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
Constructor Summary |
AlignmentBuilder(org.biojava.bio.search.SearchContentHandler delegate)
|
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 |
QUERY
public static final Object QUERY
SUBJECT
public static final Object SUBJECT
ALIGNMENT
public static final Object ALIGNMENT
AlignmentBuilder
public AlignmentBuilder(org.biojava.bio.search.SearchContentHandler delegate)
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