X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=2221f0090a29830112daf03331f4650e49dcac5c;hb=121a4b153bdd56b15ff2c528e6b84219affc09d5;hp=372690983598af0aceb00f5ce0442d657883e102;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 3726909..2221f00 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -1,20 +1,22 @@ /* - * 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 ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ // NewickFile.java // Tree I/O @@ -24,10 +26,14 @@ // 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 @@ -35,10 +41,10 @@ import jalview.datamodel.*; * 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) () : - * decimal branch length to parent node (MUST BE SECOND, IF ASSIGNED) - * () :GN= string gene name () :AC= - * string sequence accession () :ND= string node + * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED) + * () : decimal branch length to parent node (MUST BE SECOND, IF + * ASSIGNED) () :GN= string gene name () + * :AC= string sequence accession () :ND= string node * identifier - if this is being used, it has to be unique within each phylogeny * () :B= decimal confidence value for parent branch * () :D= 'T', 'F', or '?' 'T' if this node represents a @@ -81,14 +87,14 @@ 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 com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] { + new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for // requiring // quotes new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote // characters new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace - // transformation + // transformation }; char QuoteChar = '\''; @@ -97,30 +103,31 @@ public class NewickFile extends FileParse * Creates a new NewickFile object. * * @param inStr - * DOCUMENT ME! + * DOCUMENT ME! * * @throws IOException - * DOCUMENT ME! + * DOCUMENT ME! */ public NewickFile(String inStr) throws IOException { - super(inStr, "Paste"); + super(inStr, DataSourceType.PASTE); } /** * Creates a new NewickFile object. * * @param inFile - * DOCUMENT ME! - * @param type - * DOCUMENT ME! + * DOCUMENT ME! + * @param protocol + * DOCUMENT ME! * * @throws IOException - * DOCUMENT ME! + * 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 @@ -132,7 +139,7 @@ public class NewickFile extends FileParse * Creates a new NewickFile object. * * @param newtree - * DOCUMENT ME! + * DOCUMENT ME! */ public NewickFile(SequenceNode newtree) { @@ -143,9 +150,9 @@ public class NewickFile extends FileParse * Creates a new NewickFile object. * * @param newtree - * DOCUMENT ME! + * DOCUMENT ME! * @param bootstrap - * DOCUMENT ME! + * DOCUMENT ME! */ public NewickFile(SequenceNode newtree, boolean bootstrap) { @@ -157,11 +164,11 @@ public class NewickFile extends FileParse * 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) @@ -175,13 +182,13 @@ public class NewickFile extends FileParse * 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) @@ -196,28 +203,25 @@ public class NewickFile extends FileParse * 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! */ 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 @@ -246,8 +250,8 @@ public class NewickFile extends FileParse * 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 { @@ -293,6 +297,7 @@ public class NewickFile extends FileParse int nextcp = 0; int ncp = cp; + boolean parsednodename = false; while (majorsyms.searchFrom(nf, cp) && (Error == null)) { int fcp = majorsyms.matchedFrom(); @@ -350,14 +355,21 @@ public class NewickFile extends FileParse 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, - nl - 1)); - cp = fcp + 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/''/'/"); + String widernodename = xpandquotes.replaceAll(nodename); + nodename = widernodename; + // jump to after end of quoted nodename + nextcp = fcp + nl + 1; + parsednodename = true; } else { @@ -372,8 +384,8 @@ 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 } @@ -386,7 +398,8 @@ public class NewickFile extends FileParse * '"+nf.substring(cp,fcp)+"'"); } */ // verify termination. - com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]"); + com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex( + "]"); if (comment.searchFrom(nf, fcp)) { // Skip the comment field @@ -426,7 +439,7 @@ public class NewickFile extends FileParse 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! @@ -453,26 +466,24 @@ 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); } } } @@ -483,14 +494,14 @@ public class NewickFile extends FileParse { try { - distance = (new Float(ndist.stringMatched(1))).floatValue(); + distance = (Float.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); } } @@ -549,8 +560,7 @@ 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); } @@ -585,6 +595,7 @@ public class NewickFile extends FileParse distance = DefDistance; bootstrap = DefBootstrap; commentString2 = null; + parsednodename = false; } if (nextcp == 0) { @@ -599,11 +610,15 @@ 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()) @@ -646,7 +661,7 @@ public class NewickFile extends FileParse if (code.toLowerCase().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); @@ -655,8 +670,8 @@ 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); } } @@ -699,7 +714,7 @@ public class NewickFile extends FileParse * 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 */ @@ -723,9 +738,9 @@ public class NewickFile extends FileParse * 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 */ @@ -747,11 +762,11 @@ public class NewickFile extends FileParse * 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 */ @@ -784,7 +799,7 @@ public class NewickFile extends FileParse * DOCUMENT ME! * * @param c - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -800,7 +815,7 @@ public class NewickFile extends FileParse * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -820,35 +835,39 @@ public class NewickFile extends FileParse * DOCUMENT ME! * * @param c - * DOCUMENT ME! + * 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) : ""); + + ((HasBootstrap) ? ((c.getBootstrap() > -1) + ? ((c.getName() != null ? " " : "") + c.getBootstrap()) + : "") : "") + + ((HasDistances) ? (":" + c.dist) : ""); } /** * DOCUMENT ME! * * @param root - * DOCUMENT ME! + * 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) - : "")) : ""; + 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 @@ -928,8 +947,8 @@ public class NewickFile extends FileParse { 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); } @@ -947,7 +966,7 @@ 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");