X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=5979a2753c3e0eccbf399849ba5fe1cde3118d85;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=b3a22df894f169bc408c3bef653c8eb86d691723;hpb=59c3078b53669a38f4e1c1158675691fe60349b3;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index b3a22df..5979a27 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)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
@@ -14,6 +14,7 @@
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
@@ -338,12 +339,15 @@ public class AnnotationFile
rowprops.append(row.centreColLabels);
rowprops.append(newline);
}
+ if (graphLine.length()>0) {
+ text.append(graphLine.toString());
+ graphLine.setLength(0);
+ }
}
text.append(newline);
text.append(colours.toString());
- text.append(graphLine.toString());
if (graphGroup.size() > 0)
{
SequenceI oldRefSeq = refSeq;
@@ -621,11 +625,13 @@ public class AnnotationFile
}
long nlinesread=0;
String lastread="";
+ private static String GRAPHLINE="GRAPHLINE", COMBINE="COMBINE";
public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
throws Exception
{
nlinesread = 0;
ArrayList