Source+Code

=Mesquite Source Code= There are three different versions of the Mesquite source code available publicly:
 * 1) source code of the official release versions of Mesquite. These are the simple, numbered versions (e.g., version 1.0, or version 3.0).
 * 2) source code of the latest interim version. Not of "official release" quality, but still considered of sufficient quality to be generally useable.
 * 3) 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.

This page contains details on acquiring the source code, and developing your own code.

Using Eclipse for Mesquite development
We are using Eclipse as our IDE for Mesquite development, and GIT as our version control system. Here we explain how to use Eclipse to obtain and compile the Mesquite source code. This section is written for Eclipse version 4.4 ("Luna"); it will probably work generally well for subsequent versions as well. If you are using a different development environment you might skip directly to the section on GIT 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: []. There are multiple download opitons at the Eclipse download site; the standard version should work just fine.

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.

Obtaining source code
The Mesquite source is available via a version control system called GIT. There are many ways of accessing a GIT repository; we use the GIT plugin that is distributed with Eclipse. To begin, you will need to go to GitHub and create your own account.

The source code for the core of Mesquite is present on GitHub in several versions:
 * 1) source code for the official releases can be found be exploring here: [] If you wish to pull down one of these versions, you should go there and find the version you want, so that you have the URL for that particular version.
 * 2) source code for the current interim release is the **master** branch at this URL: [].
 * 3) source code for the active development version is the **development** branch at this URL: []. This branch normally is a functional version of Mesquite, but on occasion it may have notable issues.

There will be other branches in the GitHub repository containing exploratory code that should in general not be trusted.

In Eclipse, do the following steps to pull the Mesquite source code onto your computer: > > The GIT Repositories panel should now be visible. > > Enter your GitHub user name under Authentication, and your GitHub password. Then press the Next button.
 * 1) First, prepare Eclipse for the Mesquite code by choosing Preferences. In the Preferences dialog box, choose General, and then from within there touch on "Workspace". Under "Text file encoding", select "UTF-8" beside "Other". Press the Apply button, and then press OK to close the Preferences dialog box.
 * 1) Choose Window>Open Perspective>Other... and in the dialog box that appears, choose GIT
 * 1) Press on "Clone a GIT Repository". In the dialog box that appears, enter the URI for the version of Mesquite you would like to get (see addresses above) in the URI field:
 * 1) In the Branch Selection dialog box, make sure "master" (for latest official release) or "development" (for active development branch) is selected. Press Next.
 * 2) In Local Destination dialog box, check "import all existing projects after clone finishes", and press Finish.

Eclipse will now contact GitHub and download the Mesquite source to your computer. Once this is completed, you should switch back to the Java perspective where you will see a new project, called "MesquiteCore."

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.

If there are problems after acquiring or pulling the latest Mesquite code
If the icon for MesquiteCore has a red x or red ! on it, then you should:
 * 1) Right-click or Control-click on MesquiteCore in the Package Explorer and choose Properties.
 * 2) In the dialog box that appears:
 * 3) Under Java Compiler make sure the code compliance level is set to **1.6**.
 * 4) Under Java Build Path, the Libraries tab, check to see that there is not a red X beside the JRE System Library entry. If there is, then select it, press Remove. Then press Add Library, select JRE System Library, and choose Workspace default.

Creating a Mesquite launch configuration
Eclipse needs to be configured to launch Mesquite. Follow these steps to do so: > -Dmesquite.lib.noconsoleinput=true
 * 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 "MesquiteCore" 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". Select the checkbox that says "Other"
 * 7) Click the "Workspace" button to browse for the working directory. Browse to and select the "Mesquite_Folder" folder underneath the main Mesquite Core 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:
 * 1) Now press Run (or Debug)
 * 2) 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 Core 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 Core folder in your workspace.
 * Unzip the jars.zip file.
 * Move the jars folder that is created into the Mesquite Folder in the Mesquite Core folder.
 * Create and edit a classpaths.txt file so that Mesquite will know to load files in other projects.
 * On Windows, if there is no Mesquite.exe in the Mesquite_Folder, then go in to the Additional Files folder, copy the Mesquite.exe file, and paste it into Mesquite_Folder.

My copy of Mesquite won't start or is missing features; why?
On occasion Eclipse will mess up the various aspects of the installation. This will cause one of two problems:
 * 1) The Mesquite application won't start up at all. To fix this, 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. On Windows, if there is no Mesquite.exe in the Mesquite_Folder, then go in to the Additional Files folder, copy the Mesquite.exe file, and paste it into Mesquite_Folder.
 * 2) The Mesquite application will start up, but it will not complete the startup process because of an error. The message given is only "Error caught in Mesquite", or something equally cryptic. Check to see if there is a jars folder in Mesquite_Folder. There may be a jars folder in Mesquite Core (outside of the Mesquite_Folder), and copying that into Mesquite_Folder may work. However, if you still encounter problems, then unzip the jars.zip file that is Additional Files, and m ove the jars folder that is created into the Mesquite_Folder in the Mesquite Core folder.
 * 3) The Mesquite application will start up, but some separate packages (e.g. Zephyr) that you have in your Eclipse Workspace aren't showing up within Mesquite (i.e., their features are missing). Eclipse may have thrown away your classpaths.txt file (see below); you will then need to add it back to your Mesquite_Folder.

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 GitHub repositories using the same mechanism described above. You will need to find the URI for the repository. For some of the repositories, you can explore on https://github.com/MesquiteProject/ For Cartographer, the URI is https://github.com/MesquiteProject/Cartographer.

Configuring Mesquite to load other projects
The class files contained in the projects other than MesquiteCore will not be found by Mesquite unless you tell Mesquite where to look. You do this by creating a "classpaths.txt" file that contains the locations of the other classes, and placing the file in the Mesquite_Folder in MesquiteCore in your Eclipse workspace. The format of the classpaths.txt file is as follows for MacOS X and Linux: code ../../Cartographer/Mesquite_Folder

code

(For Windows, use \ rather than /) This tells Mesquite to look outside of Mesquite_Folder, outside of MesquiteCore, then inside Cartographer/Mesquite_Folder. An example classpaths.txt file, as shown above, is contained in the Additional Files folder within the MesquiteCore folder in your workspace.

If you have other projects that you want Mesquite to find, add more lines. For example, if you have a separate project called MyProject, then the classpaths.txt file would look like this: code ../../Cartographer/Mesquite_Folder ../../MyProject/Mesquite_Folder

code

It is also advisable to save a backup copy of your classpaths.txt file in another directory notunder subversion control. When updating Mesquite Project, the classpaths.txt 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.txt file every time you update your workspace.

//Note: in Mesquite 3.31 and earlier a classpaths.xml file was used to house extra classpaths. This was changed to the simpler text file format shown above in version 3.4 of Mesquite.//

Updating the latest source
Once you have your Eclipse workspace configured, you can update your source code to the latest that is present on GitHub. To do this,
 * Go to the Java perspective in Eclipse.
 * Open the Package Explorer so that you can see MesquiteCore.
 * Right-click or Ctrl-click on MesquiteCore and choose, from the menu that appears, Team>Pull. Eclipse will contact GitHub 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 MesquiteCore 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 MesquiteCore, 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 "MesquiteCore" 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.txt file located in Mesquite_Folder in MesquiteCore 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 MesquiteCore 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. If you wish for us to consider incorporation of this code, then please submit a pull request in GitHub; please provide enough descriptive details in the pull request to help us judge the value of your modifications. If you wish to be involved more extensively, please contact us directly.

Mesquite Development mailing list
You may sign up for a mailing list for discussion of Mesquite development [|here].

Software distributed with and used by Mesquite
Mesquite uses the following pieces of software:
 * [|ByteBuddy], distributed under an [|Apache 2.0 license].
 * BrowserLauncher by Eric Albert
 * corejava.Format by Horstmann & Cornell
 * iText by Lowagie & Soares.
 * JAMA by The MathWorks and NIST
 * JSci by Mark Hale, Jaco van Kooten and others (see Mesquite source code for details).
 * The PAL library by Drummond and Strimmer is used by the GTR substitution model for DNA sequence simulations.

Mesquite Source Code License
Mesquite source code is Copyright ©1997-2017 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, Oregon State University, and is intended for non-commercial use only. Copyright ©2002-2009 Arizona Board of Regents on Behalf of The University of Arizona.

GNU Lesser General Public Licence
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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. 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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.  Copyright (C) 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. , 1 April 1990 Ty Coon, President of Vice That's all there is to it!