X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=8588f202987660a143e409ca33d1ed7d9bd8159b;hb=a01f3d6d4821282f6528b927137d79750fa58e72;hp=3a7f6200beb713599842dc891424d2620e25be68;hpb=a87351ca30e9651404e42aaac9929e8fb9492d88;p=jalview.git
diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 3a7f620..8588f20 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,146 +1,636 @@
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+
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+
+
+
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+
+
+
+
+
+
+
+
+ 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Tree ID added for binding tree
+ visualization
+ settings to vamsas
+ document trees in jalview 2.4.1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+