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
{\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
}\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
{\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