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Merge branch 'develop' into features/JAL-2393customMatrices
[jalview.git]
/
src
/
jalview
/
io
/
VamsasAppDatastore.java
diff --git
a/src/jalview/io/VamsasAppDatastore.java
b/src/jalview/io/VamsasAppDatastore.java
index
d580129
..
1cab8ca
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
*
*
* This file is part of Jalview.
*
@@
-43,7
+43,6
@@
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.List;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.List;
-import java.util.Set;
import java.util.Vector;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
import java.util.Vector;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
@@
-1433,7
+1432,7
@@
public class VamsasAppDatastore
// to the align frames.
boolean gathered = false;
String newviewid = null;
// to the align frames.
boolean gathered = false;
String newviewid = null;
- Set<AlignedCodonFrame> mappings = av.getAlignment()
+ List<AlignedCodonFrame> mappings = av.getAlignment()
.getCodonFrames();
for (int i = 0; i < views.length; i++)
{
.getCodonFrames();
for (int i = 0; i < views.length; i++)
{
@@
-1943,7
+1942,7
@@
public class VamsasAppDatastore
TreePanel tp = null;
if (vstree.isValidTree())
{
TreePanel tp = null;
if (vstree.isValidTree())
{
- tp = alignFrame.ShowNewickTree(vstree.getNewickTree(),
+ tp = alignFrame.showNewickTree(vstree.getNewickTree(),
vstree.getTitle(), vstree.getInputData(), 600,
500, t * 20 + 50, t * 20 + 50);
vstree.getTitle(), vstree.getInputData(), 600,
500, t * 20 + 50, t * 20 + 50);
@@
-2732,7
+2731,7
@@
public class VamsasAppDatastore
}
// Store any sequence mappings.
}
// Store any sequence mappings.
- Set<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
+ List<AlignedCodonFrame> cframes = av.getAlignment().getCodonFrames();
if (cframes != null)
{
for (AlignedCodonFrame acf : cframes)
if (cframes != null)
{
for (AlignedCodonFrame acf : cframes)