public static boolean parsableMAGE_TAB(ResourceLocator file) throws IOException {
AsciiLineReader reader = null;
try {
reader = ParsingUtils.openAsciiReader(file);
String nextLine = null;
// skip first row
reader.readLine();
// check second row for MAGE_TAB identifiers
if ((nextLine = reader.readLine()) != null
&& (nextLine.contains("Reporter REF")
|| nextLine.contains("Composite Element REF")
|| nextLine.contains("Term Source REF")
|| nextLine.contains("CompositeElement REF")
|| nextLine.contains("TermSource REF")
|| nextLine.contains("Coordinates REF"))) {
int count = 0;
// check if this mage_tab data matrix can be parsed by this class
while ((nextLine = reader.readLine()) != null && count < 5) {
nextLine = nextLine.trim();
if (nextLine.startsWith("SNP_A") || nextLine.startsWith("CN_")) {
return true;
}
count++;
}
return false;
}
} finally {
if (reader != null) {
reader.close();
}
}
return false;
}
