PIP.IO.Blast
Class Blaster

java.lang.Object
  PIP.IO.Blast.Blaster

public class Blaster
extends java.lang.Object

Constructor Summary

Blaster()

Method Summary

static void	blast(java.lang.String sequence, java.lang.String formatDBName, java.lang.String filename)
static java.util.List<BlastStats>	blastAgainstDatabase(java.lang.String sequence1, java.lang.String formatDBName, java.lang.String filename)
static double	getSequenceIdentityConsideringLength(Domain d1, Domain d2)
static double	getSequenceIdentityConsideringLength(DomainInteraction di)
static double	getSimpleSequenceIdentity(DomainInteraction di)
static void	pairWiseBlast(java.lang.String s1, java.lang.String s2)
static void	pairWiseBlastNucleotide(java.lang.String s1, java.lang.String s2)

Methods inherited from class java.lang.Object

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

Constructor Detail

Blaster

public Blaster()

Method Detail

blast

public static void blast(java.lang.String sequence,
                         java.lang.String formatDBName,
                         java.lang.String filename)
                  throws java.io.FileNotFoundException,
                         java.io.IOException,
                         java.lang.InterruptedException

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.InterruptedException

pairWiseBlast

public static void pairWiseBlast(java.lang.String s1,
                                 java.lang.String s2)
                          throws java.io.FileNotFoundException,
                                 java.io.IOException,
                                 java.lang.InterruptedException

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.InterruptedException

pairWiseBlastNucleotide

public static void pairWiseBlastNucleotide(java.lang.String s1,
                                           java.lang.String s2)
                                    throws java.io.FileNotFoundException,
                                           java.io.IOException,
                                           java.lang.InterruptedException

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.InterruptedException

blastAgainstDatabase

public static java.util.List<BlastStats> blastAgainstDatabase(java.lang.String sequence1,
                                                              java.lang.String formatDBName,
                                                              java.lang.String filename)
                                                       throws java.io.IOException,
                                                              java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

getSequenceIdentityConsideringLength

public static double getSequenceIdentityConsideringLength(DomainInteraction di)
                                                   throws java.io.IOException,
                                                          java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

getSequenceIdentityConsideringLength

public static double getSequenceIdentityConsideringLength(Domain d1,
                                                          Domain d2)
                                                   throws java.io.IOException,
                                                          java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException

getSimpleSequenceIdentity

public static double getSimpleSequenceIdentity(DomainInteraction di)
                                        throws java.io.IOException,
                                               java.lang.InterruptedException

Throws:

java.io.IOException

java.lang.InterruptedException