Package | Description |
---|---|
org.biojava.bio.program.phred |
Parser for Phred output
|
org.biojava.bio.seq.io |
Classes and interfaces for processing and producing flat-file representations
of sequences.
|
org.biojava.utils |
Miscellaneous utility classes used by other BioJava components.
|
Modifier and Type | Class and Description |
---|---|
class |
PhredFormat
Format object representing Phred Quality files.
|
Modifier and Type | Method and Description |
---|---|
void |
PhredFormat.addParseErrorListener(ParseErrorListener theListener)
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
PhredFormat.removeParseErrorListener(ParseErrorListener theListener)
Removes a parse error listener from the list of listeners if it is
included.
|
Modifier and Type | Class and Description |
---|---|
class |
EmblLikeFormat
Deprecated.
Use org.biojavax.bio.seq.io.EMBLFormat instead
|
class |
FastaFormat
Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
|
class |
GenbankFormat
Deprecated.
Use org.biojavax.bio.seq.io.GenbankFormat
|
class |
GenbankXmlFormat
Deprecated.
Use org.biojavax.bio.seq.io.INSDseqFormat
|
class |
GenpeptFormat
Deprecated.
Use org.biojavax.bio.seq.io framework instead
|
class |
StreamReader
Parses a stream into sequences.
|
Modifier and Type | Method and Description |
---|---|
void |
SwissprotProcessor.addParseErrorListener(ParseErrorListener theListener)
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
GenbankProcessor.addParseErrorListener(ParseErrorListener theListener)
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
GenbankFormat.addParseErrorListener(ParseErrorListener theListener)
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
FastaFormat.addParseErrorListener(ParseErrorListener theListener)
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
EmblProcessor.addParseErrorListener(ParseErrorListener theListener)
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
EmblLikeFormat.addParseErrorListener(ParseErrorListener theListener)
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
SwissprotProcessor.removeParseErrorListener(ParseErrorListener theListener)
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
|
void |
GenbankProcessor.removeParseErrorListener(ParseErrorListener theListener)
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
|
void |
GenbankFormat.removeParseErrorListener(ParseErrorListener theListener)
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
|
void |
FastaFormat.removeParseErrorListener(ParseErrorListener theListener)
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
|
void |
EmblProcessor.removeParseErrorListener(ParseErrorListener theListener)
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
|
void |
EmblLikeFormat.removeParseErrorListener(ParseErrorListener theListener)
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
|
Modifier and Type | Method and Description |
---|---|
void |
ParseErrorSource.addParseErrorListener(ParseErrorListener theListener)
Adds a parse error listener to the list of listeners.
|
void |
ParseErrorSource.removeParseErrorListener(ParseErrorListener theListener)
Removes a parse error listener from the list of listeners.
|
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