ProCope Java API


This is an introduction to the Java Library and its API provided by ProCope. All functionality can be embedded in your own Java applications by linking the ProCope JAR file in the classpath and then accessing the respective classes. A detailed documentation of all classes and methods can be found in the JavaDocs of ProCope. This page provides an introduction to the main functionality along with a set of well-documented sample use cases which guide you step-by-step throught most of the functionality in the library.

Classpath

In order to use the ProCope classes in your project, be sure to include one of the .jar file delivered with the download package in your Java classpath. ProCope_core-X.Y.jar (where X.Y is the current version) is needed for the main ProCope functionality. When creating diagrams and histograms or sequence alignments, you will also need the JFreeChart and JAligner libraries. These are fully included in ProCope-X.Y.jar.

Library overview

Contains a brief overview of the ProCopa Java package structure. Show overview

Use cases

Source codes of practical applications which guide you through different parts of the library. Show use cases

Extensibility

Note that you can integrate your own clusterers and scores calculators into the graphical user interface and the command line tools of ProCope. See also: User defined classes

The protein manager

Introduction and example codes on the handling of protein identifiers in the ProCope library.  Show protein manager documentation

Note: As the protein manager is an essential part of the library, its basic usage is also covered by the example use cases (see above).


Interologs

ProCope contains some methods to transfer protein protein interactions using homology information. If you are interested in these features, read the JavaDocs of the procope.methods.interologs package. Feel free to contact me via email for further information and help.



ProCope documentation