Package | Description |
---|---|
org.biojavax.bio.db |
Interactions between biojavax objects and a DB.
|
org.biojavax.bio.seq |
Rich implementations of Sequences, Locations and Features.
|
org.biojavax.bio.seq.io |
Classes to support the I/O of RichSequence and
Bioentry objects.
|
Modifier and Type | Method and Description |
---|---|
RichSequenceIterator |
RichSequenceDB.getRichSequenceIterator()
Returns a RichSequenceIterator over all sequences in the database.
|
RichSequenceIterator |
AbstractRichSequenceDB.getRichSequenceIterator() |
Modifier and Type | Class and Description |
---|---|
static class |
RichSequence.IOTools.SingleRichSeqIterator
Used to iterate over a single rich sequence
|
Modifier and Type | Method and Description |
---|---|
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,
Namespace ns)
Read a fasta file.
|
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.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,
Namespace ns)
Guess which format a file is then attempt to read it.
|
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.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,
Namespace ns)
Guess which format a stream is then attempt to read it.
|
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.readUniProt(java.io.BufferedReader br,
Namespace ns)
Iterate over the sequences in an UniProt-format stream of RNA
sequences.
|
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.readUniProtXML(java.io.BufferedReader br,
Namespace ns)
Iterate over the sequences in an UniProt XML-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.
|
Modifier and Type | Class and Description |
---|---|
class |
HashedFastaIterator
Iterates over a Fasta file that is kept in memory for optimized access.
|
class |
RichStreamReader
Parses a stream into sequences.
|