org.biojava.bio.program.gff
Class GFFWriter
java.lang.Object
|
+--org.biojava.bio.program.gff.GFFWriter
- public class GFFWriter
- extends java.lang.Object
- implements GFFDocumentHandler
Listens to a stream of GFF events and writes the lines to a
PrintWriter.
This will ignore all exceptions. Mabey the error-handeling needs to move into
an error handeling interface?
- Author:
- Matthew Pocock
Constructor Summary |
GFFWriter(java.io.PrintWriter out)
Create a new GFFWriter that will write to
out. |
Method Summary |
void |
commentLine(java.lang.String comment)
Prints the comment directly to the PrintWriter
after adding a leading '# '. |
void |
endDocument()
Flushes the PrintWriter to make sure that everything is written. |
void |
invalidEnd(java.lang.String token,
java.lang.NumberFormatException nfe)
|
void |
invalidFrame(java.lang.String token,
java.lang.NumberFormatException nfe)
|
void |
invalidScore(java.lang.String token,
java.lang.NumberFormatException nfe)
|
void |
invalidStart(java.lang.String token,
java.lang.NumberFormatException nfe)
|
void |
invalidStrand(java.lang.String token)
|
void |
recordLine(GFFRecord record)
Prints record to the PrintWriter. |
void |
startDocument(java.lang.String locator)
Indicates that a new GFF document has been started. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
GFFWriter
public GFFWriter(java.io.PrintWriter out)
- Create a new GFFWriter that will write to
out.
- Parameters:
out
- the PrintWriter to write to
startDocument
public void startDocument(java.lang.String locator)
- Description copied from interface: GFFDocumentHandler
- Indicates that a new GFF document has been started.
This gives you a hook to set up per-document resources.
- Specified by:
- startDocument in interface GFFDocumentHandler
- Tags copied from interface: GFFDocumentHandler
- Parameters:
locator
- A URI for the stream being parsed.
endDocument
public void endDocument()
- Flushes the PrintWriter to make sure that everything is written.
- Specified by:
- endDocument in interface GFFDocumentHandler
commentLine
public void commentLine(java.lang.String comment)
- Prints the comment directly to the PrintWriter
after adding a leading '
#
'.
- Specified by:
- commentLine in interface GFFDocumentHandler
- Tags copied from interface: GFFDocumentHandler
- Parameters:
comment
- the comment String
recordLine
public void recordLine(GFFRecord record)
- Prints record to the PrintWriter.
- Specified by:
- recordLine in interface GFFDocumentHandler
- Tags copied from interface: GFFDocumentHandler
- Parameters:
record
- the GFFRecord containing all the info
invalidStart
public void invalidStart(java.lang.String token,
java.lang.NumberFormatException nfe)
throws BioException
invalidEnd
public void invalidEnd(java.lang.String token,
java.lang.NumberFormatException nfe)
throws BioException
invalidScore
public void invalidScore(java.lang.String token,
java.lang.NumberFormatException nfe)
throws BioException
invalidStrand
public void invalidStrand(java.lang.String token)
throws BioException
invalidFrame
public void invalidFrame(java.lang.String token,
java.lang.NumberFormatException nfe)
throws BioException