additional
identifier
which
properly
disambiguates
the
structure
view
from
any
other
view
with
the
same
attributes.
This
is
not
an
ID,
because
it
is
possible
to
have
many
references
to
the
same
physical
structure
view
from
different
sequences
in
an
alignment.
A
structureState
element
citing
the
same
viewId
will
appear
for
each
instance.
Flag
set
if
the
alignment
panel
containing
this
JSeq
should
be
included
in
those
used
to
perform
a
structure
superposition
(since
Jalview
2.7).
Flag
set
if
the
alignment
panel
containing
this
JSeq
should
be
included
in
those
used
to
colour
its
associated
sequences
in
this
structureState(since
Jalview
2.7).
Flag
set
if
the
structure
display
is
coloured
by
the
Jmol
state,
rather
than
by
one
or
more
linked
alignment
views.
An
identifier
for
the
viewer
type,
currently
either
JMOL
or
CHIMERA
Reference to a viewer showing
RNA structure for this sequence.
Schema supports one viewer
showing multiple annotations for
multiple sequences, though
currently only one annotation
for one sequence (gapped or
trimmed) is used
id attribute
of
Annotation
in
vamsasModel
for the
secondary
structure
annotation
shown in the
viewer
if true the
RNA
structure is
shown with
gaps, if
false
without
name of the
project jar
entry that
holds the
VARNA viewer
state for
the
structure
An id unique to the RNA
viewer panel
horizontal position of
split pane divider
Index of the selected
structure in the viewer
panel
Optional sequence group ID (only
needs to be
unique for this
alignment)
handle for the calculation which uses
this parameter set
should the calculation be performed
immediately after loading in order to refresh results
should the calculation be automatically
performed on edits
unique id used by jalview to
synchronize
between stored and
instantiated views
The viewport id of this viewport's
(cdna/protein) coding complement, if any
Set for trees associated with columns of an alignment, sequence or annotation row
Refers to annotation row the tree is provided by
Tree ID added for binding tree
visualization
settings to vamsas
document trees in jalview 2.4.1
endpoints of X, Y and Z axes in that order
name of feature attribute to colour by, or attribute and sub-attribute
optional filter(s) applied to the feature type
Optional minimum colour
for graduated
feature
colour
threshold value for
graduated feature colour
threshold type for
graduated feature colour
key2 may be used for a sub-attribute of key
base attributes for windows displayed in Jalview
desktop.
parameters that condition a similarity score calculation
The results of a PCA calculation