import com.stevesoft.pat.Regex;
import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
{
c.setRight(new SequenceNode(null, c, null, DefDistance,
DefBootstrap, false));
- c = (BinaryNode) c.right();
+ c = c.right();
}
else
{
c.setLeft(new SequenceNode(null, c, null, DefDistance,
DefBootstrap, false));
- c = (BinaryNode) c.left();
+ c = c.left();
}
if (realroot == null)
// Just advance focus, if we need to
if ((c.left() != null) && (!c.left().isLeaf()))
{
- c = (BinaryNode) c.left();
+ c = c.left();
}
}
}
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
- root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+ root = root.right().detach(); // remove the imaginary root.
if (!RootHasDistance)
{
if (args == null || args.length != 1)
{
Jalview.exit(
- "Takes one argument - file name of a newick tree file.", 0);
+ "Takes one argument - file name of a newick tree file.",
+ ExitCode.INVALID_ARGUMENT);
}
File fn = new File(args[0]);
jalview.bin.Console.outPrintln("Original file :\n");
Regex nonl = new Regex("\n+", "");
- jalview.bin.Console.outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
+ jalview.bin.Console
+ .outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
jalview.bin.Console.outPrintln("Parsed file.\n");
- jalview.bin.Console.outPrintln("Default output type for original input.\n");
+ jalview.bin.Console
+ .outPrintln("Default output type for original input.\n");
jalview.bin.Console.outPrintln(trf.print());
jalview.bin.Console.outPrintln("Without bootstraps.\n");
jalview.bin.Console.outPrintln(trf.print(false));
jalview.bin.Console.outPrintln("Without distances.\n");
jalview.bin.Console.outPrintln(trf.print(true, false));
- jalview.bin.Console.outPrintln("Without bootstraps but with distanecs.\n");
+ jalview.bin.Console
+ .outPrintln("Without bootstraps but with distanecs.\n");
jalview.bin.Console.outPrintln(trf.print(false, true));
jalview.bin.Console.outPrintln("Without bootstraps or distanecs.\n");
jalview.bin.Console.outPrintln(trf.print(false, false));
- jalview.bin.Console.outPrintln("With bootstraps and with distances.\n");
+ jalview.bin.Console
+ .outPrintln("With bootstraps and with distances.\n");
jalview.bin.Console.outPrintln(trf.print(true, true));
} catch (java.io.IOException e)
{