views_popup.sgml

    <SECT2 ID="VIEWS-POPUPMENU">
      <TITLE>The Pop-up Menu</TITLE>
      <PARA>
The pop-up menu is activated by pressing the third mouse button (see <XREF
LINKEND="MOUSEBUTTONS">) on a feature view.  The menu is split into three
sections.  The top contains functions that will act on the current view.  The
middle contains shortcuts to some of the main window menus.  The bottom
contains four toggle buttons which influence the appearance of the view.
      </PARA>

      <SECT3 ID="VIEWS-POPUPMENU-FUNCTIONS">
        <TITLE>Pop-up Menu Functions</TITLE>
        <PARA>
Note that not all of these functions are available all the time (the first two
are only shown when there are some selected features).
        </PARA>

        <ITEMIZEDLIST SPACING="compact">
          <LISTITEM ID="VIEWS-POPUPMENU-RAISE-SELECTED-FEATURES">
            <FORMALPARA>
              <TITLE>Raise Selected Features</TITLE>
              <PARA>
Raise the selected features so that they appear in front of all other
features.
              </PARA>
            </FORMALPARA>
          </LISTITEM>

          <LISTITEM ID="VIEWS-POPUPMENU-LOWER-SELECTED-FEATURES">
            <FORMALPARA>
              <TITLE>Lower Selected Features</TITLE>
              <PARA>
Make the selected features go behind all the other features.
              </PARA>
            </FORMALPARA>
          </LISTITEM>

          <LISTITEM ID="VIEWS-POPUPMENU-SMALLEST-IN-FRONT">
            <FORMALPARA>
              <TITLE>Smallest Features In Front</TITLE>
              <PARA>
Sort the visible features so that the smallest features appear in front of the
larger ones.  This is only necessary when the user has manually rearranged the
features using "Raise Selected Features" or "Lower Selected Features".
              </PARA>
            </FORMALPARA>
          </LISTITEM>

          <LISTITEM ID="VIEWS-POPUPMENU-ZOOM-TO-SELECTION">
            <FORMALPARA>
              <TITLE>Zoom to Selection</TITLE>
              <PARA>
Scroll and scale the display so that the current selection is centred and full
width.
              </PARA>
            </FORMALPARA>
          </LISTITEM>

          <LISTITEM ID="VIEWS-POPUPMENU-SELECT-VISIBLE-RANGE">
            <FORMALPARA>
              <TITLE>Select Visible Range</TITLE>
              <PARA>
Select the currently visible bases on the forward strand.
              </PARA>
            </FORMALPARA>
          </LISTITEM>

          <LISTITEM ID="VIEWS-POPUPMENU-SELECT-VISIBLE-FEATURES">
            <FORMALPARA>
              <TITLE>Select Visible Features</TITLE>
              <PARA>
Select those (and only those) features that currently visible in this view.
Any features that are off screen or have been filtered out with the "Set Score
Cutoffs ..." control.
              </PARA>
            </FORMALPARA>
          </LISTITEM>

          <LISTITEM ID="VIEWS-POPUPMENU-SET-SCORE-CUTOFFS">
            <FORMALPARA>
              <TITLE>Set Score Cutoffs ...</TITLE>
              <PARA>
The score cutoffs panel allows the user to filter the features of the active
entries so that features with low or high scores are not shown.  The "score"
of a feature is the value of the <LITERAL>/score</LITERAL> qualifier and
should be a number from 0 to 100.  The cutoffs window has two sliders.  Any
feature that has a score less than the value of the top controller or more
than the value of the bottom controller will not be shown.  Features with no
<LITERAL>/score</LITERAL> qualifier will always be shown.
              </PARA>
            </FORMALPARA>
          </LISTITEM>
        </ITEMIZEDLIST>
      </SECT3>

      <SECT3 ID="VIEWS-POPUPMENU-TOGGLES">
        <TITLE>Toggle Buttons</TITLE>
        <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-LABELS">
          <TITLE>Feature Labels</TITLE>
          <PARA>
This toggle button controls whether the feature labels are displayed on their
own line (when the toggle is on) or on the top of the features (when the
toggle is off).  The default setting for this toggle can be set in the options
file (see <XREF LINKEND="OPTIONS-FEATURE-LABELS">).
          </PARA>
        </SECT4>

        <SECT4 ID="VIEWS-POPUPMENU-ONE-LINE-PER-ENTRY">
          <TITLE>One Line Per Entry</TITLE>
          <PARA>
This toggle controls whether the entries are shown in the context of the three
frame translation or one entry per line on screen.  In the first case the
entries will be overlaid, in second case they will be shown in parallel. 
The default setting for this toggle can be set in the options file (see <XREF
LINKEND="OPTIONS-ONE-LINE-PER-ENTRY">).
          </PARA>
        </SECT4>
 
        <SECT4 ID="VIEWS-POPUPMENU-SHOW-FORWARD-FRAMES">
          <TITLE>Forward Frame Lines</TITLE>
          <PARA>
This toggle button controls whether or not to show the 3 frame translation of
the forward sequence.
          </PARA>
        </SECT4>
 
        <SECT4 ID="VIEWS-POPUPMENU-SHOW-REVERSE-FRAMES">
          <TITLE>Reverse Frame Lines</TITLE>
          <PARA>
This toggle button controls whether or not to show the 3 frame translation of
the reverse sequence.
          </PARA>
        </SECT4>

       <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-STARTCODONS">
          <TITLE>Start Codons</TITLE>
          <PARA>
Toggle the display of start codons in the view.  See <XREF
LINKEND="LAUNCH-WINDOW-OPTIONS-EUK"> to find out how to change which start
codons to use.
          </PARA>
        </SECT4>

        <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-STOPCODONS">
          <TITLE>Stop Codons</TITLE>
          <PARA>
Toggle the display of stop codons in the view.
          </PARA>
        </SECT4>

        <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-FEATURE-ARROWS">
          <TITLE>Feature Arrows</TITLE>
          <PARA>
Toggle the display of directional arrows on each feature.  The default setting
for this toggle can be set in the options file (see <XREF
LINKEND="OPTIONS-DRAWFEATUREARROWS">).
          </PARA>
        </SECT4>

        <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-FEATURE-BORDERS">
          <TITLE>Feature Borders</TITLE>
          <PARA>
Toggle the display of black borders around each feature.  The default setting
for this toggle can be set in the options file (see <XREF
LINKEND="OPTIONS-DRAWFEATUREBORDERS">).
          </PARA>
        </SECT4>

        <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-FRAMEFEATURES">
          <TITLE>All Features On Frame Lines</TITLE>
          <PARA>
Normally non-protein features are drawn on the DNA lines.  This toggle allows
the user to force all features to be drawn on the frame lines, which can
sometimes improve readability.  The default setting
for this toggle can be set in the options file (see <XREF
LINKEND="OPTIONS-FEATURES-ON-FRAME-LINES">).
          </PARA>
        </SECT4>

        <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-FLIPDISPLAY">
          <TITLE>Flip Display</TITLE>
          <PARA>
If selected the sequence and features will be drawn on screen as if they are
reverse complemented with the first base to the right of the screen.
          </PARA>
        </SECT4>

        <SECT4 ID="VIEWS-POPUPMENU-TOGGLES-COLOURISE">
          <TITLE>Colourise Bases</TITLE>
          <PARA>
This toggle turn base colouring on or off.  (Note that this feature is
completely unless, it exists for amusement only).
          </PARA>
        </SECT4>
      </SECT3>
    </SECT2>