The selection
The user can select the current object by clicking on it. The current object
will be displayed in red with a blue bounding rectangle. Depending on the
selection mode (see further), other objects than the current one will also
be selected. The selection (selected objects) are also diplayed in red, but
with a red bounding rectangle. Objects can be added or removed from
the selection by clicking while the "Control" is pressed. Dragging the pointer
over the page, will select the objects enclosed in the rectangle shown.
Some actions will be limited either to the current object or to the selected
objects (selection).
In the selection mode, the points defining the current object are highlighted
and can be edited (line containing items). New points can be added by double
clicking on a line.
RnaViz supports several different selection modes. Depending on the current
mode, the selection of the current object on the page with the mouse will
have different effects.
Select group mode
In the plain select mode, clicking on an object will select this object, or
the group it belongs to. If an object is part of a structure, the entire
structure will be selected. Objects can be grouped by selecting them, and
using the "Objects.Group" option. A group can be ungrouped by selecting it,
and applying the "Objects.Ungroup" option.
Select element mode
By default, RnaViz uses the "element selection" mode. In this mode,
clicking on a base that belongs to a helical element will select the
entire helix. In combination with the 'Control' key, elements can be added
to or removed from the selection.
The alternate mouse key can be used to select only a
segment of a helix. Helix segments are defined as the parts of a helix
separated by internal or bulge loops. Using the "Select tree" entry in
the "Edit" menu or its key shortcut the entire domain enclosed by the
two segments of the selected helix can be added to the selection.
A structure on the page can be rearranged quickly by clicking on a
base or on the selection and dragging it to a different position. When
the selection is released, the bases connecting the selection to the
rest of the structure will be rearanged so as to maintain a clear structure
drawing. If the distance between the bases reaches a given treshhold,
they will be automatically connected by a line. The treshhold and width
of the line can be selected in the structure
settings dialog.
The selected part of a structure can be rotated by changing
to rotation mode. The center of rotation is
indicated by a target, which can be repositioned with the mouse.
The selection can also be oriented in
a specific direction using the "Orient helix" or "Orient" options in
the "Geometry" menu. When more than one helix is selected, the last
helix added will determine the orientation. The "Geometry" menu also
offers options to easily straighthen or arch the single stranded areas,
or to flip a helix. Areas with unknown structure can be drawn unformatted.
Select single mode
The "single select" mode allows individual selection and positioning
of objects. It treats all object equally. There is no automatic selection of
other objects then the one clicked on, and no automatic rearrangements: Using
this mode, each object can be positioned individually if necessary. Only the
selected objects will be moved. This makes any special arrangement of objects
possible.
Select subelement mode
The first mousebutton will select helix segments (alternate mousebutton in
the element selection mode).
Select trees mode
The first mouse button will always select the tree starting from the selected helix.