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.
java ProcessBlastReport blast.out ssbind.AlignmentBuilder ssbind.Echoer
| Modifier and Type | Field and Description |
|---|---|
static Object |
ALIGNMENT |
static Object |
QUERY |
static Object |
SUBJECT |
| Constructor and Description |
|---|
AlignmentBuilder(org.biojava.bio.search.SearchContentHandler delegate) |
| Modifier and Type | Method and Description |
|---|---|
void |
addSubHitProperty(Object key,
Object val) |
void |
endSubHit() |
public static final Object QUERY
public static final Object SUBJECT
public static final Object ALIGNMENT
public AlignmentBuilder(org.biojava.bio.search.SearchContentHandler delegate)
public void addSubHitProperty(Object key, Object val)
addSubHitProperty in interface org.biojava.bio.search.SearchContentHandleraddSubHitProperty in class org.biojava.bio.search.SearchContentFilterpublic void endSubHit()
endSubHit in interface org.biojava.bio.search.SearchContentHandlerendSubHit in class org.biojava.bio.search.SearchContentFilter