Projects and Files

(updated February 2001)

Elements of information

At any given time Mesquite is using information about taxa, characters and so on. This information might consist of:

a set of taxa
a data matrix
a set of trees
a model of character evolution

Each of these is an element of information. Each corresponds roughly to a single block or command in a NEXUS file. Such an element can be created at the user's command. For instance, a command requesting a new data matrix might yield a blank matrix the user can fill in. An element might also be read from a file on disk, as happens when Mesquite reads in a NEXUS data file.

Files on Disks and servers

Since Mesquite is designed to use the NEXUS file format (Maddison, D.R., D.L. Swofford, and W.P. Maddison. 1997. NEXUS: An extensible file format for systematic information. Systematic Biology 46: 590-621) as its primary file format, we will assume for the moment that it is using NEXUS files. A typical NEXUS file might contain a TAXA block defining taxa, a CHARACTERS block giving character data, and a TREES block. After Mesquite reads in the file, Mesquite will have in its memory a list of taxa (that it got from the TAXA block), a data matrix (that it got from the CHARACTERS block), and a set of trees (from the TREES block).

However, Mesquite is not limited to NEXUS files with this set of three blocks. Mesquite is happy with files with more than one TAXA block, more than one CHARACTERs block and so on.

Mesquite can read such a file from a web server if given the URL. If run as a local application, Mesquite can read such a file from the user's computer.

Projects

Since Mesquite can accumulate and analyze a more or less indefinitely large collection of elements of information (several sets of taxa, data matrices, and so on), Mesquite doesn't need to respect the boundaries of files. That is, it could read a TAXA block from one file on the disk, and read a data matrix for those taxa from another file on disk, and a set of trees from another file. While other programs can handle external treefiles or command files, Mesquite can handle external character matrices, assumptions, and so on.

Mesquite therefore makes a distinction between the collection of elements of information that are currently interacting with one another in Mesquite's calculations, and the physical files on disk or server. The former collection, which may include information gathered from several files, is called a project. The set of files to which the elements of information in a project belong are said to be linked.

Mesquite shows a list of the projects and files currently active in the Projects and Files window:

Opening versus Including versus Linking files

In Mesquite there are three ways to read a file: Open, Include and Link.

Open — If a file is to be opened up independently of any other open files, and not share information, it should be opened using the Open submenu. A file opened in this way is treated as belonging to a project separate from any other files open at the time.
Include — To read in the contents of a file and merge them into an existing file, so that all of its information becomes part of the existing file and is saved into that existing file, use the Include submenu in the Open submenu.
Link — To read in the contents of a file and add its information to a collection of information in a project in use, but to maintain the file separate for purposes of writing to the disk, use the Link submenu in the File menu. A file opened in this way will become part of the project. Because of the interdependencies among elements of information that can exist (list of taxa in a data file matches list of taxa in a tree file), it is possible that editing information that belongs to one file will also change information in a linked file.