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PROJECT STRUCTURE


File/Folder Description
apidoc/ (autogenerated) contains autogenerated documentation
build/ (autogenerated) contains generated class files
release/ (autogenerated) output: jnlp, jar and zip package.
lib/ contains the external libraries that PathVisio needs.
example-data/ mapp and gpml files for quick testing
modules/ the java source code for each of the different modules
pathvisio.sh shortcut for running PathVisio from the command line (Linux/MacOSX)
pathvisio.bat shortcut for running PathVisio from the command line (Windows)
readme.md this file
build.xml ant build file (see below)
pathvisio.iss inno-setup script, to generate installer

HOW TO IMPORT IN ECLIPSE


For detailed instructions, please see: https://github.com/PathVisio/pathvisio/wiki/PathVisio-setup-in-Eclipse


HOW TO BUILD WITH ANT


Using the ant build file, you can build the project from the command line. You can also use ant to generate the apidocs and to create an executable jar.

It is also possible to set up eclipse to build ant targets.

First make sure ant is set up properly. It comes with eclipse, but you'll have to check if the path is set correctly if you want to run it from the command line.

The ant build file provides the following targets, which you can invoke it from the directory which contains build.xml with

ant <target>

where is one of:

compile:   just compile all classes
docs:      generate all apidocs
exe:       generate executable jar file
clean:     remove all generated files
dist:      generate zip package and windows installer. 
           The zip package only includes files needed to *run* not compile.
all:       clean, then compile, jar, dist and docs.

HOW TO RUN FROM THE TERMINAL


If you have managed to build the classes with ant or with eclipse, you can use pathvisio.bat to start java from the command line.

PathVisio's Projects

biopax-plugin icon biopax-plugin

PathVisio plugin to import and export pathways in BioPAX format

gpml icon gpml

Graphical Pathway Markup Language

libgpml icon libgpml

Java library for reading / writing GPML files

mipast icon mipast

miRNA pathway statistics plugin for PathVisio

pathvisio icon pathvisio

PathVisio - pathway editor, visualization and analysis software

pathvisiorpc icon pathvisiorpc

PathVisioRPC is an XML-RPC implementation of PathVisio that allows users to create and edit biological pathways, visualize data on pathways, perform pathway statistics and exports results in various image formats. Since most major programming languages have a library/module providing XML-RPC functionality, this application enables users to access PathVisio functionality from their favourite analytical environment.

pv-minimap icon pv-minimap

Plugin for PathVisio that adds a MiniMap side panel for navigation in large pathways

regint-plugin icon regint-plugin

Visualize regulatory interactions in the side panel of PathVisio

tutorials icon tutorials

Tutorials and workshop material for PathVisio

wp-plugin icon wp-plugin

Plugin for PathVisio that provides a WikiPathways client.

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