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IDMapperText.java

Timestamp:

08/14/09 21:50:23 (3 years ago)

Author:

jgao

Message:

IDMapperText & IDMapperBiomart driver update,
IDMapperBiomart constructor with mart

Files:

r134	r156
49	49	{
50	50	// parse arguments to determine idsep and dssep
51		// sample: dssep~~:\t,idsep:;,idsep:,~~@file:/localfile.txt
	51	// sample: dssep=\t,idsep=;,idsep=,,transitivity=false@file:/localfile.txt
52	52	// \t represents tab, \@ represents @
53	53	String path = null;
54	54	char[] dssep = null;
55	55	char[] idsep = null;
	56	boolean transitivity = false;
56	57
57	58	int idx = location.indexOf("@");
…	…
81	82
82	83	String config = location.substring(0, idx)+",";
	84	String prefixTran = "transitivity=";
	85	idx = config.indexOf(prefixTran);
	86	String tran = config.substring(idx+prefixTran.length());
	87	if (tran.toLowerCase().startsWith("true")) {
	88	transitivity = true;
	89	} else if (tran.toLowerCase().startsWith("false")) {
	90	transitivity = false;
	91	} else {
	92	throw new IDMapperException(
	93	"transivity can only be true or false");
	94	}
	95
83	96	dssep = parseConfig(config, "dssep");
84	97	idsep = parseConfig(config, "idsep");
…	…
88	101	try
89	102	{
90		return new IDMapperText(new URL(path), dssep, idsep);
	103	return new IDMapperText(new URL(path), dssep, idsep,
	104	transitivity);
91	105	}
92	106	catch (MalformedURLException ex)
…	…
98	112	private char[] parseConfig(String config, String head) {
99	113	Set<Character> delimiters = new HashSet();
100		Pattern p = Pattern.compile(head+":(.\|\\t\|\\@),", Pattern.CASE_INSENSITIVE);
	114	Pattern p = Pattern.compile(head+"=(.\|\\t\|\\@),",
	115	Pattern.CASE_INSENSITIVE);
101	116	Matcher m = p.matcher(config);
102	117	while (m.find()) {