public BiNGOOntologyDefaultReader(String filename, HashMap synonymHash)
throws IllegalArgumentException, IOException, Exception {
this.filename = filename;
this.synonymHash = synonymHash;
try {
if (filename.trim().startsWith("jar:")) {
BiNGOJarReader reader = new BiNGOJarReader(filename);
reader.read();
fullText = reader.getText();
} else if (filename.trim().startsWith("http://")) {
TextHttpReader reader = new TextHttpReader(filename);
reader.read();
fullText = reader.getText();
} else {
TextFileReader reader = new TextFileReader(filename);
reader.read();
fullText = reader.getText();
}
} catch (IOException e0) {
System.err.println("-- Exception while reading ontology default file " + filename);
System.err.println(e0.getMessage());
throw e0;
// return;
}
this.goMap = new HashMap();
lines = fullText.split("\n");
parseHeader();
parse();
} // ctor
public BiNGOConsortiumAnnotationReader(
String filename,
HashMap synonymHash,
BingoParameters params,
String annotationType,
String curator)
throws IllegalArgumentException, IOException, Exception {
// System.out.println ("AnnotationFlatFileReader on " + filename);
this.filename = filename;
try {
if (filename.trim().startsWith("jar:")) {
BiNGOJarReader reader = new BiNGOJarReader(filename);
reader.read();
fullText = reader.getText();
} else if (filename.trim().startsWith("http://")) {
TextHttpReader reader = new TextHttpReader(filename);
reader.read();
fullText = reader.getText();
} else {
TextFileReader reader = new TextFileReader(filename);
reader.read();
fullText = reader.getText();
}
} catch (IOException e0) {
System.err.println("-- Exception while reading annotation flat file " + filename);
System.err.println(e0.getMessage());
throw e0;
}
this.species = filename;
this.annotationType = annotationType;
this.curator = curator;
this.synonymHash = synonymHash;
this.deleteCodes = params.getDeleteCodes();
lines = fullText.split("\n");
int start = parseHeader();
parse(start);
}