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Revert "needed for linkedapplets_ng.html (JAL-859,JAL-469)"
[jalview.git]
/
src
/
jalview
/
io
/
vamsas
/
Tree.java
diff --git
a/src/jalview/io/vamsas/Tree.java
b/src/jalview/io/vamsas/Tree.java
index
0545839
..
9b76f91
100644
(file)
--- a/
src/jalview/io/vamsas/Tree.java
+++ b/
src/jalview/io/vamsas/Tree.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-155,8
+155,7
@@
public class Tree extends DatastoreItem
else
{
// handle conflict
else
{
// handle conflict
- log
- .info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
+ log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
}
}
}
}
@@
-220,8
+219,8
@@
public class Tree extends DatastoreItem
// or just correctly resolve the tree's seqData to the correct alignment
// in
// the document.
// or just correctly resolve the tree's seqData to the correct alignment
// in
// the document.
- Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
- .getTree().seqData.getSequences()));
+ Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
+ tp.getTree().seqData.getSequences()));
Object[] alsqs = new Object[alsqrefs.size()];
alsqrefs.copyInto(alsqs);
vInput.setObjRef(alsqs);
Object[] alsqs = new Object[alsqrefs.size()];
alsqrefs.copyInto(alsqs);
vInput.setObjRef(alsqs);
@@
-347,9
+346,7
@@
public class Tree extends DatastoreItem
else
{
leaf.setPlaceholder(true);
else
{
leaf.setPlaceholder(true);
- leaf
- .setElement(new Sequence(leaf.getName(),
- "THISISAPLACEHLDER"));
+ leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
}
}
}
}
}