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JAL-2805 getNodeSequences returns a list now instead of array (size
[jalview.git]
/
src
/
jalview
/
ext
/
forester
/
io
/
NexusFile.java
diff --git
a/src/jalview/ext/forester/io/NexusFile.java
b/src/jalview/ext/forester/io/NexusFile.java
index
2db46cc
..
51f3bc3
100644
(file)
--- a/
src/jalview/ext/forester/io/NexusFile.java
+++ b/
src/jalview/ext/forester/io/NexusFile.java
@@
-8,6
+8,7
@@
import jalview.io.FileParse;
import java.io.File;
import java.io.IOException;
import java.io.File;
import java.io.IOException;
+import java.util.List;
public class NexusFile extends AlignFile
{
public class NexusFile extends AlignFile
{
@@
-30,12
+31,13
@@
public class NexusFile extends AlignFile
TreeParserI parser = ForesterParser
.createNexusParser(new File(getDataName()));
TreeI[] trees = parser.parse();
TreeParserI parser = ForesterParser
.createNexusParser(new File(getDataName()));
TreeI[] trees = parser.parse();
- for (TreeI tree : trees) {
- for (SequenceI seq : tree.getNodeSequences()) {
+ List<SequenceI> treeSeqs = trees[0].getNodeSequences();
+ for (SequenceI seq : treeSeqs)
+ {
seqs.add(seq);
}
}
}
seqs.add(seq);
}
}
}
-}
+