static RichSequence |
RichSequence.Tools.createRichSequence(Namespace ns,
java.lang.String name,
java.lang.String seqString,
Alphabet alpha) |
Create a new RichSequence in the specified namespace.
|
static RichSequence |
RichSequence.Tools.createRichSequence(Namespace ns,
java.lang.String name,
SymbolList syms) |
Create a new RichSequence in the specified namespace.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBL(java.io.BufferedReader br,
SymbolTokenization sTok,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Read a EMBL file using a custom type of SymbolList.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBLDNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an EMBL-format stream of DNA sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBLProtein(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an EMBL-format stream of Protein
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBLRNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an EMBL-format stream of RNA sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBLxml(java.io.BufferedReader br,
SymbolTokenization sTok,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Read a EMBLxml file using a custom type of SymbolList.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBLxmlDNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an EMBLxml-format stream of DNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBLxmlProtein(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an EMBLxml-format stream of Protein
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readEMBLxmlRNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an EMBLxml-format stream of RNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readFasta(java.io.BufferedReader br,
SymbolTokenization sTok,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Read a fasta file building a custom type of RichSequence
.
|
static RichSequenceIterator |
RichSequence.IOTools.readFasta(java.io.BufferedReader br,
SymbolTokenization sTok,
Namespace ns) |
Read a fasta file.
|
static RichSequenceIterator |
RichSequence.IOTools.readFastaDNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an FASTA-format stream of DNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readFastaProtein(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an FASTA-format stream of Protein
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readFastaRNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an FASTA-format stream of RNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readFile(java.io.File file,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Guess which format a file is then attempt to read it.
|
static RichSequenceIterator |
RichSequence.IOTools.readFile(java.io.File file,
Namespace ns) |
Guess which format a file is then attempt to read it.
|
static RichSequenceIterator |
RichSequence.IOTools.readGenbank(java.io.BufferedReader br,
SymbolTokenization sTok,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Read a GenBank file using a custom type of SymbolList.
|
static RichSequenceIterator |
RichSequence.IOTools.readGenbankDNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an GenBank-format stream of DNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readGenbankProtein(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an GenBank-format stream of Protein
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readGenbankRNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an GenBank-format stream of RNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readHashedFastaDNA(java.io.BufferedInputStream is,
Namespace ns) |
Iterate over the sequences in an FASTA-format stream of DNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readINSDseq(java.io.BufferedReader br,
SymbolTokenization sTok,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Read a INSDseq file using a custom type of SymbolList.
|
static RichSequenceIterator |
RichSequence.IOTools.readINSDseqDNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an INSDseq-format stream of DNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readINSDseqProtein(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an INSDseq-format stream of Protein
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readINSDseqRNA(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an INSDseq-format stream of RNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readStream(java.io.BufferedInputStream stream,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Guess which format a stream is then attempt to read it.
|
static RichSequenceIterator |
RichSequence.IOTools.readStream(java.io.BufferedInputStream stream,
Namespace ns) |
Guess which format a stream is then attempt to read it.
|
static RichSequenceIterator |
RichSequence.IOTools.readUniProt(java.io.BufferedReader br,
SymbolTokenization sTok,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Read a UniProt file using a custom type of SymbolList.
|
static RichSequenceIterator |
RichSequence.IOTools.readUniProt(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an UniProt-format stream of RNA
sequences.
|
static RichSequenceIterator |
RichSequence.IOTools.readUniProtXML(java.io.BufferedReader br,
SymbolTokenization sTok,
RichSequenceBuilderFactory seqFactory,
Namespace ns) |
Read a UniProt XML file using a custom type of SymbolList.
|
static RichSequenceIterator |
RichSequence.IOTools.readUniProtXML(java.io.BufferedReader br,
Namespace ns) |
Iterate over the sequences in an UniProt XML-format stream of RNA
sequences.
|
static RichSequence |
RichSequence.Tools.subSequence(RichSequence s,
int from,
int to,
Namespace newNamespace,
java.lang.String newName,
java.lang.String newAccession,
java.lang.String newIdentifier,
int newVersion,
java.lang.Double seqVersion) |
Creates a new sequence from a subregion of another sequence.
|
static void |
RichSequence.IOTools.writeEMBL(java.io.OutputStream os,
SequenceIterator in,
Namespace ns) |
Writes sequences from a SequenceIterator to an
OutputStream in EMBL Format.
|
static void |
RichSequence.IOTools.writeEMBL(java.io.OutputStream os,
Sequence seq,
Namespace ns) |
Writes a single Sequence to an OutputStream
in EMBL format.
|
static void |
RichSequence.IOTools.writeEMBLxml(java.io.OutputStream os,
SequenceIterator in,
Namespace ns) |
Writes sequences from a SequenceIterator to an
OutputStream in EMBLxml Format.
|
static void |
RichSequence.IOTools.writeEMBLxml(java.io.OutputStream os,
Sequence seq,
Namespace ns) |
Writes a single Sequence to an OutputStream
in EMBLxml format.
|
static void |
RichSequence.IOTools.writeFasta(java.io.OutputStream os,
SequenceIterator in,
Namespace ns) |
Writes Sequence s from a SequenceIterator to
an OutputStream in Fasta Format.
|
static void |
RichSequence.IOTools.writeFasta(java.io.OutputStream os,
SequenceIterator in,
Namespace ns,
FastaHeader header) |
Writes Sequence s from a SequenceIterator to
an OutputStream in Fasta Format.
|
static void |
RichSequence.IOTools.writeFasta(java.io.OutputStream os,
Sequence seq,
Namespace ns) |
Writes a single Sequence to an OutputStream
in Fasta format.
|
static void |
RichSequence.IOTools.writeFasta(java.io.OutputStream os,
Sequence seq,
Namespace ns,
FastaHeader header) |
Writes a single Sequence to an OutputStream
in Fasta format.
|
static void |
RichSequence.IOTools.writeGenbank(java.io.OutputStream os,
SequenceIterator in,
Namespace ns) |
Writes sequences from a SequenceIterator to an
OutputStream in GenBank Format.
|
static void |
RichSequence.IOTools.writeGenbank(java.io.OutputStream os,
Sequence seq,
Namespace ns) |
Writes a single Sequence to an OutputStream
in GenBank format.
|
static void |
RichSequence.IOTools.writeINSDseq(java.io.OutputStream os,
SequenceIterator in,
Namespace ns) |
Writes sequences from a SequenceIterator to an
OutputStream in INSDseq Format.
|
static void |
RichSequence.IOTools.writeINSDseq(java.io.OutputStream os,
Sequence seq,
Namespace ns) |
Writes a single Sequence to an OutputStream
in INSDseq format.
|
static void |
RichSequence.IOTools.writeUniProt(java.io.OutputStream os,
SequenceIterator in,
Namespace ns) |
Writes sequences from a SequenceIterator to an
OutputStream in UniProt Format.
|
static void |
RichSequence.IOTools.writeUniProt(java.io.OutputStream os,
Sequence seq,
Namespace ns) |
Writes a single Sequence to an OutputStream
in UniProt format.
|
static void |
RichSequence.IOTools.writeUniProtXML(java.io.OutputStream os,
SequenceIterator in,
Namespace ns) |
Writes sequences from a SequenceIterator to an
OutputStream in UniProt XML Format.
|
static void |
RichSequence.IOTools.writeUniProtXML(java.io.OutputStream os,
Sequence seq,
Namespace ns) |
Writes a single Sequence to an OutputStream
in UniProt XML format.
|