X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=b86c170fd9058afad50b6aabb0bca4e6bfdd9672;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=9a7f6fb9ff0dae4dccaa96bec65f06b94f141b74;hpb=ab9e5bf849afd2f41102db0bf9893de1df0512f6;p=jalview.git diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 9a7f6fb..b86c170 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -1,22 +1,21 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ - // NewickFile.java // Tree I/O // http://evolution.genetics.washington.edu/phylip/newick_doc.html @@ -36,10 +35,10 @@ 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 @@ -84,12 +83,12 @@ public class NewickFile extends FileParse private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] { new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for - // requiring - // quotes + // requiring + // quotes new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote - // characters + // characters new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace - // transformation + // transformation }; char QuoteChar = '\''; @@ -98,10 +97,10 @@ 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 { @@ -112,12 +111,12 @@ public class NewickFile extends FileParse * 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 { @@ -133,7 +132,7 @@ public class NewickFile extends FileParse * Creates a new NewickFile object. * * @param newtree - * DOCUMENT ME! + * DOCUMENT ME! */ public NewickFile(SequenceNode newtree) { @@ -144,9 +143,9 @@ 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) { @@ -158,11 +157,11 @@ 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) @@ -176,13 +175,13 @@ 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) @@ -197,15 +196,15 @@ 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! */ @@ -217,8 +216,8 @@ public class NewickFile extends FileParse + " 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 @@ -247,8 +246,8 @@ 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 { @@ -280,20 +279,21 @@ public class NewickFile extends FileParse String commentString2 = null; // comments after simple node props float DefDistance = (float) 0.001; // @param Default distance for a node - - // very very small + // very very small int DefBootstrap = -1; // @param Default bootstrap for a node float distance = DefDistance; int bootstrap = DefBootstrap; boolean ascending = false; // flag indicating that we are leaving the - // current node + // current node com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex( "[(\\['),;]"); int nextcp = 0; int ncp = cp; + boolean parsednodename=false; while (majorsyms.searchFrom(nf, cp) && (Error == null)) { int fcp = majorsyms.matchedFrom(); @@ -351,14 +351,20 @@ 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, + 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 { @@ -427,10 +433,10 @@ 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! + // HACK! { if (nodename == null) { @@ -472,8 +478,8 @@ public class NewickFile extends FileParse } 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); } } } @@ -490,8 +496,8 @@ public class NewickFile extends FileParse } 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); } } @@ -506,8 +512,8 @@ public class NewickFile extends FileParse if (c == realroot) { RootHasDistance = nodehasdistance; // JBPNote This is really - // UGLY!!! Ensure root node gets - // its given distance + // UGLY!!! Ensure root node gets + // its given distance } parseNHXNodeProps(c, commentString2); commentString2 = null; @@ -585,7 +591,8 @@ public class NewickFile extends FileParse nodename = null; distance = DefDistance; bootstrap = DefBootstrap; - commentString2=null; + commentString2 = null; + parsednodename=false; } if (nextcp == 0) { @@ -630,39 +637,40 @@ public class NewickFile extends FileParse // tree is output if (commentString != null && commentString.startsWith("&&NHX")) { - StringTokenizer st = new StringTokenizer(commentString.substring(5),":"); + StringTokenizer st = new StringTokenizer(commentString.substring(5), + ":"); while (st.hasMoreTokens()) { String tok = st.nextToken(); - int colpos=tok.indexOf("="); + int colpos = tok.indexOf("="); - if (colpos>-1) + if (colpos > -1) { String code = tok.substring(0, colpos); - String value = tok.substring(colpos+1); - try { + String value = tok.substring(colpos + 1); + try + { // parse out code/value pairs if (code.toLowerCase().equals("b")) { - int v=-1; + int v = -1; Float iv = new Float(value); v = iv.intValue(); // jalview only does integer bootstraps - // currently + // currently c.setBootstrap(v); HasBootstrap = true; } // more codes here. - } - catch (Exception e) + } 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 +707,7 @@ 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 +731,9 @@ 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 +755,11 @@ 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 +792,7 @@ public class NewickFile extends FileParse * DOCUMENT ME! * * @param c - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -800,7 +808,7 @@ public class NewickFile extends FileParse * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -820,7 +828,7 @@ public class NewickFile extends FileParse * DOCUMENT ME! * * @param c - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -837,7 +845,7 @@ public class NewickFile extends FileParse * DOCUMENT ME! * * @param root - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */