edu.mssm.crover.mutations.drivers.tinygrap
Class TinyGrapDriver

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

public class TinyGrapDriver
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
     
    Field Summary
    static int SUBTYPE_OFFSET
              Number of tokens which are not type specific in the mutation lines.
     
    Constructor Summary
    TinyGrapDriver()
               
     
    Method Summary
     Mutant[] appendMutant(Mutant[] old, Mutant mutant)
               
     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)
               
    protected  Mutant[] tgForSequence(java.lang.String accession_code)
              Do whatever is needed to get the mutations from TinyGRAP.
     
    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
     

    Field Detail

    SUBTYPE_OFFSET

    public static int SUBTYPE_OFFSET
    Number of tokens which are not type specific in the mutation lines.

    Constructor Detail

    TinyGrapDriver

    public TinyGrapDriver()
    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

    tgForSequence

    protected Mutant[] tgForSequence(java.lang.String accession_code)
                              throws SourceNotAvailable,
                                     ProtocolError
    Do whatever is needed to get the mutations from TinyGRAP.

    SourceNotAvailable
    ProtocolError

    appendMutant

    public Mutant[] appendMutant(Mutant[] old,
                                 Mutant mutant)

    main

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


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