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org.nmdp.ngs.feature.parser.FeatureParser Maven / Gradle / Ivy
/* Generated By:JavaCC: Do not edit this line. FeatureParser.java */
/*
ngs-feature Features.
Copyright (c) 2014 National Marrow Donor Program (NMDP)
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.gnu.org/licenses/lgpl.html
*/
package org.nmdp.ngs.feature.parser;
import java.io.StringReader;
import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import java.util.NoSuchElementException;
import com.google.common.collect.ArrayListMultimap;
import com.google.common.collect.ListMultimap;
import org.biojava.bio.Annotation;
import org.biojava.bio.SimpleAnnotation;
import org.biojava.bio.program.gff.SimpleGFFRecord;
import org.biojava.bio.seq.DNATools;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.StrandedFeature;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.bio.symbol.FiniteAlphabet;
import org.biojava.bio.symbol.IllegalSymbolException;
import org.biojava.bio.symbol.RangeLocation;
import org.nmdp.ngs.feature.Locus;
import org.nmdp.ngs.feature.Sample;
import org.nmdp.ngs.feature.VcfFile;
import org.nmdp.ngs.feature.VcfFileException;
import org.nmdp.ngs.variant.vcf.VcfRecord;
/**
* Feature parser.
*/
public final class FeatureParser implements FeatureParserConstants {
public static SimpleGFFRecord parseOneRecord(final String fields) throws ParseException {
FeatureParser featureParser = new FeatureParser(new StringReader(fields));
return featureParser.parse();
}
public static Double parseNumber(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseNumber();
}
public static Double parseNumberField(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseNumberField();
}
public static List parseNumbers(final String fields) throws ParseException {
return (new FeatureParser(new StringReader(fields))).parseNumbers();
}
public static SimpleAnnotation parseAnnotations(final String fields) throws ParseException {
return (new FeatureParser(new StringReader(fields))).parseAnnotations();
}
public static BigInteger parseLocation(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseLocation();
}
public static RangeLocation parseRangeLocation(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseRangeLocation();
}
public static Locus parseLocus(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseLocus();
}
public static VcfRecord parseVcfRecord(final String field, final long lineNumber) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseVcfRecord(lineNumber);
}
public static List parseVcfSamples(final String field, final VcfFile.Header header) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseVcfSamples(header);
}
public static String parseVcfVersion(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseVcfVersion();
}
public static VcfFile.Header parseVcfHeader(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseVcfHeader();
}
public static VcfFile.Metadata parseVcfMetadata(final String field) throws ParseException {
return (new FeatureParser(new StringReader(field.replace(",", ";")))).parseVcfMetadata();
}
public static Sequence parseDnaSequence(final String field) throws ParseException {
return parseDnaSequence(field, "");
}
public static Sequence parseDnaSequence(final String field, final String name) throws ParseException {
return (new FeatureParser(new StringReader(field))).parseDna(name);
}
public static String parseDnas(final String fields) throws ParseException {
// stub
return null;
}
public static String parseSequence(final String field) throws ParseException {
// stub
return null;
}
public static String parseSequence(final String field, final String uri, final String name, final Annotation annotation) throws ParseException {
// stub
return null;
}
public static String parseSequences(final String field) throws ParseException {
// stub
return null;
}
public static StrandedFeature.Strand parseGffStrand(final String field) throws ParseException {
FeatureParser featureParser = new FeatureParser(new StringReader(field));
return featureParser.parseGffStrand();
}
final public SimpleGFFRecord parse() throws ParseException {
String sequenceName;
String source;
String feature;
BigInteger start;
BigInteger end;
//Double score;
StrandedFeature.Strand strand;
Integer frame;
String comment;
Map attributes;
//sequenceName = ""
//source = ""
//feature = ""
start = parseInteger();
jj_consume_token(TAB);
end = parseInteger();
jj_consume_token(TAB);
//score = 0
strand = parseGffStrand();
jj_consume_token(0);
{if (true) return new SimpleGFFRecord("", "", "", start.intValue(), end.intValue(), 0, strand, 0, "", null);}
throw new Error("Missing return statement in function");
}
final private String parseString() throws ParseException {
Token token;
//System.out.println("INSIDE parseString()");
String string;
if (jj_2_1(2)) {
token = jj_consume_token(DOT);
} else if (jj_2_2(2)) {
token = jj_consume_token(DNA);
} else if (jj_2_3(2)) {
token = jj_consume_token(IDENTIFIER);
} else {
jj_consume_token(-1);
throw new ParseException();
}
{if (true) return token.image;}
throw new Error("Missing return statement in function");
}
final private String parseStringSkip(long ns) throws ParseException {
Token token;
//System.out.println("parseStringSkip(" + ns + ")");
String string;
token = jj_consume_token(IDENTIFIER);
{if (true) return token.image;}
throw new Error("Missing return statement in function");
}
final private List parseStrings() throws ParseException {
String string;
List strings = new ArrayList();
if (jj_2_5(2)) {
string = parseString();
strings.add(string);
label_1:
while (true) {
if (jj_2_4(2)) {
;
} else {
break label_1;
}
jj_consume_token(COMMA);
string = parseString();
strings.add(string);
}
} else {
;
}
{if (true) return strings;}
throw new Error("Missing return statement in function");
}
final private BigInteger parseInteger() throws ParseException {
Token token;
token = jj_consume_token(INTEGER);
{if (true) return new BigInteger(token.image);}
throw new Error("Missing return statement in function");
}
final public Double parseNumber() throws ParseException {
Token token;
if (jj_2_6(2)) {
token = jj_consume_token(INTEGER);
} else if (jj_2_7(2)) {
token = jj_consume_token(REAL);
} else {
jj_consume_token(-1);
throw new ParseException();
}
{if (true) return new Double(token.image);}
throw new Error("Missing return statement in function");
}
final private Double parseNumberField() throws ParseException {
Double number;
number = parseNumber();
jj_consume_token(0);
{if (true) return number;}
throw new Error("Missing return statement in function");
}
final private List parseNumbers() throws ParseException {
Double number;
List numbers = new ArrayList();
if (jj_2_9(2)) {
number = parseNumber();
numbers.add(number);
label_2:
while (true) {
if (jj_2_8(2)) {
;
} else {
break label_2;
}
jj_consume_token(COMMA);
number = parseNumber();
numbers.add(number);
}
} else {
;
}
{if (true) return numbers;}
throw new Error("Missing return statement in function");
}
final private Object parseObject() throws ParseException {
Object object;
if (jj_2_10(2)) {
object = parseNumber();
} else if (jj_2_11(2)) {
object = parseString();
} else if (jj_2_12(2)) {
object = parseDna("");
} else {
jj_consume_token(-1);
throw new ParseException();
}
{if (true) return object;}
throw new Error("Missing return statement in function");
}
final private List parseObjects() throws ParseException {
Object object;
List objects = new ArrayList();
object = parseObject();
objects.add(object);
label_3:
while (true) {
if (jj_2_13(2)) {
;
} else {
break label_3;
}
jj_consume_token(COMMA);
object = parseObject();
objects.add(object);
}
{if (true) return objects;}
throw new Error("Missing return statement in function");
}
final private SimpleAnnotation parseAnnotations() throws ParseException {
String key;
List values = new ArrayList();
Map> map = new TreeMap>();
key = parseString();
if (jj_2_14(2)) {
jj_consume_token(EQUALS);
values = parseObjects();
} else {
;
}
map.put(key, values);
//System.out.println("map.put(" + key + ", " + values + ")");
label_4:
while (true) {
if (jj_2_15(2)) {
;
} else {
break label_4;
}
jj_consume_token(SEMICOLON);
key = parseString();
values = new ArrayList();
if (jj_2_16(2)) {
jj_consume_token(EQUALS);
values = parseObjects();
} else {
;
}
map.put(key, values);
//System.out.println("map.put(" + key + ", " + values + ")");
}
{if (true) return new SimpleAnnotation(map);}
throw new Error("Missing return statement in function");
}
final private BigInteger parseLocation() throws ParseException {
Token token;
BigInteger location;
if (jj_2_17(2)) {
location = parseInteger();
{if (true) return location;}
} else if (jj_2_18(2)) {
token = jj_consume_token(LOCATION);
{if (true) return new BigInteger(token.image.replace(",", ""));}
} else {
jj_consume_token(-1);
throw new ParseException();
}
throw new Error("Missing return statement in function");
}
final private RangeLocation parseRangeLocation() throws ParseException {
BigInteger lower = null , upper = null;
char sign = '?';
lower = parseLocation();
if (jj_2_22(2)) {
if (jj_2_21(2)) {
if (jj_2_19(2)) {
jj_consume_token(TAB);
} else if (jj_2_20(2)) {
jj_consume_token(DOT);
jj_consume_token(DOT);
} else {
jj_consume_token(-1);
throw new ParseException();
}
} else {
;
}
upper = parseLocation();
// System.out.println("tab or .. : lower = " + lower + " upper = " + upper + " negated = " + upper.negate());
if (lower.compareTo(BigInteger.ZERO) == 1 && upper.compareTo(BigInteger.ZERO) == -1) {
upper = upper.negate();
}
} else if (jj_2_23(2)) {
jj_consume_token(PLUS_SIGN);
upper = parseLocation();
//System.out.println("plus : lower = " + lower);
//System.out.println(" : upper = " + upper);
upper = BigInteger.ONE.add(lower.add(upper));
//System.out.println("plus : lower = " + lower + " upper = " + upper);
} else {
jj_consume_token(-1);
throw new ParseException();
}
if (upper == null) {
{if (true) throw new ParseException("cannot parse upper coordinate");}
}
try {
// System.out.println("new RangeLocation(" + lower.intValue() + ", " + upper.intValue() + ")");
{if (true) return new RangeLocation(lower.intValue(), upper.intValue());}
}
catch (IndexOutOfBoundsException exception) {
{if (true) throw new ParseException(exception.getMessage());}
}
throw new Error("Missing return statement in function");
}
final private Locus parseLocus() throws ParseException {
String contig;
BigInteger integer;
RangeLocation range;
if (jj_2_24(2)) {
contig = parseString();
} else if (jj_2_25(2)) {
integer = parseInteger();
contig = integer.toString();
} else {
jj_consume_token(-1);
throw new ParseException();
}
jj_consume_token(COLON);
range = parseRangeLocation();
{if (true) return new Locus(contig, range);}
throw new Error("Missing return statement in function");
}
final private List parseVcfGenotypes() throws ParseException {
BigInteger index;
List indexes = new ArrayList();
index = parseInteger();
indexes.add(index);
label_5:
while (true) {
if (jj_2_26(2)) {
;
} else {
break label_5;
}
if (jj_2_27(2)) {
jj_consume_token(BAR);
} else if (jj_2_28(2)) {
jj_consume_token(SLASH);
} else {
jj_consume_token(-1);
throw new ParseException();
}
index = parseInteger();
indexes.add(index);
}
{if (true) return indexes;}
throw new Error("Missing return statement in function");
}
final private List parseVcfFormat() throws ParseException {
String tag;
List tags = new ArrayList();
tag = parseString();
tags.add(tag);
label_6:
while (true) {
if (jj_2_29(2)) {
;
} else {
break label_6;
}
jj_consume_token(COLON);
tag = parseString();
tags.add(tag);
}
{if (true) return tags;}
throw new Error("Missing return statement in function");
}
final private List parseVcfSamples(VcfFile.Header header) throws ParseException {
int formatIndex;
int sampleIndex;
String tag;
List tags;
List genotypes;
List values = new ArrayList();
Map> map = new TreeMap>();
Sample sample;
List samples = new ArrayList();
tags = parseVcfFormat();
sampleIndex = 0;
//System.out.println("tags = " + tags);
try {
tag = tags.get(0);
if(!tag.equals("GT")) {
{if (true) throw new ParseException("genotype field 'GT' must be first in format");}
}
} catch(IndexOutOfBoundsException exception) {
{if (true) throw new ParseException("missing required genotype field 'GT' in format");}
}
label_7:
while (true) {
if (jj_2_30(2)) {
;
} else {
break label_7;
}
jj_consume_token(TAB);
genotypes = parseVcfGenotypes();
// System.out.println("genotypes = " + genotypes);
formatIndex = 0;
map.put(tags.get(formatIndex), genotypes);
label_8:
while (true) {
if (jj_2_31(2)) {
;
} else {
break label_8;
}
jj_consume_token(COLON);
values = parseObjects();
try {
map.put(tags.get(++formatIndex), values);
} catch(IndexOutOfBoundsException exception) {
{if (true) throw new ParseException("format field index out of bounds");}
}
}
try {
sample = new Sample(header.names.get(sampleIndex++), new SimpleAnnotation(map));
samples.add(sample);
} catch(IndexOutOfBoundsException exception) {
{if (true) throw new ParseException("not enough names for observed samples");}
}
map.clear();
}
{if (true) return samples;}
throw new Error("Missing return statement in function");
}
final private VcfRecord parseVcfRecord(long lineNumber) throws ParseException {
String contig;
BigInteger position;
Double quality;
List identifiers = new ArrayList();
Sequence ref;
String filter;
List filters = new ArrayList();
List alternates = new ArrayList();
String uri;
String name;
SimpleAnnotation annotation;
contig = parseString();
jj_consume_token(TAB);
position = parseInteger();
jj_consume_token(TAB);
identifiers = parseStrings();
jj_consume_token(TAB);
ref = parseDna("");
jj_consume_token(TAB);
alternates = parseDnas();
jj_consume_token(TAB);
quality = parseNumber();
jj_consume_token(TAB);
filter = parseString();
filters.add(filter);
//System.out.println("filter = " + filter);
label_9:
while (true) {
if (jj_2_32(2)) {
;
} else {
break label_9;
}
jj_consume_token(SEMICOLON);
filter = parseString();
filters.add(filter);
}
jj_consume_token(TAB);
annotation = parseAnnotations();
List alts = new ArrayList();
for(Sequence alternate : alternates) {
alts.add(alternate.seqString());
}
// todo: this needs more thinkin'
ListMultimap info = ArrayListMultimap.create();
// ...and untyped map coming from annotation is ugly
for (Object e : annotation.asMap().entrySet()) {
Map.Entry entry = (Map.Entry) e;
String key = (String) entry.getKey();
List values = (List) entry.getValue();
for (Object value : values) {
info.put(key, value == null ? "null" : value.toString());
}
}
{if (true) return VcfRecord.builder()
.withLineNumber(lineNumber)
.withChrom(contig)
.withPos(position.longValue())
.withId(identifiers.toArray(new String[identifiers.size()]))
.withRef(ref.seqString())
.withAlt(alts.toArray(new String[alts.size()]))
.withQual(quality)
.withFilter(filters.toArray(new String[filters.size()]))
.withInfo(info)
.build();}
throw new Error("Missing return statement in function");
}
final private String parseVcfVersion() throws ParseException {
SimpleAnnotation annotation;
jj_consume_token(DOUBLEHASH);
annotation = parseAnnotations();
try {
{if (true) return (String) annotation.getProperty("fileformat");}
} catch(NoSuchElementException exception) {
{if (true) throw new ParseException("expected \u005c"fileformat\u005c"");}
}
throw new Error("Missing return statement in function");
}
final private VcfFile.Metadata parseVcfMetadata() throws ParseException {
String name, description;
SimpleAnnotation annotation;
jj_consume_token(DOUBLEHASH);
name = parseString();
jj_consume_token(EQUALS);
if (jj_2_33(2)) {
description = parseString();
{if (true) return new VcfFile.Metadata(name, description);}
} else if (jj_2_34(2)) {
jj_consume_token(OPENANGLE);
annotation = parseAnnotations();
} else {
jj_consume_token(-1);
throw new ParseException();
}
if(name.equals(VcfFile.INFO)) {
try {
{if (true) return new VcfFile.Info(annotation);}
} catch(VcfFileException exception) {
{if (true) throw new ParseException(exception.getMessage());}
}
}
else if(name.equals(VcfFile.FILTER)) {
try {
{if (true) return new VcfFile.Filter(annotation);}
} catch(VcfFileException exception) {
{if (true) throw new ParseException(exception.getMessage());}
}
}
else if(name.equals(VcfFile.FORMAT)) {
try {
{if (true) return new VcfFile.Format(annotation);}
} catch(VcfFileException exception) {
{if (true) throw new ParseException(exception.getMessage());}
}
}
throw new Error("Missing return statement in function");
}
final private VcfFile.Header parseVcfHeader() throws ParseException {
String field;
List fields = new ArrayList();
jj_consume_token(HASH);
field = parseString();
fields.add(field);
label_10:
while (true) {
if (jj_2_35(2)) {
;
} else {
break label_10;
}
jj_consume_token(TAB);
field = parseString();
fields.add(field);
}
try {
{if (true) return new VcfFile.Header(fields.subList(9, fields.size()));}
} catch (IndexOutOfBoundsException exception) {
{if (true) throw new ParseException("header is improperly formed");}
}
throw new Error("Missing return statement in function");
}
final private Sequence parseDna(String name) throws ParseException {
Token token;
token = jj_consume_token(DNA);
try {
//System.out.println("parseDna() : " + token.image);
{if (true) return DNATools.createDNASequence(token.image, name);}
}
catch(IllegalSymbolException exception) {
{if (true) throw new ParseException(exception.getMessage());}
}
throw new Error("Missing return statement in function");
}
final private List parseDnas() throws ParseException {
Sequence sequence;
List sequences = new ArrayList();
sequence = parseDna("");
sequences.add(sequence);
label_11:
while (true) {
if (jj_2_36(2)) {
;
} else {
break label_11;
}
jj_consume_token(COMMA);
sequence = parseDna("");
sequences.add(sequence);
}
{if (true) return sequences;}
throw new Error("Missing return statement in function");
}
final public StrandedFeature.Strand parseGffStrand() throws ParseException {
Token token;
if (jj_2_37(2)) {
token = jj_consume_token(MINUS_SIGN);
{if (true) return StrandedFeature.NEGATIVE;}
} else if (jj_2_38(2)) {
token = jj_consume_token(PLUS_SIGN);
{if (true) return StrandedFeature.POSITIVE;}
} else if (jj_2_39(2)) {
token = jj_consume_token(DOT);
{if (true) return StrandedFeature.UNKNOWN;}
} else {
jj_consume_token(-1);
throw new ParseException();
}
throw new Error("Missing return statement in function");
}
private boolean jj_2_1(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_1(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(0, xla); }
}
private boolean jj_2_2(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_2(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(1, xla); }
}
private boolean jj_2_3(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_3(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(2, xla); }
}
private boolean jj_2_4(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_4(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(3, xla); }
}
private boolean jj_2_5(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_5(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(4, xla); }
}
private boolean jj_2_6(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_6(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(5, xla); }
}
private boolean jj_2_7(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_7(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(6, xla); }
}
private boolean jj_2_8(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_8(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(7, xla); }
}
private boolean jj_2_9(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_9(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(8, xla); }
}
private boolean jj_2_10(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_10(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(9, xla); }
}
private boolean jj_2_11(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_11(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(10, xla); }
}
private boolean jj_2_12(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_12(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(11, xla); }
}
private boolean jj_2_13(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_13(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(12, xla); }
}
private boolean jj_2_14(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_14(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(13, xla); }
}
private boolean jj_2_15(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_15(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(14, xla); }
}
private boolean jj_2_16(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_16(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(15, xla); }
}
private boolean jj_2_17(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_17(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(16, xla); }
}
private boolean jj_2_18(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_18(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(17, xla); }
}
private boolean jj_2_19(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_19(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(18, xla); }
}
private boolean jj_2_20(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_20(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(19, xla); }
}
private boolean jj_2_21(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_21(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(20, xla); }
}
private boolean jj_2_22(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_22(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(21, xla); }
}
private boolean jj_2_23(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_23(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(22, xla); }
}
private boolean jj_2_24(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_24(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(23, xla); }
}
private boolean jj_2_25(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_25(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(24, xla); }
}
private boolean jj_2_26(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_26(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(25, xla); }
}
private boolean jj_2_27(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_27(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(26, xla); }
}
private boolean jj_2_28(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_28(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(27, xla); }
}
private boolean jj_2_29(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_29(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(28, xla); }
}
private boolean jj_2_30(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_30(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(29, xla); }
}
private boolean jj_2_31(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_31(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(30, xla); }
}
private boolean jj_2_32(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_32(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(31, xla); }
}
private boolean jj_2_33(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_33(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(32, xla); }
}
private boolean jj_2_34(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_34(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(33, xla); }
}
private boolean jj_2_35(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_35(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(34, xla); }
}
private boolean jj_2_36(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_36(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(35, xla); }
}
private boolean jj_2_37(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_37(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(36, xla); }
}
private boolean jj_2_38(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_38(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(37, xla); }
}
private boolean jj_2_39(int xla) {
jj_la = xla; jj_lastpos = jj_scanpos = token;
try { return !jj_3_39(); }
catch(LookaheadSuccess ls) { return true; }
finally { jj_save(38, xla); }
}
private boolean jj_3_12() {
if (jj_3R_14()) return true;
return false;
}
private boolean jj_3_14() {
if (jj_scan_token(EQUALS)) return true;
if (jj_3R_16()) return true;
return false;
}
private boolean jj_3_18() {
if (jj_scan_token(LOCATION)) return true;
return false;
}
private boolean jj_3_4() {
if (jj_scan_token(COMMA)) return true;
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3R_18() {
Token xsp;
xsp = jj_scanpos;
if (jj_3_17()) {
jj_scanpos = xsp;
if (jj_3_18()) return true;
}
return false;
}
private boolean jj_3_5() {
if (jj_3R_12()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
if (jj_3_4()) { jj_scanpos = xsp; break; }
}
return false;
}
private boolean jj_3_17() {
if (jj_3R_17()) return true;
return false;
}
private boolean jj_3R_14() {
if (jj_scan_token(DNA)) return true;
return false;
}
private boolean jj_3_2() {
if (jj_scan_token(DNA)) return true;
return false;
}
private boolean jj_3_16() {
if (jj_scan_token(EQUALS)) return true;
if (jj_3R_16()) return true;
return false;
}
private boolean jj_3_15() {
if (jj_scan_token(SEMICOLON)) return true;
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3_32() {
if (jj_scan_token(SEMICOLON)) return true;
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3_35() {
if (jj_scan_token(TAB)) return true;
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3_11() {
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3_29() {
if (jj_scan_token(COLON)) return true;
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3R_20() {
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3_1() {
if (jj_scan_token(DOT)) return true;
return false;
}
private boolean jj_3_28() {
if (jj_scan_token(SLASH)) return true;
return false;
}
private boolean jj_3R_12() {
Token xsp;
xsp = jj_scanpos;
if (jj_3_1()) {
jj_scanpos = xsp;
if (jj_3_2()) {
jj_scanpos = xsp;
if (jj_3_3()) return true;
}
}
return false;
}
private boolean jj_3_13() {
if (jj_scan_token(COMMA)) return true;
if (jj_3R_15()) return true;
return false;
}
private boolean jj_3_27() {
if (jj_scan_token(BAR)) return true;
return false;
}
private boolean jj_3_26() {
Token xsp;
xsp = jj_scanpos;
if (jj_3_27()) {
jj_scanpos = xsp;
if (jj_3_28()) return true;
}
if (jj_3R_17()) return true;
return false;
}
private boolean jj_3R_16() {
if (jj_3R_15()) return true;
return false;
}
private boolean jj_3R_19() {
if (jj_3R_17()) return true;
return false;
}
private boolean jj_3_10() {
if (jj_3R_13()) return true;
return false;
}
private boolean jj_3R_15() {
Token xsp;
xsp = jj_scanpos;
if (jj_3_10()) {
jj_scanpos = xsp;
if (jj_3_11()) {
jj_scanpos = xsp;
if (jj_3_12()) return true;
}
}
return false;
}
private boolean jj_3_20() {
if (jj_scan_token(DOT)) return true;
if (jj_scan_token(DOT)) return true;
return false;
}
private boolean jj_3_34() {
if (jj_scan_token(OPENANGLE)) return true;
if (jj_3R_20()) return true;
return false;
}
private boolean jj_3_24() {
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3_25() {
if (jj_3R_17()) return true;
return false;
}
private boolean jj_3_33() {
if (jj_3R_12()) return true;
return false;
}
private boolean jj_3_8() {
if (jj_scan_token(COMMA)) return true;
if (jj_3R_13()) return true;
return false;
}
private boolean jj_3_19() {
if (jj_scan_token(TAB)) return true;
return false;
}
private boolean jj_3_21() {
Token xsp;
xsp = jj_scanpos;
if (jj_3_19()) {
jj_scanpos = xsp;
if (jj_3_20()) return true;
}
return false;
}
private boolean jj_3_9() {
if (jj_3R_13()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
if (jj_3_8()) { jj_scanpos = xsp; break; }
}
return false;
}
private boolean jj_3_7() {
if (jj_scan_token(REAL)) return true;
return false;
}
private boolean jj_3_22() {
Token xsp;
xsp = jj_scanpos;
if (jj_3_21()) jj_scanpos = xsp;
if (jj_3R_18()) return true;
return false;
}
private boolean jj_3_39() {
if (jj_scan_token(DOT)) return true;
return false;
}
private boolean jj_3_38() {
if (jj_scan_token(PLUS_SIGN)) return true;
return false;
}
private boolean jj_3_37() {
if (jj_scan_token(MINUS_SIGN)) return true;
return false;
}
private boolean jj_3_31() {
if (jj_scan_token(COLON)) return true;
if (jj_3R_16()) return true;
return false;
}
private boolean jj_3_6() {
if (jj_scan_token(INTEGER)) return true;
return false;
}
private boolean jj_3_23() {
if (jj_scan_token(PLUS_SIGN)) return true;
if (jj_3R_18()) return true;
return false;
}
private boolean jj_3R_13() {
Token xsp;
xsp = jj_scanpos;
if (jj_3_6()) {
jj_scanpos = xsp;
if (jj_3_7()) return true;
}
return false;
}
private boolean jj_3_36() {
if (jj_scan_token(COMMA)) return true;
if (jj_3R_14()) return true;
return false;
}
private boolean jj_3_30() {
if (jj_scan_token(TAB)) return true;
if (jj_3R_19()) return true;
return false;
}
private boolean jj_3R_17() {
if (jj_scan_token(INTEGER)) return true;
return false;
}
private boolean jj_3_3() {
if (jj_scan_token(IDENTIFIER)) return true;
return false;
}
/** Generated Token Manager. */
public FeatureParserTokenManager token_source;
SimpleCharStream jj_input_stream;
/** Current token. */
public Token token;
/** Next token. */
public Token jj_nt;
private int jj_ntk;
private Token jj_scanpos, jj_lastpos;
private int jj_la;
private int jj_gen;
final private int[] jj_la1 = new int[0];
static private int[] jj_la1_0;
static {
jj_la1_init_0();
}
private static void jj_la1_init_0() {
jj_la1_0 = new int[] {};
}
final private JJCalls[] jj_2_rtns = new JJCalls[39];
private boolean jj_rescan = false;
private int jj_gc = 0;
/** Constructor with InputStream. */
public FeatureParser(java.io.InputStream stream) {
this(stream, null);
}
/** Constructor with InputStream and supplied encoding */
public FeatureParser(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 FeatureParserTokenManager(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
for (int i = 0; i < 0; i++) jj_la1[i] = -1;
for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Reinitialise. */
public void ReInit(java.io.InputStream stream) {
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 < 0; i++) jj_la1[i] = -1;
for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Constructor. */
public FeatureParser(java.io.Reader stream) {
jj_input_stream = new SimpleCharStream(stream, 1, 1);
token_source = new FeatureParserTokenManager(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
for (int i = 0; i < 0; i++) jj_la1[i] = -1;
for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Reinitialise. */
public void ReInit(java.io.Reader stream) {
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 < 0; i++) jj_la1[i] = -1;
for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Constructor with generated Token Manager. */
public FeatureParser(FeatureParserTokenManager tm) {
token_source = tm;
token = new Token();
jj_ntk = -1;
jj_gen = 0;
for (int i = 0; i < 0; i++) jj_la1[i] = -1;
for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Reinitialise. */
public void ReInit(FeatureParserTokenManager tm) {
token_source = tm;
token = new Token();
jj_ntk = -1;
jj_gen = 0;
for (int i = 0; i < 0; i++) jj_la1[i] = -1;
for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
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++;
if (++jj_gc > 100) {
jj_gc = 0;
for (int i = 0; i < jj_2_rtns.length; i++) {
JJCalls c = jj_2_rtns[i];
while (c != null) {
if (c.gen < jj_gen) c.first = null;
c = c.next;
}
}
}
return token;
}
token = oldToken;
jj_kind = kind;
throw generateParseException();
}
static private final class LookaheadSuccess extends java.lang.Error { }
final private LookaheadSuccess jj_ls = new LookaheadSuccess();
private boolean jj_scan_token(int kind) {
if (jj_scanpos == jj_lastpos) {
jj_la--;
if (jj_scanpos.next == null) {
jj_lastpos = jj_scanpos = jj_scanpos.next = token_source.getNextToken();
} else {
jj_lastpos = jj_scanpos = jj_scanpos.next;
}
} else {
jj_scanpos = jj_scanpos.next;
}
if (jj_rescan) {
int i = 0; Token tok = token;
while (tok != null && tok != jj_scanpos) { i++; tok = tok.next; }
if (tok != null) jj_add_error_token(kind, i);
}
if (jj_scanpos.kind != kind) return true;
if (jj_la == 0 && jj_scanpos == jj_lastpos) throw jj_ls;
return false;
}
/** 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;
}
/** 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;
}
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();
private int[] jj_expentry;
private int jj_kind = -1;
private int[] jj_lasttokens = new int[100];
private int jj_endpos;
private void jj_add_error_token(int kind, int pos) {
if (pos >= 100) return;
if (pos == jj_endpos + 1) {
jj_lasttokens[jj_endpos++] = kind;
} else if (jj_endpos != 0) {
jj_expentry = new int[jj_endpos];
for (int i = 0; i < jj_endpos; i++) {
jj_expentry[i] = jj_lasttokens[i];
}
jj_entries_loop: for (java.util.Iterator it = jj_expentries.iterator(); it.hasNext();) {
int[] oldentry = (int[])(it.next());
if (oldentry.length == jj_expentry.length) {
for (int i = 0; i < jj_expentry.length; i++) {
if (oldentry[i] != jj_expentry[i]) {
continue jj_entries_loop;
}
}
jj_expentries.add(jj_expentry);
break jj_entries_loop;
}
}
if (pos != 0) jj_lasttokens[(jj_endpos = pos) - 1] = kind;
}
}
/** Generate ParseException. */
public ParseException generateParseException() {
jj_expentries.clear();
boolean[] la1tokens = new boolean[31];
if (jj_kind >= 0) {
la1tokens[jj_kind] = true;
jj_kind = -1;
}
for (int i = 0; i < 0; i++) {
if (jj_la1[i] == jj_gen) {
for (int j = 0; j < 32; j++) {
if ((jj_la1_0[i] & (1< jj_gen) {
jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
switch (i) {
case 0: jj_3_1(); break;
case 1: jj_3_2(); break;
case 2: jj_3_3(); break;
case 3: jj_3_4(); break;
case 4: jj_3_5(); break;
case 5: jj_3_6(); break;
case 6: jj_3_7(); break;
case 7: jj_3_8(); break;
case 8: jj_3_9(); break;
case 9: jj_3_10(); break;
case 10: jj_3_11(); break;
case 11: jj_3_12(); break;
case 12: jj_3_13(); break;
case 13: jj_3_14(); break;
case 14: jj_3_15(); break;
case 15: jj_3_16(); break;
case 16: jj_3_17(); break;
case 17: jj_3_18(); break;
case 18: jj_3_19(); break;
case 19: jj_3_20(); break;
case 20: jj_3_21(); break;
case 21: jj_3_22(); break;
case 22: jj_3_23(); break;
case 23: jj_3_24(); break;
case 24: jj_3_25(); break;
case 25: jj_3_26(); break;
case 26: jj_3_27(); break;
case 27: jj_3_28(); break;
case 28: jj_3_29(); break;
case 29: jj_3_30(); break;
case 30: jj_3_31(); break;
case 31: jj_3_32(); break;
case 32: jj_3_33(); break;
case 33: jj_3_34(); break;
case 34: jj_3_35(); break;
case 35: jj_3_36(); break;
case 36: jj_3_37(); break;
case 37: jj_3_38(); break;
case 38: jj_3_39(); break;
}
}
p = p.next;
} while (p != null);
} catch(LookaheadSuccess ls) { }
}
jj_rescan = false;
}
private void jj_save(int index, int xla) {
JJCalls p = jj_2_rtns[index];
while (p.gen > jj_gen) {
if (p.next == null) { p = p.next = new JJCalls(); break; }
p = p.next;
}
p.gen = jj_gen + xla - jj_la; p.first = token; p.arg = xla;
}
static final class JJCalls {
int gen;
Token first;
int arg;
JJCalls next;
}
}
