public void onMissingProtein1Column(int lineNumber) { if (parserListener != null) { parserListener.onMissingProtein1Column(lineNumber); } else if (defaultParserListener != null) { defaultParserListener.onSyntaxWarning( new DefaultFileSourceContext(new CsvSourceLocator(lineNumber, -1, -1)), "The protein1 column is missing or empty and it is required."); } }
public void onMismatchBetweenRangePositionsAndProteins( List<CsvRange> rangePositions, List<CsvProtein> proteins) { if (parserListener != null) { parserListener.onMismatchBetweenRangePositionsAndProteins(rangePositions, proteins); } else if (defaultParserListener != null) { defaultParserListener.onSyntaxWarning( !rangePositions.isEmpty() ? rangePositions.iterator().next() : proteins.iterator().next(), "The number of range/linked positions does not match the number of protein identifiers and therefore, will be ignored"); } }
public void onInvalidProteinIdentifierSyntax( String[] identifiers, int lineNumber, int columnNumber) { if (parserListener != null) { parserListener.onInvalidProteinIdentifierSyntax(identifiers, lineNumber, columnNumber); } else if (defaultParserListener != null) { defaultParserListener.onSyntaxWarning( new DefaultFileSourceContext(new CsvSourceLocator(lineNumber, -1, columnNumber)), "The protein1/protein2 columns syntax should be sp|uniprotId|name and if several proteins are provided, the identifiers " + "should be separeted by ';'"); } }
public void onMismatchBetweenPeptideAndLinkedPositions( List<CsvRange> peptidePositions, List<CsvRange> linkedPositions) { if (parserListener != null) { parserListener.onMismatchBetweenPeptideAndLinkedPositions(peptidePositions, linkedPositions); } else if (defaultParserListener != null) { defaultParserListener.onSyntaxWarning( !peptidePositions.isEmpty() ? peptidePositions.iterator().next() : linkedPositions.iterator().next(), "The number of peptide positions does not match the number of linked positions and therefore, will be ignored"); } }