com.milaboratory.core.alignment.blast

Class Blast

java.lang.Object

com.milaboratory.core.alignment.blast.Blast

public class Blast
extends Object

This class stores Blast path and manages interaction between JVM and binary blast commands. It will try to find blast on the system's PATH if it is not set explicitly. To set blast path use setBlastPath(String) or set blastPath java property.

Field Summary

Fields

Modifier and Type	Field and Description
static String	CMD_BLASTDBCMD
static String	CMD_BLASTN
static String	CMD_BLASTP
static String	CMD_MAKEBLASTDB

Constructor Summary

Constructors

Constructor and Description
Blast()

Method Summary

Methods

Modifier and Type	Method and Description
static void	setBlastPath(String path) Sets the blast path (e.g.

Methods inherited from class java.lang.Object

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

Field Detail

CMD_BLASTDBCMD

public static final String CMD_BLASTDBCMD

See Also:

Constant Field Values

CMD_MAKEBLASTDB

public static final String CMD_MAKEBLASTDB

See Also:

Constant Field Values

CMD_BLASTN

public static final String CMD_BLASTN

See Also:

Constant Field Values

CMD_BLASTP

public static final String CMD_BLASTP

See Also:

Constant Field Values

Constructor Detail

Blast

public Blast()

Method Detail

setBlastPath

public static void setBlastPath(String path)

Sets the blast path (e.g. ".../tools/blast/bin" or ".../tools/blast/").

Parameters:

path - path to blast distribution