git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (from parent 1:
6ab5d60
)
better vamsas tree io (for when there are no nodemappings)
author
jprocter
<Jim Procter>
Wed, 25 Jul 2007 17:16:54 +0000
(17:16 +0000)
committer
jprocter
<Jim Procter>
Wed, 25 Jul 2007 17:16:54 +0000
(17:16 +0000)
src/jalview/io/vamsas/Tree.java
patch
|
blob
|
history
diff --git
a/src/jalview/io/vamsas/Tree.java
b/src/jalview/io/vamsas/Tree.java
index
12c471e
..
82f4f07
100644
(file)
--- a/
src/jalview/io/vamsas/Tree.java
+++ b/
src/jalview/io/vamsas/Tree.java
@@
-1,5
+1,6
@@
package jalview.io.vamsas;
\r
\r
package jalview.io.vamsas;
\r
\r
+import java.io.IOException;
\r
import java.util.Enumeration;
\r
import java.util.Hashtable;
\r
import java.util.Vector;
\r
import java.util.Enumeration;
\r
import java.util.Hashtable;
\r
import java.util.Vector;
\r
@@
-60,7
+61,7
@@
public class Tree extends DatastoreItem
{
\r
inputData = (AlignmentView) idata[0];
\r
}
\r
{
\r
inputData = (AlignmentView) idata[0];
\r
}
\r
- ntree = new jalview.io.NewickFile(tree.getNewick(0).getContent());
\r
+ ntree = getNtree();
\r
title = tree.getNewick(0).getTitle();
\r
if (title==null || title.length()==0)
\r
{
\r
title = tree.getNewick(0).getTitle();
\r
if (title==null || title.length()==0)
\r
{
\r
@@
-74,6
+75,10
@@
public class Tree extends DatastoreItem
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
+ private NewickFile getNtree() throws IOException
\r
+ {
\r
+ return new jalview.io.NewickFile(tree.getNewick(0).getContent());
\r
+ }
\r
public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, uk.ac.vamsas.objects.core.Alignment alignment2)
\r
{
\r
super(datastore);
\r
public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2, uk.ac.vamsas.objects.core.Alignment alignment2)
\r
{
\r
super(datastore);
\r
@@
-402,5
+407,21
@@
public class Tree extends DatastoreItem
{
\r
return inputData;
\r
}
\r
{
\r
return inputData;
\r
}
\r
+ public boolean isValidTree()
\r
+ {
\r
+ try {
\r
+ ntree.parse();
\r
+ if (ntree.getTree()!=null)
\r
+ {
\r
+ ntree = getNtree();
\r
+ }
\r
+ return true;
\r
+ }
\r
+ catch (Exception e)
\r
+ {
\r
+ Cache.log.debug("Failed to parse newick tree string",e);
\r
+ }
\r
+ return false;
\r
+ }
\r
\r
}
\r
\r
}
\r