org.utgenome.format.axt
Class AXTLens

java.lang.Object
  org.utgenome.format.axt.AXTLens

All Implemented Interfaces:

org.xerial.lens.TextFormatLens

public class AXTLens
extends Object
implements org.xerial.lens.TextFormatLens

Lens for AXT format

Author:

leo

Constructor Summary

AXTLens(BufferedReader in)

AXTLens(URL axt)

Method Summary

void	convert(org.xerial.lens.ObjectStreamHandler handler)
static Iterable<AXTAlignment>	lens(BufferedReader in)
static void	lens(BufferedReader in, org.xerial.util.ObjectHandler<AXTAlignment> handler)
static void	lens(File axtFile, org.xerial.util.ObjectHandler<AXTAlignment> handler)
static AXTAlignment	lens(List<String> axtBlock)
static void	parseSummaryLine(AXTAlignment obj, String summaryLine)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AXTLens

public AXTLens(BufferedReader in)

AXTLens

public AXTLens(URL axt)
        throws IOException

Throws:

IOException

Method Detail

lens

public static AXTAlignment lens(List<String> axtBlock)
                         throws UTGBException

Throws:

UTGBException

parseSummaryLine

public static void parseSummaryLine(AXTAlignment obj,
                                    String summaryLine)
                             throws UTGBException

Throws:

UTGBException

lens

public static Iterable<AXTAlignment> lens(BufferedReader in)
                                   throws UTGBException

Throws:

UTGBException

lens

public static void lens(BufferedReader in,
                        org.xerial.util.ObjectHandler<AXTAlignment> handler)
                 throws UTGBException

Throws:

UTGBException

lens

public static void lens(File axtFile,
                        org.xerial.util.ObjectHandler<AXTAlignment> handler)
                 throws UTGBException

Throws:

UTGBException

convert

public void convert(org.xerial.lens.ObjectStreamHandler handler)
             throws Exception

Specified by:

convert in interface org.xerial.lens.TextFormatLens

Throws:

Exception