public final class VDJCDataUtils
extends java.lang.Object
| Modifier and Type | Class and Description |
|---|---|
static class |
VDJCDataUtils.FragmentsBuilder |
| 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 |
| 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) |
public static final java.util.Comparator<java.lang.String> SMART_COMPARATOR
public static final java.util.Comparator<java.lang.String> SMART_COMPARATOR_INVERSE
public static void sort(java.util.List<VDJCLibraryData> libraries)
libraries - libraries to sortpublic static void sort(VDJCLibraryData[] libraries)
libraries - libraries to sortpublic static void sort(VDJCLibraryData library)
library - librarypublic static VDJCLibraryData[] merge(java.util.List<VDJCLibraryData> libraries)
libraries - librariespublic static java.util.List<KnownSequenceFragmentData> extractFragments(java.net.URI uri, com.milaboratory.core.sequence.provider.CachedSequenceProvider<com.milaboratory.core.sequence.NucleotideSequence> provider)
public static VDJCLibraryData[] readArrayFromFile(java.lang.String file) throws java.io.IOException
java.io.IOExceptionpublic static VDJCLibraryData[] readArrayFromFile(java.nio.file.Path file) throws java.io.IOException
java.io.IOExceptionpublic static void writeToFile(VDJCLibraryData[] data, java.lang.String file, boolean compact) throws java.io.IOException
java.io.IOExceptionpublic static void writeToFile(VDJCLibraryData[] data, java.nio.file.Path file, boolean compact) throws java.io.IOException
java.io.IOExceptionpublic static void writeToFile(java.util.List<VDJCLibraryData> data, java.lang.String file, boolean compact) throws java.io.IOException
java.io.IOExceptionpublic static void writeToFile(java.util.List<VDJCLibraryData> data, java.nio.file.Path file, boolean compact) throws java.io.IOException
java.io.IOExceptionpublic static int smartCompare(java.lang.String s1,
java.lang.String s2)