X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=db888b7716c53df25d9f5660c7c7ff0852aebd39;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=92456d5aaccb7a96c5d6c39b52a8f52c3e161a4e;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java index 92456d5..db888b7 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -26,11 +26,21 @@ // TODO: Extended SequenceNodeI to hold parsed NHX strings package jalview.io; -import java.io.*; -import java.util.StringTokenizer; +import java.util.Locale; -import jalview.datamodel.*; +import jalview.datamodel.SequenceNode; import jalview.util.MessageManager; +import jalview.util.Platform; + +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; + +// TODO This class does not conform to Java standards for field name capitalization. /** * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the @@ -71,7 +81,7 @@ import jalview.util.MessageManager; */ public class NewickFile extends FileParse { - SequenceNode root; + private SequenceNode root; private boolean HasBootstrap = false; @@ -80,21 +90,90 @@ public class NewickFile extends FileParse private boolean RootHasDistance = false; // File IO Flags - boolean ReplaceUnderscores = false; + private boolean ReplaceUnderscores = false; + + private boolean printRootInfo = true; + + private static final int REGEX_PERL_NODE_REQUIRE_QUOTE = 0; + + private static final int REGEX_PERL_NODE_ESCAPE_QUOTE = 1; + + private static final int REGEX_PERL_NODE_UNQUOTED_WHITESPACE = 2; + + private static final int REGEX_MAJOR_SYMS = 3; + + private static final int REGEX_QNODE_NAME = 4; + + private static final int REGEX_COMMENT = 5; - boolean printRootInfo = true; + private static final int REGEX_UQNODE_NAME = 6; - 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 - }; + private static final int REGEX_NBOOTSTRAP = 7; - char QuoteChar = '\''; + private static final int REGEX_NDIST = 8; + + private static final int REGEX_NO_LINES = 9; + + private static final int REGEX_PERL_EXPAND_QUOTES = 10; + + private static final int REGEX_MAX = 11; + + private static final Regex[] REGEX = new Regex[REGEX_MAX]; + + private static Regex getRegex(int id) + { + if (REGEX[id] == null) + { + String code = null; + String code2 = null; + String codePerl = null; + switch (id) + { + case REGEX_PERL_NODE_REQUIRE_QUOTE: + codePerl = "m/[\\[,:'()]/"; + break; + case REGEX_PERL_NODE_ESCAPE_QUOTE: + codePerl = "s/'/''/"; + break; + case REGEX_PERL_NODE_UNQUOTED_WHITESPACE: + codePerl = "s/\\/w/_/"; + break; + case REGEX_PERL_EXPAND_QUOTES: + codePerl = "s/''/'/"; + break; + case REGEX_MAJOR_SYMS: + code = "[(\\['),;]"; + break; + case REGEX_QNODE_NAME: + code = "'([^']|'')+'"; + break; + case REGEX_COMMENT: + code = "]"; + break; + case REGEX_UQNODE_NAME: + code = "\\b([^' :;\\](),]+)"; + break; + case REGEX_NBOOTSTRAP: + code = "\\s*([0-9+]+)\\s*:"; + break; + case REGEX_NDIST: + code = ":([-0-9Ee.+]+)"; + break; + case REGEX_NO_LINES: + code = "\n+"; + code2 = ""; + break; + default: + return null; + } + return codePerl == null ? Platform.newRegex(code, code2) + : Platform.newRegexPerl(codePerl); + } + return REGEX[id]; + } + + + private char quoteChar = '\''; /** * Creates a new NewickFile object. @@ -107,7 +186,7 @@ public class NewickFile extends FileParse */ public NewickFile(String inStr) throws IOException { - super(inStr, "Paste"); + super(inStr, DataSourceType.PASTE); } /** @@ -115,15 +194,16 @@ 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 @@ -214,13 +294,10 @@ 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 - + " ( " + 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"; + ((p + r) > s.length()) ? s.length() : (p + r)) + + " )\n"; } // @tree annotations @@ -254,6 +331,7 @@ public class NewickFile extends FileParse */ public void parse() throws IOException { + Platform.ensureRegex(); String nf; { // fill nf with complete tree file @@ -291,8 +369,7 @@ public class NewickFile extends FileParse boolean ascending = false; // flag indicating that we are leaving the // current node - com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex( - "[(\\['),;]"); + Regex majorsyms = getRegex(REGEX_MAJOR_SYMS); // "[(\\['),;]" int nextcp = 0; int ncp = cp; @@ -313,8 +390,6 @@ public class NewickFile extends FileParse continue; } - - ; d++; if (c.right() == null) @@ -353,17 +428,15 @@ public class NewickFile extends FileParse // Deal with quoted fields case '\'': - com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex( - "'([^']|'')+'"); + Regex qnodename = getRegex(REGEX_QNODE_NAME);// "'([^']|'')+'"); if (qnodename.searchFrom(nf, fcp)) { int nl = qnodename.stringMatched().length(); - nodename = new String(qnodename.stringMatched().substring(1, - 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/''/'/"); + Regex xpandquotes = getRegex(REGEX_PERL_EXPAND_QUOTES); String widernodename = xpandquotes.replaceAll(nodename); nodename = widernodename; // jump to after end of quoted nodename @@ -383,8 +456,8 @@ 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 } @@ -397,7 +470,7 @@ public class NewickFile extends FileParse * '"+nf.substring(cp,fcp)+"'"); } */ // verify termination. - com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]"); + Regex comment = getRegex(REGEX_COMMENT); // "]" if (comment.searchFrom(nf, fcp)) { // Skip the comment field @@ -413,8 +486,6 @@ public class NewickFile extends FileParse Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf); } - - ; } // Parse simpler field strings String fstring = nf.substring(ncp, fcp); @@ -430,15 +501,11 @@ 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 (!parsednodename - && uqnodename.search(fstring) + Regex uqnodename = getRegex(REGEX_UQNODE_NAME);// "\\b([^' :;\\](),]+)" + Regex nbootstrap = getRegex(REGEX_NBOOTSTRAP);// "\\s*([0-9+]+)\\s*:"); + Regex ndist = getRegex(REGEX_NDIST);// ":([-0-9Ee.+]+)"); + + if (!parsednodename && uqnodename.search(fstring) && ((uqnodename.matchedFrom(1) == 0) || (fstring .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote // HACK! @@ -465,26 +532,24 @@ 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); } } } @@ -495,7 +560,7 @@ 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) @@ -561,8 +626,7 @@ 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); } @@ -612,11 +676,15 @@ public class NewickFile extends FileParse if (Error != null) { - throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{Error.toString()}))); + 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")}))); + 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()) @@ -656,10 +724,10 @@ 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); @@ -668,8 +736,8 @@ 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); } } @@ -790,7 +858,7 @@ public class NewickFile extends FileParse */ char getQuoteChar() { - return QuoteChar; + return quoteChar; } /** @@ -803,8 +871,8 @@ public class NewickFile extends FileParse */ char setQuoteChar(char c) { - char old = QuoteChar; - QuoteChar = c; + char old = quoteChar; + quoteChar = c; return old; } @@ -819,13 +887,15 @@ public class NewickFile extends FileParse */ private String nodeName(String name) { - if (NodeSafeName[0].search(name)) + if (getRegex(REGEX_PERL_NODE_REQUIRE_QUOTE).search(name)) { - return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar; + return quoteChar + + getRegex(REGEX_PERL_NODE_ESCAPE_QUOTE).replaceAll(name) + + quoteChar; } else { - return NodeSafeName[2].replaceAll(name); + return getRegex(REGEX_PERL_NODE_UNQUOTED_WHITESPACE).replaceAll(name); } } @@ -840,10 +910,10 @@ 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) : ""); } /** @@ -856,12 +926,16 @@ 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 @@ -934,15 +1008,19 @@ 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); } @@ -960,11 +1038,11 @@ 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 = getRegex(REGEX_NO_LINES);// "\n+", ""); System.out.println(nonl.replaceAll(newickfile.toString()) + "\n"); System.out.println("Parsed file.\n");