Mesquite source code
There are two different versions of the Mesquite source code:
(1) the code for the latest official release version of Mesquite,
and (2) the current, active code that is in development. This
active code is less well tested, and may contain more bugs and
incomplete features, but it does contain new features and may
also have some bug fixes. Both versions of source code are available
This page contains details on acquiring the source code, and
developing your own code.
NOTE: Instructions below are obsolete. We have switched to Git. The repository for the currently active source is at http://github.com/MesquiteProject/MesquiteCore. The repository for released versions is at http://github.com/MesquiteProject/MesquiteArchive. We will update the instructions below accordingly.
Obtaining source code
There are two ways to get Mesquite source code:
Using Eclipse for Mesquite development
We are using Eclipse as our IDE for Mesquite development, and
Subversion as our version control system. Here we explain how
to use Eclipse to obtain and compile the Mesquite source code.
If you are using a different development environment you might
skip directly to the section on subversion access.
Eclipse is an integrated development environment (IDE) that
allows a programmer to organize, edit, and compile their programs.
In order to get started with programming Mesquite, you should
download and install Eclipse. Eclipse can be downloaded here:
There are multiple projects available for download at the Eclipse
site; download either the "Eclipse IDE for Java Developers" or
Eclipse is distributed as a .zip file for
Windows and as a .tar.gz file for Mac OS X and Linux. Once you
have downloaded the distribution
file, you will need to unzip/untar it to a location on your
Once unzipped, there will be an "eclipse" directory on your
computer that contains an executable file (application) called "Eclipse" (Linux
or Mac OS X) or "Eclipse.exe" (Win32x). This is the
file that starts Eclipse. Move the eclipse directory to your
perferred place in your hard disk; e.g., with
your other applications.
Start up Eclipse or Eclipse.exe in the
eclipse directory. The first time you start Eclipse, you
will be presented with
that gives you the option to read an Overview of Eclipse or do
a tutorial to teach you about Java development in Eclipse.
are very helpful and are recommended for new Eclipse users.
Installing a Subversion plugin within Eclipse
The Mesquite source is available via a version control system
called Subversion. There are many ways of accessing a Subversion
repository; we use the Subclipse plugin for Eclipse.
Detailed instructions for installing Subclipse can be found here:
If you already have Subclipse installed, make sure you have the
latest version as a number of bugs have been fixed since it was
For more detailed instructions on Subversion and version control in general,
please refer to this free online book: http://svnbook.red-bean.com/
You could use instead the Subversive plugin, which appears to have some advantages over Subclipse.
Subversion checkout of Mesquite Source
In order to download the Mesquite source code, you will need
to switch your Eclipse perspective to the "SVN Repository
Browsing" perspective. In Eclipse, perspectives define
the initial set and layout of views in the Workbench window.
the SNV Repository Browsing perspective in the dialog box that
appears when you choose Window>Open Perspective>Others...
For more information about Eclipse perspectives, visit the Eclipse
manual page on perspectives.
Once you have switched to the "SVN Repository Browsing"
perspective, you need to add the Mesquite SVN Repository using
the SVN+ button ()
located at the top-right
corner of the left-hand
SVN Repository panel. Once you
touch the SVN+ button, you will presented with a dialog box
in which you enter the URL of the source code repository.
If you wish to acquire the source code for the latest
official release, then enter the following in the URL box:
and press Finish (you will not need to enter a user name or password). You should now see the Mesquite repository URL on the left in your SVN Repository
If you wish to acquire the source code that is actively
under development, then enter the following in the URL box:
and press Finish (you will not need to enter a user name or password). You should now see the Mesquite repository URL on the left in your SVN Repository
Expand (using the triangle) the URL to reveal a single item,
Mesquite Project. Right-click (Ctrl-click on Mac with one mouse
folder and select "Checkout As Project."
This will begin the process of checking out the Mesquite source
code to your computer. Once this is completed, you should switch
back to the Java perspective where you will see a new project,
called "Mesquite Project."
Given the number of classes in Mesquite, you will probably want to switch the Layout to "Hierarchical". You can do this by touching on the little triangle at the upper right of the Package Explorer panel, and choosing Layout>Hierarchical in the popup menu.
Checking out source for other projects
Mesquite packages that are distributed separately from Mesquite
are organized into their own Eclipse source code projects. If
you have access to some of these projects,
you can also check them out from the Mesquite SVN repository.
Cartographer source is available.
For example, to checkout the Cartographer source, switch to
Repository Browsing" perspective, touch on the SVN+
and in the dialog box that will appear, enter
the following in the URL box:
and press Finish. You will not need to enter a username and
password to get the active Cartographer source, but you will
likely need a username and password to acquire source from other
Cartographer repository URL on the left in
Expand the URL (using the triangle) to reveal a single item,
Cartographer. Right-click (Ctrl-click on a Mac with one mouse
folder and select "Checkout As Project."
This will begin the process of checking out the Cartographer
source code to your computer.
Use the exact same mechanism to check out other projects to
which you have access.
These other projects will be placed in your Eclipse workspace,
but in a different folder than the main Mesquite Project. Because
if this, you will need configure Mesquite to find them (as described
in the next section).
Configuring Mesquite to load other projects
The class files contained in the projects other than Mesquite
Project will not be found by Mesquite unless you tell Mesquite
where to look. You do this by creating a "classpaths.xml" file
that contains the locations of the other classes, and placing
the file in the Mesquite_Folder in
Mesquite Project in your Eclipse workspace. The format of
file is as follows.
This tells Mesquite to look outside of Mesquite_Folder, outside
of Mesquite Project, then inside Cartographer/Mesquite_Folder.
An example classpaths.xml file, as shown above, is contained
in the Additional Files folder within the Mesquite Project
in your workspace.
If you have other projects that you want
Mesquite to find, add
more <classpath></classpath> lines.
For example, if you have a separate project called MyProject,
file would look like this:
It is also advisable to save a backup copy of your classpaths.xml file
in another directory not under
subversion control. When updating Mesquite Project, the classpaths.xml
file is sometimes deleted, so a backup copy would allow you to copy and paste
the file into the Mesquite_Folder directory as opposed to creating
a new classpaths.xml file every time you update your workspace.
Creating a Mesquite launch configuration
Eclipse needs to be configured to launch Mesquite. Follow these
steps to do so:
- From the main Mesquite workspace window, select the "Run"
menu then select the "Run..." menu item.
- In the ensuing dialog, select "Java Application"
in the left-side panel, then click the "New" button
underneath the left-side panel.
- There should be a new element underneath the "Java Application"
element on the left-side entitled "New_configuration".
Rename this to "Mesquite" by typing in the name
text field on the right hand side.
- Browse for the project and select "Mesquite Project"
in the dialog that pops up.
- Browse for the Main class and select Mesquite
in the dialog that pops up. "mesquite.Mesquite" show
now appear in the field under "Main class".
- Click on the "Arguments" tab on the right half
on the window. Near the bottom of the panel there is a section
entitled "Working directory". Deselect the checkbox
that says "Use default working directory"
- Click the "Workspace" button to browse for the
working directory. Browse to and select the "Mesquite_Folder"
folder underneath the main Mesquite Project directory.
- (THIS STEP IS NEEDED ONLY IF YOU ARE RUNNING WINDOWS) In
order to make file opening function properly, add the following
into the VM arguments textbox above the Working Directory section:
- Now press Run (or Debug)
- You should now be able to launch or debug Mesquite whenever
you wish by opening the Run (or Debug) menu, selecting the "Mesquite"
item in the list and clicking the Run (or Debug) button.
Running a development copy of Mesquite outside of Eclipse
If you wish to run Mesquite outside of Eclipse (for example,
by directly starting up the Mesquite file in the Mesquite Folder
in Mesquite Project in your workspace), then you will need to
do the following:
- Find the jars.zip file that is in the Additional Files
folder in the Mesquite Project folder in your workspace.
- Unzip the jars.zip file.
- Move the jars folder that is created into the Mesquite
Folder in the Mesquite Project folder.
- Create and edit a classpaths.xml file so that Mesquite will know to load files in other projects
- On MacOS X, for reasons that we don't understand yet,
Eclipse seems to damage the executable files that are needed
to launch Mesquite in the standard way. If on a Mac you
find Mesquite does not launch appropriately, then open
unzip the file executables.zip that is contained in the
Additional Files folder, and move its contents into Mesquite_Folder,
replacing the existing files of the same name.
Updating a project to the latest source
Once you have your Eclipse workspace configured, you can update your source
code to the latest that is present on Mesquite's SVN server. To
- Go to the Java perspective in Eclipse.
- Open the Package Explorer so that you can see Mesquite
- Right-click or Ctrl-click on Mesquite Project and choose from the menu that appears Team>Update. Eclipse will contact the SVN server at mesquiteproject.org and pull down the latest source.
Developing your own modules
The developer's documentation
explains how Mesquite works and in general how to program for
it. It is incomplete and out of date, but should assist orienting
you. We here describe how you can establish your own project
in order to build modules within Eclipse.
In order to extend Mesquite with your own analyses or tools,
first check out the Mesquite Project within Eclipse as described
above. For your own modules, it's best
to create a separate Java project with all of your code.
To create a new Java project in Eclipse and configure it to
refer to the main Mesquite Project, follow these steps:
- From the main Mesquite workspace window, select the "File"
menu, select the "New" menu item, then select the
"Project" menu item in the "New" submenu.
- In the "New Project" dialog, keep the default selection,
"Java Project", selected and click Next.
- Type a name for your project in the "Project name:"
field. This should match the name of the Mesquite package you
will eventually distribute.
- In the "Project layout" area of the dialog, select
the option that says "Create separate source and output
folders." Click next.
- In the bottom of the Java settings dialog, click the "Browse"
button next to the Default Output folder textfield.
- In the dialog that comes up select the root folder (the folder
that is named as the same as your project) then click on the
"Create New Folder" button. Name your new folder "Mesquite_Folder"
and click "OK". In the Folder Selection dialog select
the new Mesquite_Folder and click "OK".
- Click the "Projects" tab in the Java Settings dialog.
Click "Add" and select "Mesquite Project"
in the Required Project Selection dialog. Click Finish to create
your project in the workspace.
- Expand the contents of your new project by clicking on the
triangle next to it. Right click (Ctrl-click on a Mac with
a single-button mouse) on the
"src" folder and select the "Refactor" menu
and choose "Rename." For the new name type "Source."
- Right-click on the "Source" folder, select the "New"
menu then choose "Package" in the "New"
menu. In the name field, start your package name with "mesquite."
and finish it with whatever the name of your Mesquite feature
will be. Click "Finish" to create your new package.
- You can start creating new packages and classes underneath
your new package as described in the developer's
documentation. We also encourage you to use existing
modules as models. Remember that for a module with class
to be found by Mesquite, its immediate package needs to have
the same name (i.e., the module needs to be mesquite.mypackage.MyModule.MyModule.class).
- You can test your project classes by launching Mesquite from
within Eclipse as specified here. However,
for Mesquite to find your class files at runtime, you need
edit the classpaths.xml file located in Mesquite_Folder in
Mesquite Project in your Eclipse workspace to include the
classpath of your project's class files (see above).
Contributing changes to the
official Mesquite code
If you check out the Mesquite Project from the Mesquite repository, you
will have Mesquite's main code base. You can make
changes to this core code, if you wish. It may be the case that
as you write your own modules, you will discover bugs in the main
Mesquite code that need to be fixed or you will have methods that
you would like to add to some of the standard classes such as
DNAData. We suggest that you contact us with recommendations for such
we will consider incorporating them into the
official Mesquite code.
Mesquite Development mailing list
You may sign up for a mailing list for discussion of Mesquite
Copyright © 2007-2011 W.P. & D.R. Maddison
Mesquite source code is Copyright ©1997-2011 W.P. Maddison
and D.R. Maddison unless otherwise stated in a source code file
itself. Mesquite is distributed under the terms of the GNU
Lesser General Public Licence. The example data files ARE
NOT distributed under the GNU LGPL.
This open source code is provided by Wayne Maddison, University
of British Columbia and David Maddison, University of Arizona,
and is intended for non-commercial use only. Copyright ©2002-2009
Arizona Board of Regents on Behalf of The University of Arizona.
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patents or other property right claims or to contest validity
such claims; this section has the sole purpose of protecting
integrity of the free software distribution system which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of
system; it is up to the author/donor to decide if he or she is
to distribute software through any other system and a licensee
impose that choice.
This section is intended to make thoroughly clear what is believed
be a consequence of the rest of this License.
12. If the distribution and/or use of the Library is restricted
certain countries either by patents or by copyrighted interfaces,
original copyright holder who places the Library under this License
an explicit geographical distribution limitation excluding those
so that distribution is permitted only in or among countries
excluded. In such case, this License incorporates the limitation
written in the body of this License.
13. The Free Software Foundation may publish revised and/or new
versions of the Lesser General Public License from time to time.
Such new versions will be similar in spirit to the present version,
but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the
specifies a version number of this License which applies to it
"any later version", you have the option of following
the terms and
conditions either of that version or of any later version published
the Free Software Foundation. If the Library does not specify
license version number, you may choose any version ever published
the Free Software Foundation.
14. If you wish to incorporate parts of the Library into other
programs whose distribution conditions are incompatible with
write to the author to ask for permission. For software which
copyrighted by the Free Software Foundation, write to the Free
Software Foundation; we sometimes make exceptions for this. Our
decision will be guided by the two goals of preserving the free
of all derivatives of our free software and of promoting the
and reuse of software generally.
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS
OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF
LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY
AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO
LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES
FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Libraries
If you develop a new library, and you want it to be of the greatest
possible use to the public, we recommend making it free software
everyone can redistribute and change. You can do so by permitting
redistribution under these terms (or, alternatively, under the
terms of the
ordinary General Public License).
To apply these terms, attach the following notices to the library.
safest to attach them to the start of each source file to most
convey the exclusion of warranty; and each file should have at
"copyright" line and a pointer to where the full notice
<one line to give the library's name and a brief idea of what
Copyright (C) <year> <name of author>
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
Also add information on how to contact you by electronic and
You should also get your employer (if you work as a programmer)
school, if any, to sign a "copyright disclaimer" for
the library, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the
library `Frob' (a library for tweaking knobs) written by James
<signature of Ty Coon>, 1 April 1990
Ty Coon, President of Vice
That's all there is to it!