Class AgaveWriter


  • public class AgaveWriter
    extends java.lang.Object
    Writes Sequence into AGAVE XML document. The AGAVE format is defined in agave.dtd which can be downloaded from http://www.agavexml.org.
    Author:
    Hanning Ni, Brian King
    • Field Detail

      • INDENT

        public static final java.lang.String INDENT
        use a two space indent
        See Also:
        Constant Field Values
      • mOut

        protected java.io.PrintWriter mOut
        Write to XML document
      • mFilter

        protected org.biojava.bio.seq.io.agave.PCDATAFilterWriter mFilter
        writes PCDATA replacing XML characters with escape entities
      • mAnnotFilter

        protected AGAVEAnnotFilter mAnnotFilter
        The AnnotationMap to use for getting AGAVE XML attributes from a Sequence Annotation.
      • mWriteDocType

        protected boolean mWriteDocType
        write DOCTYPE if true
    • Constructor Detail

      • AgaveWriter

        public AgaveWriter()
        Default constructor uses generic annotation to attribute mapping.
      • AgaveWriter

        public AgaveWriter​(AGAVEAnnotFilter filter)
        Construct with data source specific annotation to attribute mapping.
    • Method Detail

      • setWriteDocType

        public void setWriteDocType​(boolean writeDocType)
        Set flag that determines if XML DOCTYPE is written or not. Default is true.
      • writeSequence

        public void writeSequence​(Sequence seq,
                                  java.io.PrintStream os)
                           throws java.io.IOException
        Write sequence into AGAVE XML format.
        Parameters:
        seq - maybe the or simple sequence
         if annotation of seq has chromosome information , generate  tag
         if seq is SimpleAssembly, generate  tag
         otherwise, generate  tag
         currently  each top-level sequence is wrapped into seperated sciobj xml file
         
        Throws:
        java.io.IOException
      • writeHeader

        protected void writeHeader()
        Write <sciobj>
      • writeFooter

        protected void writeFooter()
        Write </sciobj>
      • write

        protected void write​(Sequence seq)
                      throws java.io.IOException
        Writing Sequence.
        Parameters:
        seq - is simple sequence or simple assembly
        Throws:
        java.io.IOException
      • writeContig

        protected void writeContig​(Annotatable seq)
                            throws java.io.IOException
        Throws:
        java.io.IOException
      • writeAssembly

        protected void writeAssembly​(Annotatable seq)
                              throws java.io.IOException
        Throws:
        java.io.IOException
      • writeBioSequence

        protected void writeBioSequence​(Annotatable seq)
                                 throws java.io.IOException
        Throws:
        java.io.IOException
      • writeSequenceMap

        protected void writeSequenceMap​(Annotatable seq)
                                 throws java.io.IOException
        group sequence_map by getSource()
        Throws:
        java.io.IOException
      • writeClassification

        protected void writeClassification​(Annotatable seq)
                                    throws java.io.IOException
        Throws:
        java.io.IOException
      • writeSequenceMap2

        protected void writeSequenceMap2​(Annotatable f)
                                  throws java.io.IOException
        Write SequenceMap XML
        Throws:
        java.io.IOException
      • writeAnnotations

        protected void writeAnnotations​(FeatureHolder f)
                                 throws java.io.IOException
        Throws:
        java.io.IOException
      • writeGene

        protected void writeGene​(Annotatable f)
                          throws java.io.IOException
        Throws:
        java.io.IOException
      • writeTranscript

        protected void writeTranscript​(Annotatable f)
                                throws java.io.IOException
        Throws:
        java.io.IOException
      • writeSeqFeature

        protected void writeSeqFeature​(Annotatable f)
                                throws java.io.IOException
        Write SeqFeature XML
        Throws:
        java.io.IOException
      • writeCompResult

        protected void writeCompResult​(Annotatable f)
                                throws java.io.IOException
        Throws:
        java.io.IOException