updated version to 2.6.1

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2721fb2..a96ff67 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,5 +1,5 @@
 /*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)\r
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
  * \r
  * This file is part of Jalview.\r
@@ -416,7 +416,7 @@ public class AnnotationFile
       text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
       text.append("displayText=" + sg.getDisplayText() + "\t");\r
       text.append("colourText=" + sg.getColourText() + "\t");\r
-      text.append("showUnconserved=" + sg.getShowunconserved() + "\t");\r
+      text.append("showUnconserved=" + sg.getShowNonconserved() + "\t");\r
       if (sg.textColour != java.awt.Color.black)\r
       {\r
         text.append("textCol1="\r
@@ -508,14 +508,16 @@ public class AnnotationFile
             if (aa[aai].autoCalculated)\r
             {\r
               // make a note of the name and description\r
-              autoAnnots.put(aa[aai].graph\r
-                      + "\t"\r
-                      + aa[aai].label\r
-                      + "\t"\r
-                      + aa[aai].description\r
-                      + "\t"\r
-                      + (aa[aai].sequenceRef != null ? aa[aai].sequenceRef\r
-                              .getDisplayId(true) : ""), new Integer(1));\r
+              autoAnnots\r
+                      .put(aa[aai].graph\r
+                              + "\t"\r
+                              + aa[aai].label\r
+                              + "\t"\r
+                              + aa[aai].description\r
+                              + "\t"\r
+                              + (aa[aai].sequenceRef != null ? aa[aai].sequenceRef\r
+                                      .getDisplayId(true) : ""),\r
+                              new Integer(1));\r
             }\r
           }\r
         }\r
@@ -1121,9 +1123,7 @@ public class AnnotationFile
         }\r
         else\r
         {\r
-          sg\r
-                  .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),\r
-                          false);\r
+          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);\r
         }\r
       }\r
     }\r
@@ -1234,8 +1234,8 @@ public class AnnotationFile
         {\r
           sg.cs.setConservationInc(Integer.parseInt(value));\r
           Conservation c = new Conservation("Group",\r
-                  ResidueProperties.propHash, 3, sg.getSequences(null), sg\r
-                          .getStartRes(), sg.getEndRes() + 1);\r
+                  ResidueProperties.propHash, 3, sg.getSequences(null),\r
+                  sg.getStartRes(), sg.getEndRes() + 1);\r
 \r
           c.calculate();\r
           c.verdict(false, 25);\r
@@ -1253,7 +1253,7 @@ public class AnnotationFile
         }\r
         else if (key.equalsIgnoreCase("showUnconserved"))\r
         {\r
-          sg.setShowunconserved(Boolean.valueOf(value).booleanValue());\r
+          sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());\r
         }\r
         else if (key.equalsIgnoreCase("displayText"))\r
         {\r
@@ -1314,7 +1314,7 @@ public class AnnotationFile
       token = st.nextToken();\r
       if (ala == null)\r
       {\r
-        System.err.print(" "+token);\r
+        System.err.print(" " + token);\r
       }\r
       else\r
       {\r
@@ -1328,7 +1328,7 @@ public class AnnotationFile
         }\r
       }\r
     }\r
-    if (ala==null)\r
+    if (ala == null)\r
     {\r
       System.err.print("\n");\r
     }\r