PIP.IO.Blast
Class ParseBlastOutput

java.lang.Object
  PIP.IO.Blast.ParseBlastOutput

public class ParseBlastOutput
extends java.lang.Object

Constructor Summary

ParseBlastOutput()

Method Summary

static char[]	getAlignmentDBBlast(BlastStats stats, java.lang.String filename)
static java.lang.String	getEValuePairWiseBlast(java.lang.String filename)
static java.util.List<BlastStats>	getStatsFromBlastDBSearch(java.lang.String filename)
static char[]	parsePairWiseBlastOutput(java.lang.String filename, int maxDomainLength)

Methods inherited from class java.lang.Object

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

Constructor Detail

ParseBlastOutput

public ParseBlastOutput()

Method Detail

getStatsFromBlastDBSearch

public static java.util.List<BlastStats> getStatsFromBlastDBSearch(java.lang.String filename)
                                                            throws java.io.FileNotFoundException,
                                                                   java.io.IOException

Throws:

java.io.FileNotFoundException

java.io.IOException

getEValuePairWiseBlast

public static java.lang.String getEValuePairWiseBlast(java.lang.String filename)
                                               throws java.io.IOException

Throws:

java.io.IOException

getAlignmentDBBlast

public static char[] getAlignmentDBBlast(BlastStats stats,
                                         java.lang.String filename)
                                  throws java.io.IOException

Throws:

java.io.IOException

parsePairWiseBlastOutput

public static char[] parsePairWiseBlastOutput(java.lang.String filename,
                                              int maxDomainLength)
                                       throws java.io.IOException

Throws:

java.io.IOException