Package | Description |
---|---|
org.biojavax.bio.seq.io |
Classes to support the I/O of RichSequence and
Bioentry objects.
|
Modifier and Type | Interface and Description |
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interface |
RichSequenceBuilder
An interface for objects that can build RichSequences.
|
Modifier and Type | Class and Description |
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class |
DebuggingRichSeqIOListener
This is purely for debugging purposes.
|
class |
RichSeqIOAdapter
This class implements all methods of RichSeqIOListener and takes no action.
|
class |
SimpleRichSequenceBuilder
Constructs BioEntry objects by listening to events.
|
Modifier and Type | Method and Description |
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void |
FastaFormat.processHeader(String line,
RichSeqIOListener rsiol,
Namespace ns)
Parse the Header information from the Fasta Description line
|
boolean |
UniProtFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
INSDseqFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
UniProtXMLFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
FastaFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rsiol,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
RichSequenceFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener listener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
EMBLxmlFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
GenbankFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
EMBLFormat.readRichSequence(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
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