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");
}
}