The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:
| GroupId | ArtifactId | Version | Classifier | Type | Optional |
|---|---|---|---|---|---|
| commons-beanutils | commons-beanutils | 1.7.0 | - | jar | |
| commons-cli | commons-cli | 1.1 | - | jar | |
| org.moltools | probemaker-stdext | 1.5.0 | - | jar | |
| log4j | log4j | 1.2.14 | - | jar | (optional) |
The following is a list of runtime dependencies for this project. These dependencies are required to run the application:
| GroupId | ArtifactId | Version | Classifier | Type | Optional |
|---|---|---|---|---|---|
| net.genefront | piecemaker-swingui | 1.3.2 | - | jar | (optional) |
The following is a list of transitive dependencies for this project. Transitive dependencies are the dependencies of the project dependencies.
The following is a list of compile dependencies for this project. These dependencies are required to compile and run the application:
| GroupId | ArtifactId | Version | Classifier | Type | Optional |
|---|---|---|---|---|---|
| commons-codec | commons-codec | 1.2 | - | jar | |
| commons-collections | commons-collections | 3.2 | - | jar | |
| commons-httpclient | commons-httpclient | 3.0 | - | jar | |
| commons-io | commons-io | 1.2 | - | jar | |
| commons-logging | commons-logging | 1.0 | - | jar | |
| jdom | jdom | 1.0 | - | jar | |
| net.genefront | piecemaker-core | 1.3.3 | - | jar | |
| net.sf.apptools | apptools-core | 1.5.1 | - | jar | |
| net.sf.apptools | apptools-platform | 1.5.1 | - | jar | |
| net.sf.apptools | apptools-workbench | 1.5.1 | - | jar | |
| net.sf.apptools | textio | 0.2 | - | jar | |
| org.moltools | moltools-core | 1.4.1 | - | jar | |
| org.moltools | moltools-design | 1.4.1 | - | jar | |
| org.moltools | moltools-workbench | 1.4.1 | - | jar | |
| org.moltools | probemaker-core | 1.5.0 | - | jar |
The following is a list of test dependencies for this project. These dependencies are only required to compile and run unit tests for the application:
| GroupId | ArtifactId | Version | Classifier | Type | Optional |
|---|---|---|---|---|---|
| junit | junit | 3.8.1 | - | jar |
A Java and Perl software suite for design of selector probes for exon resequencing applications.
http://bioinformatics.org/disperse/
Swing-based graphical user interface for PieceMaker
PieceMaker data model and core functionality
ProbeMaker Standard Extensions
Standard function extensions to the ProbeMaker framework
http://probemaker.sourceforge.net/probemaker-stdext
The HttpClient component supports the client-side of RFC 1945 (HTTP/1.0) and RFC 2616 (HTTP/1.1) , several related specifications (RFC 2109 (Cookies) , RFC 2617 (HTTP Authentication) , etc.), and provides a framework by which new request types (methods) or HTTP extensions can be created easily.
http://jakarta.apache.org/commons/httpclient/
ProbeMaker data and processing model
http://probemaker.sourceforge.net/probemaker-core
The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
http://moltools-lib.sourceforge.net/moltools-core
The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
http://moltools-lib.sourceforge.net/moltools-design
Log4j
http://logging.apache.org/log4j/docs/
Commons CLI provides a simple API for presenting, processing and validating a command line interface.
http://jakarta.apache.org/commons/cli/