/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
// NewickFile.java
// Tree I/O
// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
-import java.io.*;
-import java.util.StringTokenizer;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
-import jalview.datamodel.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.StringTokenizer;
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
* this: NHX codes are appended in comments beginning with &&NHX. The codes are
* given below (from http://www.phylosoft.org/forester/NHX.html): Element Type
* Description Corresponding phyloXML element (parent element in parentheses) no
- * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED) <name>(<clade>) :
- * decimal branch length to parent node (MUST BE SECOND, IF ASSIGNED)
- * <branch_length>(<clade>) :GN= string gene name <name>(<sequence>) :AC=
- * string sequence accession <accession>(<sequence>) :ND= string node
+ * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
+ * <name>(<clade>) : decimal branch length to parent node (MUST BE SECOND, IF
+ * ASSIGNED) <branch_length>(<clade>) :GN= string gene name <name>(<sequence>)
+ * :AC= string sequence accession <accession>(<sequence>) :ND= string node
* identifier - if this is being used, it has to be unique within each phylogeny
* <node_id>(<clade>) :B= decimal confidence value for parent branch
* <confidence>(<clade>) :D= 'T', 'F', or '?' 'T' if this node represents a
* Creates a new NewickFile object.
*
* @param inStr
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NewickFile(String inStr) throws IOException
{
* Creates a new NewickFile object.
*
* @param inFile
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param type
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @throws IOException
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NewickFile(String inFile, String type) throws IOException
{
* Creates a new NewickFile object.
*
* @param newtree
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NewickFile(SequenceNode newtree)
{
* Creates a new NewickFile object.
*
* @param newtree
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param bootstrap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NewickFile(SequenceNode newtree, boolean bootstrap)
{
* Creates a new NewickFile object.
*
* @param newtree
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param bootstrap
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param distances
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NewickFile(SequenceNode newtree, boolean bootstrap,
boolean distances)
* Creates a new NewickFile object.
*
* @param newtree
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param bootstrap
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param distances
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param rootdistance
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NewickFile(SequenceNode newtree, boolean bootstrap,
boolean distances, boolean rootdistance)
* DOCUMENT ME!
*
* @param Error
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param Er
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param r
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param p
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
+ " at position "
+ p
+ " ( "
- + s.substring(((p - r) < 0) ? 0 : (p - r), ((p + r) > s
- .length()) ? s.length() : (p + r)) + " )\n";
+ + s.substring(((p - r) < 0) ? 0 : (p - r),
+ ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
}
// @tree annotations
* parse the filesource as a newick file (new hampshire and/or extended)
*
* @throws IOException
- * with a line number and character position for badly
- * formatted NH strings
+ * with a line number and character position for badly formatted NH
+ * strings
*/
public void parse() throws IOException
{
int nextcp = 0;
int ncp = cp;
+ boolean parsednodename = false;
while (majorsyms.searchFrom(nf, cp) && (Error == null))
{
int fcp = majorsyms.matchedFrom();
case '\'':
com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
- "([^']|'')+'");
+ "'([^']|'')+'");
if (qnodename.searchFrom(nf, fcp))
{
int nl = qnodename.stringMatched().length();
- nodename = new String(qnodename.stringMatched().substring(0,
+ nodename = new String(qnodename.stringMatched().substring(1,
nl - 1));
- cp = fcp + nl + 1;
+ // unpack any escaped colons
+ com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
+ .perlCode("s/''/'/");
+ String widernodename = xpandquotes.replaceAll(nodename);
+ nodename = widernodename;
+ // jump to after end of quoted nodename
+ nextcp = fcp + nl + 1;
+ parsednodename = true;
}
else
{
com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
":([-0-9Ee.+]+)");
- if (uqnodename.search(fstring)
+ if (!parsednodename
+ && uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
// HACK!
} catch (Exception e)
{
Error = ErrorStringrange(Error,
- "Can't parse bootstrap value", 4, ncp
- + nbootstrap.matchedFrom(), nf);
+ "Can't parse bootstrap value", 4,
+ ncp + nbootstrap.matchedFrom(), nf);
}
}
}
} catch (Exception e)
{
Error = ErrorStringrange(Error,
- "Can't parse node distance value", 7, ncp
- + ndist.matchedFrom(), nf);
+ "Can't parse node distance value", 7,
+ ncp + ndist.matchedFrom(), nf);
}
}
distance = DefDistance;
bootstrap = DefBootstrap;
commentString2 = null;
+ parsednodename = false;
}
if (nextcp == 0)
{
if (Error != null)
{
- throw (new IOException("NewickFile: " + Error + "\n"));
+ throw (new IOException(MessageManager.formatMessage(
+ "exception.newfile", new String[] { Error.toString() })));
}
if (root == null)
{
- throw (new IOException("NewickFile: No Tree read in\n"));
+ 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())
* root distances and user specificied writing of bootstraps.
*
* @param withbootstraps
- * controls if bootstrap values are explicitly written.
+ * controls if bootstrap values are explicitly written.
*
* @return new hampshire tree in a single line
*/
* node distances.
*
* @param withbootstraps
- * explicitly write bootstrap values
+ * explicitly write bootstrap values
* @param withdists
- * explicitly write distances
+ * explicitly write distances
*
* @return new hampshire tree in a single line
*/
* Generate newick format tree according to user specified flags
*
* @param withbootstraps
- * explicitly write bootstrap values
+ * explicitly write bootstrap values
* @param withdists
- * explicitly write distances
+ * explicitly write distances
* @param printRootInfo
- * explicitly write root distance
+ * explicitly write root distance
*
* @return new hampshire tree in a single line
*/
* DOCUMENT ME!
*
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param name
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param c
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
* DOCUMENT ME!
*
* @param root
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
git://source.jalview.org / jalview.git / blobdiff