io.repseq.dto

Class VDJCDataUtils

java.lang.Object

io.repseq.dto.VDJCDataUtils

public final class VDJCDataUtils
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VDJCDataUtils.FragmentsBuilder

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Comparator<java.lang.String>	SMART_COMPARATOR
static java.util.Comparator<java.lang.String>	SMART_COMPARATOR_INVERSE

Method Summary

Modifier and Type	Method and Description
static java.util.List<KnownSequenceFragmentData>	extractFragments(java.net.URI uri, com.milaboratory.core.sequence.provider.CachedSequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> provider)
static VDJCLibraryData[]	merge(java.util.List<VDJCLibraryData> libraries) Merges VDJCLibraryData objects for the same species into single object.
static VDJCLibraryData[]	readArrayFromFile(java.nio.file.Path file)
static VDJCLibraryData[]	readArrayFromFile(java.lang.String file)
static int	smartCompare(java.lang.String s1, java.lang.String s2)
static void	sort(java.util.List<VDJCLibraryData> libraries) Sort libraries and genes inside them.
static void	sort(VDJCLibraryData library) Sort records inside library
static void	sort(VDJCLibraryData[] libraries) Sort libraries and genes inside them.
static void	writeToFile(java.util.List<VDJCLibraryData> data, java.nio.file.Path file, boolean compact)
static void	writeToFile(java.util.List<VDJCLibraryData> data, java.lang.String file, boolean compact)
static void	writeToFile(VDJCLibraryData[] data, java.nio.file.Path file, boolean compact)
static void	writeToFile(VDJCLibraryData[] data, java.lang.String file, boolean compact)

Methods inherited from class java.lang.Object

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

Field Detail

SMART_COMPARATOR

public static final java.util.Comparator<java.lang.String> SMART_COMPARATOR

SMART_COMPARATOR_INVERSE

public static final java.util.Comparator<java.lang.String> SMART_COMPARATOR_INVERSE

Method Detail

sort

public static void sort(java.util.List<VDJCLibraryData> libraries)

Sort libraries and genes inside them.

Parameters:

libraries - libraries to sort

sort

public static void sort(VDJCLibraryData[] libraries)

Sort libraries and genes inside them.

Parameters:

libraries - libraries to sort

sort

public static void sort(VDJCLibraryData library)

Sort records inside library

Parameters:

library - library

merge

public static VDJCLibraryData[] merge(java.util.List<VDJCLibraryData> libraries)

Merges VDJCLibraryData objects for the same species into single object.

Parameters:

libraries - libraries

Returns:

list of merged libraries

extractFragments

public static java.util.List<KnownSequenceFragmentData> extractFragments(java.net.URI uri,
                                                                         com.milaboratory.core.sequence.provider.CachedSequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> provider)

readArrayFromFile

public static VDJCLibraryData[] readArrayFromFile(java.lang.String file)
                                           throws java.io.IOException

Throws:

java.io.IOException

readArrayFromFile

public static VDJCLibraryData[] readArrayFromFile(java.nio.file.Path file)
                                           throws java.io.IOException

Throws:

java.io.IOException

writeToFile

public static void writeToFile(VDJCLibraryData[] data,
                               java.lang.String file,
                               boolean compact)
                        throws java.io.IOException

Throws:

java.io.IOException

writeToFile

public static void writeToFile(VDJCLibraryData[] data,
                               java.nio.file.Path file,
                               boolean compact)
                        throws java.io.IOException

Throws:

java.io.IOException

writeToFile

public static void writeToFile(java.util.List<VDJCLibraryData> data,
                               java.lang.String file,
                               boolean compact)
                        throws java.io.IOException

Throws:

java.io.IOException

writeToFile

public static void writeToFile(java.util.List<VDJCLibraryData> data,
                               java.nio.file.Path file,
                               boolean compact)
                        throws java.io.IOException

Throws:

java.io.IOException

smartCompare

public static int smartCompare(java.lang.String s1,
                               java.lang.String s2)