uk.ac.ebi.intact.application.intSeq.struts.framework
Interface SeqIdConstants

public interface SeqIdConstants

Contains constants required for the IntSeq application.

Version:

: $Id: SeqIdConstants.java,v 1.3 2003/07/16 13:56:25 skerrien Exp $

Author:

shuet (shuet@ebi.ac.uk)

Field Summary

static java.lang.String	DIR_INPUT_BLAST
static java.lang.String	DIR_OUTPUT_BLAST
static java.lang.String	DIR_OUTPUT_WGETZ
static java.lang.String	DIR_OUTPUT_WGETZ_SEQ
static java.lang.String	FORWARD_ACC_ERROR command error from the page which display the list of accession number.
static java.lang.String	FORWARD_END_SESSION the key to forward on the welcome session when a session is put down.
static java.lang.String	FORWARD_ERROR The key to some errors.
static java.lang.String	FORWARD_FAILURE command error from the page which display the list of accession number.
static java.lang.String	FORWARD_RESULT Forward to the result page which another template of the idseq page.
static java.lang.String	FORWARD_SUCCESS_ID The key to success ProteinSearchAction action.
static java.lang.String	FORWARD_SUCCESS_SEQ The key to success SequenceSimilarityAction action.
static java.lang.String	INPUT_OUTPUT_DIR Manager files ------- to arrange files in their directory.
static java.lang.String	INTACT_SERVICE The key to store an Intact Service object.
static java.lang.String	INTACT_USER The key to access a user session object.
static java.lang.String	PARSING_BEGIN_FRAGMENT_QUERY
static java.lang.String	PARSING_BEGIN_FRAGMENT_SUBJECT
static java.lang.String	PARSING_END_FRAGMENT_QUERY
static java.lang.String	PARSING_END_FRAGMENT_SUBJECT
static java.lang.String	PARSING_ID WU BLAST regular expressions to parse the standard blast output file (-m 0 and wu-blast output file)
static java.lang.String	PARSING_PERCENTAGE
static java.lang.String	PARSING_TABLE_BLAST_FILE NCBI BLAST regular expression to parse the table blast output file (-m 9 ~ ncbi blast option)
static java.lang.String	PARSING_TABLE_FASTA_FILE FASTA regular expression to parse the table fasta output file (-m 9 ~ ncbi fasta option)
static java.lang.String	PARSING_TABLE_WGETZ_AC WGETZ (to run SRS) regular expression to parse the table wgetz ouput file (+-vn3+-ascii option = 4 columns) SWALL:A1AF_CAVPO P22324 Alpha-1-antiproteinase F precursor (Alpha-1-antitrypsin) (Alpha-1- proteinase inhibitor) (APF) (Fragment).
static java.lang.String	SEARCH_STRING

Field Detail

INTACT_SERVICE

public static final java.lang.String INTACT_SERVICE

The key to store an Intact Service object.

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Constant Field Values

INTACT_USER

public static final java.lang.String INTACT_USER

The key to access a user session object.

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Constant Field Values

SEARCH_STRING

public static final java.lang.String SEARCH_STRING

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Constant Field Values

FORWARD_SUCCESS_SEQ

public static final java.lang.String FORWARD_SUCCESS_SEQ

The key to success SequenceSimilarityAction action.

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Constant Field Values

FORWARD_SUCCESS_ID

public static final java.lang.String FORWARD_SUCCESS_ID

The key to success ProteinSearchAction action.

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Constant Field Values

FORWARD_ERROR

public static final java.lang.String FORWARD_ERROR

The key to some errors.

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Constant Field Values

FORWARD_FAILURE

public static final java.lang.String FORWARD_FAILURE

command error from the page which display the list of accession number.

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Constant Field Values

FORWARD_ACC_ERROR

public static final java.lang.String FORWARD_ACC_ERROR

command error from the page which display the list of accession number.

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Constant Field Values

FORWARD_END_SESSION

public static final java.lang.String FORWARD_END_SESSION

the key to forward on the welcome session when a session is put down.

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Constant Field Values

FORWARD_RESULT

public static final java.lang.String FORWARD_RESULT

Forward to the result page which another template of the idseq page.

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Constant Field Values

INPUT_OUTPUT_DIR

public static final java.lang.String INPUT_OUTPUT_DIR

Manager files ------- to arrange files in their directory. Be aware that the directory /ebi/sp/misc1/intact is visible within bsub !!!

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Constant Field Values

DIR_INPUT_BLAST

public static final java.lang.String DIR_INPUT_BLAST

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Constant Field Values

DIR_OUTPUT_BLAST

public static final java.lang.String DIR_OUTPUT_BLAST

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Constant Field Values

DIR_OUTPUT_WGETZ

public static final java.lang.String DIR_OUTPUT_WGETZ

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Constant Field Values

DIR_OUTPUT_WGETZ_SEQ

public static final java.lang.String DIR_OUTPUT_WGETZ_SEQ

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Constant Field Values

PARSING_ID

public static final java.lang.String PARSING_ID

WU BLAST regular expressions to parse the standard blast output file (-m 0 and wu-blast output file)

 ----- example of the output file to parse ---

      >SWALL:O88613 (3873) MUSCARINIC ACETYLCHOLINE RECEPTOR M1 (FRAGMENT)
              Length = 200

      Score = 61 (26.5 bits), Expect = 4.4, Sum P(2) = 0.99
      Identities = 26/78 (33%), Positives = 36/78 (46%)

      Query:   317 TEKQARELSVPQG---PGAGAESTGEIINNTVPLENSI---PGNCCSALFKNLLLK---- 366
                  TE +AREL+  QG   PG G  S+     +    E S    PG CC       LL+
      Sbjct:    58 TENRARELAALQGSETPGKGGGSSSSSERSQPGAEGSPESPPGRCCRCCRTPRLLQAYSW 117

      Query:   367 KIKRCERKGT-ESVTEEK 383
                  K +  E +G+ ES+T  +
      Sbjct:   118 KEEEEEDEGSMESLTSSE 135

      Score = 37 (18.1 bits), Expect = 4.4, Sum P(2) = 0.99
      Identities = 7/14 (50%), Positives = 8/14 (57%)

      Query:   655 PLPTPELQMPTMVP 668
                  P+  PE Q PT  P
      Sbjct:   148 PMVDPEAQAPTKQP 161

      >SWALL:O55068 (3829) ALPHA1B-ADRENERGIC RECEPTOR (FRAGMENT)
             Length = 85

      Score = 51 (23.0 bits), Expect = 5.6, P = 0.996
      Identities = 13/33 (39%), Positives = 19/33 (57%)

      Query:   164 SLIETPANGTGPSEALAMLLQETTGELEAAKAL 196
                  +L T A G  P  ++A+ L + + E EAAK L
      Sbjct:    47 TLSSTKAKGHNPRSSIAVKLFKFSREKEAAKTL 79
 

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Constant Field Values

PARSING_PERCENTAGE

public static final java.lang.String PARSING_PERCENTAGE

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Constant Field Values

PARSING_BEGIN_FRAGMENT_QUERY

public static final java.lang.String PARSING_BEGIN_FRAGMENT_QUERY

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Constant Field Values

PARSING_BEGIN_FRAGMENT_SUBJECT

public static final java.lang.String PARSING_BEGIN_FRAGMENT_SUBJECT

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Constant Field Values

PARSING_END_FRAGMENT_QUERY

public static final java.lang.String PARSING_END_FRAGMENT_QUERY

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Constant Field Values

PARSING_END_FRAGMENT_SUBJECT

public static final java.lang.String PARSING_END_FRAGMENT_SUBJECT

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Constant Field Values

PARSING_TABLE_BLAST_FILE

public static final java.lang.String PARSING_TABLE_BLAST_FILE

NCBI BLAST regular expression to parse the table blast output file (-m 9 ~ ncbi blast option)

      # BLASTP 2.2.2 [Dec-14-2001]
      # Database: /ebi/sp/misc1/tmp/shuet/intactblast/bank/seqSigHum.fasta
      # Query: sptrembl:Q9BQD2 Q9BQD2; Signal transducer and activator of transcription 6, interleukin-4 induced.
      # Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
      sptrembl:Q9BQD2 sptrembl:Q9BQD2 100.00  679     0       0       1       679     1       679     0.0     1337.0
      sptrembl:Q9BQD2 sptrembl:Q8WWS8 40.14   715     356     17      1       650     1       708     1e-125  438.7
      sptrembl:Q9BQD2 sptrembl:Q8WWS9 39.80   711     356     17      1       650     1       700     1e-123  431.8
 

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Constant Field Values

PARSING_TABLE_FASTA_FILE

public static final java.lang.String PARSING_TABLE_FASTA_FILE

FASTA regular expression to parse the table fasta output file (-m 9 ~ ncbi fasta option)

      FASTA (3.39 May 2001) function [optimized, BL50 matrix (15:-5)] ktup: 2
      join: 38, opt: 26, gap-pen: -12/ -2, width:  16
      The best scores are:                                       opt bits E(55)       %_id  %_gid   sw  alen  mn0  mx0  mn1  mx1 gapq gapl
      intact:EBI-1234 Q8WWS8; Partial STAT5B signal tra  ( 787) 1443  398 5.1e-113    0.410 0.459 1548  717    1  650    1  708  67   9
             --------                                                                 -----                    -  ---    -  ---
 

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Constant Field Values

PARSING_TABLE_WGETZ_AC

public static final java.lang.String PARSING_TABLE_WGETZ_AC

WGETZ (to run SRS) regular expression to parse the table wgetz ouput file (+-vn3+-ascii option = 4 columns) SWALL:A1AF_CAVPO P22324 Alpha-1-antiproteinase F precursor (Alpha-1-antitrypsin) (Alpha-1- proteinase inhibitor) (APF) (Fragment). 403 SWALL:A1AF_RABIT P23035 Alpha-1-antiproteinase F precursor (Alpha-1-antitrypsin) (Alpha-1- proteinase inhibitor) (APF). 413 SWALL:A1AS_CAVPO P22325 Alpha-1-antiproteinase S precursor (Alpha-1-antitrypsin) (Alpha-1- proteinase inhibitor) (APS). 405

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Constant Field Values