// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
-import java.util.Locale;
-
-import jalview.datamodel.BinaryNode;
-import jalview.datamodel.SequenceNode;
-import jalview.util.MessageManager;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
+import java.util.Locale;
import java.util.StringTokenizer;
import com.stevesoft.pat.Regex;
+import jalview.bin.Jalview;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
+
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
* tree distances and topology are unreliable when they are parsed. TODO: on
{
try
{
- distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
+ distance = (Double.valueOf(ndist.stringMatched(1)))
+ .floatValue();
HasDistances = true;
nodehasdistance = true;
} catch (Exception e)
{
if (root.isDummy())
{
- _print(tf, root.right());
- _print(tf, root.left());
+ _print(tf, root.right());
+ _print(tf, root.left());
}
else
{
tf.append("(");
- _print(tf, root.right());
+ _print(tf, root.right());
if (root.left() != null)
{
tf.append(",");
}
- _print(tf, root.left());
+ _print(tf, root.left());
tf.append(")" + printRootField(root));
}
}
{
if (c.isDummy())
{
- _print(tf, c.left());
+ _print(tf, c.left());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, c.right());
+ _print(tf, c.right());
}
else
{
tf.append("(");
- _print(tf, c.right());
+ _print(tf, c.right());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, c.left());
+ _print(tf, c.left());
tf.append(")" + printNodeField(c));
}
}
{
if (args == null || args.length != 1)
{
- System.err.println(
- "Takes one argument - file name of a newick tree file.");
- System.exit(0);
+ Jalview.exit(
+ "Takes one argument - file name of a newick tree file.", 0);
}
File fn = new File(args[0]);