/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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 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.
-*
-* 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
-*/\r
-\r
-// NewickFile.java\r
-// Tree I/O\r
-// http://evolution.genetics.washington.edu/phylip/newick_doc.html\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.io.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-public class NewickFile extends FileParse {\r
- SequenceNode root;\r
- private boolean HasBootstrap = false;\r
- private boolean HasDistances = false;\r
- private boolean RootHasDistance = false;\r
-\r
- // File IO Flags\r
- boolean ReplaceUnderscores = false;\r
- boolean printRootInfo = false;\r
- private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] {\r
- new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes\r
- new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters\r
- new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation\r
- };\r
- char QuoteChar = '\'';\r
-\r
- public NewickFile(String inStr) throws IOException {\r
- super(inStr, "Paste");\r
- }\r
-\r
- public NewickFile(String inFile, String type) throws IOException {\r
- super(inFile, type);\r
- }\r
-\r
- public NewickFile(SequenceNode newtree) {\r
- root = newtree;\r
- }\r
-\r
- public NewickFile(SequenceNode newtree, boolean bootstrap) {\r
- HasBootstrap = bootstrap;\r
- root = newtree;\r
- }\r
-\r
- public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {\r
- root = newtree;\r
- HasBootstrap = bootstrap;\r
- HasDistances = distances;\r
- }\r
-\r
- public NewickFile(SequenceNode newtree, boolean bootstrap,\r
- boolean distances, boolean rootdistance) {\r
- root = newtree;\r
- HasBootstrap = bootstrap;\r
- HasDistances = distances;\r
- RootHasDistance = rootdistance;\r
- }\r
-\r
- private String ErrorStringrange(String Error, String Er, int r, int p,\r
- String s) {\r
- return ((Error == null) ? "" : Error) + Er + " at position " + p +\r
- " ( " +\r
- s.substring(((p - r) < 0) ? 0 : (p - r),\r
- ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";\r
- }\r
-\r
- // @tree annotations\r
- // These are set automatically by the reader\r
- public boolean HasBootstrap() {\r
- return HasBootstrap;\r
- }\r
-\r
- public boolean HasDistances() {\r
- return HasDistances;\r
- }\r
-\r
- public void parse() throws IOException {\r
- String nf;\r
-\r
- { // fill nf with complete tree file\r
-\r
- StringBuffer file = new StringBuffer();\r
-\r
- while ((nf = nextLine()) != null) {\r
- file.append(nf);\r
- }\r
-\r
- nf = file.toString();\r
- }\r
-\r
- root = new SequenceNode();\r
-\r
- SequenceNode realroot = null;\r
- SequenceNode c = root;\r
-\r
- int d = -1;\r
- int cp = 0;\r
- int flen = nf.length();\r
-\r
- String Error = null;\r
- String nodename = null;\r
-\r
- float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small\r
- int DefBootstrap = 0; // @param Default bootstrap for a node\r
-\r
- float distance = DefDistance;\r
- int bootstrap = DefBootstrap;\r
-\r
- boolean ascending = false; // flag indicating that we are leaving the current node\r
-\r
- com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(\r
- "[(\\['),;]");\r
-\r
- while (majorsyms.searchFrom(nf, cp) && (Error == null)) {\r
- int fcp = majorsyms.matchedFrom();\r
-\r
- switch (nf.charAt(fcp)) {\r
- case '[': // Comment or structured/extended NH format info\r
-\r
- com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(\r
- "]");\r
-\r
- if (comment.searchFrom(nf, fcp)) {\r
- // Skip the comment field\r
- cp = 1 + comment.matchedFrom();\r
- } else {\r
- Error = ErrorStringrange(Error, "Unterminated comment", 3,\r
- fcp, nf);\r
- }\r
-\r
- ;\r
-\r
- break;\r
-\r
- case '(':\r
-\r
- // ascending should not be set\r
- // New Internal node\r
- if (ascending) {\r
- Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);\r
-\r
- continue;\r
- }\r
-\r
- ;\r
- d++;\r
-\r
- if (c.right() == null) {\r
- c.setRight(new SequenceNode(null, c, null, DefDistance,\r
- DefBootstrap, false));\r
- c = (SequenceNode) c.right();\r
- } else {\r
- if (c.left() != null) {\r
- // Dummy node for polytomy - keeps c.left free for new node\r
- SequenceNode tmpn = new SequenceNode(null, c, null, 0,\r
- 0, true);\r
- tmpn.SetChildren(c.left(), c.right());\r
- c.setRight(tmpn);\r
- }\r
-\r
- c.setLeft(new SequenceNode(null, c, null, DefDistance,\r
- DefBootstrap, false));\r
- c = (SequenceNode) c.left();\r
- }\r
-\r
- if (realroot == null) {\r
- realroot = c;\r
- }\r
-\r
- nodename = null;\r
- distance = DefDistance;\r
- bootstrap = DefBootstrap;\r
- cp = fcp + 1;\r
-\r
- break;\r
-\r
- // Deal with quoted fields\r
- case '\'':\r
-\r
- com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(\r
- "([^']|'')+'");\r
-\r
- if (qnodename.searchFrom(nf, fcp)) {\r
- int nl = qnodename.stringMatched().length();\r
- nodename = new String(qnodename.stringMatched().substring(0,\r
- nl - 1));\r
- cp = fcp + nl + 1;\r
- } else {\r
- Error = ErrorStringrange(Error,\r
- "Unterminated quotes for nodename", 7, fcp, nf);\r
- }\r
-\r
- break;\r
-\r
- case ';':\r
-\r
- if (d != -1) {\r
- Error = ErrorStringrange(Error,\r
- "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);\r
- }\r
-\r
- // cp advanced at the end of default\r
- default:\r
-\r
- // Parse simpler field strings\r
- String fstring = nf.substring(cp, fcp);\r
- com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(\r
- "\\b([^' :;\\](),]+)");\r
- com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(\r
- "\\S+([0-9+]+)\\S*:");\r
- com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(\r
- ":([-0-9.+]+)");\r
-\r
- if (uqnodename.search(fstring) &&\r
- ((uqnodename.matchedFrom(1) == 0) ||\r
- (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!\r
- {\r
- if (nodename == null) {\r
- if (ReplaceUnderscores) {\r
- nodename = uqnodename.stringMatched(1).replace('_',\r
- ' ');\r
- } else {\r
- nodename = uqnodename.stringMatched(1);\r
- }\r
- } else {\r
- Error = ErrorStringrange(Error,\r
- "File has broken algorithm - overwritten nodename",\r
- 10, fcp, nf);\r
- }\r
- }\r
-\r
- if (nbootstrap.search(fstring) &&\r
- (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +\r
- uqnodename.stringMatched().length()))) {\r
- try {\r
- bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();\r
- HasBootstrap = true;\r
- } catch (Exception e) {\r
- Error = ErrorStringrange(Error,\r
- "Can't parse bootstrap value", 4,\r
- cp + nbootstrap.matchedFrom(), nf);\r
- }\r
- }\r
-\r
- boolean nodehasdistance = false;\r
-\r
- if (ndist.search(fstring)) {\r
- try {\r
- distance = (new Float(ndist.stringMatched(1))).floatValue();\r
- HasDistances = true;\r
- nodehasdistance = true;\r
- } catch (Exception e) {\r
- Error = ErrorStringrange(Error,\r
- "Can't parse node distance value", 7,\r
- cp + ndist.matchedFrom(), nf);\r
- }\r
- }\r
-\r
- if (ascending) {\r
- // Write node info here\r
- c.setName(nodename);\r
- c.dist = (HasDistances) ? distance : 0;\r
- c.setBootstrap((HasBootstrap) ? bootstrap : 0);\r
-\r
- if (c == realroot) {\r
- RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!\r
- }\r
- } else {\r
- // Find a place to put the leaf\r
- SequenceNode newnode = new SequenceNode(null, c, nodename,\r
- (HasDistances) ? distance : DefDistance,\r
- (HasBootstrap) ? bootstrap : DefBootstrap, false);\r
-\r
- if (c.right() == null) {\r
- c.setRight(newnode);\r
- } else {\r
- if (c.left() == null) {\r
- c.setLeft(newnode);\r
- } else {\r
- // Insert a dummy node for polytomy\r
- SequenceNode newdummy = new SequenceNode(null, c,\r
- null, 0, 0, true);\r
- newdummy.SetChildren(c.left(), newnode);\r
- c.setLeft(newdummy);\r
- }\r
- }\r
- }\r
-\r
- if (ascending) {\r
- // move back up the tree from preceding closure\r
- c = c.AscendTree();\r
-\r
- if ((d > -1) && (c == null)) {\r
- Error = ErrorStringrange(Error,\r
- "File broke algorithm: Lost place in tree (is there an extra ')' ?)",\r
- 7, fcp, nf);\r
- }\r
- }\r
-\r
- if (nf.charAt(fcp) == ')') {\r
- d--;\r
- ascending = true;\r
- } else {\r
- if (nf.charAt(fcp) == ',') {\r
- if (ascending) {\r
- ascending = false;\r
- } else {\r
- // Just advance focus, if we need to\r
- if ((c.left() != null) && (!c.left().isLeaf())) {\r
- c = (SequenceNode) c.left();\r
- }\r
- }\r
- }\r
- // else : We do nothing if ';' is encountered.\r
- }\r
-\r
- // Reset new node properties to obvious fakes\r
- nodename = null;\r
- distance = DefDistance;\r
- bootstrap = DefBootstrap;\r
-\r
- cp = fcp + 1;\r
- }\r
- }\r
-\r
- if (Error != null) {\r
- throw (new IOException("NewickFile: " + Error + "\n"));\r
- }\r
-\r
- root = (SequenceNode) root.right().detach(); // remove the imaginary root.\r
-\r
- if (!RootHasDistance) {\r
- root.dist = 0;\r
- }\r
- }\r
-\r
- public SequenceNode getTree() {\r
- return root;\r
- }\r
-\r
- public String print() {\r
- synchronized (this) {\r
- StringBuffer tf = new StringBuffer();\r
- print(tf, root);\r
-\r
- return (tf.append(";").toString());\r
- }\r
- }\r
-\r
- public String print(boolean withbootstraps) {\r
- synchronized (this) {\r
- boolean boots = this.HasBootstrap;\r
- this.HasBootstrap = withbootstraps;\r
-\r
- String rv = print();\r
- this.HasBootstrap = boots;\r
-\r
- return rv;\r
- }\r
- }\r
-\r
- public String print(boolean withbootstraps, boolean withdists) {\r
- synchronized (this) {\r
- boolean dists = this.HasDistances;\r
- this.HasDistances = withdists;\r
-\r
- String rv = print(withbootstraps);\r
- this.HasDistances = dists;\r
-\r
- return rv;\r
- }\r
- }\r
-\r
- public String print(boolean withbootstraps, boolean withdists,\r
- boolean printRootInfo) {\r
- synchronized (this) {\r
- boolean rootinfo = printRootInfo;\r
- this.printRootInfo = printRootInfo;\r
-\r
- String rv = print(withbootstraps, withdists);\r
- this.printRootInfo = rootinfo;\r
-\r
- return rv;\r
- }\r
- }\r
-\r
- char getQuoteChar() {\r
- return QuoteChar;\r
- }\r
-\r
- char setQuoteChar(char c) {\r
- char old = QuoteChar;\r
- QuoteChar = c;\r
-\r
- return old;\r
- }\r
-\r
- private String nodeName(String name) {\r
- if (NodeSafeName[0].search(name)) {\r
- return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;\r
- } else {\r
- return NodeSafeName[2].replaceAll(name);\r
- }\r
- }\r
-\r
- private String printNodeField(SequenceNode c) {\r
- return ((c.getName() == null) ? "" : nodeName(c.getName())) +\r
- ((HasBootstrap)\r
- ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +\r
- ((HasDistances) ? (":" + c.dist) : "");\r
- }\r
-\r
- private String printRootField(SequenceNode root) {\r
- return (printRootInfo)\r
- ? (((root.getName() == null) ? "" : nodeName(root.getName())) +\r
- ((HasBootstrap)\r
- ? ((root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") : "") +\r
- ((RootHasDistance) ? (":" + root.dist) : "")) : "";\r
- }\r
-\r
- // Non recursive call deals with root node properties\r
- public void print(StringBuffer tf, SequenceNode root) {\r
- if (root != null) {\r
- if (root.isLeaf() && printRootInfo) {\r
- tf.append(printRootField(root));\r
- } else {\r
- if (root.isDummy()) {\r
- _print(tf, (SequenceNode) root.right());\r
- _print(tf, (SequenceNode) root.left());\r
- } else {\r
- tf.append("(");\r
- _print(tf, (SequenceNode) root.right());\r
-\r
- if (root.left() != null) {\r
- tf.append(",");\r
- }\r
-\r
- _print(tf, (SequenceNode) root.left());\r
- tf.append(")" + printRootField(root));\r
- }\r
- }\r
- }\r
- }\r
-\r
- // Recursive call for non-root nodes\r
- public void _print(StringBuffer tf, SequenceNode c) {\r
- if (c != null) {\r
- if (c.isLeaf()) {\r
- tf.append(printNodeField(c));\r
- } else {\r
- if (c.isDummy()) {\r
- _print(tf, (SequenceNode) c.right());\r
- _print(tf, (SequenceNode) c.left());\r
- } else {\r
- tf.append("(");\r
- _print(tf, (SequenceNode) c.right());\r
-\r
- if (c.left() != null) {\r
- tf.append(",");\r
- }\r
-\r
- _print(tf, (SequenceNode) c.left());\r
- tf.append(")" + printNodeField(c));\r
- }\r
- }\r
- }\r
- }\r
-\r
- // Test\r
- public static void main(String[] args) {\r
- try {\r
- File fn = new File(args[0]);\r
-\r
- StringBuffer newickfile = new StringBuffer();\r
- BufferedReader treefile = new BufferedReader(new FileReader(fn));\r
- String l;\r
-\r
- while ((l = treefile.readLine()) != null) {\r
- newickfile.append(l);\r
- }\r
-\r
- treefile.close();\r
- System.out.println("Read file :\n");\r
-\r
- NewickFile trf = new NewickFile(args[0], "File");\r
- trf.parse();\r
- System.out.println("Original file :\n");\r
-\r
- com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");\r
- System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");\r
-\r
- System.out.println("Parsed file.\n");\r
- System.out.println("Default output type for original input.\n");\r
- System.out.println(trf.print());\r
- System.out.println("Without bootstraps.\n");\r
- System.out.println(trf.print(false));\r
- System.out.println("Without distances.\n");\r
- System.out.println(trf.print(true, false));\r
- System.out.println("Without bootstraps but with distanecs.\n");\r
- System.out.println(trf.print(false, true));\r
- System.out.println("Without bootstraps or distanecs.\n");\r
- System.out.println(trf.print(false, false));\r
- System.out.println("With bootstraps and with distances.\n");\r
- System.out.println(trf.print(true, true));\r
- } catch (java.io.IOException e) {\r
- System.err.println("Exception\n" + e);\r
- e.printStackTrace();\r
- }\r
- }\r
-}\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+// NewickFile.java
+// Tree I/O
+// http://evolution.genetics.washington.edu/phylip/newick_doc.html
+// TODO: Implement Basic NHX tag parsing and preservation
+// TODO: http://evolution.genetics.wustl.edu/eddy/forester/NHX.html
+// TODO: Extended SequenceNodeI to hold parsed NHX strings
+package jalview.io;
+
+import java.util.Locale;
+
+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.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
+ * 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
+ * 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
+ * duplication event - 'F' if this node represents a speciation event, '?' if
+ * this node represents an unknown event (D= tag should be replaced by Ev= tag)
+ * n/a :Ev=duplications>speciations>gene losses>event type>duplication type int
+ * int int string string event (replaces the =D tag), number of duplication,
+ * speciation, and gene loss events, type of event (transfer, fusion, root,
+ * unknown, other, speciation_duplication_loss, unassigned) <events>(<clade>)
+ * :E= string EC number at this node <annotation>(<sequence>) :Fu= string
+ * function at this node <annotation>(<sequence>)
+ * :DS=protein-length>from>to>support>name>from>... int int int double string
+ * int ... domain structure at this node <domain_architecture>(<sequence>) :S=
+ * string species name of the species/phylum at this node <taxonomy>(<clade>)
+ * :T= integer taxonomy ID of the species/phylum at this node <id>(<taxonomy>)
+ * :W= integer width of parent branch <width>(<clade>) :C=rrr.ggg.bbb
+ * integer.integer.integer color of parent branch <color>(<clade>) :Co= 'Y' or
+ * 'N' collapse this node when drawing the tree (default is not to collapse) n/a
+ * :XB= string custom data associated with a branch <property>(<clade>) :XN=
+ * string custom data associated with a node <property>(<clade>) :O= integer
+ * orthologous to this external node n/a :SN= integer subtree neighbors n/a :SO=
+ * integer super orthologous (no duplications on paths) to this external node
+ * n/a
+ *
+ * @author Jim Procter
+ * @version $Revision$
+ */
+public class NewickFile extends FileParse
+{
+ SequenceNode root;
+
+ private boolean HasBootstrap = false;
+
+ private boolean HasDistances = false;
+
+ private boolean RootHasDistance = false;
+
+ // File IO Flags
+ boolean ReplaceUnderscores = false;
+
+ boolean printRootInfo = true;
+
+ private Regex[] NodeSafeName = new Regex[] {
+ new Regex().perlCode("m/[\\[,:'()]/"), // test for
+ // requiring
+ // quotes
+ new Regex().perlCode("s/'/''/"), // escaping quote
+ // characters
+ new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
+ // transformation
+ };
+
+ char QuoteChar = '\'';
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param inStr
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public NewickFile(String inStr) throws IOException
+ {
+ super(inStr, DataSourceType.PASTE);
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param protocol
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public NewickFile(String inFile, DataSourceType protocol)
+ throws IOException
+ {
+ super(inFile, protocol);
+ }
+
+ public NewickFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree
+ * DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree)
+ {
+ root = newtree;
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree
+ * DOCUMENT ME!
+ * @param bootstrap
+ * DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree, boolean bootstrap)
+ {
+ HasBootstrap = bootstrap;
+ root = newtree;
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree
+ * DOCUMENT ME!
+ * @param bootstrap
+ * DOCUMENT ME!
+ * @param distances
+ * DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree, boolean bootstrap,
+ boolean distances)
+ {
+ root = newtree;
+ HasBootstrap = bootstrap;
+ HasDistances = distances;
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree
+ * DOCUMENT ME!
+ * @param bootstrap
+ * DOCUMENT ME!
+ * @param distances
+ * DOCUMENT ME!
+ * @param rootdistance
+ * DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree, boolean bootstrap,
+ boolean distances, boolean rootdistance)
+ {
+ root = newtree;
+ HasBootstrap = bootstrap;
+ HasDistances = distances;
+ RootHasDistance = rootdistance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Error
+ * DOCUMENT ME!
+ * @param Er
+ * DOCUMENT ME!
+ * @param r
+ * DOCUMENT ME!
+ * @param p
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String ErrorStringrange(String Error, String Er, int r, int p,
+ String s)
+ {
+ 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";
+ }
+
+ // @tree annotations
+ // These are set automatically by the reader
+ public boolean HasBootstrap()
+ {
+ return HasBootstrap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean HasDistances()
+ {
+ return HasDistances;
+ }
+
+ public boolean HasRootDistance()
+ {
+ return RootHasDistance;
+ }
+
+ /**
+ * 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
+ */
+ public void parse() throws IOException
+ {
+ String nf;
+
+ { // fill nf with complete tree file
+
+ StringBuffer file = new StringBuffer();
+
+ while ((nf = nextLine()) != null)
+ {
+ file.append(nf);
+ }
+
+ nf = file.toString();
+ }
+
+ root = new SequenceNode();
+
+ SequenceNode realroot = null;
+ SequenceNode c = root;
+
+ int d = -1;
+ int cp = 0;
+ // int flen = nf.length();
+
+ String Error = null;
+ String nodename = null;
+ String commentString2 = null; // comments after simple node props
+
+ double DefDistance = (float) 0.001; // @param Default distance for a node -
+ // very very small
+ int DefBootstrap = -1; // @param Default bootstrap for a node
+
+ double distance = DefDistance;
+ int bootstrap = DefBootstrap;
+
+ boolean ascending = false; // flag indicating that we are leaving the
+ // current node
+
+ Regex majorsyms = new Regex("[(\\['),;]");
+
+ int nextcp = 0;
+ int ncp = cp;
+ boolean parsednodename = false;
+ while (majorsyms.searchFrom(nf, cp) && (Error == null))
+ {
+ int fcp = majorsyms.matchedFrom();
+ char schar;
+ switch (schar = nf.charAt(fcp))
+ {
+ case '(':
+
+ // ascending should not be set
+ // New Internal node
+ if (ascending)
+ {
+ Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
+
+ continue;
+ }
+ d++;
+
+ if (c.right() == null)
+ {
+ c.setRight(new SequenceNode(null, c, null, DefDistance,
+ DefBootstrap, false));
+ c = (SequenceNode) 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);
+ tmpn.SetChildren(c.left(), c.right());
+ c.setRight(tmpn);
+ }
+
+ c.setLeft(new SequenceNode(null, c, null, DefDistance,
+ DefBootstrap, false));
+ c = (SequenceNode) c.left();
+ }
+
+ if (realroot == null)
+ {
+ realroot = c;
+ }
+
+ nodename = null;
+ distance = DefDistance;
+ bootstrap = DefBootstrap;
+ cp = fcp + 1;
+
+ break;
+
+ // Deal with quoted fields
+ case '\'':
+
+ Regex qnodename = new Regex("'([^']|'')+'");
+
+ if (qnodename.searchFrom(nf, fcp))
+ {
+ int nl = qnodename.stringMatched().length();
+ nodename = new String(
+ qnodename.stringMatched().substring(1, nl - 1));
+ // unpack any escaped colons
+ Regex xpandquotes = Regex.perlCode("s/''/'/");
+ String widernodename = xpandquotes.replaceAll(nodename);
+ nodename = widernodename;
+ // jump to after end of quoted nodename
+ nextcp = fcp + nl + 1;
+ parsednodename = true;
+ }
+ else
+ {
+ Error = ErrorStringrange(Error,
+ "Unterminated quotes for nodename", 7, fcp, nf);
+ }
+
+ break;
+
+ default:
+ if (schar == ';')
+ {
+ if (d != -1)
+ {
+ Error = ErrorStringrange(Error,
+ "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
+ }
+ // cp advanced at the end of default
+ }
+ if (schar == '[')
+ {
+ // node string contains Comment or structured/extended NH format info
+ /*
+ * if ((fcp-cp>1 && nf.substring(cp,fcp).trim().length()>1)) { // will
+ * process in remains System.err.println("skipped text:
+ * '"+nf.substring(cp,fcp)+"'"); }
+ */
+ // verify termination.
+ Regex comment = new Regex("]");
+ if (comment.searchFrom(nf, fcp))
+ {
+ // Skip the comment field
+ nextcp = comment.matchedFrom() + 1;
+ warningMessage = "Tree file contained comments which may confuse input algorithm.";
+ break;
+
+ // cp advanced at the end of default to nextcp, ncp is unchanged so
+ // any node info can be read.
+ }
+ else
+ {
+ Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
+ nf);
+ }
+ }
+ // Parse simpler field strings
+ String fstring = nf.substring(ncp, fcp);
+ // remove any comments before we parse the node info
+ // TODO: test newick file with quoted square brackets in node name (is
+ // this allowed?)
+ while (fstring.indexOf(']') > -1)
+ {
+ int cstart = fstring.indexOf('[');
+ int cend = fstring.indexOf(']');
+ commentString2 = fstring.substring(cstart + 1, cend);
+ fstring = fstring.substring(0, cstart)
+ + fstring.substring(cend + 1);
+
+ }
+ 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 (nodename == null)
+ {
+ if (ReplaceUnderscores)
+ {
+ nodename = uqnodename.stringMatched(1).replace('_', ' ');
+ }
+ else
+ {
+ nodename = uqnodename.stringMatched(1);
+ }
+ }
+ else
+ {
+ Error = ErrorStringrange(Error,
+ "File has broken algorithm - overwritten nodename", 10,
+ fcp, nf);
+ }
+ }
+ // get comment bootstraps
+
+ if (nbootstrap.search(fstring))
+ {
+ 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()))
+ {
+ try
+ {
+ 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);
+ }
+ }
+ }
+
+ boolean nodehasdistance = false;
+
+ if (ndist.search(fstring))
+ {
+ try
+ {
+ distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
+ HasDistances = true;
+ nodehasdistance = true;
+ } catch (Exception e)
+ {
+ Error = ErrorStringrange(Error,
+ "Can't parse node distance value", 7,
+ ncp + ndist.matchedFrom(), nf);
+ }
+ }
+
+ if (ascending)
+ {
+ // Write node info here
+ c.setName(nodename);
+ // Trees without distances still need a render distance
+ c.dist = (HasDistances) ? distance : DefDistance;
+ // be consistent for internal bootstrap defaults too
+ c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
+ if (c == realroot)
+ {
+ RootHasDistance = nodehasdistance; // JBPNote This is really
+ // UGLY!!! Ensure root node gets
+ // its given distance
+ }
+ parseNHXNodeProps(c, commentString2);
+ commentString2 = null;
+ }
+ else
+ {
+ // Find a place to put the leaf
+ SequenceNode newnode = new SequenceNode(null, c, nodename,
+ (HasDistances) ? distance : DefDistance,
+ (HasBootstrap) ? bootstrap : DefBootstrap, false);
+ parseNHXNodeProps(c, commentString2);
+ commentString2 = null;
+
+ if (c.right() == null)
+ {
+ c.setRight(newnode);
+ }
+ else
+ {
+ if (c.left() == null)
+ {
+ c.setLeft(newnode);
+ }
+ else
+ {
+ // Insert a dummy node for polytomy
+ // dummy nodes have distances
+ SequenceNode newdummy = new SequenceNode(null, c, null,
+ (HasDistances ? 0 : DefDistance), 0, true);
+ newdummy.SetChildren(c.left(), newnode);
+ c.setLeft(newdummy);
+ }
+ }
+ }
+
+ if (ascending)
+ {
+ // move back up the tree from preceding closure
+ c = c.AscendTree();
+
+ if ((d > -1) && (c == null))
+ {
+ Error = ErrorStringrange(Error,
+ "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
+ 7, fcp, nf);
+ }
+ }
+
+ if (nf.charAt(fcp) == ')')
+ {
+ d--;
+ ascending = true;
+ }
+ else
+ {
+ if (nf.charAt(fcp) == ',')
+ {
+ if (ascending)
+ {
+ ascending = false;
+ }
+ else
+ {
+ // Just advance focus, if we need to
+ if ((c.left() != null) && (!c.left().isLeaf()))
+ {
+ c = (SequenceNode) c.left();
+ }
+ }
+ }
+ }
+
+ // Reset new node properties to obvious fakes
+ nodename = null;
+ distance = DefDistance;
+ bootstrap = DefBootstrap;
+ commentString2 = null;
+ parsednodename = false;
+ }
+ if (nextcp == 0)
+ {
+ ncp = cp = fcp + 1;
+ }
+ else
+ {
+ cp = nextcp;
+ nextcp = 0;
+ }
+ }
+
+ if (Error != null)
+ {
+ 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") })));
+ }
+ // 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.
+
+ if (!RootHasDistance)
+ {
+ root.dist = (HasDistances) ? 0 : DefDistance;
+ }
+ }
+
+ /**
+ * parse NHX codes in comment strings and update NewickFile state flags for
+ * distances and bootstraps, and add any additional properties onto the node.
+ *
+ * @param c
+ * @param commentString
+ * @param commentString2
+ */
+ private void parseNHXNodeProps(SequenceNode c, String commentString)
+ {
+ // TODO: store raw comment on the sequenceNode so it can be recovered when
+ // tree is output
+ if (commentString != null && commentString.startsWith("&&NHX"))
+ {
+ StringTokenizer st = new StringTokenizer(commentString.substring(5),
+ ":");
+ while (st.hasMoreTokens())
+ {
+ String tok = st.nextToken();
+ int colpos = tok.indexOf("=");
+
+ if (colpos > -1)
+ {
+ String code = tok.substring(0, colpos);
+ String value = tok.substring(colpos + 1);
+ try
+ {
+ // parse out code/value pairs
+ if (code.toLowerCase(Locale.ROOT).equals("b"))
+ {
+ int v = -1;
+ Float iv = Float.valueOf(value);
+ v = iv.intValue(); // jalview only does integer bootstraps
+ // currently
+ c.setBootstrap(v);
+ HasBootstrap = true;
+ }
+ // more codes here.
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Couldn't parse code '" + code + "' = '" + value + "'");
+ e.printStackTrace(System.err);
+ }
+ }
+ }
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode getTree()
+ {
+ return root;
+ }
+
+ /**
+ * Generate a newick format tree according to internal flags for bootstraps,
+ * distances and root distances.
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print()
+ {
+ synchronized (this)
+ {
+ StringBuffer tf = new StringBuffer();
+ print(tf, root);
+
+ return (tf.append(";").toString());
+ }
+ }
+
+ /**
+ *
+ *
+ * Generate a newick format tree according to internal flags for distances and
+ * root distances and user specificied writing of bootstraps.
+ *
+ * @param withbootstraps
+ * controls if bootstrap values are explicitly written.
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print(boolean withbootstraps)
+ {
+ synchronized (this)
+ {
+ boolean boots = this.HasBootstrap;
+ this.HasBootstrap = withbootstraps;
+
+ String rv = print();
+ this.HasBootstrap = boots;
+
+ return rv;
+ }
+ }
+
+ /**
+ *
+ * Generate newick format tree according to internal flags for writing root
+ * node distances.
+ *
+ * @param withbootstraps
+ * explicitly write bootstrap values
+ * @param withdists
+ * explicitly write distances
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print(boolean withbootstraps, boolean withdists)
+ {
+ synchronized (this)
+ {
+ boolean dists = this.HasDistances;
+ this.HasDistances = withdists;
+
+ String rv = print(withbootstraps);
+ this.HasDistances = dists;
+
+ return rv;
+ }
+ }
+
+ /**
+ * Generate newick format tree according to user specified flags
+ *
+ * @param withbootstraps
+ * explicitly write bootstrap values
+ * @param withdists
+ * explicitly write distances
+ * @param printRootInfo
+ * explicitly write root distance
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print(boolean withbootstraps, boolean withdists,
+ boolean printRootInfo)
+ {
+ synchronized (this)
+ {
+ boolean rootinfo = printRootInfo;
+ this.printRootInfo = printRootInfo;
+
+ String rv = print(withbootstraps, withdists);
+ this.printRootInfo = rootinfo;
+
+ return rv;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ char getQuoteChar()
+ {
+ return QuoteChar;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ char setQuoteChar(char c)
+ {
+ char old = QuoteChar;
+ QuoteChar = c;
+
+ return old;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String nodeName(String name)
+ {
+ if (NodeSafeName[0].search(name))
+ {
+ return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
+ }
+ else
+ {
+ return NodeSafeName[2].replaceAll(name);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String printNodeField(SequenceNode c)
+ {
+ return ((c.getName() == null) ? "" : nodeName(c.getName()))
+ + ((HasBootstrap) ? ((c.getBootstrap() > -1)
+ ? ((c.getName() != null ? " " : "") + c.getBootstrap())
+ : "") : "")
+ + ((HasDistances) ? (":" + c.dist) : "");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String printRootField(SequenceNode root)
+ {
+ 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)
+ {
+ if (root != null)
+ {
+ if (root.isLeaf() && printRootInfo)
+ {
+ tf.append(printRootField(root));
+ }
+ else
+ {
+ if (root.isDummy())
+ {
+ _print(tf, (SequenceNode) root.right());
+ _print(tf, (SequenceNode) root.left());
+ }
+ else
+ {
+ tf.append("(");
+ _print(tf, (SequenceNode) root.right());
+
+ if (root.left() != null)
+ {
+ tf.append(",");
+ }
+
+ _print(tf, (SequenceNode) root.left());
+ tf.append(")" + printRootField(root));
+ }
+ }
+ }
+ }
+
+ // Recursive call for non-root nodes
+ public void _print(StringBuffer tf, SequenceNode c)
+ {
+ if (c != null)
+ {
+ if (c.isLeaf())
+ {
+ tf.append(printNodeField(c));
+ }
+ else
+ {
+ if (c.isDummy())
+ {
+ _print(tf, (SequenceNode) c.left());
+ if (c.left() != null)
+ {
+ tf.append(",");
+ }
+ _print(tf, (SequenceNode) c.right());
+ }
+ else
+ {
+ tf.append("(");
+ _print(tf, (SequenceNode) c.right());
+
+ if (c.left() != null)
+ {
+ tf.append(",");
+ }
+
+ _print(tf, (SequenceNode) c.left());
+ tf.append(")" + printNodeField(c));
+ }
+ }
+ }
+ }
+
+ /**
+ *
+ * @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.exit(0);
+ }
+
+ File fn = new File(args[0]);
+
+ StringBuffer newickfile = new StringBuffer();
+ BufferedReader treefile = new BufferedReader(new FileReader(fn));
+ String l;
+
+ while ((l = treefile.readLine()) != null)
+ {
+ newickfile.append(l);
+ }
+
+ treefile.close();
+ System.out.println("Read file :\n");
+
+ NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
+ trf.parse();
+ System.out.println("Original file :\n");
+
+ Regex nonl = new Regex("\n+", "");
+ System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
+
+ System.out.println("Parsed file.\n");
+ System.out.println("Default output type for original input.\n");
+ System.out.println(trf.print());
+ System.out.println("Without bootstraps.\n");
+ System.out.println(trf.print(false));
+ System.out.println("Without distances.\n");
+ System.out.println(trf.print(true, false));
+ System.out.println("Without bootstraps but with distanecs.\n");
+ System.out.println(trf.print(false, true));
+ System.out.println("Without bootstraps or distanecs.\n");
+ System.out.println(trf.print(false, false));
+ System.out.println("With bootstraps and with distances.\n");
+ System.out.println(trf.print(true, true));
+ } catch (java.io.IOException e)
+ {
+ System.err.println("Exception\n" + e);
+ e.printStackTrace();
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff