/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
// 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.IOException;
import java.util.StringTokenizer;
+import com.stevesoft.pat.Regex;
+
/**
* 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
*/
public class NewickFile extends FileParse
{
- SequenceNode root;
+ BinaryNode root;
private boolean HasBootstrap = false;
boolean printRootInfo = true;
- private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
- { new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
+ private Regex[] NodeSafeName = new Regex[] {
+ new Regex().perlCode("m/[\\[,:'()]/"), // test for
// requiring
// quotes
- new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
+ new Regex().perlCode("s/'/''/"), // escaping quote
// characters
- new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
- // transformation
+ new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
+ // transformation
};
char QuoteChar = '\'';
*/
public NewickFile(String inStr) throws IOException
{
- super(inStr, "Paste");
+ super(inStr, DataSourceType.PASTE);
}
/**
*
* @param inFile
* DOCUMENT ME!
- * @param type
+ * @param protocol
* DOCUMENT ME!
*
* @throws IOException
* DOCUMENT ME!
*/
- public NewickFile(String inFile, String type) throws IOException
+ public NewickFile(String inFile, DataSourceType protocol)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, protocol);
}
public NewickFile(FileParse source) throws IOException
* @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;
private String ErrorStringrange(String Error, String Er, int r, int p,
String s)
{
- return ((Error == null) ? "" : Error)
- + Er
- + " at position "
- + p
- + " ( "
+ return ((Error == null) ? "" : Error) + Er + " at position " + p + " ( "
+ s.substring(((p - r) < 0) ? 0 : (p - r),
- ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
+ ((p + r) > s.length()) ? s.length() : (p + r))
+ + " )\n";
}
// @tree annotations
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
- com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
- "[(\\['),;]");
+ Regex majorsyms = new Regex("[(\\['),;]");
int nextcp = 0;
int ncp = cp;
continue;
}
-
- ;
d++;
if (c.right() == null)
{
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 '\'':
- com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
- "'([^']|'')+'");
+ Regex qnodename = new Regex("'([^']|'')+'");
if (qnodename.searchFrom(nf, fcp))
{
int nl = qnodename.stringMatched().length();
- nodename = new String(qnodename.stringMatched().substring(1,
- nl - 1));
+ nodename = new String(
+ qnodename.stringMatched().substring(1, nl - 1));
// unpack any escaped colons
- com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
- .perlCode("s/''/'/");
+ Regex xpandquotes = Regex.perlCode("s/''/'/");
String widernodename = xpandquotes.replaceAll(nodename);
nodename = widernodename;
// jump to after end of quoted nodename
{
if (d != -1)
{
- Error = ErrorStringrange(Error, "Wayward semicolon (depth=" + d
- + ")", 7, fcp, nf);
+ Error = ErrorStringrange(Error,
+ "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
}
// cp advanced at the end of default
}
* '"+nf.substring(cp,fcp)+"'"); }
*/
// verify termination.
- com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
+ Regex comment = new Regex("]");
if (comment.searchFrom(nf, fcp))
{
// Skip the comment field
Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
nf);
}
-
- ;
}
// Parse simpler field strings
String fstring = nf.substring(ncp, fcp);
+ fstring.substring(cend + 1);
}
- com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
- "\\b([^' :;\\](),]+)");
- com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
- "\\s*([0-9+]+)\\s*:");
- com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
- ":([-0-9Ee.+]+)");
-
- if (!parsednodename
- && uqnodename.search(fstring)
+ 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
.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
// HACK!
if (nbootstrap.search(fstring))
{
- if (nbootstrap.stringMatched(1).equals(
- uqnodename.stringMatched(1)))
+ if (nbootstrap.stringMatched(1)
+ .equals(uqnodename.stringMatched(1)))
{
nodename = null; // no nodename here.
}
- if (nodename == null
- || nodename.length() == 0
- || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) + uqnodename
- .stringMatched().length()))
+ if (nodename == null || nodename.length() == 0
+ || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1)
+ + uqnodename.stringMatched().length()))
{
try
{
- bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+ bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
.intValue();
HasBootstrap = true;
} catch (Exception e)
{
- Error = ErrorStringrange(Error,
- "Can't parse bootstrap value", 4,
- ncp + nbootstrap.matchedFrom(), nf);
+ Error = ErrorStringrange(Error, "Can't parse bootstrap value",
+ 4, ncp + nbootstrap.matchedFrom(), nf);
}
}
}
{
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);
if ((d > -1) && (c == null))
{
- Error = ErrorStringrange(
- Error,
+ Error = ErrorStringrange(Error,
"File broke algorithm: Lost place in tree (is there an extra ')' ?)",
7, fcp, nf);
}
// Just advance focus, if we need to
if ((c.left() != null) && (!c.left().isLeaf()))
{
- c = (SequenceNode) c.left();
+ c = (BinaryNode) c.left();
}
}
}
if (Error != null)
{
- throw (new IOException(MessageManager.formatMessage(
- "exception.newfile", new String[] { Error.toString() })));
+ throw (new IOException(
+ MessageManager.formatMessage("exception.newfile", new String[]
+ { Error.toString() })));
}
if (root == null)
{
- throw (new IOException(MessageManager.formatMessage(
- "exception.newfile", new String[] { MessageManager
- .getString("label.no_tree_read_in") })));
+ throw (new IOException(
+ MessageManager.formatMessage("exception.newfile", new String[]
+ { MessageManager.getString("label.no_tree_read_in") })));
}
// THe next line is failing for topali trees - not sure why yet. if
// (root.right()!=null && root.isDummy())
* @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);
// more codes here.
} catch (Exception e)
{
- System.err.println("Couldn't parse code '" + code + "' = '"
- + value + "'");
+ System.err.println(
+ "Couldn't parse code '" + code + "' = '" + value + "'");
e.printStackTrace(System.err);
}
}
*
* @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) ? ((c.getName() != null ? " "
- : "") + c.getBootstrap())
- : "")
- : "") + ((HasDistances) ? (":" + c.dist) : "");
+ + ((HasBootstrap) ? ((c.getBootstrap() > -1)
+ ? ((c.getName() != null ? " " : "") + c.getBootstrap())
+ : "") : "")
+ + ((HasDistances) ? (":" + c.dist) : "");
}
/**
*
* @return DOCUMENT ME!
*/
- private String printRootField(SequenceNode root)
+ private String printRootField(BinaryNode root)
{
- return (printRootInfo) ? (((root.getName() == null) ? ""
- : nodeName(root.getName()))
- + ((HasBootstrap) ? ((root.getBootstrap() > -1) ? ((root
- .getName() != null ? " " : "") + +root.getBootstrap())
- : "") : "") + ((RootHasDistance) ? (":" + root.dist)
- : "")) : "";
+ return (printRootInfo)
+ ? (((root.getName() == null) ? "" : nodeName(root.getName()))
+ + ((HasBootstrap)
+ ? ((root.getBootstrap() > -1)
+ ? ((root.getName() != null ? " " : "")
+ + +root.getBootstrap())
+ : "")
+ : "")
+ + ((RootHasDistance) ? (":" + root.dist) : ""))
+ : "";
}
// 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));
}
}
}
}
- // Test
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
try
{
if (args == null || args.length != 1)
{
- System.err
- .println("Takes one argument - file name of a newick tree file.");
+ System.err.println(
+ "Takes one argument - file name of a newick tree file.");
System.exit(0);
}
treefile.close();
System.out.println("Read file :\n");
- NewickFile trf = new NewickFile(args[0], "File");
+ NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
trf.parse();
System.out.println("Original file :\n");
- com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+ Regex nonl = new Regex("\n+", "");
System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
System.out.println("Parsed file.\n");
git://source.jalview.org / jalview.git / blobdiff