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Merge branch 'develop' into groovy/JAL-2074_upgradeto2.4.4
[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
02ce434
..
0bf4096
100644
(file)
--- a/
src/jalview/io/vamsas/Tree.java
+++ b/
src/jalview/io/vamsas/Tree.java
@@
-1,29
+1,25
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* 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.
*
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
import jalview.analysis.NJTree;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.analysis.NJTree;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
@@
-33,10
+29,17
@@
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignViewport;
import jalview.gui.TreePanel;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
import jalview.gui.TreePanel;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.Entry;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.Entry;
@@
-419,8
+422,7
@@
public class Tree extends DatastoreItem
tnv.copyInto(tn);
return tn;
}
tnv.copyInto(tn);
return tn;
}
- return new Treenode[]
- {};
+ return new Treenode[] {};
}
private String makeNodeSpec(Hashtable nodespecs,
}
private String makeNodeSpec(Hashtable nodespecs,
@@
-508,7
+510,7
@@
public class Tree extends DatastoreItem
*/
public Object[] recoverInputData(Provenance tp)
{
*/
public Object[] recoverInputData(Provenance tp)
{
- AlignViewport javport = null;
+ AlignmentViewport javport = null;
jalview.datamodel.AlignmentI jal = null;
jalview.datamodel.CigarArray view = null;
for (int pe = 0; pe < tp.getEntryCount(); pe++)
jalview.datamodel.AlignmentI jal = null;
jalview.datamodel.CigarArray view = null;
for (int pe = 0; pe < tp.getEntryCount(); pe++)
@@
-593,8
+595,7
@@
public class Tree extends DatastoreItem
// off by
// one for to
}
// off by
// one for to
}
- return new Object[]
- { new AlignmentView(view), jal };
+ return new Object[] { new AlignmentView(view), jal };
}
}
Cache.log
}
}
Cache.log
@@
-602,7
+603,7
@@
public class Tree extends DatastoreItem
return null;
}
return null;
}
- private AlignViewport getViewport(Vobject v_parent)
+ private AlignmentViewport getViewport(Vobject v_parent)
{
if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
{
{
if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
{