<CHAPTER ID="MAINWINDOW-CHAPTER">
  <TITLE>The &prog; Main Window</TITLE>
  <PARA>
This chapter describes the main viewing window of &prog;.  First is an
overview of the window and a description of the three main window menus -
File, Graphs (Top) and Graphs (Bottom).  The other menus are accessible only
from the pop-up menu in the view windows (see <XREF
LINKEND="VIEWS-OTHERMOUSE"> and <XREF LINKEND="VIEWS-POPUPMENU"> for more).
  </PARA>

  <SECT1 ID="MAINWINDOW-OVERVIEW">
    <TITLE>Overview of the Comparison Window</TITLE>
    <PARA>
The following images show a breakdown of the main &prog; window taken from a
<ULINK
URL="http://www.sanger.ac.uk/Software/Artemis/ACT/gfx/user_manual_screen_shot.gif"
TYPE="external">screen shot</ULINK>.
    </PARA>

    <ORDEREDLIST ID="MAINWINDOW-BREAKDOWN-LIST">
      <LISTITEM>
        <PARA ID="MAINWINDOW-BREAKDOWN-MENU">
          <SCREENSHOT>
            <SCREENINFO>
The menu bar of the main &prog; window
            </SCREENINFO>

            <![ %html-flag; [
            <GRAPHIC FORMAT="gif" FILEREF="act_main_window_1.gif">
            ]]>

            <![ %ps-flag; [
            <GRAPHIC FORMAT="eps" FILEREF="act_main_window_1.eps">
            ]]>
          </SCREENSHOT>
        </PARA>
      </LISTITEM>

      <LISTITEM>
        <PARA ID="MAINWINDOW-BREAKDOWN-ENTRY-BUTTONS">
          <SCREENSHOT>
            <SCREENINFO>
The buttons controlling from the main &prog; window
            </SCREENINFO>

            <![ %html-flag; [
            <GRAPHIC FORMAT="gif" FILEREF="act_main_window_2.gif">
            ]]>

            <![ %ps-flag; [
            <GRAPHIC FORMAT="eps" FILEREF="act_main_window_2.eps">
            ]]>
          </SCREENSHOT>
        </PARA>
      </LISTITEM>

      <LISTITEM ID="MAINWINDOW-BREAKDOWN-OVERVIEW">
        <PARA>
          <SCREENSHOT>
            <SCREENINFO>
An overview of the subject sequence
            </SCREENINFO>

            <![ %html-flag; [
            <GRAPHIC FORMAT="gif" FILEREF="act_main_window_3.gif">
            ]]>

            <![ %ps-flag; [
            <GRAPHIC FORMAT="eps" FILEREF="act_main_window_3.eps">
            ]]>
          </SCREENSHOT>
        </PARA>
      </LISTITEM>

      <LISTITEM ID="MAINWINDOW-BREAKDOWN-DNAVIEW">
        <PARA>
          <SCREENSHOT>
            <SCREENINFO>
The alignment view
            </SCREENINFO>

            <![ %html-flag; [
            <GRAPHIC FORMAT="gif" FILEREF="act_main_window_4.gif">
            ]]>

            <![ %ps-flag; [
            <GRAPHIC FORMAT="eps" FILEREF="act_main_window_4.eps">
            ]]>
          </SCREENSHOT>
        </PARA>
      </LISTITEM>

      <LISTITEM ID="MAINWINDOW-BREAKDOWN-FEATURELIST">
        <PARA>
          <SCREENSHOT>
            <SCREENINFO>
An overview of the query sequence
            </SCREENINFO>

            <![ %html-flag; [
            <GRAPHIC FORMAT="gif" FILEREF="act_main_window_5.gif">
            ]]>

            <![ %ps-flag; [
            <GRAPHIC FORMAT="eps" FILEREF="act_main_window_5.eps">
            ]]>
          </SCREENSHOT>
        </PARA>
      </LISTITEM>
    </ORDEREDLIST>
    <PARA>
Key:
    </PARA>
    <ORDEREDLIST ID="MAINWINDOW-INFO">
      <LISTITEM ID="MAINWINDOW-INFO-MENU">
        <PARA>
The File and Display menus for the main window (described later in this
chapter).  
        </PARA>
      </LISTITEM>
      <LISTITEM ID="MAINWINDOW-INFO-BUTTONS">
        <PARA>
Buttons controlling the view.  Currently the only button is the "lock" button
which controls whether the two sequences should be scrolled together.  When
the button is off, the sequences can be scrolled independently.
        </PARA>
      </LISTITEM>
      <LISTITEM ID="MAINWINDOW-INFO-SUBJECT">
        <PARA>
This a view of the subject sequence of the comparison.  See <XREF
LINKEND="VIEWS"> for more information on how to operate this part of the
window.  Note that all the menus apart from the File menu and the Display
menus are accessed via a pop-up menu on the third mouse button.  See <XREF
LINKEND="VIEWS-OTHERMOUSE"> and <XREF LINKEND="VIEWS-POPUPMENU"> for
more.
        </PARA>
      </LISTITEM>
      <LISTITEM ID="MAINWINDOW-INFO-COMPARISON">
        <PARA>
This part of the window shows the comparison between the two sequences.  See
<XREF LINKEND="COMPARISON-VIEW"> for more information.
        </PARA>
      </LISTITEM>
      <LISTITEM ID="MAINWINDOW-INFO-QUERY">
        <PARA>
The query sequence of the comparison.  See <XREF
LINKEND="VIEWS"> for more.
        </PARA>
      </LISTITEM>
    </ORDEREDLIST>
  </SECT1>

  &act-filemenu;
  &act-displaymenus;
  &menus;

  <SECT1 ID="VIEWS">
    <TITLE>The DNA Views</TITLE>
    <PARA>
The two sequence views in &prog; show the forward and reverse strands of the
sequence and a representation of the three translation frames in each
direction.  The top view shows the subject sequence of the comparison (see
<XREF LINKEND="MAINWINDOW-INFO-SUBJECT">), the bottom view shows the query
sequence (see <XREF LINKEND="MAINWINDOW-INFO-QUERY">).  The horizontal
scrollbar controls which part of the sequence is currently visible.  The
scroll bar at the left controls the zoom level.  By default the view shows
only the stop codons in each translation frame, but if the view is zoomed in
it will show the complete six frame translation.
    </PARA>
    <PARA>
See also <XREF LINKEND="MAINWINDOW-OVERVIEW">.
    </PARA>

&views-selection;

    <SECT2 ID="VIEWS-OTHERMOUSE">
      <TITLE>Other Mouse Controlled Functions</TITLE>
      <PARA>
Double clicking on a feature with the first mouse button causes the view to
centre itself on that feature.  Similarly, double clicking the first mouse
button on a base or amino acid will centre the view on that base/amino acid.
      </PARA>
      <PARA>
A double click of the middle mouse button on a feature will open an edit
window for that feature.  This is the same as clicking once and then choosing
the Edit Selected Features menu item (see <XREF
LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
      </PARA>
      <PARA>
The third button activates a pop-up menu with functions specific to this
view.  See <XREF LINKEND="VIEWS-POPUPMENU"> for more.
      </PARA>
    </SECT2>

&views-popup;
&views-scrolling;
&views-scale;
  </SECT1>

  <SECT1 ID="COMPARISON-VIEW">
    <TITLE>Comparison View</TITLE>
    <PARA>
This part of the window shows the comparison between the two sequences.  Each
red/pink box corresponds to single match, with red representing a good match
and white/pale pink a lower scoring match.  This view cannot be scrolled
directly, instead it tracks the movement of the subject and query sequence
views (see <XREF LINKEND="VIEWS">).
    </PARA>
    <PARA>
See <XREF LINKEND="MAINWINDOW-INFO-COMPARISON"> to see where this view fits in
the main window.
    </PARA>
    <SECT2>
      <TITLE>Controls</TITLE>
      <PARA>
The vertical scrollbar at the right of the view sets the minimum size (in
bases on the subject sequence) of the matches that are displayed.  The default
is 1, so when started &prog; will show all matches.
      </PARA>
      <PARA>
Double clicking the mouse on one of the matches will cause the sequence views
to align around that match.
      </PARA>
      <PARA>
The third mouse button will pop up a gadget that allows the matches to be
filtered on score.  Currently the "score" for blast matches is actually the
percent identity.   (See <XREF LINKEND="MOUSEBUTTONS"> if you don't have three
buttons on your mouse).
      </PARA>
    </SECT2>

  </SECT1>

&featurelist;

  <SECT1 ID="GRAPHS">
    <TITLE>Graphs and Plots</TITLE>
    <PARA>
The DNA plots are accessed from the Graphs(top) and Graphs(bottom) menus (see
<XREF LINKEND="DISPLAYMENU">).  When a graph is turned on it is locked to the
overview window, so it will follow the overview window when the overview is
scrolled.  It will also automatically change the viewing scale to match the
scale of the overview window.  The vertical scrollbar to the right of the
graph controls the window size of algorithm.
    </PARA>

    <PARA>
The feature plots window (see <XREF LINKEND="VIEWMENU-SHOW-FEATURE-PLOTS">)
has a horizontal scroll bar that sets the position of the plot in the feature.
As with the DNA plots, the vertical scrollbar to the right of the graph
controls the window size of algorithm.
    </PARA>

    <PARA>
Note that clicking the left mouse button on the plot will show the base or
residue at that position.  Clicking the right mouse button will pop-up a menu.
The menu contains a toggle which controls whether the graph is scaled and some
menu items which allow the maximum window size to be set.
    </PARA>
  </SECT1>

&mousebuttons;
</CHAPTER>
