TinyGrapDriver (edu.mssm.crover API)

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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 Øyvind 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.