Class RichSequenceFormat.BasicFormat

java.lang.Object
org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
All Implemented Interfaces:
SequenceFormat, RichSequenceFormat
Direct Known Subclasses:
EMBLxmlFormat, INSDseqFormat, RichSequenceFormat.HeaderlessFormat, UniProtXMLFormat
Enclosing interface:
RichSequenceFormat

public abstract static class RichSequenceFormat.BasicFormat extends Object implements RichSequenceFormat
Provides a basic format with simple things like line-widths precoded.
  • Constructor Details

  • Method Details

    • canRead

      public boolean canRead(File file) throws 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.
      Specified by:
      canRead in interface RichSequenceFormat
      Parameters:
      file - the File to check.
      Returns:
      true if the file is readable by this format, false if not.
      Throws:
      IOException - in case the file is inaccessible.
    • guessSymbolTokenization

      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.
      Specified by:
      guessSymbolTokenization in interface RichSequenceFormat
      Parameters:
      file - the File object to guess the format of.
      Returns:
      a SymbolTokenization to read the file with.
      Throws:
      IOException - if the file is unrecognisable or inaccessible.
    • getLineWidth

      public int getLineWidth()
      Retrive the current line width. Defaults to 80.
      Specified by:
      getLineWidth in interface RichSequenceFormat
      Returns:
      the line width
    • setLineWidth

      public void setLineWidth(int width)
      Set the line width. When writing, the lines of sequence will never be longer than the line width. Defaults to 80.
      Specified by:
      setLineWidth in interface RichSequenceFormat
      Parameters:
      width - the new line width
    • getElideSymbols

      public boolean getElideSymbols()
      Is the format going to emit events when sequence data is read?
      Specified by:
      getElideSymbols in interface RichSequenceFormat
      Returns:
      true if it is not otherwise false (false is default) .
    • setElideSymbols

      public void setElideSymbols(boolean elideSymbols)
      Use this method to toggle reading of sequence data.
      Specified by:
      setElideSymbols in interface RichSequenceFormat
      Parameters:
      elideSymbols - set to true if you don't want the sequence data.
    • getElideFeatures

      public boolean getElideFeatures()
      Is the format going to emit events when feature data is read?
      Specified by:
      getElideFeatures in interface RichSequenceFormat
      Returns:
      true if it is not otherwise false (false is default).
    • setElideFeatures

      public void setElideFeatures(boolean elideFeatures)
      Use this method to toggle reading of feature data.
      Specified by:
      setElideFeatures in interface RichSequenceFormat
      Parameters:
      elideFeatures - set to true if you don't want the feature data.
    • getElideReferences

      public boolean getElideReferences()
      Is the format going to emit events when bibliographic reference data is read?
      Specified by:
      getElideReferences in interface RichSequenceFormat
      Returns:
      true if it is not otherwise false (false is default) .
    • setElideReferences

      public void setElideReferences(boolean elideReferences)
      Use this method to toggle reading of bibliographic reference data.
      Specified by:
      setElideReferences in interface RichSequenceFormat
      Parameters:
      elideReferences - set to true if you don't want the bibliographic reference data.
    • getElideComments

      public boolean getElideComments()
      Is the format going to emit events when comments data or remarks from bibliographic references are read?
      Specified by:
      getElideComments in interface RichSequenceFormat
      Returns:
      true if it is not otherwise false (false is default).
    • setElideComments

      public void setElideComments(boolean elideComments)
      Use this method to toggle reading of comments data. Will also ignore remarks lines in bibliographic references.
      Specified by:
      setElideComments in interface RichSequenceFormat
      Parameters:
      elideComments - set to true if you don't want the comments data.
    • setPrintStream

      public void setPrintStream(PrintStream os)
      Sets the stream to write to.
      Specified by:
      setPrintStream in interface RichSequenceFormat
      Parameters:
      os - the PrintStream to write to.
    • getPrintStream

      Gets the print stream currently being written to.
      Specified by:
      getPrintStream in interface RichSequenceFormat
      Returns:
      the current print stream.