR\t");
           colours.append(row.label);
           colours.append("\t");
-          colours.append(jalview.util.Format.getHexString(color));
+          colours.append(Format.getHexString(color));
           colours.append(newline);
         }
         if (row.scaleColLabel || row.showAllColLabels
@@ -597,7 +599,7 @@ public class AnnotationFile
         }
       }
       text.append("outlineColour=");
-      text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+      text.append(Format.getHexString(sg.getOutlineColour()));
       text.append("\t");
 
       text.append("displayBoxes=");
@@ -615,13 +617,13 @@ public class AnnotationFile
       if (sg.textColour != java.awt.Color.black)
       {
         text.append("textCol1=");
-        text.append(jalview.util.Format.getHexString(sg.textColour));
+        text.append(Format.getHexString(sg.textColour));
         text.append("\t");
       }
       if (sg.textColour2 != java.awt.Color.white)
       {
         text.append("textCol2=");
-        text.append(jalview.util.Format.getHexString(sg.textColour2));
+        text.append(Format.getHexString(sg.textColour2));
         text.append("\t");
       }
       if (sg.thresholdTextColour != 0)
@@ -633,7 +635,7 @@ public class AnnotationFile
       if (sg.idColour != null)
       {
         text.append("idColour=");
-        text.append(jalview.util.Format.getHexString(sg.idColour));
+        text.append(Format.getHexString(sg.idColour));
         text.append("\t");
       }
       if (sg.isHidereps())