Package org.biojavax.bio.seq.io

Class INSDseqFormat

  • All Implemented Interfaces:
    SequenceFormat, RichSequenceFormat
    public class INSDseqFormat
extends RichSequenceFormat.BasicFormat
    Format reader for INSDseq files. This version of INSDseq format will generate and write RichSequence objects. Loosely Based on code from the old, deprecated, org.biojava.bio.seq.io.GenbankXmlFormat object. Understands http://www.ebi.ac.uk/embl/Documentation/DTD/INSDC_V1.4.dtd.txt Does NOT understand the "sites" keyword in INSDReference_position. Interprets this instead as an empty location. This is because there is no obvious way of representing the "sites" keyword in BioSQL. Note also that the INSDInterval tags and associate stuff are not read, as this is duplicate information to the INSDFeature_location tag which is already fully parsed. However, they are written on output, although there is no guarantee that the INSDInterval tags will exactly match the INSDFeature_location tag as it is not possible to exactly reflect its contents using these.
    Since:
    1.5
    Author:
    Alan Li (code based on his work), Richard Holland, George Waldon

    • Constructor Detail

      • INSDseqFormat

        public INSDseqFormat()

    • Method Detail

      • canRead

        public boolean canRead​(java.io.File file)
                throws java.io.IOException
        Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in INSDseq format if the second XML line contains the phrase "http://www.ebi.ac.uk/dtd/INSD_INSDSeq.dtd".
        Specified by:
        canRead in interface RichSequenceFormat
        Overrides:
        canRead in class RichSequenceFormat.BasicFormat
        Parameters:
        file - the File to check.
        Returns:
        true if the file is readable by this format, false if not.
        Throws:
        java.io.IOException - in case the file is inaccessible.

      • guessSymbolTokenization

        public SymbolTokenization guessSymbolTokenization​(java.io.File file)
                                           throws java.io.IOException
        On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
        Specified by:
        guessSymbolTokenization in interface RichSequenceFormat
        Overrides:
        guessSymbolTokenization in class RichSequenceFormat.BasicFormat
        Parameters:
        file - the File object to guess the format of.
        Returns:
        a SymbolTokenization to read the file with.
        Throws:
        java.io.IOException - if the file is unrecognisable or inaccessible.

      • canRead

        public boolean canRead​(java.io.BufferedInputStream stream)
                throws java.io.IOException
        Check to see if a given stream is in our format. A stream is in INSDseq format if the second XML line contains the phrase "http://www.ebi.ac.uk/dtd/INSD_INSDSeq.dtd".
        Parameters:
        stream - the BufferedInputStream to check.
        Returns:
        true if the stream is readable by this format, false if not.
        Throws:
        java.io.IOException - in case the stream is inaccessible.

      • guessSymbolTokenization

        public SymbolTokenization guessSymbolTokenization​(java.io.BufferedInputStream stream)
                                           throws java.io.IOException
        On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the stream. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
        Parameters:
        stream - the BufferedInputStream object to guess the format of.
        Returns:
        a SymbolTokenization to read the stream with.
        Throws:
        java.io.IOException - if the stream is unrecognisable or inaccessible.

      • readSequence

        public boolean readSequence​(java.io.BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener listener)
                     throws IllegalSymbolException,
                            java.io.IOException,
                            ParseException
        Read a sequence and pass data on to a SeqIOListener.
        Parameters:
        reader - The stream of data to parse.
        symParser - A SymbolParser defining a mapping from character data to Symbols.
        listener - A listener to notify when data is extracted from the stream.
        Returns:
        a boolean indicating whether or not the stream contains any more sequences.
        Throws:
        IllegalSymbolException - if it is not possible to translate character data from the stream into valid BioJava symbols.
        java.io.IOException - if an error occurs while reading from the stream.
        ParseException

      • readRichSequence

        public boolean readRichSequence​(java.io.BufferedReader reader,
                                SymbolTokenization symParser,
                                RichSeqIOListener rlistener,
                                Namespace ns)
                         throws IllegalSymbolException,
                                java.io.IOException,
                                ParseException
        Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. Events are passed to the listener, and the namespace used for sequences read is the one given. If the namespace is null, then the default namespace for the parser is used, which may depend on individual implementations of this interface.
        Parameters:
        reader - the input source
        symParser - the tokenizer which understands the sequence being read
        rlistener - the listener to send sequence events to
        ns - the namespace to read sequences into.
        Returns:
        true if there is more to read after this, false otherwise.
        Throws:
        IllegalSymbolException - if the tokenizer couldn't understand one of the sequence symbols in the file.
        java.io.IOException - if there was a read error.
        ParseException

      • beginWriting

        public void beginWriting()
                  throws java.io.IOException
        Informs the writer that we want to start writing. This will do any initialisation required, such as writing the opening tags of an XML file that groups sequences together.
        Throws:
        java.io.IOException - if writing fails.

      • finishWriting

        public void finishWriting()
                   throws java.io.IOException
        Informs the writer that are done writing. This will do any finalisation required, such as writing the closing tags of an XML file that groups sequences together.
        Throws:
        java.io.IOException - if writing fails.

      • writeSequence

        public void writeSequence​(Sequence seq,
                          java.io.PrintStream os)
                   throws java.io.IOException
        writeSequence writes a sequence to the specified PrintStream, using the default format.
        Parameters:
        seq - the sequence to write out.
        os - the printstream to write to.
        Throws:
        java.io.IOException

      • writeSequence

        public void writeSequence​(Sequence seq,
                          java.lang.String format,
                          java.io.PrintStream os)
                   throws java.io.IOException
        writeSequence writes a sequence to the specified PrintStream, using the specified format.
        Parameters:
        seq - a Sequence to write out.
        format - a String indicating which sub-format of those available from a particular SequenceFormat implemention to use when writing.
        os - a PrintStream object.
        Throws:
        java.io.IOException - if an error occurs.

      • writeSequence

        public void writeSequence​(Sequence seq,
                          Namespace ns)
                   throws java.io.IOException
        Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is given, sequences will be written with that namespace, otherwise they will be written with the default namespace of the implementing class (which is usually the namespace of the sequence itself). If you pass this method a sequence which is not a RichSequence, it will attempt to convert it using RichSequence.Tools.enrich(). Obviously this is not going to guarantee a perfect conversion, so it's better if you just use RichSequences to start with! Namespace is ignored as INSDseq has no concept of it.
        Parameters:
        seq - the sequence to write
        ns - the namespace to write it with
        Throws:
        java.io.IOException - in case it couldn't write something

      • getDefaultFormat

        public java.lang.String getDefaultFormat()
        getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
        Returns:
        a String.