See: Description
| Interface | Description |
|---|---|
| BitSet | |
| GeneralAnnotation |
Provide generalized annotations (descriptors).
|
| Graph<T> |
Created by Eli Rodgers-Melnick on 7/2/2014
This interface is implemented by graphs, both directed and undirected.
|
| ProgressListener | |
| SuperByteMatrix | |
| TableReport |
Interface for classes with data that can be presented in tables
|
| Class | Description |
|---|---|
| AbstractTableReport | |
| ArgsEngine |
A reusable solution for Command Line Arguments Parsing in Java.
|
| BasicFileFilter |
Title:
|
| BitSet.BitSetListCollector | |
| BitUtil |
A variety of high efficiency bit twiddling routines.
|
| BuilderFromVCFUtil | |
| CheckSum | |
| ConvertOldFastqToModernFormatPlugin |
This plugin takes a single fastq or a directory of fastq files
in the "old" format and converts them to the "modern" illumina format.
|
| DirectedGraph<T> |
Class used to represent a directed graph
The design is inspired by the Python networkx library (https://networkx.github.io/)
|
| DirectoryCrawler |
Directory crawler that matches REGEX or Glob patterns.
|
| DoubleFormat | |
| ExceptionUtils | |
| FormattedInput |
tools to simplify formatted input from an input stream
|
| FormattedOutput |
tools to simplify formatted output to a stream
|
| GeneralAnnotationStorage | |
| GeneralAnnotationStorage.Builder | |
| GraphBuilder<T> |
Builder for graphs, directed and undirected
|
| GraphUtils<T> |
Functions used for Graph traversal and analysis
|
| HDF5TableReport | |
| HDF5Utils | |
| InputSource |
convenience class to open input streams
linked to files, stdin, and strings
|
| LoggingUtils | |
| MultiMemberGZIPInputStream | |
| OpenBitSet |
An "open" BitSet implementation that allows direct access to the array of
words storing the bits.
|
| SimpleTableReport |
Created by IntelliJ IDEA.
|
| Sizeof | |
| SMTPClient |
This class can be used to send email.
|
| StringNumberComparator |
Title: TASSEL
Description: A java program to deal with diversity
Copyright: Copyright (c) 2000
Company: USDA-ARS/NCSU
|
| SuperByteMatrixBuilder | |
| SuperByteMatrixMultiple | |
| SuperByteMatrixSingle | |
| SuperByteMatrixSingleValue | |
| SuperByteMatrixTranspose | |
| TableReportBuilder | |
| TableReportUtils | |
| Tassel5HDF5Constants |
Definition of attributes and paths for Tassel HDF5 file format.
|
| Tuple<X,Y> |
Based on response in http://stackoverflow.com/questions/2670982/using-pairs-or-2-tuples-in-java
|
| UndirectedGraph<T> |
Class used to represent an undirected graph.
|
| UnmodifiableBitSet | |
| Utils |
| Enum | Description |
|---|---|
| Graph.GraphType |
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