X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=adaa3ee8ecd0804efa8c434ddc5d81c6a29de5b2;hb=fbd682c00e543eadb48074ac354ade57c04c20cb;hp=65cf2f89e55dd97e6e05fdbd16da4b1d041520f8;hpb=8c4f77adba0521e7dc89dcb77fe2f8b28c62f70d;p=jalview.git
diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 65cf2f8..adaa3ee 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -1,172 +1,795 @@
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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
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+