Difference between revisions of "rig input"
From irefindex
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=== Using the IRefIndex_digester === | === Using the IRefIndex_digester === | ||
*you require the IRefIndex_digester.jar in your class path) | *you require the IRefIndex_digester.jar in your class path) | ||
| − | + | ||
IRefIndex_digester digetster = new IRefIndex_digester(); | IRefIndex_digester digetster = new IRefIndex_digester(); | ||
String seq = "PQITLWQRPLVTVKIGGQLKEALLDTGEICGHKAIGT"; | String seq = "PQITLWQRPLVTVKIGGQLKEALLDTGEICGHKAIGT"; | ||
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String ROGID_1 = digetster.getROGID(seq, 9606); | String ROGID_1 = digetster.getROGID(seq, 9606); | ||
String ROGID_2 = digetster.getROGID(seq2, 9606); | String ROGID_2 = digetster.getROGID(seq2, 9606); | ||
| − | |||
ArrayList<String> data = new ArrayList<String>(); | ArrayList<String> data = new ArrayList<String>(); | ||
data.add(ROGID_1); | data.add(ROGID_1); | ||
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System.out.println("concat string = "+rig_input); | System.out.println("concat string = "+rig_input); | ||
System.out.println("RIGID = "+digetster.getSeguForWithNum(rig_input)); | System.out.println("RIGID = "+digetster.getSeguForWithNum(rig_input)); | ||
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=== Creating ROGID without IRefIndex_digester === | === Creating ROGID without IRefIndex_digester === | ||
Revision as of 15:31, 17 November 2008
Generating ROGIDs and RIGIDs
The following examples expalins how to generate ROGIDs from primary amino acid sequence and also the methods to sort ROGs before creating RIGIDs
Using the IRefIndex_digester
- you require the IRefIndex_digester.jar in your class path)
IRefIndex_digester digetster = new IRefIndex_digester();
String seq = "PQITLWQRPLVTVKIGGQLKEALLDTGEICGHKAIGT";
String seq2 = "ADDTVLEEMNLPGKWKPKMIGGIGGFIKARQYDQIAI";
String ROGID_1 = digetster.getROGID(seq, 9606);
String ROGID_2 = digetster.getROGID(seq2, 9606);
ArrayList<String> data = new ArrayList<String>();
data.add(ROGID_1);
data.add(ROGID_2);
try {
data = digetster.sortBase64ASCII(data);
} catch (InvalidBase64Exception ex) {
ex.printStackTrace();
}
System.out.println("ROGID of 1 = " + ROGID_1);
System.out.println("ROGID of 1 = " + ROGID_2);
System.out.println("Sorted list = "+data );
String rig_input = "";
for (int i = 0; i < data.size(); i++) {
rig_input = rig_input + data.get(i);
}
System.out.println("concat string = "+rig_input);
System.out.println("RIGID = "+digetster.getSeguForWithNum(rig_input));
