ssbind

Class AlignmentBuilder

java.lang.Object

org.biojava.bio.search.SearchContentFilter

ssbind.AlignmentBuilder

All Implemented Interfaces:

org.biojava.bio.search.SearchContentHandler

public class AlignmentBuilder
extends org.biojava.bio.search.SearchContentFilter

This filter intercepts the querySequence and subjectSequence events to build an alignment.

It will collect up the sequence information per sub hit, and then pass on a newly built alignment object with labels AlignmentBuilder.QUERY and AlignmentBuilder.SUBJECT under the event key AlignmentBuilder.ALIGNMEMT.

Example

 java ProcessBlastReport blast.out ssbind.AlignmentBuilder ssbind.Echoer
 

Author:

Matthew Pocock

Field Summary

Fields

Modifier and Type	Field and Description
static Object	ALIGNMENT
static Object	QUERY
static Object	SUBJECT

Constructor Summary

Constructors

Constructor and Description
AlignmentBuilder(org.biojava.bio.search.SearchContentHandler delegate)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSubHitProperty(Object key, Object val)
void	endSubHit()

Methods inherited from class org.biojava.bio.search.SearchContentFilter

addHitProperty, addSearchProperty, endHeader, endHit, endSearch, getMoreSearches, setDatabaseID, setMoreSearches, setQueryID, startHeader, startHit, startSearch, startSubHit

Methods inherited from class java.lang.Object

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

Field Detail

QUERY

public static final Object QUERY

SUBJECT

public static final Object SUBJECT

ALIGNMENT

public static final Object ALIGNMENT

Constructor Detail

AlignmentBuilder

public AlignmentBuilder(org.biojava.bio.search.SearchContentHandler delegate)

Method Detail

addSubHitProperty

public void addSubHitProperty(Object key,
                     Object val)

Specified by:

addSubHitProperty in interface org.biojava.bio.search.SearchContentHandler

Overrides:

addSubHitProperty in class org.biojava.bio.search.SearchContentFilter

endSubHit

public void endSubHit()

Specified by:

endSubHit in interface org.biojava.bio.search.SearchContentHandler

Overrides:

endSubHit in class org.biojava.bio.search.SearchContentFilter