Difference between revisions of "rig input"
From irefindex
(New page: == 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 === U...) |
|||
Line 1: | Line 1: | ||
− | |||
== Generating ROGIDs and RIGIDs == | == 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 | The following examples expalins how to generate ROGIDs from primary amino acid sequence and also the methods to sort ROGs before creating RIGIDs | ||
Line 5: | Line 4: | ||
=== Using the IRefIndex_digester === | === 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)); |
Revision as of 15:29, 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));