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java.lang.Objectorg.biojava.bio.program.gff.GFFEntrySet
A set of entries and comments as a representation of a GFF file.
This is an intermediate storage solution for GFF stuff. It lets you collect together an arbitrary set of GFF records and comments, and then do something with them later.
Field Summary | |
static java.lang.String |
PROPERTY_GFF_SCORE
|
Constructor Summary | |
GFFEntrySet()
Make an empty GFFEntrySet. |
Method Summary | |
void |
add(GFFRecord record)
Add a GFFRecord to the end of this set. |
void |
add(java.lang.String comment)
Add a comment to the end of this set. |
GFFEntrySet |
filter(GFFRecordFilter filter)
Filter this entry set into another set. |
GFFDocumentHandler |
getAddHandler()
Get the GFFDocumentHandler for adding to this set. |
SequenceAnnotator |
getAnnotator()
Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet. |
SequenceAnnotator |
getAnnotator(boolean checkSeqName)
Get an annotator that can add GFF features to a Sequence using the features in this GFFEntrySet. |
java.util.Iterator |
lineIterator()
Loop over all lines in the set. |
int |
size()
Return how many lines are in this set. |
void |
streamRecords(GFFDocumentHandler handler)
Write all records in this set out to a handler. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
public static final java.lang.String PROPERTY_GFF_SCORE
Constructor Detail |
public GFFEntrySet()
Method Detail |
public java.util.Iterator lineIterator()
The Iterator will return String and GFFRecord objects in the order that they were added to this set. It is your responsibility to check the type of hasNext() before casting it.
public void add(java.lang.String comment)
This should be the text of the comment, without the leading
'#
'.
comment
- a String giving the commentpublic void add(GFFRecord record)
public int size()
public SequenceAnnotator getAnnotator()
Sequences are only annotated if their getName() method returns a name equal to the sequence name field of one or more records in this GFFEntrySet.
public SequenceAnnotator getAnnotator(boolean checkSeqName)
If checkSeqName is set to true, Sequences are only annotated if their getName() method returns a name equal to the sequence name field of one or more records in this GFFEntrySet. If checkSeqName is false, then all features are added to the sequence regardless of name.
checkSeqName
- boolean to indicate if only records with names
matching the sequences name should be added
public GFFEntrySet filter(GFFRecordFilter filter)
filter
- the GFFRecordFilter to filter with
public GFFDocumentHandler getAddHandler()
public void streamRecords(GFFDocumentHandler handler)
handler
- the GFFDocumentHandler to inform of the records
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