X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=027390a1e8fc6facd4f7ae1e5852df515acacf38;hb=c6977851625f96831a95b45901aa1d84bd7774fe;hp=8e374ac0d722eab205ae4112b8f53545ac4059f2;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 8e374ac..027390a 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -1,19 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ // NewickFile.java // Tree I/O @@ -23,10 +26,18 @@ // TODO: Extended SequenceNodeI to hold parsed NHX strings package jalview.io; -import java.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 jalview.datamodel.*; +import com.stevesoft.pat.Regex; /** * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the @@ -80,14 +91,14 @@ public class NewickFile extends FileParse 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 = '\''; @@ -103,7 +114,7 @@ public class NewickFile extends FileParse */ public NewickFile(String inStr) throws IOException { - super(inStr, "Paste"); + super(inStr, DataSourceType.PASTE); } /** @@ -111,15 +122,16 @@ public class NewickFile extends FileParse * * @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 @@ -210,13 +222,10 @@ public class NewickFile extends FileParse 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"; + 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 @@ -277,21 +286,21 @@ public class NewickFile extends FileParse 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; + boolean parsednodename = false; while (majorsyms.searchFrom(nf, cp) && (Error == null)) { int fcp = majorsyms.matchedFrom(); @@ -308,8 +317,6 @@ public class NewickFile extends FileParse continue; } - - ; d++; if (c.right() == null) @@ -348,15 +355,20 @@ public class NewickFile extends FileParse // 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(0, - nl - 1)); - cp = fcp + nl + 1; + 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 { @@ -371,8 +383,8 @@ public class NewickFile extends FileParse { 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 } @@ -385,7 +397,7 @@ public class NewickFile extends FileParse * '"+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 @@ -401,8 +413,6 @@ public class NewickFile extends FileParse Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf); } - - ; } // Parse simpler field strings String fstring = nf.substring(ncp, fcp); @@ -418,14 +428,11 @@ public class NewickFile extends FileParse + 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 (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! @@ -452,26 +459,24 @@ public class NewickFile extends FileParse 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); } } } @@ -482,14 +487,14 @@ public class NewickFile extends FileParse { try { - distance = (new Float(ndist.stringMatched(1))).floatValue(); + 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); + "Can't parse node distance value", 7, + ncp + ndist.matchedFrom(), nf); } } @@ -548,8 +553,7 @@ public class NewickFile extends FileParse 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); } @@ -584,6 +588,7 @@ public class NewickFile extends FileParse distance = DefDistance; bootstrap = DefBootstrap; commentString2 = null; + parsednodename = false; } if (nextcp == 0) { @@ -598,11 +603,15 @@ public class NewickFile extends FileParse 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()) @@ -642,10 +651,10 @@ public class NewickFile extends FileParse 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); @@ -654,8 +663,8 @@ public class NewickFile extends FileParse // 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); } } @@ -826,10 +835,10 @@ public class NewickFile extends FileParse private String printNodeField(SequenceNode 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) : ""); } /** @@ -842,12 +851,16 @@ public class NewickFile extends FileParse */ 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) - : "")) : ""; + 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 @@ -920,15 +933,19 @@ public class NewickFile extends FileParse } } - // 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); } @@ -946,11 +963,11 @@ public class NewickFile extends FileParse 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");