edu.mssm.crover.tools.blast
Class BlastCommand

java.lang.Object
  |
  +--edu.mssm.crover.tools.blast.BlastCommand

public class BlastCommand

extends java.lang.Object

This implementation wraps around Blast. It is responsible for knowing the peculiarities of the Blast installation (executable location, database directory path, etc.).

Field Summary

static int	OUTPUT_PAIRWISE
static int	OUTPUT_XML Selects the XML Blast output.
static int	TYPE_DNA Sequence is nucleotide.
static int	TYPE_PROTEIN Sequence is a protein.

Constructor Summary

BlastCommand()

BlastCommand(BlastContext ctx)

Method Summary

BlastResult	blast(int seqType, BiologicalSequence seq, java.lang.String database) Runs BLAST.
BlastResult	blast(java.lang.String blastType, BiologicalSequence querySequence, java.lang.String database)
boolean	checkSequenceDB(java.lang.String dbname, java.lang.String path) Checks if the command is installed on this machine.
void	copy(java.io.File from, java.io.File dest)
void	copy(java.io.InputStream is, java.io.File dest)
BlastResult	createBlastResult(java.io.StringReader sr) Creates a BlastResult from a StringReader.
void	dispose(java.io.File Output)
java.lang.String	getBlastType(int seqType, java.lang.String database) Predicts the BLAST program to be used depending on the sequence type (DNA or protein) and the type of sequence in the database.
BlastContext	getContext()
boolean	installed(java.lang.String cmdPath, java.lang.String execName) Checks if the command is installed on this machine.
static void	main(java.lang.String[] args)
void	read(java.io.InputStream is)
java.io.File	run(int seqType, java.io.File seqFile, java.lang.String database) Run BLAST with a (multiple) sequence file.
java.io.File	run(java.lang.String blastType, BiologicalSequence querySequence, java.lang.String database) Run BLAST with a query sequence.
java.io.File	run(java.lang.String blastType, BiologicalSequence querySequence, java.lang.String database, int mValue) Predicts the product of the genes encoded by the sequence passed as argument.
java.io.File	run(java.lang.String blastType, java.io.File seqFile, java.lang.String database, int mValue) Runs BLAST on the sequences encoded by the sequence(s) in the File seqFile passed as argument.
java.io.File	runbl2(java.lang.String blastType, BiologicalSequence querySequence, BiologicalSequence subjSequence)
void	setContext(BlastContext ctx)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

OUTPUT_PAIRWISE

public static final int OUTPUT_PAIRWISE

See Also:

Constant Field Values

OUTPUT_XML

public static final int OUTPUT_XML

Selects the XML Blast output.

See Also:

Constant Field Values

TYPE_PROTEIN

public static final int TYPE_PROTEIN

Sequence is a protein.

See Also:

Constant Field Values

TYPE_DNA

public static final int TYPE_DNA

Sequence is nucleotide.

See Also:

Constant Field Values

Constructor Detail

BlastCommand

public BlastCommand()

BlastCommand

public BlastCommand(BlastContext ctx)

Method Detail

installed

public boolean installed(java.lang.String cmdPath,
                         java.lang.String execName)

Checks if the command is installed on this machine. Check to see if both /usr/local/softs/blast/blastall (or blast.executable.path/blast.executable.name) and /data/db/blast/ (or blast.database.path/)

Returns:

True when blast is installed on the machine, False otherwise.

checkSequenceDB

public boolean checkSequenceDB(java.lang.String dbname,
                               java.lang.String path)
                        throws DatabaseNotFound

Checks if the command is installed on this machine. Check to see if both /usr/local/softs/blast/blastall (or blast.executable.path/blast.executable.name) and /data/db/blast/ (or blast.database.path/)

Returns:

True when blast is installed on the machine, False otherwise.

DatabaseNotFound

blast

public BlastResult blast(int seqType,
                         BiologicalSequence seq,
                         java.lang.String database)
                  throws java.io.FileNotFoundException,
                         UnsupportedFormat,
                         CommandNotInstalled,
                         DatabaseNotFound

Runs BLAST. Determines the BLAST program to be used from the sequence types of the query sequence and the database

java.io.FileNotFoundException

UnsupportedFormat

CommandNotInstalled

DatabaseNotFound

See Also:

blast(int, edu.mssm.crover.representation.BiologicalSequence, java.lang.String)

blast

public BlastResult blast(java.lang.String blastType,
                         BiologicalSequence querySequence,
                         java.lang.String database)
                  throws java.io.FileNotFoundException,
                         UnsupportedFormat,
                         CommandNotInstalled,
                         DatabaseNotFound

Throws:

java.io.FileNotFoundException - Thrown when there is a Runtime error during the execution of run, such as the tmp directory becoming full or if the execution of BLAST fails.

UnsupportedFormat - Thrown when the output file is not in XML format

CommandNotInstalled

DatabaseNotFound

getBlastType

public java.lang.String getBlastType(int seqType,
                                     java.lang.String database)
                              throws DatabaseNotFound

Predicts the BLAST program to be used depending on the sequence type (DNA or protein) and the type of sequence in the database. The sequence type in the database is determined by the initial letter of database file suffix: "n" implies a DNA database, "p" implies a protein database. blastn: dna seq vs dna db blastp: protein seq vs protein db blastx: dna seq vs protein db tblastn: protein seq vs dna db

DatabaseNotFound

run

public java.io.File run(java.lang.String blastType,
                        BiologicalSequence querySequence,
                        java.lang.String database)
                 throws CommandNotInstalled,
                        DatabaseNotFound

Run BLAST with a query sequence.

CommandNotInstalled

DatabaseNotFound

See Also:

run(java.lang.String, edu.mssm.crover.representation.BiologicalSequence, java.lang.String)

run

public java.io.File run(int seqType,
                        java.io.File seqFile,
                        java.lang.String database)
                 throws CommandNotInstalled,
                        DatabaseNotFound

Run BLAST with a (multiple) sequence file.

CommandNotInstalled

DatabaseNotFound

See Also:

run(java.lang.String, edu.mssm.crover.representation.BiologicalSequence, java.lang.String)

run

public java.io.File run(java.lang.String blastType,
                        java.io.File seqFile,
                        java.lang.String database,
                        int mValue)
                 throws CommandNotInstalled,
                        DatabaseNotFound

Runs BLAST on the sequences encoded by the sequence(s) in the File seqFile passed as argument. Returns a file.

CommandNotInstalled

DatabaseNotFound

createBlastResult

public BlastResult createBlastResult(java.io.StringReader sr)
                              throws CommandNotInstalled,
                                     org.exolab.castor.xml.MarshalException,
                                     org.exolab.castor.xml.ValidationException

Creates a BlastResult from a StringReader. Checks to see if the XML version is supported.

CommandNotInstalled

org.exolab.castor.xml.MarshalException

org.exolab.castor.xml.ValidationException

run

public java.io.File run(java.lang.String blastType,
                        BiologicalSequence querySequence,
                        java.lang.String database,
                        int mValue)
                 throws CommandNotInstalled,
                        DatabaseNotFound

Predicts the product of the genes encoded by the sequence passed as argument. Returns an array of protein sequences. The path to the blast executable is found in the "blast.executable.path" property. If the blast executable is in /usr/local/softs/blast/blastall, the path should be /usr/local/softs/blast. Default: "blastall".

Parameters:

blastType - The type of blast analysis to be performed (blastp, tblastn, tblastx, blastx, blastn).

querySequence - File that contains the sequence to be used as query.

CommandNotInstalled

DatabaseNotFound

read

public void read(java.io.InputStream is)

copy

public void copy(java.io.InputStream is,
                 java.io.File dest)

copy

public void copy(java.io.File from,
                 java.io.File dest)

dispose

public void dispose(java.io.File Output)

getContext

public BlastContext getContext()

setContext

public void setContext(BlastContext ctx)

runbl2

public java.io.File runbl2(java.lang.String blastType,
                           BiologicalSequence querySequence,
                           BiologicalSequence subjSequence)
                    throws CommandNotInstalled

CommandNotInstalled

main

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