To save a new project to a file or to save a project that was loaded from a file to a different file, select Save Project As from the File menu. A dialog box similar to the following will appear, but may differ according to the operating system (Windows XP interface shown here):
The box provides the interface for choosing the file name and the information about the location where the file is to be saved.
By default, MorphoJ suggests a file name consisting of the name of the project ("myProject" in the example) with the extension ".morphoj". This extension was chosen to minimize the potential for confusion, but users are free to use any other file name extension or none at all.
During the process of saving the file, the cursor will change shape. The program can be used, but to avoid possible problems, users should avoid operations that change the structure of the project tree (deleting items or adding new analyses).
Saving a file does not interrupt the current session of MorphoJ, and work can be continued when the process is complete. The file can later be loaded into MorphoJ again by selecting Open Existing Project in the File menu.
The file with the project information is a special type of XML file that reflects the structure of the project tree. Users can open it with text editor software to view its contents, but are strongly advised against making any changes in the file, because this may make the file unreadable for MorphoJ or parts of the project may be lost.