X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fjalview.xsd;h=1d2235ed1a7663d0997592d703f2ac24b515d4d1;hb=14e1f9dbb9c7a4535734fd3be7ddeee2a5ae72dc;hp=5aae6aef60b1163b8f00c31cbe4fca9d5bff6ed0;hpb=9adf6bc4eac154c1f96a2be5867ce24d7c6470f1;p=jalview.git diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index 5aae6ae..1d2235e 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -1,75 +1,226 @@ - + - - - + + + + + - - - + + + - + - + - + - - - - + + + + - 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. + + 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 + 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. + + - - - - 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). - - + + + + An + identifier + for + the + viewer + type, + currently + either + JMOL + or + CHIMERA + + - - - Flag set if the structure display is coloured by the Jmol state, rather than by one or more linked alignment views. - - + - + @@ -77,169 +228,390 @@ - + + + + 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) - - + + + + + + + + + + + + + + + + + + + + + + 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 + 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 - - - + + + + + + + + + + + + + + + + + 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 - - - - - - + + + Optional minimum colour + for graduated + feature + colour + + + + + + + + threshold value for + graduated feature colour + + + + + + + threshold type for + graduated feature colour + + + + + + + + - - + + @@ -252,53 +624,106 @@ - - + + + + 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 + + + + + + + + + + + + + + + + + + + + + - --> - - - - base attributes for windows displayed in Jalview desktop. - - - - - - -