X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=33caf531d40abda95b99f1d1469b57871444859e;hb=977eba6d0cdd5683a583d1ad39abf83e0c68d3ac;hp=2296ab12e9a7da44373933f5190022bc7966ffb1;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2296ab1..33caf53 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* 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 .
+ * 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.appletgui;
@@ -348,7 +351,7 @@ public class SeqCanvas extends Panel
String mask = "0";
int maxWidth = 0;
int tmp;
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (int i = 0; i < alignment.getHeight(); i++)
{
tmp = alignment.getSequenceAt(i).getEnd();
@@ -643,7 +646,7 @@ public class SeqCanvas extends Panel
if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
- group = (SequenceGroup) av.getAlignment().getGroups().elementAt(0);
+ group = (SequenceGroup) av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
@@ -675,7 +678,8 @@ public class SeqCanvas extends Panel
{
if ((bottom == -1)
&& (i >= alHeight || !group.getSequences(null)
- .contains(av.getAlignment().getSequenceAt(i + 1))))
+ .contains(
+ av.getAlignment().getSequenceAt(i + 1))))
{
bottom = sy + av.charHeight;
}
@@ -799,8 +803,8 @@ public class SeqCanvas extends Panel
break;
}
- group = (SequenceGroup) av.getAlignment().getGroups().elementAt(
- groupIndex);
+ group = (SequenceGroup) av.getAlignment().getGroups()
+ .get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
}