MSFTBX Examples

Companion repo for MSFTBX - mass spectrometry data readers library: http://github.com/chhh/msftbx.
Provides a complete example java app built with Gradle that prints some information about MS2 scans.

Running it

You don't need to have gradle or any libraries installed. Bootstrapping feature will get everything needed automatically.

Automatically build and run

./gradlew run --args "path-to-mzml-or-mzxml-file"

This command will build the application jar and start it with your default Java, passing it the values you specify after --args.

Manually build and run

Alternatively you can tell gradle to build the app and create launch scripts for it (windows and linux)

./gradlew clean install

This command will produce output in build/install/msftbx-examples. Run scripts will be in bin sub-directory, and all the jar dependencies will be in lib sub-directory.
You just start the script for your OS from the bin directory.

By modifying the build.gradle file it's also easy to package the whole application in a single fat jar file. See gradle-shadow plugin.

Run from Intellij Idea

You can just import the project into Intellij IDEA and click the green Run triangle icon next to main() method of msftbx.examples.App. To import, start IDEA, if you get into its launcher First, click Open or Import. if you already have it running with some project open: File -> New -> Project from Existing Sources. Select the build.gradle file. IDEA will offer you to open the project in a new window.

If it's your first time using gradle, it might take a while to initially download all dependencies. After the initial import everything will be very fast.