From 203b9b073d95d320f7f4898e9419fe4ae89c4032 Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum Date: Sun, 19 Nov 2017 16:35:50 +0100 Subject: [PATCH] getNotPrimaryAlignmentFlag deprecated; tests for bamstats04 --- .../tools/bam2graphics/PaintContext.java | 2 +- .../jvarkit/tools/bamstats01/BamStats01.java | 2 +- .../lindenb/jvarkit/tools/tests/TestNg01.java | 15 + .../util/bio/samfilter/ParseException.java | 38 +- .../util/bio/samfilter/SamFilterParser.java | 407 +++---- .../SamFilterParserTokenManager.java | 1016 +++++++++-------- .../util/bio/samfilter/SimpleCharStream.java | 15 +- .../jvarkit/util/bio/samfilter/Token.java | 6 +- .../util/bio/samfilter/TokenMgrError.java | 23 +- .../util/bio/samfilter/SamFilterParser.jj | 4 +- 10 files changed, 766 insertions(+), 762 deletions(-) diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/PaintContext.java b/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/PaintContext.java index f22e60b6f..4825beb79 100644 --- a/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/PaintContext.java +++ b/src/main/java/com/github/lindenb/jvarkit/tools/bam2graphics/PaintContext.java @@ -161,7 +161,7 @@ private void writeBamSection( { SAMRecord rec=iter.next(); if(rec.getReadUnmappedFlag()) continue; - if(rec.getNotPrimaryAlignmentFlag()) continue; + if(rec.isSecondaryAlignment()) continue; if(rec.getDuplicateReadFlag()) continue; if(rec.getReadFailsVendorQualityCheckFlag()) continue; for(int i1= Math.max(interval.start+1,rec.getAlignmentStart()); diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/bamstats01/BamStats01.java b/src/main/java/com/github/lindenb/jvarkit/tools/bamstats01/BamStats01.java index eebb67782..bda4a3d39 100644 --- a/src/main/java/com/github/lindenb/jvarkit/tools/bamstats01/BamStats01.java +++ b/src/main/java/com/github/lindenb/jvarkit/tools/bamstats01/BamStats01.java @@ -245,7 +245,7 @@ void watch(SAMRecord rec) } - if(!rec.getNotPrimaryAlignmentFlag()) + if(!rec.isSecondaryAlignment()) { this.increment(Category.PRIMARY_ALIGNMENT); } diff --git a/src/main/java/com/github/lindenb/jvarkit/tools/tests/TestNg01.java b/src/main/java/com/github/lindenb/jvarkit/tools/tests/TestNg01.java index 879e45fc6..6d0e618fe 100644 --- a/src/main/java/com/github/lindenb/jvarkit/tools/tests/TestNg01.java +++ b/src/main/java/com/github/lindenb/jvarkit/tools/tests/TestNg01.java @@ -46,6 +46,7 @@ of this software and associated documentation files (the "Software"), to deal import com.github.lindenb.jvarkit.tools.bam2graphics.Bam2Raster; import com.github.lindenb.jvarkit.tools.bam2graphics.LowResBam2Raster; import com.github.lindenb.jvarkit.tools.bam2wig.Bam2Wig; +import com.github.lindenb.jvarkit.tools.bamstats04.BamStats04; import com.github.lindenb.jvarkit.tools.bioalcidae.BioAlcidaeJdk; import com.github.lindenb.jvarkit.tools.biostar.Biostar59647; import com.github.lindenb.jvarkit.tools.biostar.Biostar86480; @@ -121,6 +122,7 @@ class TestNg01 { static final File TEST_RESULTS_DIR= new File("test-results"); static final File JETER_VCF = new File(TEST_RESULTS_DIR,"jeter.vcf"); static final String TOY_FA="src/test/resources/toy.fa"; + static final String TOY_BED_GZ="src/test/resources/toy.bed.gz"; static final String TOY_VCF_GZ="src/test/resources/toy.vcf.gz"; static final String TOY_BAM="src/test/resources/toy.bam"; static final String TOY_DICT="src/test/resources/toy.dict"; @@ -1060,4 +1062,17 @@ public void testVcfToSql(final String path) throws IOException { })); Assert.assertTrue(outvcf.delete()); } + + @Test + public void testBamStats04() throws IOException { + final File output =new File(TEST_RESULTS_DIR,"jeter.tsv"); + Assert.assertEquals(0,new BamStats04().instanceMain(new String[]{ + "-o",output.getPath(), + "-R",TOY_FA, + "-B",TOY_BED_GZ, + TOY_BAM + })); + Assert.assertTrue(output.delete()); + } + } diff --git a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/ParseException.java b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/ParseException.java index 34a114a40..79beede37 100644 --- a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/ParseException.java +++ b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/ParseException.java @@ -1,5 +1,5 @@ -/* Generated By:JavaCC: Do not edit this line. ParseException.java Version 7.0 */ -/* JavaCCOptions:KEEP_LINE_COLUMN=true */ +/* Generated By:JavaCC: Do not edit this line. ParseException.java Version 5.0 */ +/* JavaCCOptions:KEEP_LINE_COL=null */ /* The MIT License (MIT) @@ -44,11 +44,6 @@ public class ParseException extends Exception { */ private static final long serialVersionUID = 1L; - /** - * The end of line string for this machine. - */ - protected static String EOL = System.getProperty("line.separator", "\n"); - /** * This constructor is used by the method "generateParseException" * in the generated parser. Calling this constructor generates @@ -117,7 +112,7 @@ public ParseException(String message) { private static String initialise(Token currentToken, int[][] expectedTokenSequences, String[] tokenImage) { - + String eol = System.getProperty("line.separator", "\n"); StringBuffer expected = new StringBuffer(); int maxSize = 0; for (int i = 0; i < expectedTokenSequences.length; i++) { @@ -130,7 +125,7 @@ private static String initialise(Token currentToken, if (expectedTokenSequences[i][expectedTokenSequences[i].length - 1] != 0) { expected.append("..."); } - expected.append(EOL).append(" "); + expected.append(eol).append(" "); } String retval = "Encountered \""; Token tok = currentToken.next; @@ -147,23 +142,20 @@ private static String initialise(Token currentToken, tok = tok.next; } retval += "\" at line " + currentToken.next.beginLine + ", column " + currentToken.next.beginColumn; - retval += "." + EOL; - - - if (expectedTokenSequences.length == 0) { - // Nothing to add here + retval += "." + eol; + if (expectedTokenSequences.length == 1) { + retval += "Was expecting:" + eol + " "; } else { - if (expectedTokenSequences.length == 1) { - retval += "Was expecting:" + EOL + " "; - } else { - retval += "Was expecting one of:" + EOL + " "; - } - retval += expected.toString(); + retval += "Was expecting one of:" + eol + " "; } - + retval += expected.toString(); return retval; } + /** + * The end of line string for this machine. + */ + protected String eol = System.getProperty("line.separator", "\n"); /** * Used to convert raw characters to their escaped version @@ -176,6 +168,8 @@ static String add_escapes(String str) { for (int i = 0; i < str.length(); i++) { switch (str.charAt(i)) { + case 0 : + continue; case '\b': retval.append("\\b"); continue; @@ -214,4 +208,4 @@ static String add_escapes(String str) { } } -/* JavaCC - OriginalChecksum=8f1e51aa4b916bc256163d0c1bebb8ed (do not edit this line) */ +/* JavaCC - OriginalChecksum=2478e7e15dfcd9937c47bf4e1260ae77 (do not edit this line) */ diff --git a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.java b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.java index f7975578e..eb232adc8 100644 --- a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.java +++ b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.java @@ -1,4 +1,3 @@ -/* SamFilterParser.java */ /* Generated By:JavaCC: Do not edit this line. SamFilterParser.java */ /* The MIT License (MIT) @@ -244,18 +243,18 @@ private static String unescape(final String s) throws ParseException int i=0; while(i group(final String s) { }; } private static Predicate notPrimaryAlignmentFlag() { return new Predicate() { - @Override public boolean test(final SAMRecord rec) { return rec.getNotPrimaryAlignmentFlag();} + @Override public boolean test(final SAMRecord rec) { return rec.isSecondaryAlignment();} }; } private static Predicate supplementaryAlignmentFlag() { return new Predicate() { @@ -357,13 +356,13 @@ private static Predicate mapqLowerThan(final int mapq) { } }; } - final private Predicate anyNode() throws ParseException {Predicate other; - switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { - case NOT:{ + final private Predicate anyNode() throws ParseException { + Predicate other; + switch ((jj_ntk==-1)?jj_ntk():jj_ntk) { + case NOT: other = NegateExpr(); -{if ("" != null) return other;} + {if (true) return other;} break; - } case DUPLICATE: case UNMAPPED: case MAPPED: @@ -380,235 +379,217 @@ private static Predicate mapqLowerThan(final int mapq) { case GROUP: case HASFLAG: case DISCORDANT: - case MAPQLT:{ + case MAPQLT: other = OrExpr(); -{if ("" != null) return other;} + {if (true) return other;} break; - } - case OPAR:{ + case OPAR: jj_consume_token(OPAR); other = anyNode(); jj_consume_token(CPAR); -{if ("" != null) return other;} + {if (true) return other;} break; - } default: jj_la1[0] = jj_gen; jj_consume_token(-1); throw new ParseException(); } throw new Error("Missing return statement in function"); -} + } final private Predicate NegateExpr() throws ParseException { jj_consume_token(NOT); OrExpr(); -{if ("" != null) return null;} + {if (true) return null;} throw new Error("Missing return statement in function"); -} + } - final private Predicate OrExpr() throws ParseException {Predicate root,other; + final private Predicate OrExpr() throws ParseException { + Predicate root,other; root = AndExpr(); label_1: while (true) { - switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { - case OR:{ + switch ((jj_ntk==-1)?jj_ntk():jj_ntk) { + case OR: ; break; - } default: jj_la1[1] = jj_gen; break label_1; } jj_consume_token(OR); other = AndExpr(); -root = root.or(other); + root = root.or(other); } -{if ("" != null) return root;} + {if (true) return root;} throw new Error("Missing return statement in function"); -} + } - final private Predicate AndExpr() throws ParseException {Predicate root,other; + final private Predicate AndExpr() throws ParseException { + Predicate root,other; root = UnaryExpr(); label_2: while (true) { - switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { - case AND:{ + switch ((jj_ntk==-1)?jj_ntk():jj_ntk) { + case AND: ; break; - } default: jj_la1[2] = jj_gen; break label_2; } jj_consume_token(AND); other = UnaryExpr(); -root = root.and(other); + root = root.and(other); } -{if ("" != null) return root;} + {if (true) return root;} throw new Error("Missing return statement in function"); -} + } - final private Predicate UnaryExpr() throws ParseException {String str; Token t; int flg; - switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { - case DUPLICATE:{ + final private Predicate UnaryExpr() throws ParseException { + String str; Token t; int flg; + switch ((jj_ntk==-1)?jj_ntk():jj_ntk) { + case DUPLICATE: jj_consume_token(DUPLICATE); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return duplicateFilter();} + {if (true) return duplicateFilter();} break; - } - case UNMAPPED:{ + case UNMAPPED: jj_consume_token(UNMAPPED); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return unmappedFilter();} + {if (true) return unmappedFilter();} break; - } - case MAPPED:{ + case MAPPED: jj_consume_token(MAPPED); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return mappedFilter();} + {if (true) return mappedFilter();} break; - } - case FAILSVENDORQUALITY:{ + case FAILSVENDORQUALITY: jj_consume_token(FAILSVENDORQUALITY); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return failsVendorQuality();} + {if (true) return failsVendorQuality();} break; - } - case PAIRED:{ + case PAIRED: jj_consume_token(PAIRED); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return readPaired();} + {if (true) return readPaired();} break; - } - case CLIPPED:{ + case CLIPPED: jj_consume_token(CLIPPED); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return readClipped();} + {if (true) return readClipped();} break; - } - case MAPQUNAVAILABLE:{ + case MAPQUNAVAILABLE: jj_consume_token(MAPQUNAVAILABLE); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return mapqUnavailable();} + {if (true) return mapqUnavailable();} break; - } - case MATEUNMAPPED:{ + case MATEUNMAPPED: jj_consume_token(MATEUNMAPPED); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return mateUnmapped();} + {if (true) return mateUnmapped();} break; - } - case NOTPRIMARYALIGNMENT:{ + case NOTPRIMARYALIGNMENT: jj_consume_token(NOTPRIMARYALIGNMENT); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return notPrimaryAlignmentFlag();} + {if (true) return notPrimaryAlignmentFlag();} break; - } - case SUPPLEMENTARYALIGNMENT:{ + case SUPPLEMENTARYALIGNMENT: jj_consume_token(SUPPLEMENTARYALIGNMENT); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return supplementaryAlignmentFlag();} + {if (true) return supplementaryAlignmentFlag();} break; - } - case OVERLAP:{ + case OVERLAP: jj_consume_token(OVERLAP); jj_consume_token(OPAR); str = characters(); jj_consume_token(CPAR); -{if ("" != null) return overlapBed(str);} + {if (true) return overlapBed(str);} break; - } - case SAMFLAG:{ + case SAMFLAG: jj_consume_token(SAMFLAG); jj_consume_token(OPAR); t = jj_consume_token(INT); jj_consume_token(CPAR); -{if ("" != null) return samFlag(Integer.parseInt(t.image));} + {if (true) return samFlag(Integer.parseInt(t.image));} break; - } - case SAMPLE:{ + case SAMPLE: jj_consume_token(SAMPLE); jj_consume_token(OPAR); str = characters(); jj_consume_token(CPAR); -{if ("" != null) return sample(str);} + {if (true) return sample(str);} break; - } - case GROUP:{ + case GROUP: jj_consume_token(GROUP); jj_consume_token(OPAR); str = characters(); jj_consume_token(CPAR); -{if ("" != null) return group(str);} + {if (true) return group(str);} break; - } - case HASFLAG:{ + case HASFLAG: jj_consume_token(HASFLAG); jj_consume_token(OPAR); flg = integer(); jj_consume_token(CPAR); -{if ("" != null) return hasFlag(flg);} + {if (true) return hasFlag(flg);} break; - } - case DISCORDANT:{ + case DISCORDANT: jj_consume_token(DISCORDANT); jj_consume_token(OPAR); jj_consume_token(CPAR); -{if ("" != null) return discordant();} + {if (true) return discordant();} break; - } - case MAPQLT:{ + case MAPQLT: jj_consume_token(MAPQLT); jj_consume_token(OPAR); flg = integer(); jj_consume_token(CPAR); -{if ("" != null) return mapqLowerThan(flg);} + {if (true) return mapqLowerThan(flg);} break; - } default: jj_la1[3] = jj_gen; jj_consume_token(-1); throw new ParseException(); } throw new Error("Missing return statement in function"); -} + } - final private String characters() throws ParseException {Token t; - switch ((jj_ntk==-1)?jj_ntk_f():jj_ntk) { - case SIMPLE_QUOTE_LITERAL:{ + final private String characters() throws ParseException { + Token t; + switch ((jj_ntk==-1)?jj_ntk():jj_ntk) { + case SIMPLE_QUOTE_LITERAL: t = jj_consume_token(SIMPLE_QUOTE_LITERAL); -{if ("" != null) return unescape(t.image.substring(1,t.image.length()-1));} + {if (true) return unescape(t.image.substring(1,t.image.length()-1));} break; - } - case DOUBLE_QUOTE_LITERAL:{ + case DOUBLE_QUOTE_LITERAL: t = jj_consume_token(DOUBLE_QUOTE_LITERAL); -{if ("" != null) return unescape(t.image.substring(1,t.image.length()-1));} + {if (true) return unescape(t.image.substring(1,t.image.length()-1));} break; - } default: jj_la1[4] = jj_gen; jj_consume_token(-1); throw new ParseException(); } throw new Error("Missing return statement in function"); -} + } - final private int integer() throws ParseException {Token t; + final private int integer() throws ParseException { + Token t; t = jj_consume_token(INT); -{if ("" != null) return Integer.parseInt(t.image);} + {if (true) return Integer.parseInt(t.image);} throw new Error("Missing return statement in function"); -} + } /** Generated Token Manager. */ public SamFilterParserTokenManager token_source; @@ -623,129 +604,121 @@ final private Predicate NegateExpr() throws ParseException { static private int[] jj_la1_0; static private int[] jj_la1_1; static { - jj_la1_init_0(); - jj_la1_init_1(); - } - private static void jj_la1_init_0() { - jj_la1_0 = new int[] {0xfffc1400,0x100,0x200,0xfffc0000,0x30000,}; - } - private static void jj_la1_init_1() { - jj_la1_1 = new int[] {0x7,0x0,0x0,0x7,0x0,}; - } + jj_la1_init_0(); + jj_la1_init_1(); + } + private static void jj_la1_init_0() { + jj_la1_0 = new int[] {0xfffc1400,0x100,0x200,0xfffc0000,0x30000,}; + } + private static void jj_la1_init_1() { + jj_la1_1 = new int[] {0x7,0x0,0x0,0x7,0x0,}; + } /** Constructor with InputStream. */ public SamFilterParser(java.io.InputStream stream) { - this(stream, null); + this(stream, null); } /** Constructor with InputStream and supplied encoding */ public SamFilterParser(java.io.InputStream stream, String encoding) { - try { jj_input_stream = new SimpleCharStream(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); } - token_source = new SamFilterParserTokenManager(jj_input_stream); - token = new Token(); - jj_ntk = -1; - jj_gen = 0; - for (int i = 0; i < 5; i++) jj_la1[i] = -1; + try { jj_input_stream = new SimpleCharStream(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); } + token_source = new SamFilterParserTokenManager(jj_input_stream); + token = new Token(); + jj_ntk = -1; + jj_gen = 0; + for (int i = 0; i < 5; i++) jj_la1[i] = -1; } /** Reinitialise. */ public void ReInit(java.io.InputStream stream) { - ReInit(stream, null); + ReInit(stream, null); } /** Reinitialise. */ public void ReInit(java.io.InputStream stream, String encoding) { - try { jj_input_stream.ReInit(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); } - token_source.ReInit(jj_input_stream); - token = new Token(); - jj_ntk = -1; - jj_gen = 0; - for (int i = 0; i < 5; i++) jj_la1[i] = -1; + try { jj_input_stream.ReInit(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); } + token_source.ReInit(jj_input_stream); + token = new Token(); + jj_ntk = -1; + jj_gen = 0; + for (int i = 0; i < 5; i++) jj_la1[i] = -1; } /** Constructor. */ public SamFilterParser(java.io.Reader stream) { - jj_input_stream = new SimpleCharStream(stream, 1, 1); - token_source = new SamFilterParserTokenManager(jj_input_stream); - token = new Token(); - jj_ntk = -1; - jj_gen = 0; - for (int i = 0; i < 5; i++) jj_la1[i] = -1; + jj_input_stream = new SimpleCharStream(stream, 1, 1); + token_source = new SamFilterParserTokenManager(jj_input_stream); + token = new Token(); + jj_ntk = -1; + jj_gen = 0; + for (int i = 0; i < 5; i++) jj_la1[i] = -1; } /** Reinitialise. */ public void ReInit(java.io.Reader stream) { - if (jj_input_stream == null) { - jj_input_stream = new SimpleCharStream(stream, 1, 1); - } else { - jj_input_stream.ReInit(stream, 1, 1); - } - if (token_source == null) { - token_source = new SamFilterParserTokenManager(jj_input_stream); - } - - token_source.ReInit(jj_input_stream); - token = new Token(); - jj_ntk = -1; - jj_gen = 0; - for (int i = 0; i < 5; i++) jj_la1[i] = -1; + jj_input_stream.ReInit(stream, 1, 1); + token_source.ReInit(jj_input_stream); + token = new Token(); + jj_ntk = -1; + jj_gen = 0; + for (int i = 0; i < 5; i++) jj_la1[i] = -1; } /** Constructor with generated Token Manager. */ public SamFilterParser(SamFilterParserTokenManager tm) { - token_source = tm; - token = new Token(); - jj_ntk = -1; - jj_gen = 0; - for (int i = 0; i < 5; i++) jj_la1[i] = -1; + token_source = tm; + token = new Token(); + jj_ntk = -1; + jj_gen = 0; + for (int i = 0; i < 5; i++) jj_la1[i] = -1; } /** Reinitialise. */ public void ReInit(SamFilterParserTokenManager tm) { - token_source = tm; - token = new Token(); - jj_ntk = -1; - jj_gen = 0; - for (int i = 0; i < 5; i++) jj_la1[i] = -1; + token_source = tm; + token = new Token(); + jj_ntk = -1; + jj_gen = 0; + for (int i = 0; i < 5; i++) jj_la1[i] = -1; } private Token jj_consume_token(int kind) throws ParseException { - Token oldToken; - if ((oldToken = token).next != null) token = token.next; - else token = token.next = token_source.getNextToken(); - jj_ntk = -1; - if (token.kind == kind) { - jj_gen++; - return token; - } - token = oldToken; - jj_kind = kind; - throw generateParseException(); + Token oldToken; + if ((oldToken = token).next != null) token = token.next; + else token = token.next = token_source.getNextToken(); + jj_ntk = -1; + if (token.kind == kind) { + jj_gen++; + return token; + } + token = oldToken; + jj_kind = kind; + throw generateParseException(); } /** Get the next Token. */ final public Token getNextToken() { - if (token.next != null) token = token.next; - else token = token.next = token_source.getNextToken(); - jj_ntk = -1; - jj_gen++; - return token; + if (token.next != null) token = token.next; + else token = token.next = token_source.getNextToken(); + jj_ntk = -1; + jj_gen++; + return token; } /** Get the specific Token. */ final public Token getToken(int index) { - Token t = token; - for (int i = 0; i < index; i++) { - if (t.next != null) t = t.next; - else t = t.next = token_source.getNextToken(); - } - return t; + Token t = token; + for (int i = 0; i < index; i++) { + if (t.next != null) t = t.next; + else t = t.next = token_source.getNextToken(); + } + return t; } - private int jj_ntk_f() { - if ((jj_nt=token.next) == null) - return (jj_ntk = (token.next=token_source.getNextToken()).kind); - else - return (jj_ntk = jj_nt.kind); + private int jj_ntk() { + if ((jj_nt=token.next) == null) + return (jj_ntk = (token.next=token_source.getNextToken()).kind); + else + return (jj_ntk = jj_nt.kind); } private java.util.List jj_expentries = new java.util.ArrayList(); @@ -754,44 +727,36 @@ private int jj_ntk_f() { /** Generate ParseException. */ public ParseException generateParseException() { - jj_expentries.clear(); - boolean[] la1tokens = new boolean[35]; - if (jj_kind >= 0) { - la1tokens[jj_kind] = true; - jj_kind = -1; - } - for (int i = 0; i < 5; i++) { - if (jj_la1[i] == jj_gen) { - for (int j = 0; j < 32; j++) { - if ((jj_la1_0[i] & (1<= 0) { + la1tokens[jj_kind] = true; + jj_kind = -1; + } + for (int i = 0; i < 5; i++) { + if (jj_la1[i] == jj_gen) { + for (int j = 0; j < 32; j++) { + if ((jj_la1_0[i] & (1< 7) kind = 7; - { jjCheckNAdd(0); } + jjCheckNAdd(0); } else if (curChar == 34) - { jjCheckNAddStates(0, 2); } + jjCheckNAddStates(0, 2); else if (curChar == 39) - { jjCheckNAddStates(3, 5); } + jjCheckNAddStates(3, 5); break; case 0: if ((0x3ff000000000000L & l) == 0L) break; if (kind > 7) kind = 7; - { jjCheckNAdd(0); } + jjCheckNAdd(0); break; case 2: if ((0xffffff7fffffdbffL & l) != 0L) - { jjCheckNAddStates(3, 5); } + jjCheckNAddStates(3, 5); break; case 4: if ((0x8400000000L & l) != 0L) - { jjCheckNAddStates(3, 5); } + jjCheckNAddStates(3, 5); break; case 5: if (curChar == 39 && kind > 16) @@ -347,15 +356,15 @@ else if (curChar == 39) break; case 6: if (curChar == 34) - { jjCheckNAddStates(0, 2); } + jjCheckNAddStates(0, 2); break; case 7: if ((0xfffffffbffffdbffL & l) != 0L) - { jjCheckNAddStates(0, 2); } + jjCheckNAddStates(0, 2); break; case 9: if ((0x8400000000L & l) != 0L) - { jjCheckNAddStates(0, 2); } + jjCheckNAddStates(0, 2); break; case 10: if (curChar == 34 && kind > 17) @@ -372,77 +381,83 @@ else if (curChar < 128) { switch(jjstateSet[--i]) { - case 154: - if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 187; - else if ((0x10000000100000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 169; - if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 153; - break; - case 1: - if ((0x200000002000L & l) != 0L) - { jjCheckNAddStates(6, 8); } - else if ((0x4000000040000L & l) != 0L) - { jjCheckNAddStates(9, 12); } - else if ((0x1000000010L & l) != 0L) - { jjCheckNAddTwoStates(142, 217); } - else if ((0x8000000080L & l) != 0L) - { jjAddStates(13, 22); } - else if ((0x20000000200L & l) != 0L) - { jjAddStates(23, 33); } - else if ((0x800000008L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 117; + case 117: + if ((0x2000000020000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 205; else if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 110; - else if ((0x8000000080000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 104; - else if ((0x400000004000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 68; - else if ((0x4000000040L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 35; - else if ((0x20000000200000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 17; + jjstateSet[jjnewStateCnt++] = 116; break; - case 221: + case 238: if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 238; + jjstateSet[jjnewStateCnt++] = 255; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 236; + jjstateSet[jjnewStateCnt++] = 253; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 234; + jjstateSet[jjnewStateCnt++] = 251; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 232; + jjstateSet[jjnewStateCnt++] = 249; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 230; + jjstateSet[jjnewStateCnt++] = 247; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 228; + jjstateSet[jjnewStateCnt++] = 245; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 226; + jjstateSet[jjnewStateCnt++] = 243; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 224; + jjstateSet[jjnewStateCnt++] = 241; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 222; + jjstateSet[jjnewStateCnt++] = 239; if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 220; + jjstateSet[jjnewStateCnt++] = 237; break; - case 243: + case 261: + if ((0x20000000200000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 190; + else if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 153; + break; + case 118: + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 204; + else if ((0x10000000100000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 133; + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 117; + break; + case 262: if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 205; + jjstateSet[jjnewStateCnt++] = 222; if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 170; + jjstateSet[jjnewStateCnt++] = 134; if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 154; + jjstateSet[jjnewStateCnt++] = 118; break; - case 153: - if ((0x2000000020000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 188; + case 1: + if ((0x8000000080000L & l) != 0L) + jjCheckNAddTwoStates(154, 191); + else if ((0x200000002000L & l) != 0L) + jjCheckNAddStates(6, 8); + else if ((0x4000000040000L & l) != 0L) + jjCheckNAddStates(9, 12); + else if ((0x1000000010L & l) != 0L) + jjCheckNAddTwoStates(106, 234); + else if ((0x8000000080L & l) != 0L) + jjAddStates(13, 22); + else if ((0x20000000200L & l) != 0L) + jjAddStates(23, 33); + else if ((0x800000008L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 81; else if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 152; + jjstateSet[jjnewStateCnt++] = 74; + else if ((0x400000004000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 68; + else if ((0x4000000040L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 35; + else if ((0x20000000200000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 17; break; case 2: if ((0xffffffffefffffffL & l) != 0L) - { jjCheckNAddStates(3, 5); } + jjCheckNAddStates(3, 5); break; case 3: if (curChar == 92) @@ -450,11 +465,11 @@ else if ((0x1000000010000L & l) != 0L) break; case 4: if ((0x14404410144044L & l) != 0L) - { jjCheckNAddStates(3, 5); } + jjCheckNAddStates(3, 5); break; case 7: if ((0xffffffffefffffffL & l) != 0L) - { jjCheckNAddStates(0, 2); } + jjCheckNAddStates(0, 2); break; case 8: if (curChar == 92) @@ -462,7 +477,7 @@ else if ((0x1000000010000L & l) != 0L) break; case 9: if ((0x14404410144044L & l) != 0L) - { jjCheckNAddStates(0, 2); } + jjCheckNAddStates(0, 2); break; case 11: if ((0x1000000010L & l) != 0L && kind > 19) @@ -573,7 +588,7 @@ else if ((0x1000000010000L & l) != 0L) break; if (kind > 23) kind = 23; - { jjAddStates(34, 35); } + jjAddStates(34, 35); break; case 38: if ((0x8000000080L & l) != 0L && kind > 23) @@ -582,7 +597,7 @@ else if ((0x1000000010000L & l) != 0L) case 39: case 46: if ((0x200000002L & l) != 0L) - { jjCheckNAdd(38); } + jjCheckNAdd(38); break; case 40: if ((0x100000001000L & l) != 0L) @@ -594,7 +609,7 @@ else if ((0x1000000010000L & l) != 0L) break; case 42: if ((0x4000000040000L & l) != 0L) - { jjAddStates(36, 37); } + jjAddStates(36, 37); break; case 43: if ((0x1000000010L & l) != 0L && kind > 23) @@ -629,8 +644,9 @@ else if ((0x1000000010000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 50; break; case 52: + case 139: if ((0x400000004000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 37; + jjCheckNAdd(37); break; case 53: if ((0x2000000020L & l) != 0L) @@ -701,684 +717,752 @@ else if ((0x1000000010000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 68; break; case 70: - if ((0x10000000100000L & l) == 0L) - break; - if (kind > 24) - kind = 24; - { jjAddStates(38, 39); } + if ((0x1000000010L & l) != 0L && kind > 25) + kind = 25; break; case 71: - if ((0x8000000080L & l) != 0L && kind > 24) - kind = 24; + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 70; break; case 72: - case 79: - if ((0x200000002L & l) != 0L) - { jjCheckNAdd(71); } + if ((0x4000000040000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 71; break; case 73: - if ((0x100000001000L & l) != 0L) + if ((0x20000000200L & l) != 0L) jjstateSet[jjnewStateCnt++] = 72; break; case 74: - if ((0x4000000040L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 73; break; case 75: - if ((0x4000000040000L & l) != 0L) - { jjAddStates(40, 41); } + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 74; break; case 76: - if ((0x1000000010L & l) != 0L && kind > 24) - kind = 24; + if ((0x1000000010L & l) != 0L && kind > 26) + kind = 26; break; case 77: - if ((0x200000002L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 76; break; case 78: - if ((0x2000000020L & l) != 0L) + if ((0x1000000010000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 77; break; + case 79: + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 78; + break; case 80: - if ((0x100000001000L & l) != 0L) + if ((0x20000000200L & l) != 0L) jjstateSet[jjnewStateCnt++] = 79; break; case 81: - if ((0x4000000040L & l) != 0L) + if ((0x100000001000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 80; break; case 82: - if ((0x1000000010L & l) != 0L) + if ((0x800000008L & l) != 0L) jjstateSet[jjnewStateCnt++] = 81; break; case 83: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 82; + if ((0x20000000200L & l) != 0L) + jjAddStates(23, 33); break; case 84: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 83; + if ((0x8000000080000L & l) != 0L) + jjCheckNAdd(107); break; case 85: - if ((0x400000004000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 70; + if ((0x2000000020L & l) == 0L) + break; + if (kind > 18) + kind = 18; + jjAddStates(38, 39); break; case 86: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 85; + if ((0x8000000080L & l) != 0L && kind > 18) + kind = 18; break; case 87: - if ((0x200000002000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 86; + case 94: + if ((0x200000002L & l) != 0L) + jjCheckNAdd(86); break; case 88: - if ((0x400000004000L & l) != 0L) + if ((0x100000001000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 87; break; case 89: - if ((0x8000000080L & l) != 0L) + if ((0x4000000040L & l) != 0L) jjstateSet[jjnewStateCnt++] = 88; break; case 90: - if ((0x20000000200L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 89; + if ((0x4000000040000L & l) != 0L) + jjAddStates(40, 41); break; case 91: - if ((0x100000001000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 90; + if ((0x1000000010L & l) != 0L && kind > 18) + kind = 18; break; case 92: if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 91; break; case 93: - if ((0x200000002000000L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 92; break; - case 94: - if ((0x4000000040000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 93; - break; case 95: - if ((0x200000002L & l) != 0L) + if ((0x100000001000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 94; break; case 96: - if ((0x10000000100000L & l) != 0L) + if ((0x4000000040L & l) != 0L) jjstateSet[jjnewStateCnt++] = 95; break; case 97: - if ((0x400000004000L & l) != 0L) + if ((0x1000000010L & l) != 0L) jjstateSet[jjnewStateCnt++] = 96; break; case 98: - if ((0x2000000020L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 97; break; case 99: - if ((0x200000002000L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 98; break; case 100: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 99; + if ((0x10000000100000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 85; break; case 101: - if ((0x100000001000L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 100; break; case 102: - if ((0x1000000010000L & l) != 0L) + if ((0x800000008L & l) != 0L) jjstateSet[jjnewStateCnt++] = 101; break; case 103: - if ((0x1000000010000L & l) != 0L) + if ((0x20000000200L & l) != 0L) jjstateSet[jjnewStateCnt++] = 102; break; case 104: - if ((0x20000000200000L & l) != 0L) + if ((0x100000001000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 103; break; case 105: - if ((0x8000000080000L & l) != 0L) + if ((0x1000000010000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 104; break; case 106: - if ((0x1000000010L & l) != 0L && kind > 25) - kind = 25; + if ((0x20000000200000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 105; break; case 107: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 106; + if ((0x1000000010L & l) != 0L) + jjCheckNAdd(106); break; case 108: - if ((0x4000000040000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 107; + if ((0x8000000080000L & l) != 0L) + jjCheckNAddTwoStates(112, 18); break; case 109: - if ((0x20000000200L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 108; + if ((0x1000000010L & l) != 0L) + jjCheckNAdd(18); break; case 110: if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 109; break; case 111: - if ((0x1000000010000L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 110; break; case 112: - if ((0x1000000010L & l) != 0L && kind > 26) - kind = 26; + if ((0x4000000040000L & l) != 0L) + jjCheckNAdd(111); break; case 113: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 112; + if ((0x8000000080000L & l) != 0L) + jjCheckNAddTwoStates(123, 120); break; case 114: - if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 113; + if ((0x1000000010L & l) != 0L) + jjCheckNAdd(120); break; case 115: - if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 114; + if ((0x1000000010L & l) != 0L && kind > 20) + kind = 20; break; case 116: - if ((0x20000000200L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 115; break; - case 117: - if ((0x100000001000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 116; - break; - case 118: - if ((0x800000008L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 117; - break; case 119: - if ((0x20000000200L & l) != 0L) - { jjAddStates(23, 33); } + if ((0x200000002L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 118; break; case 120: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAdd(143); } + if ((0x200000002000L & l) != 0L) + jjCheckNAdd(119); break; case 121: - if ((0x2000000020L & l) == 0L) - break; - if (kind > 18) - kind = 18; - { jjAddStates(42, 43); } + if ((0x200000002L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 114; break; case 122: - if ((0x8000000080L & l) != 0L && kind > 18) - kind = 18; + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 121; break; case 123: - case 130: - if ((0x200000002L & l) != 0L) - { jjCheckNAdd(122); } + if ((0x4000000040000L & l) != 0L) + jjCheckNAdd(122); break; case 124: - if ((0x100000001000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 123; + if ((0x8000000080000L & l) != 0L) + jjCheckNAdd(136); break; case 125: - if ((0x4000000040L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 124; + if ((0x1000000010L & l) != 0L && kind > 21) + kind = 21; break; case 126: - if ((0x4000000040000L & l) != 0L) - { jjAddStates(44, 45); } + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 125; break; case 127: - if ((0x1000000010L & l) != 0L && kind > 18) - kind = 18; + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 126; break; case 128: - if ((0x200000002L & l) != 0L) + if ((0x1000000010000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 127; break; case 129: - if ((0x2000000020L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 128; break; + case 130: + if ((0x200000002000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 129; + break; case 131: - if ((0x100000001000L & l) != 0L) + if ((0x400000004000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 130; break; case 132: - if ((0x4000000040L & l) != 0L) + if ((0x20000000200000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 131; break; case 133: - if ((0x1000000010L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 132; break; case 134: - if ((0x200000002L & l) != 0L) + if ((0x10000000100000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 133; break; case 135: - if ((0x2000000020L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 134; break; case 136: - if ((0x10000000100000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 121; + if ((0x200000002000L & l) != 0L) + jjCheckNAdd(135); break; case 137: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 136; + if ((0x8000000080000L & l) != 0L) + jjCheckNAdd(36); break; case 138: - if ((0x800000008L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 137; - break; - case 139: - if ((0x20000000200L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 138; + if ((0x8000000080000L & l) != 0L) + jjCheckNAddTwoStates(69, 155); break; case 140: - if ((0x100000001000L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 139; break; case 141: - if ((0x1000000010000L & l) != 0L) + if ((0x200000002000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 140; break; case 142: - if ((0x20000000200000L & l) != 0L) + if ((0x400000004000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 141; break; case 143: - if ((0x1000000010L & l) != 0L) - { jjCheckNAdd(142); } + if ((0x8000000080L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 142; break; case 144: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAddTwoStates(148, 18); } + if ((0x20000000200L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 143; break; case 145: - if ((0x1000000010L & l) != 0L) - { jjCheckNAdd(18); } + if ((0x100000001000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 144; break; case 146: if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 145; break; case 147: - if ((0x2000000020L & l) != 0L) + if ((0x200000002000000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 146; break; case 148: if ((0x4000000040000L & l) != 0L) - { jjCheckNAdd(147); } + jjstateSet[jjnewStateCnt++] = 147; break; case 149: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAddTwoStates(159, 156); } + if ((0x200000002L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 148; break; case 150: if ((0x1000000010L & l) != 0L) - { jjCheckNAdd(156); } + jjstateSet[jjnewStateCnt++] = 149; break; case 151: - if ((0x1000000010L & l) != 0L && kind > 20) - kind = 20; + if ((0x400000004000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 150; break; case 152: - if ((0x2000000020L & l) != 0L) + if ((0x800000008000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 151; break; + case 153: + if ((0x800000008L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 152; + break; + case 154: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 153; + break; case 155: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 154; + if ((0x8000000080000L & l) != 0L) + jjCheckNAdd(154); break; case 156: - if ((0x200000002000L & l) != 0L) - { jjCheckNAdd(155); } + if ((0x8000000080000L & l) != 0L) + jjCheckNAdd(192); break; case 157: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 150; + if ((0x10000000100000L & l) == 0L) + break; + if (kind > 24) + kind = 24; + jjAddStates(42, 43); break; case 158: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 157; + if ((0x8000000080L & l) != 0L && kind > 24) + kind = 24; break; case 159: - if ((0x4000000040000L & l) != 0L) - { jjCheckNAdd(158); } + case 166: + if ((0x200000002L & l) != 0L) + jjCheckNAdd(158); break; case 160: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAdd(172); } + if ((0x100000001000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 159; break; case 161: - if ((0x1000000010L & l) != 0L && kind > 21) - kind = 21; + if ((0x4000000040L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 160; break; case 162: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 161; + if ((0x4000000040000L & l) != 0L) + jjAddStates(44, 45); break; case 163: - if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 162; + if ((0x1000000010L & l) != 0L && kind > 24) + kind = 24; break; case 164: - if ((0x1000000010000L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 163; break; case 165: - if ((0x200000002L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 164; break; - case 166: - if ((0x200000002000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 165; - break; case 167: - if ((0x400000004000L & l) != 0L) + if ((0x100000001000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 166; break; case 168: - if ((0x20000000200000L & l) != 0L) + if ((0x4000000040L & l) != 0L) jjstateSet[jjnewStateCnt++] = 167; break; case 169: - if ((0x2000000020L & l) != 0L) + if ((0x1000000010L & l) != 0L) jjstateSet[jjnewStateCnt++] = 168; break; case 170: - if ((0x10000000100000L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 169; break; case 171: - if ((0x200000002L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 170; break; case 172: - if ((0x200000002000L & l) != 0L) - { jjCheckNAdd(171); } + if ((0x400000004000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 157; break; case 173: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAdd(36); } + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 172; break; case 174: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAdd(69); } + if ((0x200000002000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 173; break; case 175: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAdd(105); } + if ((0x400000004000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 174; break; case 176: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAddTwoStates(180, 111); } + if ((0x8000000080L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 175; break; case 177: - if ((0x1000000010L & l) != 0L) - { jjCheckNAdd(111); } + if ((0x20000000200L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 176; break; case 178: - if ((0x200000002L & l) != 0L) + if ((0x100000001000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 177; break; case 179: - if ((0x2000000020L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 178; break; case 180: - if ((0x4000000040000L & l) != 0L) - { jjCheckNAdd(179); } + if ((0x200000002000000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 179; break; case 181: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAddTwoStates(185, 118); } + if ((0x4000000040000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 180; break; case 182: - if ((0x1000000010L & l) != 0L) - { jjCheckNAdd(118); } + if ((0x200000002L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 181; break; case 183: - if ((0x200000002L & l) != 0L) + if ((0x10000000100000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 182; break; case 184: - if ((0x2000000020L & l) != 0L) + if ((0x400000004000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 183; break; case 185: - if ((0x4000000040000L & l) != 0L) - { jjCheckNAdd(184); } + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 184; break; case 186: - if ((0x8000000080000L & l) != 0L) - { jjCheckNAdd(207); } + if ((0x200000002000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 185; break; case 187: - if ((0x2000000020000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 188; + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 186; break; case 188: - if ((0x20000000200000L & l) != 0L) - { jjCheckNAddTwoStates(204, 199); } + if ((0x100000001000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 187; break; case 189: - if ((0x200000002000000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 200; + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 188; break; case 190: - if ((0x2000000020L & l) != 0L && kind > 27) - kind = 27; + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 189; break; case 191: - if ((0x100000001000L & l) != 0L) + if ((0x20000000200000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 190; break; case 192: - if ((0x400000004L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 191; + if ((0x8000000080000L & l) != 0L) + jjCheckNAdd(191); break; case 193: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 192; + if ((0x8000000080000L & l) != 0L) + jjCheckNAddTwoStates(197, 75); break; case 194: - if ((0x100000001000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 193; + if ((0x1000000010L & l) != 0L) + jjCheckNAdd(75); break; case 195: - if ((0x20000000200L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 194; break; case 196: - if ((0x200000002L & l) != 0L) + if ((0x2000000020L & l) != 0L) jjstateSet[jjnewStateCnt++] = 195; break; case 197: - if ((0x40000000400000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 196; + if ((0x4000000040000L & l) != 0L) + jjCheckNAdd(196); break; case 198: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 197; + if ((0x8000000080000L & l) != 0L) + jjCheckNAddTwoStates(202, 82); break; case 199: - if ((0x400000004000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 198; + if ((0x1000000010L & l) != 0L) + jjCheckNAdd(82); break; case 200: - if ((0x20000000200000L & l) != 0L) - { jjCheckNAdd(199); } + if ((0x200000002L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 199; break; case 201: - if ((0x10000000100000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 189; + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 200; break; case 202: - if ((0x20000000200L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 201; + if ((0x4000000040000L & l) != 0L) + jjCheckNAdd(201); break; case 203: - if ((0x100000001000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 202; + if ((0x8000000080000L & l) != 0L) + jjCheckNAdd(224); break; case 204: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 203; + if ((0x2000000020000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 205; break; case 205: - if ((0x1000000010000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 187; + if ((0x20000000200000L & l) != 0L) + jjCheckNAddTwoStates(221, 216); break; case 206: - if ((0x200000002L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 205; + if ((0x200000002000000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 217; break; case 207: - if ((0x200000002000L & l) != 0L) - { jjCheckNAdd(206); } + if ((0x2000000020L & l) != 0L && kind > 27) + kind = 27; break; case 208: - if ((0x8000000080000L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 218; + if ((0x100000001000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 207; break; case 209: - if ((0x10000000100000L & l) != 0L && kind > 33) - kind = 33; + if ((0x400000004L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 208; break; case 210: - if ((0x400000004000L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 209; break; case 211: - if ((0x200000002L & l) != 0L) + if ((0x100000001000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 210; break; case 212: - if ((0x1000000010L & l) != 0L) + if ((0x20000000200L & l) != 0L) jjstateSet[jjnewStateCnt++] = 211; break; case 213: - if ((0x4000000040000L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 212; break; case 214: - if ((0x800000008000L & l) != 0L) + if ((0x40000000400000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 213; break; case 215: - if ((0x800000008L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 214; break; case 216: - if ((0x8000000080000L & l) != 0L) + if ((0x400000004000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 215; break; case 217: - if ((0x20000000200L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 216; + if ((0x20000000200000L & l) != 0L) + jjCheckNAdd(216); break; case 218: - if ((0x1000000010L & l) != 0L) - { jjCheckNAdd(217); } + if ((0x10000000100000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 206; break; case 219: - if ((0x8000000080L & l) != 0L) - { jjAddStates(13, 22); } + if ((0x20000000200L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 218; break; case 220: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAdd(143); } + if ((0x100000001000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 219; + break; + case 221: + if ((0x200000002L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 220; break; case 222: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAddTwoStates(148, 18); } + if ((0x1000000010000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 204; break; case 223: - if ((0x2000000020L & l) != 0L) + if ((0x200000002L & l) != 0L) jjstateSet[jjnewStateCnt++] = 222; break; case 224: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAddTwoStates(159, 156); } + if ((0x200000002000L & l) != 0L) + jjCheckNAdd(223); break; case 225: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 224; + if ((0x8000000080000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 235; break; case 226: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAdd(172); } + if ((0x10000000100000L & l) != 0L && kind > 33) + kind = 33; break; case 227: - if ((0x2000000020L & l) != 0L) + if ((0x400000004000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 226; break; case 228: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAdd(36); } + if ((0x200000002L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 227; break; case 229: - if ((0x2000000020L & l) != 0L) + if ((0x1000000010L & l) != 0L) jjstateSet[jjnewStateCnt++] = 228; break; case 230: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAdd(69); } + if ((0x4000000040000L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 229; break; case 231: - if ((0x2000000020L & l) != 0L) + if ((0x800000008000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 230; break; case 232: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAdd(105); } + if ((0x800000008L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 231; break; case 233: - if ((0x2000000020L & l) != 0L) + if ((0x8000000080000L & l) != 0L) jjstateSet[jjnewStateCnt++] = 232; break; case 234: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAddTwoStates(180, 111); } + if ((0x20000000200L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 233; break; case 235: - if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 234; + if ((0x1000000010L & l) != 0L) + jjCheckNAdd(234); break; case 236: - if ((0x10000000100000L & l) != 0L) - { jjCheckNAddTwoStates(185, 118); } + if ((0x8000000080L & l) != 0L) + jjAddStates(13, 22); break; case 237: + if ((0x10000000100000L & l) != 0L) + jjCheckNAdd(107); + break; + case 239: + if ((0x10000000100000L & l) != 0L) + jjCheckNAddTwoStates(112, 18); + break; + case 240: if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 236; + jjstateSet[jjnewStateCnt++] = 239; break; - case 238: + case 241: if ((0x10000000100000L & l) != 0L) - { jjCheckNAdd(207); } + jjCheckNAddTwoStates(123, 120); break; - case 239: + case 242: if ((0x2000000020L & l) != 0L) - jjstateSet[jjnewStateCnt++] = 238; + jjstateSet[jjnewStateCnt++] = 241; break; - case 240: + case 243: + if ((0x10000000100000L & l) != 0L) + jjCheckNAdd(136); + break; + case 244: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 243; + break; + case 245: + if ((0x10000000100000L & l) != 0L) + jjCheckNAdd(36); + break; + case 246: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 245; + break; + case 247: + if ((0x10000000100000L & l) != 0L) + jjCheckNAddTwoStates(69, 155); + break; + case 248: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 247; + break; + case 249: + if ((0x10000000100000L & l) != 0L) + jjCheckNAdd(192); + break; + case 250: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 249; + break; + case 251: + if ((0x10000000100000L & l) != 0L) + jjCheckNAddTwoStates(197, 75); + break; + case 252: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 251; + break; + case 253: + if ((0x10000000100000L & l) != 0L) + jjCheckNAddTwoStates(202, 82); + break; + case 254: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 253; + break; + case 255: + if ((0x10000000100000L & l) != 0L) + jjCheckNAdd(224); + break; + case 256: + if ((0x2000000020L & l) != 0L) + jjstateSet[jjnewStateCnt++] = 255; + break; + case 257: if ((0x1000000010L & l) != 0L) - { jjCheckNAddTwoStates(142, 217); } + jjCheckNAddTwoStates(106, 234); break; - case 241: + case 258: if ((0x4000000040000L & l) != 0L) - { jjCheckNAddStates(9, 12); } + jjCheckNAddStates(9, 12); break; - case 242: + case 259: if ((0x200000002000L & l) != 0L) - { jjCheckNAddStates(6, 8); } + jjCheckNAddStates(6, 8); + break; + case 260: + if ((0x8000000080000L & l) != 0L) + jjCheckNAddTwoStates(154, 191); break; default : break; } @@ -1394,11 +1478,11 @@ else if ((0x1000000010000L & l) != 0L) { case 2: if ((jjbitVec0[i2] & l2) != 0L) - { jjAddStates(3, 5); } + jjAddStates(3, 5); break; case 7: if ((jjbitVec0[i2] & l2) != 0L) - { jjAddStates(0, 2); } + jjAddStates(0, 2); break; default : break; } @@ -1411,18 +1495,83 @@ else if ((0x1000000010000L & l) != 0L) kind = 0x7fffffff; } ++curPos; - if ((i = jjnewStateCnt) == (startsAt = 243 - (jjnewStateCnt = startsAt))) + if ((i = jjnewStateCnt) == (startsAt = 261 - (jjnewStateCnt = startsAt))) return curPos; try { curChar = input_stream.readChar(); } catch(java.io.IOException e) { return curPos; } } } +static final int[] jjnextStates = { + 7, 8, 10, 2, 3, 5, 119, 135, 223, 111, 122, 196, 201, 238, 240, 242, + 244, 246, 248, 250, 252, 254, 256, 84, 108, 113, 124, 137, 138, 156, 193, 198, + 203, 225, 41, 42, 45, 51, 89, 90, 93, 99, 161, 162, 165, 171, +}; /** Token literal values. */ public static final String[] jjstrLiteralImages = { "", null, null, null, null, null, null, null, "\174\174", "\46\46", "\50", "\51", "\41", null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, }; + +/** Lexer state names. */ +public static final String[] lexStateNames = { + "DEFAULT", +}; +static final long[] jjtoToken = { + 0x7ffff1f81L, +}; +static final long[] jjtoSkip = { + 0x1eL, +}; +protected SimpleCharStream input_stream; +private final int[] jjrounds = new int[261]; +private final int[] jjstateSet = new int[522]; +protected char curChar; +/** Constructor. */ +public SamFilterParserTokenManager(SimpleCharStream stream){ + if (SimpleCharStream.staticFlag) + throw new Error("ERROR: Cannot use a static CharStream class with a non-static lexical analyzer."); + input_stream = stream; +} + +/** Constructor. */ +public SamFilterParserTokenManager(SimpleCharStream stream, int lexState){ + this(stream); + SwitchTo(lexState); +} + +/** Reinitialise parser. */ +public void ReInit(SimpleCharStream stream) +{ + jjmatchedPos = jjnewStateCnt = 0; + curLexState = defaultLexState; + input_stream = stream; + ReInitRounds(); +} +private void ReInitRounds() +{ + int i; + jjround = 0x80000001; + for (i = 261; i-- > 0;) + jjrounds[i] = 0x80000000; +} + +/** Reinitialise parser. */ +public void ReInit(SimpleCharStream stream, int lexState) +{ + ReInit(stream); + SwitchTo(lexState); +} + +/** Switch to specified lex state. */ +public void SwitchTo(int lexState) +{ + if (lexState >= 1 || lexState < 0) + throw new TokenMgrError("Error: Ignoring invalid lexical state : " + lexState + ". State unchanged.", TokenMgrError.INVALID_LEXICAL_STATE); + else + curLexState = lexState; +} + protected Token jjFillToken() { final Token t; @@ -1446,11 +1595,6 @@ protected Token jjFillToken() return t; } -static final int[] jjnextStates = { - 7, 8, 10, 2, 3, 5, 155, 171, 206, 147, 158, 179, 184, 221, 223, 225, - 227, 229, 231, 233, 235, 237, 239, 120, 144, 149, 160, 173, 174, 175, 176, 181, - 186, 208, 41, 42, 45, 51, 74, 75, 78, 84, 125, 126, 129, 135, -}; int curLexState = 0; int defaultLexState = 0; @@ -1472,10 +1616,9 @@ public Token getNextToken() { curChar = input_stream.BeginToken(); } - catch(Exception e) + catch(java.io.IOException e) { jjmatchedKind = 0; - jjmatchedPos = -1; matchedToken = jjFillToken(); return matchedToken; } @@ -1525,31 +1668,6 @@ public Token getNextToken() } } -void SkipLexicalActions(Token matchedToken) -{ - switch(jjmatchedKind) - { - default : - break; - } -} -void MoreLexicalActions() -{ - jjimageLen += (lengthOfMatch = jjmatchedPos + 1); - switch(jjmatchedKind) - { - default : - break; - } -} -void TokenLexicalActions(Token matchedToken) -{ - switch(jjmatchedKind) - { - default : - break; - } -} private void jjCheckNAdd(int state) { if (jjrounds[state] != jjround) @@ -1577,90 +1695,4 @@ private void jjCheckNAddStates(int start, int end) } while (start++ != end); } - /** Constructor. */ - public SamFilterParserTokenManager(SimpleCharStream stream){ - - if (SimpleCharStream.staticFlag) - throw new Error("ERROR: Cannot use a static CharStream class with a non-static lexical analyzer."); - - input_stream = stream; - } - - /** Constructor. */ - public SamFilterParserTokenManager (SimpleCharStream stream, int lexState){ - ReInit(stream); - SwitchTo(lexState); - } - - /** Reinitialise parser. */ - - public void ReInit(SimpleCharStream stream) - { - - - jjmatchedPos = - jjnewStateCnt = - 0; - curLexState = defaultLexState; - input_stream = stream; - ReInitRounds(); - } - - private void ReInitRounds() - { - int i; - jjround = 0x80000001; - for (i = 243; i-- > 0;) - jjrounds[i] = 0x80000000; - } - - /** Reinitialise parser. */ - public void ReInit(SimpleCharStream stream, int lexState) - - { - ReInit(stream); - SwitchTo(lexState); - } - - /** Switch to specified lex state. */ - public void SwitchTo(int lexState) - { - if (lexState >= 1 || lexState < 0) - throw new TokenMgrError("Error: Ignoring invalid lexical state : " + lexState + ". State unchanged.", TokenMgrError.INVALID_LEXICAL_STATE); - else - curLexState = lexState; - } - - -/** Lexer state names. */ -public static final String[] lexStateNames = { - "DEFAULT", -}; - -/** Lex State array. */ -public static final int[] jjnewLexState = { - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, - -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -}; -static final long[] jjtoToken = { - 0x7ffff1f81L, -}; -static final long[] jjtoSkip = { - 0x1eL, -}; -static final long[] jjtoSpecial = { - 0x0L, -}; -static final long[] jjtoMore = { - 0x0L, -}; - protected SimpleCharStream input_stream; - - private final int[] jjrounds = new int[243]; - private final int[] jjstateSet = new int[2 * 243]; - private final StringBuilder jjimage = new StringBuilder(); - private StringBuilder image = jjimage; - private int jjimageLen; - private int lengthOfMatch; - protected int curChar; } diff --git a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SimpleCharStream.java b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SimpleCharStream.java index 8e98e3a07..1800b7236 100644 --- a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SimpleCharStream.java +++ b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/SimpleCharStream.java @@ -1,4 +1,4 @@ -/* Generated By:JavaCC: Do not edit this line. SimpleCharStream.java Version 7.0 */ +/* Generated By:JavaCC: Do not edit this line. SimpleCharStream.java Version 5.0 */ /* JavaCCOptions:STATIC=false,SUPPORT_CLASS_VISIBILITY_PUBLIC=true */ /* The MIT License (MIT) @@ -54,12 +54,10 @@ public class SimpleCharStream protected char[] buffer; protected int maxNextCharInd = 0; protected int inBuf = 0; - protected int tabSize = 1; - protected boolean trackLineColumn = true; - - public void setTabSize(int i) { tabSize = i; } - public int getTabSize() { return tabSize; } + protected int tabSize = 8; + protected void setTabSize(int i) { tabSize = i; } + protected int getTabSize(int i) { return tabSize; } protected void ExpandBuff(boolean wrapAround) @@ -492,7 +490,6 @@ public void adjustBeginLineColumn(int newLine, int newCol) line = bufline[j]; column = bufcolumn[j]; } - boolean getTrackLineColumn() { return trackLineColumn; } - void setTrackLineColumn(boolean tlc) { trackLineColumn = tlc; } + } -/* JavaCC - OriginalChecksum=b62a6db3e3b53ada56d9a1db13f2afae (do not edit this line) */ +/* JavaCC - OriginalChecksum=e623f56108a6e684bfd277d3cdc28161 (do not edit this line) */ diff --git a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/Token.java b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/Token.java index 01663923e..6a0f48cf0 100644 --- a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/Token.java +++ b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/Token.java @@ -1,5 +1,5 @@ -/* Generated By:JavaCC: Do not edit this line. Token.java Version 7.0 */ -/* JavaCCOptions:TOKEN_EXTENDS=,KEEP_LINE_COLUMN=true,SUPPORT_CLASS_VISIBILITY_PUBLIC=true */ +/* Generated By:JavaCC: Do not edit this line. Token.java Version 5.0 */ +/* JavaCCOptions:TOKEN_EXTENDS=,KEEP_LINE_COL=null,SUPPORT_CLASS_VISIBILITY_PUBLIC=true */ /* The MIT License (MIT) @@ -152,4 +152,4 @@ public static Token newToken(int ofKind) } } -/* JavaCC - OriginalChecksum=fe33dc347fdd4e1d9c31d6f09016589c (do not edit this line) */ +/* JavaCC - OriginalChecksum=0ae03bee36365c6aa4a40a6ddf389a09 (do not edit this line) */ diff --git a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/TokenMgrError.java b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/TokenMgrError.java index 365b5cb7e..0025fcef6 100644 --- a/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/TokenMgrError.java +++ b/src/main/java/com/github/lindenb/jvarkit/util/bio/samfilter/TokenMgrError.java @@ -1,4 +1,4 @@ -/* Generated By:JavaCC: Do not edit this line. TokenMgrError.java Version 7.0 */ +/* Generated By:JavaCC: Do not edit this line. TokenMgrError.java Version 5.0 */ /* JavaCCOptions: */ /* The MIT License (MIT) @@ -44,22 +44,22 @@ public class TokenMgrError extends Error /** * Lexical error occurred. */ - public static final int LEXICAL_ERROR = 0; + static final int LEXICAL_ERROR = 0; /** * An attempt was made to create a second instance of a static token manager. */ - public static final int STATIC_LEXER_ERROR = 1; + static final int STATIC_LEXER_ERROR = 1; /** * Tried to change to an invalid lexical state. */ - public static final int INVALID_LEXICAL_STATE = 2; + static final int INVALID_LEXICAL_STATE = 2; /** * Detected (and bailed out of) an infinite loop in the token manager. */ - public static final int LOOP_DETECTED = 3; + static final int LOOP_DETECTED = 3; /** * Indicates the reason why the exception is thrown. It will have @@ -77,6 +77,8 @@ protected static final String addEscapes(String str) { for (int i = 0; i < str.length(); i++) { switch (str.charAt(i)) { + case 0 : + continue; case '\b': retval.append("\\b"); continue; @@ -126,12 +128,11 @@ protected static final String addEscapes(String str) { * curchar : the offending character * Note: You can customize the lexical error message by modifying this method. */ - protected static String LexicalErr(boolean EOFSeen, int lexState, int errorLine, int errorColumn, String errorAfter, int curChar) { - char curChar1 = (char)curChar; + protected static String LexicalError(boolean EOFSeen, int lexState, int errorLine, int errorColumn, String errorAfter, char curChar) { return("Lexical error at line " + errorLine + ", column " + errorColumn + ". Encountered: " + - (EOFSeen ? " " : ("\"" + addEscapes(String.valueOf(curChar1)) + "\"") + " (" + (int)curChar + "), ") + + (EOFSeen ? " " : ("\"" + addEscapes(String.valueOf(curChar)) + "\"") + " (" + (int)curChar + "), ") + "after : \"" + addEscapes(errorAfter) + "\""); } @@ -163,8 +164,8 @@ public TokenMgrError(String message, int reason) { } /** Full Constructor. */ - public TokenMgrError(boolean EOFSeen, int lexState, int errorLine, int errorColumn, String errorAfter, int curChar, int reason) { - this(LexicalErr(EOFSeen, lexState, errorLine, errorColumn, errorAfter, curChar), reason); + public TokenMgrError(boolean EOFSeen, int lexState, int errorLine, int errorColumn, String errorAfter, char curChar, int reason) { + this(LexicalError(EOFSeen, lexState, errorLine, errorColumn, errorAfter, curChar), reason); } } -/* JavaCC - OriginalChecksum=52d4899c137f891f59d6daaf0fffa5cb (do not edit this line) */ +/* JavaCC - OriginalChecksum=b55e658e98994f28543c7fb1c3b50e62 (do not edit this line) */ diff --git a/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj b/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj index 0f0c0cbfe..77d98e65f 100644 --- a/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj +++ b/src/main/resources/javacc/com/github/lindenb/jvarkit/util/bio/samfilter/SamFilterParser.jj @@ -314,7 +314,7 @@ public class SamFilterParser { }; } private static Predicate notPrimaryAlignmentFlag() { return new Predicate() { - @Override public boolean test(final SAMRecord rec) { return rec.getNotPrimaryAlignmentFlag();} + @Override public boolean test(final SAMRecord rec) { return rec.isSecondaryAlignment();} }; } private static Predicate supplementaryAlignmentFlag() { return new Predicate() { @@ -396,7 +396,7 @@ TOKEN: | ) ? ("Read")? "mapped" > | )? "MateUnmapped" > | ) ? "FailsVendorQuality" > -| ) ? "NotPrimaryAlignment" ()?> +| ) ? ("NotPrimaryAlignment"|"SecondaryAlignment") ()?> | ) ? "SupplementaryAlignment" ()?> | ) ? ("Read")? "Paired" > | ) ? ("Read")? "Clipped" >