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.