|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object htsjdk.samtools.SAMFileWriterImpl htsjdk.samtools.SAMTextWriter
public class SAMTextWriter
Writer for text-format SAM files.
Constructor Summary | |
---|---|
SAMTextWriter(java.io.File file)
Constructs a SAMTextWriter that writes to a File. |
|
SAMTextWriter(java.io.OutputStream stream)
Constructs a SAMTextWriter that writes to an OutputStream. |
|
SAMTextWriter(java.io.Writer out)
Constructs a SAMTextWriter that outputs to a Writer. |
Method Summary | |
---|---|
void |
finish()
Do any required flushing here. |
java.lang.String |
getFilename()
For producing error messages. |
java.io.Writer |
getWriter()
Returns the Writer used by this instance. |
void |
writeAlignment(SAMRecord alignment)
Write the record. |
void |
writeHeader(java.lang.String textHeader)
Write the header text. |
Methods inherited from class htsjdk.samtools.SAMFileWriterImpl |
---|
addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getSortOrder, setDefaultMaxRecordsInRam, setHeader, setProgressLogger, setSortOrder |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public SAMTextWriter(java.io.Writer out)
out
- Writer.public SAMTextWriter(java.io.File file)
file
- Where to write the output.public SAMTextWriter(java.io.OutputStream stream)
stream
- Need not be buffered because this class provides buffering.Method Detail |
---|
public java.io.Writer getWriter()
public void writeAlignment(SAMRecord alignment)
writeAlignment
in class SAMFileWriterImpl
alignment
- SAMRecord.public void writeHeader(java.lang.String textHeader)
writeHeader
in class SAMFileWriterImpl
textHeader
- String containing the text to write.public void finish()
finish
in class SAMFileWriterImpl
public java.lang.String getFilename()
getFilename
in class SAMFileWriterImpl
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |