project_manager.sgml

<CHAPTER ID="PROJ-MANAGER-CHAPTER">
  <TITLE>Project File Manager</TITLE>

  <SECT1 ID="PROJ-OVERVIEW">
    <TITLE>Overview</TITLE>
    <PARA>
The Project File Manager can be used to facilitate the launching of groups
of files together. The project details are stored between sessions of &prog;,
so that it is straightforward to return to a project and open up all the relevant
files.

     <SCREENSHOT>
       <SCREENINFO>
The Project File Manager window
       </SCREENINFO>
       <MEDIAOBJECT>
         <IMAGEOBJECT>
           <IMAGEDATA FORMAT="png" FILEREF="projMgr.png">
         </IMAGEOBJECT>
       </MEDIAOBJECT>
     </SCREENSHOT>
    </PARA>
  </SECT1>

  <SECT1 ID="PROJ-USING">
     <TITLE>Using the Project File Manager</TITLE>
    <PARA>
The Project File Manager can be opened from the <EMPHASIS>File</EMPHASIS> menu in the Artemis launch window (see <XREF LINKEND="LAUNCH-WINDOW">).
It opens with some example projects in the list on the left hand side of the panel.
Selecting a project in the list shows the associated files in the right hand side of the
window.
   </PARA>
   <PARA>
To add a new project click on the green '+' button at the top of the Project File Manager
window and enter a name for the project. The new project opens with a blank form with a 'sequence'
field. <EMPHASIS>Note that each project has to have an associated sequence file (e.g. FASTA, EMBL, GenBank or GFF) that
contains the nucleotide sequence for Artemis to open up.</EMPHASIS> New files can be added to the project 
by selecting the type of file from the drop down list at the bottom and clicking the
'NEW PROPERTY' button.
   </PARA>
   <PARA>
The project list and details are saved between sessions when Artemis is closed down. This information is
stored in the home directory in a file called '.artemis.project.properties'. When Artemis is run it looks
for a 'project.properties' file in the local directory as well as for the '.artemis.project.properties'
file in the home directory. 
   </PARA>
   <PARA>
Before opening a project the optional files can be toggled on and off in the
Project File Manager so that each can optionally be deselected and not opened.
Once a project has been set up it can be selected from the list and clicking 'OPEN' will
open the main Artemis window. 
   </PARA>
   <PARA>
To remove a project from the list, select the project name and click the red '-' button
at the top of the window.
   </PARA>
  </SECT1>

</CHAPTER>