Mesquite
   

 

 

 

 

 
     

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 for download.

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.

Installing Eclipse

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: http://www.eclipse.org/downloads/. There are multiple projects available for download at the Eclipse download site; download either the "Eclipse IDE for Java Developers" or the "Eclipse Classic" version.

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 hard drive. 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 a Welcome screen that gives you the option to read an Overview of Eclipse or do a tutorial to teach you about Java development in Eclipse. Both 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: http://subclipse.tigris.org/install.html. If you already have Subclipse installed, make sure you have the latest version as a number of bugs have been fixed since it was first released.

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. Choose 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:

http://svn.mesquiteproject.org:8080/repository/mesquite/releases/current/

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 view.

 

If you wish to acquire the source code that is actively under development, then enter the following in the URL box:

http://svn.mesquiteproject.org:8080/repository/mesquite/trunk/

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 view.

 

Expand (using the triangle) the URL to reveal a single item, Mesquite Project. Right-click (Ctrl-click on Mac with one mouse button) the Mesquite Project 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 (e.g., Cartographer) 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 the "SVN Repository Browsing" perspective, touch on the SVN+ button (), and in the dialog box that will appear, enter the following in the URL box:

http://svn.mesquiteproject.org:8080/repository/cartographer/trunk/

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 Mesquite projects.

You should now see the Cartographer repository URL on the left in your SVN Repository view.

Expand the URL (using the triangle) to reveal a single item, Cartographer. Right-click (Ctrl-click on a Mac with one mouse button) the Cartographer 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 the classpaths.xml file is as follows.

	<?xml version="1.0"?>
	<mesquite>
		<classpath>../../Cartographer/Mesquite_Folder</classpath>
	</mesquite>	
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 folder 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, then the classpaths.xml file would look like this:
	<?xml version="1.0"?>
	<mesquite>
		<classpath>../../Cartographer/Mesquite_Folder</classpath>
		<classpath>../../MyProject/Mesquite_Folder</classpath>
	</mesquite>	
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:

  1. From the main Mesquite workspace window, select the "Run" menu then select the "Run..." menu item.
  2. In the ensuing dialog, select "Java Application" in the left-side panel, then click the "New" button underneath the left-side panel.
  3. 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.
  4. Browse for the project and select "Mesquite Project" in the dialog that pops up.
  5. 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".
  6. 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"
  7. Click the "Workspace" button to browse for the working directory. Browse to and select the "Mesquite_Folder" folder underneath the main Mesquite Project directory.
  8. (THIS STEP IS NEEDED ONLY IF YOU ARE RUNNING WINDOWS) In order to make file opening function properly, add the following text into the VM arguments textbox above the Working Directory section:
    -Dmesquite.lib.noconsoleinput=true
  9. Now press Run (or Debug)
  10. 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 do this,
  • Go to the Java perspective in Eclipse.
  • Open the Package Explorer so that you can see Mesquite Project.
  • 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:

  1. 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.
  2. In the "New Project" dialog, keep the default selection, "Java Project", selected and click Next.
  3. Type a name for your project in the "Project name:" field. This should match the name of the Mesquite package you will eventually distribute.
  4. In the "Project layout" area of the dialog, select the option that says "Create separate source and output folders." Click next.
  5. In the bottom of the Java settings dialog, click the "Browse" button next to the Default Output folder textfield.
  6. 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".
  7. 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.
  8. 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."
  9. 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.
  10. 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 name MyModule 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).
  11. 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 to 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 changes; 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 development here.



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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original licensor to copy, distribute, link with or modify the Library
subject to these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties with
this License.

11. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Library at all. For example, if a patent
license would not permit royalty-free redistribution of the Library by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Library.

If any portion of this section is held invalid or unenforceable under any
particular circumstance, the balance of the section is intended to apply,
and the section as a whole is intended to apply in other circumstances.

It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
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 that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.

This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.

12. If the distribution and/or use of the Library is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Library under this License may add
an explicit geographical distribution limitation excluding those countries,
so that distribution is permitted only in or among countries not thus
excluded. In such case, this License incorporates the limitation as if
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 Library
specifies a version number of this License which applies to it and
"any later version", you have the option of following the terms and
conditions either of that version or of any later version published by
the Free Software Foundation. If the Library does not specify a
license version number, you may choose any version ever published by
the Free Software Foundation.

14. If you wish to incorporate parts of the Library into other free
programs whose distribution conditions are incompatible with these,
write to the author to ask for permission. For software which is
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 status
of all derivatives of our free software and of promoting the sharing
and reuse of software generally.

NO WARRANTY

15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.

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 that
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. It is
safest to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least the
"copyright" line and a pointer to where the full notice is found.

<one line to give the library's name and a brief idea of what it does.>
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 GNU
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 USA

Also add information on how to contact you by electronic and paper mail.

You should also get your employer (if you work as a programmer) or your
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 Random Hacker.

<signature of Ty Coon>, 1 April 1990
Ty Coon, President of Vice

That's all there is to it!





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