ssbind
Class AlignmentBuilder

java.lang.Object
  extended by org.biojava.bio.search.SearchContentFilter
      extended by 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
static Object ALIGNMENT
           
static Object QUERY
           
static Object SUBJECT
           
 
Constructor Summary
AlignmentBuilder(org.biojava.bio.search.SearchContentHandler delegate)
           
 
Method Summary
 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