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Merge branch 'develop' into bug/JAL-1803_JAL-2157
[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
b5ada26
..
a3781a7
100644
(file)
--- a/
src/jalview/io/vamsas/Tree.java
+++ b/
src/jalview/io/vamsas/Tree.java
@@
-20,12
+20,6
@@
*/
package jalview.io.vamsas;
*/
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;
@@
-39,6
+33,13
@@
import jalview.gui.TreePanel;
import jalview.io.NewickFile;
import jalview.io.VamsasAppDatastore;
import jalview.viewmodel.AlignmentViewport;
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;
@@
-290,8
+291,10
@@
public class Tree extends DatastoreItem
}
}
if (alsq.size() < sequences.length)
}
}
if (alsq.size() < sequences.length)
+ {
Cache.log
.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
Cache.log
.warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+ }
return alsq;
}
return alsq;
}
@@
-305,15
+308,18
@@
public class Tree extends DatastoreItem
public void UpdateSequenceTreeMap(TreePanel tp)
{
if (tp == null || tree == null)
public void UpdateSequenceTreeMap(TreePanel tp)
{
if (tp == null || tree == null)
+ {
return;
return;
- Vector leaves = new Vector();
+ }
+
if (tp.getTree() == null)
{
Cache.log.warn("Not updating SequenceTreeMap for "
+ tree.getVorbaId());
return;
}
if (tp.getTree() == null)
{
Cache.log.warn("Not updating SequenceTreeMap for "
+ tree.getVorbaId());
return;
}
- tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
+ Vector<SequenceNode> leaves = tp.getTree().findLeaves(
+ tp.getTree().getTopNode());
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
// particular tree
int sz = tn.length;
Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
// particular tree
int sz = tn.length;
@@
-370,8
+376,7
@@
public class Tree extends DatastoreItem
*/
public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
{
*/
public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
{
- Vector leaves = new Vector();
- ntree.findLeaves(ntree.getTopNode(), leaves);
+ Vector<SequenceNode> leaves = ntree.findLeaves(ntree.getTopNode());
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
Vector tnv = new Vector();
Enumeration l = leaves.elements();
Hashtable nodespecs = new Hashtable();
@@
-421,8
+426,7
@@
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,
@@
-473,7
+477,9
@@
public class Tree extends DatastoreItem
--occurence;
}
else
--occurence;
}
else
+ {
bn = null;
bn = null;
+ }
}
return bn;
}
}
return bn;
}
@@
-595,8
+601,7
@@
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