// 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;
*/
public class NewickFile extends FileParse
{
- SequenceNode root;
+ BinaryNode root;
private boolean HasBootstrap = false;
* @param newtree
* DOCUMENT ME!
*/
- public NewickFile(SequenceNode newtree)
+ public NewickFile(BinaryNode newtree)
{
root = newtree;
}
* @param distances
* DOCUMENT ME!
*/
- public NewickFile(SequenceNode newtree, boolean bootstrap,
+ public NewickFile(BinaryNode newtree, boolean bootstrap,
boolean distances)
{
root = newtree;
* @param rootdistance
* DOCUMENT ME!
*/
- public NewickFile(SequenceNode newtree, boolean bootstrap,
+ public NewickFile(BinaryNode newtree, boolean bootstrap,
boolean distances, boolean rootdistance)
{
root = newtree;
root = new SequenceNode();
- SequenceNode realroot = null;
- SequenceNode c = root;
+ BinaryNode realroot = null;
+ BinaryNode c = root;
int d = -1;
int cp = 0;
String nodename = null;
String commentString2 = null; // comments after simple node props
- float DefDistance = (float) 0.001; // @param Default distance for a node -
+ double DefDistance = (float) 0.001; // @param Default distance for a node -
// very very small
int DefBootstrap = -1; // @param Default bootstrap for a node
- float distance = DefDistance;
+ double distance = DefDistance;
int bootstrap = DefBootstrap;
boolean ascending = false; // flag indicating that we are leaving the
// current node
- Regex majorsyms = new Regex(
- "[(\\['),;]");
+ Regex majorsyms = new Regex("[(\\['),;]");
int nextcp = 0;
int ncp = cp;
{
c.setRight(new SequenceNode(null, c, null, DefDistance,
DefBootstrap, false));
- c = (SequenceNode) c.right();
+ c = (BinaryNode) c.right();
}
else
{
if (c.left() != null)
{
// Dummy node for polytomy - keeps c.left free for new node
- SequenceNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
+ BinaryNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
tmpn.SetChildren(c.left(), c.right());
c.setRight(tmpn);
}
c.setLeft(new SequenceNode(null, c, null, DefDistance,
DefBootstrap, false));
- c = (SequenceNode) c.left();
+ c = (BinaryNode) c.left();
}
if (realroot == null)
// Deal with quoted fields
case '\'':
- Regex qnodename = new Regex(
- "'([^']|'')+'");
+ Regex qnodename = new Regex("'([^']|'')+'");
if (qnodename.searchFrom(nf, fcp))
{
nodename = new String(
qnodename.stringMatched().substring(1, nl - 1));
// unpack any escaped colons
- Regex xpandquotes = Regex
- .perlCode("s/''/'/");
+ Regex xpandquotes = Regex.perlCode("s/''/'/");
String widernodename = xpandquotes.replaceAll(nodename);
nodename = widernodename;
// jump to after end of quoted nodename
* '"+nf.substring(cp,fcp)+"'"); }
*/
// verify termination.
- Regex comment = new Regex(
- "]");
+ Regex comment = new Regex("]");
if (comment.searchFrom(nf, fcp))
{
// Skip the comment field
+ fstring.substring(cend + 1);
}
- Regex uqnodename = new Regex(
- "\\b([^' :;\\](),]+)");
- Regex nbootstrap = new Regex(
- "\\s*([0-9+]+)\\s*:");
- Regex ndist = new Regex(
- ":([-0-9Ee.+]+)");
+ Regex uqnodename = new Regex("\\b([^' :;\\](),]+)");
+ Regex nbootstrap = new Regex("\\s*([0-9+]+)\\s*:");
+ Regex ndist = new Regex(":([-0-9Ee.+]+)");
if (!parsednodename && uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
{
try
{
- bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+ bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
.intValue();
HasBootstrap = true;
} catch (Exception e)
{
try
{
- distance = (new Float(ndist.stringMatched(1))).floatValue();
+ distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
HasDistances = true;
nodehasdistance = true;
} catch (Exception e)
else
{
// Find a place to put the leaf
- SequenceNode newnode = new SequenceNode(null, c, nodename,
+ BinaryNode newnode = new SequenceNode(null, c, nodename,
(HasDistances) ? distance : DefDistance,
(HasBootstrap) ? bootstrap : DefBootstrap, false);
parseNHXNodeProps(c, commentString2);
{
// Insert a dummy node for polytomy
// dummy nodes have distances
- SequenceNode newdummy = new SequenceNode(null, c, null,
+ BinaryNode newdummy = new SequenceNode(null, c, null,
(HasDistances ? 0 : DefDistance), 0, true);
newdummy.SetChildren(c.left(), newnode);
c.setLeft(newdummy);
// Just advance focus, if we need to
if ((c.left() != null) && (!c.left().isLeaf()))
{
- c = (SequenceNode) c.left();
+ c = (BinaryNode) c.left();
}
}
}
* @param commentString
* @param commentString2
*/
- private void parseNHXNodeProps(SequenceNode c, String commentString)
+ private void parseNHXNodeProps(BinaryNode c, String commentString)
{
// TODO: store raw comment on the sequenceNode so it can be recovered when
// tree is output
try
{
// parse out code/value pairs
- if (code.toLowerCase().equals("b"))
+ if (code.toLowerCase(Locale.ROOT).equals("b"))
{
int v = -1;
- Float iv = new Float(value);
+ Float iv = Float.valueOf(value);
v = iv.intValue(); // jalview only does integer bootstraps
// currently
c.setBootstrap(v);
*
* @return DOCUMENT ME!
*/
- public SequenceNode getTree()
+ public BinaryNode getTree()
{
return root;
}
*
* @return DOCUMENT ME!
*/
- private String printNodeField(SequenceNode c)
+ private String printNodeField(BinaryNode c)
{
return ((c.getName() == null) ? "" : nodeName(c.getName()))
+ ((HasBootstrap) ? ((c.getBootstrap() > -1)
*
* @return DOCUMENT ME!
*/
- private String printRootField(SequenceNode root)
+ private String printRootField(BinaryNode root)
{
return (printRootInfo)
? (((root.getName() == null) ? "" : nodeName(root.getName()))
}
// Non recursive call deals with root node properties
- public void print(StringBuffer tf, SequenceNode root)
+ public void print(StringBuffer tf, BinaryNode root)
{
if (root != null)
{
{
if (root.isDummy())
{
- _print(tf, (SequenceNode) root.right());
- _print(tf, (SequenceNode) root.left());
+ _print(tf, root.right());
+ _print(tf, root.left());
}
else
{
tf.append("(");
- _print(tf, (SequenceNode) root.right());
+ _print(tf, root.right());
if (root.left() != null)
{
tf.append(",");
}
- _print(tf, (SequenceNode) root.left());
+ _print(tf, root.left());
tf.append(")" + printRootField(root));
}
}
}
// Recursive call for non-root nodes
- public void _print(StringBuffer tf, SequenceNode c)
+ public void _print(StringBuffer tf, BinaryNode c)
{
if (c != null)
{
{
if (c.isDummy())
{
- _print(tf, (SequenceNode) c.left());
+ _print(tf, c.left());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, (SequenceNode) c.right());
+ _print(tf, c.right());
}
else
{
tf.append("(");
- _print(tf, (SequenceNode) c.right());
+ _print(tf, c.right());
if (c.left() != null)
{
tf.append(",");
}
- _print(tf, (SequenceNode) c.left());
+ _print(tf, c.left());
tf.append(")" + printNodeField(c));
}
}
git://source.jalview.org / jalview.git / blobdiff