edu.mssm.crover.mutations.drivers.dimlib
Class DiMLibDriver

java.lang.Object
  |
  +--edu.mssm.crover.mutations.drivers.MutationDriverCache
        |
        +--edu.mssm.crover.mutations.drivers.dimlib.DiMLibDriver
All Implemented Interfaces:
MutationDriver

public class DiMLibDriver
extends MutationDriverCache

A driver for TinyGRAP /cgi-bin/tG script. The driver supports the following kind of mutations (the TinyGRAP mutation type is given in parenthesis):

  • point mutations (PM),
  • deletions (DL),
  • insertions (IS),
  • subsitutions (SB)
    The Driver connects via HTTP and retrieve the mutation as an HTML file that follows a specific format, agreed between Řyvind Edvardsen and Fabien Campagne. The format is described here for future reference. The format is line-oriented. Tokens are separated by spaces.

    Mutant

    Mutants are described by lines that start with "MUTANT". The tokens encode the following:
  • Token 1 MUTANT
  • Token 2 mutant-id
  • Token 3 URL for the mutant description

    Mutations

    Mutations are described by lines that start with "MUTATION". The tokens encode the following:
  • Token 1 MUTATION
  • Token 2 mutant-id : identify the mutant to which this mutation belongs.
  • Token 3 URL for the mutation description
  • Token 4 Type of the mutation
  • Following tokens are type dependent. An example of the format is given below.
    MUTANT 14169 http://tinyGRAP.uit.no/cgi-bin/tG?14169
    
    MUTANT 14169 http://tinyGRAP.uit.no/cgi-bin/tG?14169
    MUTATION 14169 mutation_id http://tinyGRAP.uit.no/cgi-bin/tG?P32301+1 CR P32301 1 135 P30082 1 132 MAVTPSLLRLALLLLGAVGRAGPRPQGATVSLSETVQKWREYRHQCQRFLTEAPLLATGLFCNRTFDDYACWPDGPPGSFVNVSCPWYLPWASSVLQGHVYRFCTAEGIWLHKDNSSLPWRDLSECEESKQGERN MLLTQLHCPYLLLLLVVLSCLPKAPSAQVMDFLFEKWKLYSDQCHHNLSLLPPPTELVCNRTFDKYSCWPDTPPNTTANISCPWYLPWYHKVQHRLVFKRCGPDGQWVRGPRGQSWRDASQCQMDDDEIEVQ
    
    
    MUTANT 17247 http://tinyGRAP.uit.no/cgi-bin/tG?17247
    MUTATION 17247 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+1 DL 1 MLLTQLHCPYLLLLLVVLSCLPKAPSAQVMDFLFEKWKLYSDQCHHNLSLLPPPTELVCNRTFDKYSCWPDTPPNTTANISCPWYLPWYHKVQHRLVFKRCGPDGQWVRGPRGQSWRDASQCQMDDDEIEVQKGVA
    MUTATION 17247 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+178 PM 178 H R
    
    MUTANT 17246 http://tinyGRAP.uit.no/cgi-bin/tG?17246
    MUTATION 17246 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+1 DL 1 MLLTQLHCPYLLLLLVVLSCLPKAPSAQVMDFLFEKWKLYSDQCHHNLSLLPPPTELVCNRTFDKYSCWPDTPPNTTANISCPWYLPWYHKVQHRLVFKRCGPDGQWVRGPRGQSWRDASQCQMDDDEIEVQKGVAK
    
    MUTANT 17245 http://tinyGRAP.uit.no/cgi-bin/tG?17245
    MUTATION 17245 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+352 PM 352 T A
    
    MUTANT 17244 http://tinyGRAP.uit.no/cgi-bin/tG?17244
    MUTATION 17244 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+352 PM 352 T P
    
    MUTANT 17243 http://tinyGRAP.uit.no/cgi-bin/tG?17243
    MUTATION 17243 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+352 PM 352 T S
    
    MUTANT 17242 http://tinyGRAP.uit.no/cgi-bin/tG?17242
    MUTATION 17242 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+178 PM 178 H E
    
    MUTANT 17241 http://tinyGRAP.uit.no/cgi-bin/tG?17241
    MUTATION 17241 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+178 PM 178 H K
    
    MUTANT 17240 http://tinyGRAP.uit.no/cgi-bin/tG?17240
    MUTATION 17240 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+178 PM 178 H A
    
    MUTANT 17239 http://tinyGRAP.uit.no/cgi-bin/tG?17239
    MUTATION 17239 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+178 PM 178 H R
    
    MUTANT 16463 http://tinyGRAP.uit.no/cgi-bin/tG?16463
    MUTATION 16463 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+258 SB 258 T R
    MUTATION 16463 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+259 SB 259 F K
    MUTATION 16463 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+260 SB 260 S L
    MUTATION 16463 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+261 SB 261 E H
    MUTATION 16463 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+262 DL 262 KSFFSLYLCIGWGSPLLFVIPWVVVKCLFENVQCWTSNDNMGFWWILRIPVLLAILINFFIFVRIIHLLVAKLRAHQMHYADYKFRLARSTLTLIPLLGVHEVVFAFVTDEHAQGTLRSTKLFFDLFFSSFQGLLVAVLYCFLNKEVQAELLRRWRRWQEGKALQEERMASSHGSHMAPAGTCHGDPCEKLQLMSAGSSSGTGCEPSAKTSLASSLPRLADSPT
    
    MUTANT 15172 http://tinyGRAP.uit.no/cgi-bin/tG?15172
    MUTATION 15172 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+258 DL 258 TFSEKSFFSLYLCIGWGSPLLFVIPWVVVKCLFENVQCWTSNDNMGFWWILRIPVLLAILINFFIFVRIIHLLVAKLRAHQMHYADYKFRLARSTLTLIPLLGVHEVVFAFVTDEHAQGTLRSTKLFFDLFFSSFQGLLVAVLYCFLNKEVQAELLRRWRRWQEGKALQEERMASSHGSHMAPAGTCHGDPCEKLQLMSAGSSSGTGCEPSAKTSLASSLPRLADSPT
    
    MUTANT 14387 http://tinyGRAP.uit.no/cgi-bin/tG?14387
    MUTATION 14387 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+444 DL 444 CHGDPCEKLQLMSAGSSSGTGCEPSAKTSLASSLPRLADSPT
    
    MUTANT 14386 http://tinyGRAP.uit.no/cgi-bin/tG?14386
    MUTATION 14386 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+416 DL 416 WRRWQEGKALQEERMASSHGSHMAPAGTCHGDPCEKLQLMSAGSSSGTGCEPSAKTSLASSLPRLADSPT
    
    MUTANT 14385 http://tinyGRAP.uit.no/cgi-bin/tG?14385
    MUTATION 14385 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+341 DL 341 YADYKFRLARSTLTLIPLLGVHEVVFAFVTDEHAQGTLRSTKLFFDLFFSSFQGLLVAVLYCFLNKEVQAELLRRWRRWQEGKALQEERMASSHGSHMAPAGTCHGDPCEKLQLMSAGSSSGTGCEPSAKTSLASSLPRLADSPT
    
    MUTANT 14384 http://tinyGRAP.uit.no/cgi-bin/tG?14384
    MUTATION 14384 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+172 DL 172 CTRNYIHGNLFASFVLKAGSVLVIDWLLKTRYSQKIGDDLSVSVWLSDGAVAGCRVATVIMQYGIIANYCWLLVEGVYLYSLLSITTFSEKSFFSLYLCIGWGSPLLFVIPWVVVKCLFENVQCWTSNDNMGFWWILRIPVLLAILINFFIFVRIIHLLVAKLRAHQMHYADYKFRLARSTLTLIPLLGVHEVVFAFVTDEHAQGTLRSTKLFFDLFFSSFQGLLVAVLYCFLNKEVQAELLRRWRRWQEGKALQEERMASSHGSHMAPAGTCHGDPCEKLQLMSAGSSSGTGCEPSAKTSLASSLPRLADSPT
    
    MUTANT 14383 http://tinyGRAP.uit.no/cgi-bin/tG?14383
    MUTATION 14383 http://tinyGRAP.uit.no/cgi-bin/tG?P30082+27 DL 27 AQVMDFLFEKWKLYSDQCHHNLSLLPPPTELVCNRTFDKYSCWPDTPPNTTANISCPWYLPWYHKVQHRLVFKRCGPDGQWVRGPRGQS
    

    Author:
    Fabien Campagne

    Nested Class Summary
     
    Nested classes inherited from class edu.mssm.crover.mutations.drivers.MutationDriverCache
    MutationDriverCache.CachedMutants
     
    Constructor Summary
    DiMLibDriver()
               
     
    Method Summary
    protected  Mutant[] dlForSequence(java.lang.String accession_code)
              Search the DiMLib database for the WildTypeProtein corresponding to the DiMLib ID.
     DriverInformation getInformation()
               
    protected  Mutant[] getMutantsFor(java.lang.String origin, java.lang.String accession_code)
              Not Cached, implemented by each driver specialization.
    static void main(java.lang.String[] args)
               
     
    Methods inherited from class edu.mssm.crover.mutations.drivers.MutationDriverCache
    getAccessionCodeMap, getCachedMutants, getMutants, getMutantsFor, getMutationsFor, pushInCache
     
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
     

    Constructor Detail

    DiMLibDriver

    public DiMLibDriver()
    Method Detail

    getInformation

    public DriverInformation getInformation()
    Specified by:
    getInformation in interface MutationDriver
    Specified by:
    getInformation in class MutationDriverCache

    getMutantsFor

    protected Mutant[] getMutantsFor(java.lang.String origin,
                                     java.lang.String accession_code)
                              throws SourceNotAvailable,
                                     ProtocolError,
                                     UnsupportedOrigin
    Description copied from class: MutationDriverCache
    Not Cached, implemented by each driver specialization. Returns all the mutants known on this sequence.

    Specified by:
    getMutantsFor in class MutationDriverCache
    SourceNotAvailable
    ProtocolError
    UnsupportedOrigin

    dlForSequence

    protected Mutant[] dlForSequence(java.lang.String accession_code)
                              throws SourceNotAvailable,
                                     ProtocolError
    Search the DiMLib database for the WildTypeProtein corresponding to the DiMLib ID. Return the Mutants associated with that protein.

    SourceNotAvailable
    ProtocolError

    main

    public static void main(java.lang.String[] args)


    Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.