List of usage examples for java.lang Integer parseUnsignedInt
public static int parseUnsignedInt(String s) throws NumberFormatException
From source file:ffx.potential.parsers.ConversionFilter.java
/** * Parses a numerical argument for an atom-specific flag. Intended to reduce * the amount of repetitive code in applyAtomProperties by parsing and * checking for validity, and then returning the appropriate range. Input * should be 1-indexed (user end), output 0-indexed. * @param keyType Type of key//from w w w. jav a 2 s. co m * @param st Input string * @param nAtoms Number of atoms in the MolecularAssembly * @throws IllegalArgumentException if an invalid argument * @return An int[2] with start, end indices (inclusive). */ private int[] parseAtNumArg(String keyType, String st, int nAtoms) throws IllegalArgumentException { Matcher m = intrangePattern.matcher(st); if (m.matches()) { int start = Integer.parseInt(m.group(1)) - 1; int end = Integer.parseInt(m.group(2)) - 1; if (start > end) { throw new IllegalArgumentException( String.format(" %s input %s not " + "valid; start > end", keyType, st)); } else if (start < 0) { throw new IllegalArgumentException(String.format( " %s input %s not " + "valid; atoms should be indexed starting from 1", keyType, st)); } else if (start >= nAtoms) { throw new IllegalArgumentException(String.format( " %s input %s not " + "valid; atom range is out of bounds for assembly of " + "length %d", keyType, st, nAtoms)); /*for (int j = start; j <= end; j++) { if (j >= nAtoms) { logger.log(Level.INFO, String.format(" Atom index %d is " + "out of bounds for molecular assembly of " + "length %d", j + 1, nAtoms)); break; } }*/ } else { if (end >= nAtoms) { logger.log(Level.INFO, String.format(" Truncating range %s " + "to end of valid range %d", st, nAtoms)); end = nAtoms - 1; } int[] indices = { start, end }; return indices; } } else { try { int atNum = Integer.parseUnsignedInt(st) - 1; if (atNum < 0 || atNum >= nAtoms) { throw new IllegalArgumentException(String.format( " %s numerical " + "argument %s out-of-bounds for range 1 to %d", keyType, st, nAtoms)); } int[] indices = { atNum, atNum }; return indices; } catch (NumberFormatException ex) { throw new IllegalArgumentException( String.format(" %s input %s " + "could not be parsed as a positive number or range of " + "positive integers", keyType, st)); } } }
From source file:com.ge.research.semtk.load.utility.ImportSpecHandler.java
/** * Check that an input string is loadable as a certain SPARQL data type, and tweak it if necessary. * Throws exception if not./* w w w . j a va 2 s . co m*/ * Expects to only get the last part of the type, e.g. "float" */ @SuppressWarnings("deprecation") public static String validateDataType(String input, String expectedSparqlGraphType) throws Exception { // from the XSD data types: // string | boolean | decimal | int | integer | negativeInteger | nonNegativeInteger | // positiveInteger | nonPositiveInteger | long | float | double | duration | // dateTime | time | date | unsignedByte | unsignedInt | anySimpleType | // gYearMonth | gYear | gMonthDay; // added for the runtimeConstraint: // NODE_URI /** * Please keep the wiki up to date * https://github.com/ge-semtk/semtk/wiki/Ingestion-type-handling */ String ret = input; if (expectedSparqlGraphType.equalsIgnoreCase("string")) { } else if (expectedSparqlGraphType.equalsIgnoreCase("boolean")) { try { Boolean.parseBoolean(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("decimal")) { try { Double.parseDouble(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("int")) { try { Integer.parseInt(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("integer")) { try { Integer.parseInt(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("negativeInteger")) { try { int test = Integer.parseInt(input); if (test >= 0) { throw new Exception("value in model is negative integer. non-negative integer given as input"); } } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("nonNegativeInteger")) { try { int test = Integer.parseInt(input); if (test < 0) { throw new Exception("value in model is nonnegative integer. negative integer given as input"); } } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("positiveInteger")) { try { int test = Integer.parseInt(input); if (test <= 0) { throw new Exception("value in model is positive integer. integer <= 0 given as input"); } } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("nonPositiveInteger")) { try { int test = Integer.parseInt(input); if (test > 0) { throw new Exception("value in model is nonpositive integer. integer > 0 given as input"); } } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("long")) { try { long test = Long.parseLong(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("float")) { try { float test = Float.parseFloat(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("double")) { try { double test = Double.parseDouble(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("duration")) { // not sure how to check this one. this might not match the expectation from SADL try { Duration.parse(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("dateTime")) { try { return Utility.getSPARQLDateTimeString(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("time")) { try { Time.parse(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("date")) { try { return Utility.getSPARQLDateString(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("unsignedByte")) { try { Byte.parseByte(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("unsignedint")) { try { Integer.parseUnsignedInt(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("anySimpleType")) { // do nothing. } else if (expectedSparqlGraphType.equalsIgnoreCase("gYearMonth")) { try { String[] all = input.split("-"); // check them all if (all.length != 2) { throw new Exception("year-month did not have two parts."); } if (all[0].length() != 4 && all[1].length() != 2) { throw new Exception("year-month format was wrong. " + input + " given was not YYYY-MM"); } } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("gYear")) { try { if (input.length() != 4) { throw new Exception("year-month format was wrong. " + input + " given was not YYYY-MM"); } } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("gMonthDay")) { try { String[] all = input.split("-"); // check them all if (all.length != 2) { throw new Exception("month-day did not have two parts."); } if (all[0].length() != 2 && all[1].length() != 2) { throw new Exception("month-day format was wrong. " + input + " given was not MM-dd"); } } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause:" + e.getMessage()); } } else if (expectedSparqlGraphType.equalsIgnoreCase("NODE_URI")) { try { // check that this looks like a URI URI uri = new URI(input); } catch (Exception e) { throw new Exception("attempt to use value \"" + input + "\" as type \"" + expectedSparqlGraphType + "\" failed. assumed cause: " + e.getMessage()); } } else { // assume it is cool for now. } return ret; }
From source file:com.gmt2001.TwitchAPIv5.java
/** * Returns the channel Id// w w w.j ava2 s . c o m * * @param channel channel name * @return int the channel id. */ public int getChannelId(String channel) { return Integer.parseUnsignedInt(UsernameCache.instance().getID(channel)); }
From source file:org.esa.snap.smart.configurator.ui.PerformancePanel.java
boolean valid() { boolean isValid = true; File userDir = new File(cachePathTextField.getText()); if (userDir.exists() && !userDir.isDirectory()) { cachePathTextField.setForeground(ERROR_VALUES_COLOR); isValid = false;/*from ww w . ja v a 2 s.c o m*/ } else { cachePathTextField.setForeground(CURRENT_VALUES_COLOR); } String defaultTileSize = this.defaultTileSizeTextField.getText(); try { Integer.parseInt(defaultTileSize); defaultTileSizeTextField.setForeground(CURRENT_VALUES_COLOR); } catch (NumberFormatException ex) { this.defaultTileSizeTextField.setForeground(ERROR_VALUES_COLOR); isValid = false; } String readerCacheSize = this.cacheSizeTextField.getText(); try { Integer.parseInt(readerCacheSize); cacheSizeTextField.setForeground(CURRENT_VALUES_COLOR); } catch (NumberFormatException ex) { this.cacheSizeTextField.setForeground(ERROR_VALUES_COLOR); isValid = false; } String nbThreadsString = nbThreadsTextField.getText(); try { int nbThreads = Integer.parseUnsignedInt(nbThreadsString); if (nbThreads > nbCores) { nbThreadsTextField.setForeground(ERROR_VALUES_COLOR); isValid = false; } else { nbThreadsTextField.setForeground(CURRENT_VALUES_COLOR); } } catch (NumberFormatException ex) { nbThreadsTextField.setForeground(ERROR_VALUES_COLOR); isValid = false; } return isValid; }
From source file:ffx.potential.parsers.SystemFilter.java
/** * Parses a numerical argument for an atom-specific flag. Intended to reduce * the amount of repetitive code in applyAtomProperties by parsing and * checking for validity, and then returning the appropriate range. Input * should be 1-indexed (user end), output 0-indexed. * * @param keyType Type of key/*from ww w .java2 s .com*/ * @param st Input string * @param nAtoms Number of atoms in the MolecularAssembly * @throws IllegalArgumentException if an invalid argument * @return An int[2] with start, end indices (inclusive). */ public static int[] parseAtNumArg(String keyType, String st, int nAtoms) throws IllegalArgumentException { Matcher m = intrangePattern.matcher(st); if (m.matches()) { int start = Integer.parseInt(m.group(1)) - 1; int end = Integer.parseInt(m.group(2)) - 1; if (start > end) { throw new IllegalArgumentException( String.format(" %s input %s not " + "valid; start > end", keyType, st)); } else if (start < 0) { throw new IllegalArgumentException(String.format( " %s input %s not " + "valid; atoms should be indexed starting from 1", keyType, st)); } else if (start >= nAtoms) { throw new IllegalArgumentException(String.format( " %s input %s not " + "valid; atom range is out of bounds for assembly of " + "length %d", keyType, st, nAtoms)); /*for (int j = start; j <= end; j++) { if (j >= nAtoms) { logger.log(Level.INFO, String.format(" Atom index %d is " + "out of bounds for molecular assembly of " + "length %d", j + 1, nAtoms)); break; } }*/ } else { if (end >= nAtoms) { logger.log(Level.INFO, String.format(" Truncating range %s " + "to end of valid range %d", st, nAtoms)); end = nAtoms - 1; } int[] indices = { start, end }; return indices; } } else { try { int atNum = Integer.parseUnsignedInt(st) - 1; if (atNum < 0 || atNum >= nAtoms) { throw new IllegalArgumentException(String.format( " %s numerical " + "argument %s out-of-bounds for range 1 to %d", keyType, st, nAtoms)); } int[] indices = { atNum, atNum }; return indices; } catch (NumberFormatException ex) { throw new IllegalArgumentException( String.format(" %s input %s " + "could not be parsed as a positive number or range of " + "positive integers", keyType, st)); } } }
From source file:massbank.RecordParserDefinition.java
public RecordParserDefinition(Record callback) { def("start", ref("accession").seq(ref("record_title")).seq(ref("date")).seq(ref("authors")) .seq(ref("license")).seq(ref("copyright").optional()).seq(ref("publication").optional()) .seq(ref("comment").optional()).seq(ref("ch_name")).seq(ref("ch_compound_class")) .seq(ref("ch_formula")).seq(ref("ch_exact_mass")).seq(ref("ch_smiles")).seq(ref("ch_iupac")) .seq(ref("ch_link").optional()).seq(ref("sp_scientific_name").optional()) .seq(ref("sp_lineage").optional()).seq(ref("sp_link").optional()).seq(ref("sp_sample").optional()) .seq(ref("ac_instrument")).seq(ref("ac_instrument_type")).seq(ref("ac_mass_spectrometry_ms_type")) .seq(ref("ac_mass_spectrometry_ion_mode")).seq(ref("ac_mass_spectrometry").optional()) .seq(ref("ac_chromatography").optional()).seq(ref("ms_focused_ion").optional()) .seq(ref("ms_data_processing").optional()).seq(ref("pk_splash")) .seq(ref("pk_annotation").optional()).seq(ref("pk_num_peak")).seq(ref("pk_peak")).seq(ref("endtag")) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) .end());//from w ww . j a v a2 s . c om // 1.1 Syntax Rules // Single line information is either one of the followings: // Tag : space Value ( ; space Value) // Tag : space subtag space Value ( ; space Value) // Multiple line information // First line is Tag: space // Following lines are space space Value // Last line of a MassBank Record is // . def("tagsep", StringParser.of(": ")); def("valuesep", StringParser.of("; ")); def("endtag", StringParser.of("//").trim()); def("multiline_start", StringParser.of(" ")); // 2.1 Record Specific Information // 2.1.1 ACCESSION // Identifier of the MassBank Record. Mandatory // Example // ACCESSION: ZMS00006 // 8-character fix-length string. // Prefix two or three alphabetical capital characters. def("accession", StringParser.of("ACCESSION").seq(ref("tagsep")) .seq(letter().times(2).flatten().seq(digit().times(6).flatten()).map((List<String> value) -> { callback.ACCESSION(value.get(0) + value.get(1)); return value; }).or(letter().times(3).flatten().seq(digit().times(5).flatten()).map((List<String> value) -> { callback.ACCESSION(value.get(0) + value.get(1)); return value; }))).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.1.2 RECORD_TITLE (CH$NAME ; AC$INSTRUMENT_TYPE ; AC$MASS_SPECTROMETRY: MS_TYPE) // Brief Description of MassBank Record. Mandatory // Example: RECORD_TITLE: (-)-Nicotine; ESI-QQ; MS2; CE 40 V; [M+H]+ // It consists of the values of CH$NAME; AC$INSTRUMENT_TYPE; AC$MASS_SPECTROMETRY: MS_TYPE;. def("record_title", StringParser.of("RECORD_TITLE").seq(ref("tagsep")) .seq(ref("ch_name_value").seq(ref("valuesep")).pick(0)) .seq(ref("ac_instrument_type_value").seq(ref("valuesep")).pick(0)) .seq(ref("ac_mass_spectrometry_ms_type_value")) // TODO curation required because ionisation energy is not in format doc .seq(ref("valuesep").seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()) .pick(1).optional()) .seq(Token.NEWLINE_PARSER).map((List<?> value) -> { //System.out.println(value); if (value.get(value.size() - 2) == null) callback.RECORD_TITLE(value.subList(2, value.size() - 2).toString()); else callback.RECORD_TITLE(value.subList(2, value.size() - 1).toString()); return value; })); // 2.1.3 DATE // Date of the Creation or the Last Modification of MassBank Record. Mandatory // Example // DATE: 2011.02.21 (Created 2007.07.07) // DATE: 2016.01.15 // DATE: 2016.01.19 (Created 2006.12.21, modified 2011.05.06) def("date_value", CharacterParser.digit().times(4).flatten().trim(CharacterParser.of('.')) .map((String value) -> Integer.parseInt(value)) .seq(CharacterParser.digit().times(2).flatten().trim(CharacterParser.of('.')) .map((String value) -> Integer.parseInt(value))) .seq(CharacterParser.digit().times(2).flatten().map((String value) -> Integer.parseInt(value))) .map((List<Integer> value) -> { return LocalDate.of(value.get(0), value.get(1), value.get(2)); })); def("date", StringParser.of("DATE").seq(ref("tagsep")).seq(ref("date_value")) .seq(ref("date_value").trim(StringParser.of(" (Created "), StringParser.of(", modified ")) .seq(ref("date_value").trim(CharacterParser.none(), CharacterParser.of(')'))) .or(ref("date_value").trim(StringParser.of(" (Created "), CharacterParser.of(')'))) .optional()) .seq(Token.NEWLINE_PARSER).map((List<?> value) -> { //System.out.println(value); callback.DATE((LocalDate) value.get(2)); return value; })); // 2.1.4 AUTHORS // Authors and Affiliations of MassBank Record. Mandatory // Example // AUTHORS: Akimoto N, Grad Sch Pharm Sci, Kyoto Univ and Maoka T, Res Inst Prod Dev. // Only single-byte characters are allowed. For example, is not allowed. def("authors", StringParser.of("AUTHORS").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.AUTHORS(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.1.5 LICENSE // License of MassBank Record. Mandatory // Example // LICENSE: CC BY // TODO fix format doc def("license", StringParser.of("LICENSE").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.LICENSE(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.1.6 COPYRIGHT // Copyright of MassBank Record. Optional // Example // COPYRIGHT: Keio University def("copyright", StringParser.of("COPYRIGHT").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.COPYRIGHT(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.1.7 PUBLICATION // Reference of the Mass Spectral Data. Optional // Example // PUBLICATION: Iida T, Tamura T, et al, J Lipid Res. 29, 165-71 (1988). [PMID: 3367086] // Citation with PubMed ID is recommended. def("publication", StringParser.of("PUBLICATION").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.PUBLICATION(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.1.8 COMMENT // Comments. Optional and Iterative // In MassBank, COMMENT fields are often used to show the relations of the present record with other MassBank // records and with data files. In these cases, the terms in brackets [ and ] are reserved for the comments // specific to the following five examples. // Example 1 // COMMENT: This record is a MS3 spectrum. Link to the MS2 spectrum is added in the following comment field. // COMMENT: [MS2] KO008089 // Example 2 // COMMENT: This record was generated by merging the following three MassBank records. // COMMENT: [Merging] KO006229 Tiglate; ESI-QTOF; MS2; CE:10 V [M-H]-. // COMMENT: [Merging] KO006230 Tiglate; ESI-QTOF; MS2; CE:20 V [M-H]-. // COMMENT: [Merging] KO006231 Tiglate; ESI-QTOF; MS2; CE:30 V [M-H]-. // Example 3 // COMMENT: This record was merged into a MassBank record, KOX00012, with other records. // COMMENT: [Merged] KOX00012 // Example 4 // COMMENT: Analytical conditions of LC-MS were described in separate files. // COMMENT: [Mass spectrometry] ms1.txt // COMMENT: [Chromatography] lc1.txt. // Example 5 // COMMENT: Profile spectrum of this record is given as a JPEG file. // COMMENT: [Profile] CA000185.jpg def("comment", StringParser.of("COMMENT").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()) .seq(Token.NEWLINE_PARSER).pick(3).plus().map((List<String> value) -> { callback.COMMENT(value); return value; })); // 2.2.1 CH$NAME // Name of the Chemical Compound Analyzed. Mandatory and Iterative // Example // CH$NAME: D-Tartaric acid // CH$NAME: (2S,3S)-Tartaric acid // No prosthetic molecule of adducts (HCl, H2SO3, H2O, etc), conjugate ions (Chloride, etc) , and // protecting groups (TMS, etc.) is included. // Chemical names which are listed in the compound list are recommended. Synonyms could be added. // If chemical compound is a stereoisomer, stereochemistry should be indicated. // TODO no ';' in CH$NAME def("ch_name_value", CharacterParser.word().or(CharacterParser.anyOf("-+, ()[]{}/.:$^'`_*?<>#;")) .plusLazy(ref("valuesep").or(Token.NEWLINE_PARSER)).flatten()); def("ch_name", StringParser.of("CH$NAME").seq(ref("tagsep")).seq(ref("ch_name_value")) .seq(Token.NEWLINE_PARSER).pick(2).plus().map((List<String> value) -> { //System.out.println(value); callback.CH_NAME(value); return value; })); // 2.2.2 CH$COMPOUND_CLASS // Category of Chemical Compound. Mandatory // Example // CH$COMPOUND_CLASS: Natural Product; Carotenoid; Terpenoid; Lipid // Either Natural Product or Non-Natural Product should be precedes the other class names . def("ch_compound_class", StringParser.of("CH$COMPOUND_CLASS").seq(ref("tagsep")) .seq(CharacterParser.word().or(CharacterParser.anyOf("-+,()[]{}/.:$^'`_*?<> ")).plus().flatten()) .seq(ref("valuesep").seq( CharacterParser.word().or(CharacterParser.anyOf("-+,()[]{}/.:$^'`_*?<> ")).plus().flatten()) .pick(1).star()) .seq(Token.NEWLINE_PARSER).map((List<?> value) -> { @SuppressWarnings("unchecked") List<String> list = (List<String>) value.get(3); list.add(0, (String) value.get(2)); callback.CH_COMPOUND_CLASS(list); return value; })); // 2.2.3 CH$FORMULA // Molecular Formula of Chemical Compound. Mandatory // Example // CH$FORMULA: C9H10ClNO3 // It follows the Hill's System. // No prosthetic molecule is included (see 2.2.1 CH$NAME). // Molecular formulae of derivatives by chemical modification with TMS, etc. should be given in the MS$FOCUSED_ION: DERIVATIVE_FORM (2.5.1) field. def("ch_formula", StringParser.of("CH$FORMULA").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { IMolecularFormula m = MolecularFormulaManipulator.getMolecularFormula((String) value, DefaultChemObjectBuilder.getInstance()); callback.CH_FORMULA(m); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value.toString()); // return value; // }) ); // 2.2.4 CH$EXACT_MASS // Monoisotopic Mass of Chemical Compound. Mandatory // Example // CH$EXACT_MASS: 430.38108 // A value with 5 digits after the decimal point is recommended. def("number", digit().plus().seq(CharacterParser.of('.').seq(digit().plus()).optional()) .seq(CharacterParser.anyOf("eE").seq(digit().plus()).optional()).flatten()); def("ch_exact_mass", StringParser.of("CH$EXACT_MASS").seq(ref("tagsep")).seq(ref("number").map((String value) -> { Double d = Double.parseDouble(value); callback.CH_EXACT_MASS(d); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value.toString()); // return value; // }) ); // 2.2.5 CH$SMILES * // SMILES String. Mandatory // Example // CH$SMILES: NCC(O)=O // Isomeric SMILES but not a canonical one. def("ch_smiles", StringParser.of("CH$SMILES").seq(ref("tagsep")) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten() // call a Continuation Parser to validate content of SMILES string .callCC((Function<Context, Result> continuation, Context context) -> { Result r = continuation.apply(context); if (r.isSuccess()) { try { if (r.get().equals("N/A")) callback.CH_SMILES(new AtomContainer()); else callback.CH_SMILES( new SmilesParser(DefaultChemObjectBuilder.getInstance()) .parseSmiles(r.get())); } catch (InvalidSmilesException e) { return r = context.failure( "Can not parse SMILES string in \"CH$SMILES\" field.\nError: " + e.getMessage() + " for " + r.get()); } } return r; })) .seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value.toString()); // return value; // }) ); // 2.2.6 CH$IUPAC * // IUPAC International Chemical Identifier (InChI Code). Mandatory // Example // CH$IUPAC: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) // Not IUPAC name. def("ch_iupac", StringParser.of("CH$IUPAC").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten() // call a Continuation Parser to validate content of InChi string .callCC((Function<Context, Result> continuation, Context context) -> { Result r = continuation.apply(context); if (r.isSuccess()) { try { if (r.get().equals("N/A")) callback.CH_IUPAC(new AtomContainer()); else { // Get InChIToStructure InChIToStructure intostruct = InChIGeneratorFactory.getInstance() .getInChIToStructure(r.get(), DefaultChemObjectBuilder.getInstance()); INCHI_RET ret = intostruct.getReturnStatus(); if (ret == INCHI_RET.WARNING) { // Structure generated, but with warning message System.out.println("InChI warning: " + intostruct.getMessage()); System.out.println(callback.ACCESSION()); } else if (ret != INCHI_RET.OKAY) { // Structure generation failed return context.failure( "Can not parse INCHI string in \"CH$IUPAC\" field. Structure generation failed: " + ret.toString() + " [" + intostruct.getMessage() + "] for " + r.get()); } IAtomContainer m = intostruct.getAtomContainer(); callback.CH_IUPAC(m); } } catch (CDKException e) { return context .failure("\"Can not parse INCHI string in \"CH$IUPAC\" field."); } } return r; })) .seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value.toString()); // return value; // }) ); // TODO no record implements CH$CDK_DEPICT // 2.2.7 CH$CDK_DEPICT // 2.2.8 CH$LINK: subtag identifier // Identifier and Link of Chemical Compound to External Databases. // Optional and Iterative // Example // CH$LINK: CAS 56-40-6 // CH$LINK: COMPTOX DTXSID50274017 // CH$LINK: INCHIKEY UFFBMTHBGFGIHF-UHFFFAOYSA-N // CH$LINK: KEGG C00037 // CH$LINK: PUBCHEM SID: 11916 CID:182232 // CH$LINK fields should be arranged by the alphabetical order of database names. def("ch_link_subtag", StringParser.of("CAS ").or(StringParser.of("CAYMAN ")).or(StringParser.of("CHEBI ")) .or(StringParser.of("CHEMPDB ")).or(StringParser.of("CHEMSPIDER ")).or(StringParser.of("COMPTOX ")) .or(StringParser.of("HMDB ")).or(StringParser.of("INCHIKEY ")).or(StringParser.of("KAPPAVIEW ")) .or(StringParser.of("KEGG ")).or(StringParser.of("KNAPSACK ")).or(StringParser.of("LIPIDBANK ")) .or(StringParser.of("LIPIDMAPS ")).or(StringParser.of("NIKKAJI ")).or(StringParser.of("PUBCHEM "))); def("ch_link", StringParser.of("CH$LINK").seq(ref("tagsep")).seq(ref("ch_link_subtag")) .seq(Token.NEWLINE_PARSER.not()).pick(2) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()).map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0).plus().map((List<Pair<String, String>> value) -> { // System.out.println(value); callback.CH_LINK(value); return value; })); // 2.3.1 SP$SCIENTIFIC_NAME // Scientific Name of Biological Species, from Which Sample was Prepared. Optional // Example // SP$SCIENTIFIC_NAME: Mus musculus def("sp_scientific_name", StringParser.of("SP$SCIENTIFIC_NAME").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.SP_SCIENTIFIC_NAME(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.3.2 SP$LINEAGE // Evolutionary lineage of the species, from which the sample was prepared. Optional // Example: SP$LINEAGE: cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus def("sp_lineage", StringParser.of("SP$LINEAGE").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.SP_LINEAGE(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.3.3 SP$LINK subtag identifier // Identifier of Biological Species in External Databases. Optional and iterative // Example // SP$LINK: NCBI-TAXONOMY 10090 def("sp_link", StringParser.of("SP$LINK").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(CharacterParser.whitespace()).flatten()) .seq(CharacterParser.whitespace()).pick(3) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()).map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0).plus().map((List<Pair<String, String>> value) -> { //System.out.println(value); callback.SP_LINK(value); return value; })); // 2.3.4 SP$SAMPLE // Tissue or Cell, from which Sample was Prepared. Optional and iterative // Example // SP$SAMPLE: Liver extracts def("sp_sample", StringParser.of("SP$SAMPLE").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()) .seq(Token.NEWLINE_PARSER).pick(3).plus().map((List<String> value) -> { //System.out.println(value); callback.SP_SAMPLE(value); return value; })); // 2.4.1 AC$INSTRUMENT // Commercial Name and Model of Chromatographic Separation Instrument, // if any were coupled, and Mass Spectrometer and Manufacturer. Mandatory // Example: AC$INSTRUMENT: LC-10ADVPmicro HPLC, Shimadzu; LTQ Orbitrap, Thermo Electron. // Cross-reference to mzOntology: Instrument model [MS:1000031] All the instruments // are given together in a single line. This record is not iterative. def("ac_instrument", StringParser.of("AC$INSTRUMENT").seq(ref("tagsep")).seq(Token.NEWLINE_PARSER.not()) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.AC_INSTRUMENT(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.4.2 AC$INSTRUMENT_TYPE // General Type of Instrument. Mandatory // Example // AC$INSTRUMENT_TYPE: LC-ESI-QTOF // Format is: // (Separation tool type-)Ionization method-Ion analyzer type(Ion analyzer type). // Separation tool types are CE, GC, LC. // Ionization methods are APCI, APPI, EI, ESI, FAB, MALDI. // Ion analyzer types are B, E, FT, IT, Q, TOF. // In tandem mass analyzers, no is inserted between ion analyzers. // FT includes FTICR and other type analyzers using FT, such as Orbitrap(R). // IT comprises quadrupole ion trap analyzers such as 3D ion trap and linear ion trap. // Other examples of AC$INSTRUMENT_TYPE data are as follows. // ESI-QQ // ESI-QTOF // GC-EI-EB // LC-ESI-ITFT // Cross-reference to mzOntology: Ionization methods [MS:1000008]; APCI [MS:1000070]; APPI [MS:1000382]; EI [MS:1000389]; ESI [MS:1000073]; B [MS:1000080]; IT [MS:1000264], Q [MS:1000081], TOF [MS:1000084]. def("ac_instrument_type_sep", StringParser.of("CE").or(StringParser.of("GC")).or(StringParser.of("LC")) .seq(CharacterParser.of('-')).pick(0)); def("ac_instrument_type_ionisation", StringParser.of("APCI").or(StringParser.of("APPI")).or(StringParser.of("EI")) .or(StringParser.of("ESI")).or(StringParser.of("FAB")).or(StringParser.of("MALDI")) .or(StringParser.of("FD")).or(StringParser.of("CI")).or(StringParser.of("FI")) .seq(CharacterParser.of('-')).pick(0)); def("ac_instrument_type_analyzer", StringParser.of("B").or(StringParser.of("E")).or(StringParser.of("FT")) .or(StringParser.of("IT")).or(StringParser.of("Q")).or(StringParser.of("TOF"))); def("ac_instrument_type_value", ref("ac_instrument_type_sep").optional() .seq(ref("ac_instrument_type_ionisation")).seq(ref("ac_instrument_type_analyzer").plus())); def("ac_instrument_type", StringParser.of("AC$INSTRUMENT_TYPE").seq(ref("tagsep")) .seq(ref("ac_instrument_type_value").map((List<?> value) -> { // System.out.println(value); List<String> list = new ArrayList<String>(); for (int idx = 0; idx < value.size(); idx++) { if (value.get(idx) instanceof String) // string list.add((String) value.get(idx)); if (value.get(idx) instanceof List) // list of strings list.addAll((List<String>) value.get(idx)); } String ac_instrument_type_konkat = String.join("-", list.toArray(new String[list.size()])); callback.AC_INSTRUMENT_TYPE(ac_instrument_type_konkat); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.4.3 AC$MASS_SPECTROMETRY: MS_TYPE // Data Type. Mandatory // Example // AC$MASS_SPECTROMETRY: MS_TYPE MS2 // Either of MS, MS2, MS3, MS4, , , . // Brief definition of terms used in MS_TYPE // MS2 is 1st generation product ion spectrum(of MS) // MS3 is 2nd generation product ion spectrum(of MS) // MS2 is the precursor ion spectrum of MS3 // IUPAC Recommendations 2006 (http://old.iupac.org/reports/provisional/abstract06/murray_prs.pdf) def("ac_mass_spectrometry_ms_type_value", StringParser.of("MS4").or(StringParser.of("MS3")) .or(StringParser.of("MS2")).or(StringParser.of("MS"))); def("ac_mass_spectrometry_ms_type", StringParser.of("AC$MASS_SPECTROMETRY").seq(ref("tagsep")).seq(StringParser.of("MS_TYPE ")) .seq(ref("ac_mass_spectrometry_ms_type_value").map((String value) -> { callback.AC_MASS_SPECTROMETRY_MS_TYPE(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.4.4 AC$MASS_SPECTROMETRY: ION_MODE // Polarity of Ion Detection. Mandatory // Example: AC$MASS_SPECTROMETRY: ION_MODE POSITIVE // Either of POSITIVE or NEGATIVE is allowed. Cross-reference to mzOntology: POSITIVE [MS:1000030] // or NEGATIVE [MS:1000129]; Ion mode [MS:1000465] def("ac_mass_spectrometry_ion_mode_value", StringParser.of("POSITIVE").or(StringParser.of("NEGATIVE"))); def("ac_mass_spectrometry_ion_mode", StringParser.of("AC$MASS_SPECTROMETRY").seq(ref("tagsep")).seq(StringParser.of("ION_MODE ")) .seq(ref("ac_mass_spectrometry_ion_mode_value").map((String value) -> { callback.AC_MASS_SPECTROMETRY_ION_MODE(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.4.5 AC$MASS_SPECTROMETRY: subtag Description // Other Experimental Methods and Conditions of Mass Spectrometry. Optional // Description is a list of numerical values with/without unit or a sentence. // AC$MASS_SPECTROMETRY fields should be arranged by the alphabetical order of subtag names. // 2.4.5 Subtag: COLLISION_ENERGY // Collision Energy for Dissociation. // Example 1: AC$MASS_SPECTROMETRY: COLLISION_ENERGY 20 kV // Example 2: AC$MASS_SPECTROMETRY: COLLISION_ENERGY Ramp 10-50 kV // 2.4.5 Subtag: COLLISION_GAS // Name of Collision Gas. // Example: AC$MASS_SPECTROMETRY: COLLISION_GAS N2 // Cross-reference to mzOntology: Collision gas [MS:1000419] // 2.4.5 Subtag: DATE // Date of Analysis. // 2.4.5 Subtag: DESOLVATION_GAS_FLOW // Flow Rate of Desolvation Gas. // Example: AC$MASS_SPECTROMETRY: DESOLVATION_GAS_FLOW 600.0 l/h // 2.4.5 Subtag: DESOLVATION_TEMPERATURE // Temperature of Desolvation Gas. // Example: AC$MASS_SPECTROMETRY: DESOLVATION_TEMPERATURE 400 C // 2.4.5 Subtag: IONIZATION_ENERGY // Energy of Ionization. // Example: AC$MASS_SPECTROMETRY: IONIZATION_ENERGY 70 eV // 2.4.5 Subtag: LASER // Desorption /Ionization Conditions in MALDI. // Example: AC$MASS_SPECTROMETRY: LASER 337 nm nitrogen laser, 20 Hz, 10 nsec // 2.4.5 Subtag: MATRIX // Matrix Used in MALDI and FAB. // Example: AC$MASS_SPECTROMETRY: MATRIX 1-2 uL m-NBA // 2.4.5. Subtag : MASS_ACCURACY // Relative Mass Accuracy. // Example: AC$MASS_SPECTROMETRY: MASS_ACCURACY 50 ppm over a range of about m/z 100-1000 // 2.4.5 Subtag: REAGENT_GAS // Name of Reagent Gas. // Example: AC$MASS_SPECTROMETRY: REAGENT_GAS ammonia // 2.4.5 Subtag: SCANNING // Scan Cycle and Range. // Example: AC$MASS_SPECTROMETRY: SCANNING 0.2 sec/scan (m/z 50-500) def("ac_mass_spectrometry_subtag", StringParser.of("ACTIVATION_PARAMETER ").or(StringParser.of("ACTIVATION_TIME ")) .or(StringParser.of("ATOM_GUN_CURRENT ")).or(StringParser.of("AUTOMATIC_GAIN_CONTROL ")) .or(StringParser.of("BOMBARDMENT ")).or(StringParser.of("CAPILLARY_TEMPERATURE ")) .or(StringParser.of("CAPILLARY_VOLTAGE ")) .or(StringParser.of("CDL_SIDE_OCTOPOLES_BIAS_VOLTAGE ")) .or(StringParser.of("CDL_TEMPERATURE ")).or(StringParser.of("COLLISION_ENERGY ")) .or(StringParser.of("COLLISION_GAS ")).or(StringParser.of("DATAFORMAT ")) .or(StringParser.of("DATE ")).or(StringParser.of("DESOLVATION_GAS_FLOW ")) .or(StringParser.of("DESOLVATION_TEMPERATURE ")).or(StringParser.of("DRY_GAS_FLOW ")) .or(StringParser.of("DRY_GAS_TEMP ")).or(StringParser.of("FRAGMENTATION_METHOD ")) .or(StringParser.of("FRAGMENTATION_MODE ")).or(StringParser.of("FRAGMENT_VOLTAGE ")) .or(StringParser.of("GAS_PRESSURE ")).or(StringParser.of("HELIUM_FLOW ")) .or(StringParser.of("INTERFACE_VOLTAGE ")).or(StringParser.of("IONIZATION ")) .or(StringParser.of("IONIZATION_ENERGY ")).or(StringParser.of("IONIZATION_POTENTIAL ")) .or(StringParser.of("IONIZATION_VOLTAGE ")).or(StringParser.of("ION_GUIDE_PEAK_VOLTAGE ")) .or(StringParser.of("ION_GUIDE_VOLTAGE ")).or(StringParser.of("ION_SOURCE_TEMPERATURE ")) .or(StringParser.of("ION_SPRAY_VOLTAGE ")).or(StringParser.of("ISOLATION_WIDTH ")) .or(StringParser.of("IT_SIDE_OCTOPOLES_BIAS_VOLTAGE ")).or(StringParser.of("LASER ")) .or(StringParser.of("LENS_VOLTAGE ")).or(StringParser.of("MASS_ACCURACY ")) .or(StringParser.of("MASS_RANGE_M/Z ")).or(StringParser.of("MATRIX ")) .or(StringParser.of("MASS_ACCURACY ")).or(StringParser.of("NEBULIZER ")) .or(StringParser.of("NEBULIZING_GAS ")).or(StringParser.of("NEEDLE_VOLTAGE ")) .or(StringParser.of("OCTPOLE_VOLTAGE ")).or(StringParser.of("ORIFICE_TEMP ")) .or(StringParser.of("ORIFICE_TEMPERATURE ")).or(StringParser.of("ORIFICE_VOLTAGE ")) .or(StringParser.of("PEAK_WIDTH ")).or(StringParser.of("PROBE_TIP ")) .or(StringParser.of("REAGENT_GAS ")).or(StringParser.of("RESOLUTION ")) .or(StringParser.of("RESOLUTION_SETTING ")).or(StringParser.of("RING_VOLTAGE ")) .or(StringParser.of("SAMPLE_DRIPPING ")).or(StringParser.of("SCANNING ")) .or(StringParser.of("SCANNING_CYCLE ")).or(StringParser.of("SCANNING_RANGE ")) .or(StringParser.of("SCAN_RANGE_M/Z ")).or(StringParser.of("SKIMMER_VOLTAGE ")) .or(StringParser.of("SOURCE_TEMPERATURE ")).or(StringParser.of("SPRAY_CURRENT ")) .or(StringParser.of("SPRAY_VOLTAGE ")).or(StringParser.of("TUBE_LENS_VOLTAGE "))); def("ac_mass_spectrometry", StringParser.of("AC$MASS_SPECTROMETRY").seq(ref("tagsep")) .seq(ref("ac_mass_spectrometry_subtag")).seq(Token.NEWLINE_PARSER.not()).pick(2) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()).map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0).plus().map((List<Pair<String, String>> value) -> { //System.out.println(value); callback.AC_MASS_SPECTROMETRY(value); return value; })); // 2.4.6 AC$CHROMATOGRAPHY: subtag Description // Experimental Method and Conditions of Chromatographic Separation. Optional // AC$CHROMATOGRAPHY fields should be arranged by the alphabetical order of subtag names. // 2.4.6 Subtag: CAPILLARY_VOLTAGE // Voltage Applied to Capillary Electrophoresis or Voltage Applied to the Interface of LC-MS. // Example: AC$CHROMATOGRAPHY: CAPILLARY_VOLTAGE 4 kV // 2.4.6 Subtag: COLUMN_NAME // Commercial Name of Chromatography Column and Manufacture. // Example of LC: AC$CHROMATOGRAPHY: COLUMN_NAME Acquity UPLC BEH C18 2.1 by 50 mm (Waters, Milford, MA, USA) Example of CE: AC$CHROMATOGRAPHY: COLUMN_NAME Fused silica capillary id=50 um L=100 cm (HMT, Tsuruoka, Japan) // 2.4.6 Subtag: COLUMN_TEMPERATURE // Column Temperature. // Example: AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE 40 C // 2.4.6 Subtag: FLOW_GRADIENT // Gradient of Elusion Solutions. // Example: AC$CHROMATOGRAPHY: FLOW_GRADIENT 0/100 at 0 min, 15/85 at 5 min, 21/79 at 20 min, 90/10 at 24 min, 95/5 at 26 min, 0/100, 30 min // 2.4.6 Subtag: FLOW_RATE // Flow Rate of Migration Phase. // Example: AC$CHROMATOGRAPHY: FLOW_RATE 0.25 ml/min // 2.4.6 Subtag: RETENTION_TIME // Retention Time on Chromatography. // Example: AC$CHROMATOGRAPHY: RETENTION_TIME 40.3 min // Cross-reference to mzOntology: Retention time [MS:1000016] // 2.4.6 Subtag: SOLVENT // Chemical Composition of Buffer Solution. Iterative // Example: // AC$CHROMATOGRAPHY: SOLVENT A acetonitrile-methanol-water (19:19:2) with 0.1% acetic acid // AC$CHROMATOGRAPHY: SOLVENT B 2-propanol with 0.1% acetic acid and 0.1% ammonium hydroxide (28%) // 2.4.6 Subtag: NAPS_RTI // N-alkylpyrinium-3-sulfonate based retention time index. // Reference: http://nparc.cisti-icist.nrc-cnrc.gc.ca/eng/view/object/?id=b4db3589-ae0b-497e-af03-264785d7922f // Example: AC$CHROMATOGRAPHY: NAPS_RTI 100 def("ac_chromatography_subtag", StringParser.of("ANALYTICAL_TIME ").or(StringParser.of("CAPILLARY_VOLTAGE ")) .or(StringParser.of("COLUMN_NAME ")).or(StringParser.of("COLUMN_PRESSURE ")) .or(StringParser.of("COLUMN_TEMPERATURE ")).or(StringParser.of("FLOW_GRADIENT ")) .or(StringParser.of("FLOW_RATE ")).or(StringParser.of("INJECTION_TEMPERATURE ")) .or(StringParser.of("INTERNAL_STANDARD ")).or(StringParser.of("INTERNAL_STANDARD_MT ")) .or(StringParser.of("NAPS_RTI ")).or(StringParser.of("MIGRATION_TIME ")) .or(StringParser.of("OVEN_TEMPERATURE ")).or(StringParser.of("PRECONDITIONING ")) .or(StringParser.of("RETENTION_INDEX ")).or(StringParser.of("RETENTION_TIME ")) .or(StringParser.of("RUNNING_BUFFER ")).or(StringParser.of("RUNNING_VOLTAGE ")) .or(StringParser.of("SAMPLE_INJECTION ")).or(StringParser.of("SAMPLING_CONE ")) .or(StringParser.of("SHEATH_LIQUID ")).or(StringParser.of("SOLVENT ")) .or(StringParser.of("TIME_PROGRAM ")).or(StringParser.of("TRANSFARLINE_TEMPERATURE ")) .or(StringParser.of("WASHING_BUFFER "))); def("ac_chromatography", StringParser.of("AC$CHROMATOGRAPHY").seq(ref("tagsep")) .seq(ref("ac_chromatography_subtag")).seq(Token.NEWLINE_PARSER.not()).pick(2) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()).map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0).plus().map((List<Pair<String, String>> value) -> { //System.out.println(value); callback.AC_CHROMATOGRAPHY(value); return value; })); // 2.5.1 MS$FOCUSED_ION: subtag Description // Information of Precursor or Molecular Ion. Optional // MS$FOCUSED_ION fields should be arranged by the alphabetical order of subtag names. // 2.5.1 Subtag: BASE_PEAK // m/z of Base Peak. // Example: MS$FOCUSED_ION: BASE_PEAK 73 // 2.5.1 Subtag: DERIVATIVE_FORM // Molecular Formula of Derivative for GC-MS. // Example // MS$FOCUSED_ION: DERIVATIVE_FORM C19H42O5Si4 // MS$FOCUSED_ION: DERIVATIVE_FORM C{9+3*n}H{16+8*n}NO5Si{n} // 2.5.1 Subtag: DERIVATIVE_MASS // Exact Mass of Derivative for GC-MS. // Example: MS$FOCUSED_ION: DERIVATIVE_MASS 462.21093 // 2.5.1 Subtag: DERIVATIVE_TYPE // Type of Derivative for GC-MS. // Example: MS$FOCUSED_ION: DERIVATIVE_TYPE 4 TMS // 2.5.1 Subtag: ION_TYPE // Type of Focused Ion. // Example: MS$FOCUSED_ION: ION_TYPE [M+H]+ // Types currently used in MassBank are [M]+, [M]+*, [M+H]+, [2M+H]+, [M+Na]+, [M-H+Na]+, [2M+Na]+, [M+2Na-H]+, [(M+NH3)+H]+, [M+H-H2O]+, [M+H-C6H10O4]+, [M+H-C6H10O5]+, [M]-, [M-H]-, [M-2H]-, [M-2H+H2O]-, [M-H+OH]-, [2M-H]-, [M+HCOO-]-, [(M+CH3COOH)-H]-, [2M-H-CO2]- and [2M-H-C6H10O5]-. // 2.5.1 Subtag: PRECURSOR_M/Z // m/z of Precursor Ion in MSn spectrum. // Example: MS$FOCUSED_ION: PRECURSOR_M/Z 289.07123 // Calculated exact mass is preferred to the measured accurate mass of the precursor ion. Cross-reference to mzOntology: precursor m/z [MS:1000504] // 2.5.1 Subtag: PRECURSOR_TYPE // Type of Precursor Ion in MSn. // Example: MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]- // Types currently used in MassBank are [M]+, [M]+*, [M+H]+, [2M+H]+, [M+Na]+, // [M-H+Na]+, [2M+Na]+, [M+2Na-H]+, [(M+NH3)+H]+, [M+H-H2O]+, [M+H-C6H10O4]+, // [M+H-C6H10O5]+, [M]-, [M-H]-, [M-2H]-, [M-2H+H2O]-, [M-H+OH]-, [2M-H]-, [M+HCOO-]-, // [(M+CH3COOH)-H]-, [2M-H-CO2]- and [2M-H-C6H10O5]-. Cross-reference to mzOntology: Precursor type [MS: 1000792] def("precursor_type", StringParser.of("[M]+*").or(StringParser.of("[M]++")).or(StringParser.of("[M]+")) .or(StringParser.of("[M+H]+,[M-H2O+H]+")).or(StringParser.of("[M+H]+")) .or(StringParser.of("[M+2H]++")).or(StringParser.of("[2M+H]+")).or(StringParser.of("[M+Li]+*")) .or(StringParser.of("[M-H+Li]+*")).or(StringParser.of("[M+Na]+*")).or(StringParser.of("[M-H+Na]+*")) .or(StringParser.of("[M+Na]+")).or(StringParser.of("[M+K]+")).or(StringParser.of("[M+K]+")) .or(StringParser.of("[M-H2O+H]+,[M-2H2O+H]+")).or(StringParser.of("[M-H2O+H]+")) .or(StringParser.of("[M+15]+")).or(StringParser.of("[M-H+Na]+")).or(StringParser.of("[2M+Na]+")) .or(StringParser.of("[M+2Na-H]+")).or(StringParser.of("[(M+NH3)+H]+")) .or(StringParser.of("[M+NH4]+")).or(StringParser.of("[M+H-H2O]+")) .or(StringParser.of("[M-2H2O+H]+,[M-H2O+H]+")).or(StringParser.of("[M-2H2O+H]+")) .or(StringParser.of("[M+H-C6H10O4]+")).or(StringParser.of("[M+H-C6H10O5]+")) .or(StringParser.of("[M+H-C12H20O9]+")).or(StringParser.of("[M-H]+")).or(StringParser.of("[M-OH]+")) .or(StringParser.of("[M-3]+,[M-H2O+H]+")) .or(StringParser.of("[M]-")).or(StringParser.of("[M-H]-/[M-Ser]-")).or(StringParser.of("[M-H]-")) .or(StringParser.of("[M-2H]--")).or(StringParser.of("[M-2H]-")).or(StringParser.of("[M+K-2H]-")) .or(StringParser.of("[M-2H+H2O]-")).or(StringParser.of("[M-H+OH]-")).or(StringParser.of("[M-CH3]-")) .or(StringParser.of("[2M-H]-")).or(StringParser.of("[M+HCOO-]-")).or(StringParser.of("[M-C2H3O]-")) .or(StringParser.of("[M-C3H7O2]-")).or(StringParser.of("[M-H-C6H10O5]-")) .or(StringParser.of("[M-H-CO2]-")).or(StringParser.of("[(M+CH3COOH)-H]-")) .or(StringParser.of("[M+CH3COO]-/[M-CH3]-")).or(StringParser.of("[M+CH3COO]-")) .or(StringParser.of("[2M-H-CO2]-")).or(StringParser.of("[2M-H-C6H10O5]-")) .or(StringParser.of("[M-H-CO2-2HF]-"))); def("ms_focused_ion_subtag", StringParser.of("BASE_PEAK ").or(StringParser.of("DERIVATIVE_FORM ")) .or(StringParser.of("DERIVATIVE_MASS ")).or(StringParser.of("DERIVATIVE_TYPE ")) .or(StringParser.of("FULL_SCAN_FRAGMENT_ION_PEAK ")).or(StringParser.of("PRECURSOR_M/Z "))); def("ms_focused_ion", StringParser.of("MS$FOCUSED_ION").seq(ref("tagsep")).seq(StringParser.of("ION_TYPE ")) .pick(2).seq(ref("precursor_type")).map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0) .or(StringParser.of("MS$FOCUSED_ION").seq(ref("tagsep")).seq(StringParser.of("PRECURSOR_TYPE ")) .pick(2).seq(ref("precursor_type")).map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0)) .or(StringParser.of("MS$FOCUSED_ION").seq(ref("tagsep")).seq(ref("ms_focused_ion_subtag")) .seq(Token.NEWLINE_PARSER.not()).pick(2) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()) .map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0)) .plus().map((List<Pair<String, String>> value) -> { //System.out.println(value); callback.MS_FOCUSED_ION(value); return value; })); // 2.5.3 MS$DATA_PROCESSING: subtag // Data Processing Method of Peak Detection. Optional // MS$DATA_PROCESSING fields should be arranged by the alphabetical order of subtag names. Cross-reference to mzOntology: Data processing [MS:1000543] // 2.5.3 Subtag: FIND_PEAK // Peak Detection. // Example: MS$DATA_PROCESSING: FIND_PEAK convexity search; threshold = 9.1 // 2.5.3 Subtag: WHOLE // Whole Process in Single Method / Software. // Example: MS$DATA_PROCESSING: WHOLE Analyst 1.4.2 def("ms_data_processing_subtag", StringParser.of("CHARGE_DECONVOLUTION ").or(StringParser.of("DEPROFILE ")) .or(StringParser.of("FIND_PEAK ")).or(StringParser.of("IGNORE ")) .or(StringParser.of("INTENSITY CUTOFF ")).or(StringParser.of("REANALYZE ")) .or(StringParser.of("RECALIBRATE ")).or(StringParser.of("RELATIVE_M/Z ")) .or(StringParser.of("REMOVE_PEAK ")).or(StringParser.of("WHOLE "))); def("ms_data_processing", StringParser.of("MS$DATA_PROCESSING").seq(ref("tagsep")) .seq(ref("ms_data_processing_subtag")).seq(Token.NEWLINE_PARSER.not()).pick(2) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten()).map((List<String> value) -> { return Pair.of(value.get(0).trim(), value.get(1)); }).seq(Token.NEWLINE_PARSER).pick(0).plus() .map((List<Pair<String, String>> value) -> { //System.out.println(value); callback.MS_DATA_PROCESSING(value); return value; })); // 2.6.1 PK$SPLASH // Hashed Identifier of Mass Spectra. Mandatory and Single Line Information // Example: PK$SPLASH: splash10-z200000000-87bb3c76b8e5f33dd07f def("pk_splash", StringParser.of("PK$SPLASH").seq(ref("tagsep")) .seq(CharacterParser.any().plusLazy(Token.NEWLINE_PARSER).flatten().map((String value) -> { callback.PK_SPLASH(value); return value; })).seq(Token.NEWLINE_PARSER) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); // 2.6.2 PK$ANNOTATION // Chemical Annotation of Peaks with Molecular Formula. Optional and Multiple Line Information // TODO call callback function def("pk_annotation", StringParser.of("PK$ANNOTATION").seq(ref("tagsep")) .seq(CharacterParser.word().or(CharacterParser.anyOf("-+,()[]{}\\/.:$^'`_*?<>=")).plus() .flatten().trim(CharacterParser.of(' ')).plus().map((List<String> value) -> { // System.out.println(value); callback.PK_ANNOTATION_HEADER(value); return value; }).seq(Token.NEWLINE_PARSER)) .seq(StringParser.of(" ") // .map((String value) -> { // //System.out.println(value); // callback.ADD_PK_ANNOTATION_LINE(); // return value; // }) .seq(CharacterParser.word().or(CharacterParser.anyOf("-+,()[]{}\\/.:$^'`_*?<>=")) .plus().flatten().trim(CharacterParser.of(' ')).plus() .map((List<String> value) -> { // System.out.println(value); callback.PK_ANNOTATION_ADD_LINE(value); return value; }).seq(Token.NEWLINE_PARSER) // call a Continuation Parser to validate the count of PK$ANNOTATION items per line .callCC((Function<Context, Result> continuation, Context context) -> { Result r = continuation.apply(context); if (r.isSuccess()) { List<String> pk_annotation_header = callback.PK_ANNOTATION_HEADER(); List<List<String>> pk_annotation = callback.PK_ANNOTATION(); if (pk_annotation_header.size() != pk_annotation .get(pk_annotation.size() - 1).size()) { StringBuilder sb = new StringBuilder(); sb.append( "Incorrect number of fields per PK$ANNOTATION line. "); sb.append(pk_annotation_header.size() + " fields expected, but " + pk_annotation.get(pk_annotation.size() - 1).size() + " fields found.\n"); sb.append("Defined by:\n"); sb.append("PK$ANNOTATION:"); for (String annotation_header_item : callback .PK_ANNOTATION_HEADER()) sb.append(" " + annotation_header_item); System.out.println(sb.toString()); return context.failure(sb.toString()); } } return r; })) .plus())); def("pk_num_peak", StringParser.of("PK$NUM_PEAK").seq(ref("tagsep")) .seq(digit().plus().flatten().map((String value) -> { Integer i = Integer.parseUnsignedInt(value); callback.PK_NUM_PEAK(i); return value; })).seq(Token.NEWLINE_PARSER)); def("pk_peak", StringParser.of("PK$PEAK").seq(ref("tagsep")).seq(StringParser.of("m/z int. rel.int.")) .seq(Token.NEWLINE_PARSER).seq(StringParser.of(" ").seq(ref("number").trim()).pick(1) .seq(ref("number").trim()).seq(ref("number")).map((List<String> value) -> { // System.out.println(value); List<Double> list = new ArrayList<Double>(); for (String val : value) list.add(Double.parseDouble(val)); callback.PK_PEAK_ADD_LINE(list); return value; }).seq(Token.NEWLINE_PARSER).plus()) // call a Continuation Parser to validate the number of peaks in the peaklist .callCC((Function<Context, Result> continuation, Context context) -> { Result r = continuation.apply(context); if (r.isSuccess()) { Integer num_peak = callback.PK_NUM_PEAK(); List<List<Double>> pk_peak = callback.PK_PEAK(); if (pk_peak.size() != num_peak) { StringBuilder sb = new StringBuilder(); sb.append("Incorrect number of peaks in peaklist. "); sb.append(num_peak + " peaks are declared in PK$NUM_PEAK line, but " + pk_peak.size() + " peaks are found.\n"); return context.failure(sb.toString()); } List<Ion> ions = new ArrayList<Ion>(); for (List<Double> peak_line : pk_peak) { ions.add(new Ion(peak_line.get(0), peak_line.get(1))); } Splash splashFactory = SplashFactory.create(); Spectrum spectrum = new SpectrumImpl(ions, SpectraType.MS); String splash_from_peaks = splashFactory.splashIt(spectrum); String splash_from_record = callback.PK_SPLASH(); if (!splash_from_peaks.equals(splash_from_record)) { StringBuilder sb = new StringBuilder(); sb.append( "SPLASH from record file does not match SPLASH calculated from peaklist. "); sb.append(splash_from_record + " defined in record file, but " + splash_from_peaks + " calculated from peaks.\n"); return context.failure(sb.toString()); } } return r; }) // .map((List<?> value) -> { // System.out.println(value); // return value; // }) ); }