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PathVisio / GPML

Graphical Pathway Markup Language
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DataNode should have elementRef and groupRef (type=Alias) #51

Closed Finterly closed 3 years ago

Finterly commented 3 years ago

To create new DataNode type: "Alias", DataNode will have both elementRef and groupRef.

In the case of an Alias, GPML will Look something like this:

"<DataNode type=”Alias” elementId=”...” elementRef=”abc”>" (not part of group! Represents group!)

"<DataNode elementId=”” groupRef=”abc”>(part of group!)

<Group elementId=”abc”>

Finterly commented 3 years ago

I have added groupRef to DataNode.

@mkutmon DataNode, GraphicalLine, Group, Interaction, Label and Shape can all be part of a group. However we recently renamed all groupRef to elementRef. Should property name be reverted back to groupRef for these elements?

Therefore properties name will then return to how it was in 2013a. DataNode, GraphicalLine, Group, Interaction, Label and Shape will have groupRef (able to belong to group) Point and State will still have elementRef.

Finterly commented 3 years ago

DataNode, Interaction, GraphicalLine, Label, Shape, and Group elements can belong to a group and have groupRef. DataNode will have elementRef in addition to groupRef when a DataNode has type="Alias" and refers to a Group.

Example for Group with Alias: <DataNode elementId="c27d1" elementRef="d4107" textLabel="Alias_for_abc" .../> <DataNode elementId="ed3f8" groupRef="d4107" textLabel="DataNode" type="GeneProduct" .../ > <Label elementId="e180c" groupRef="d4107" textLabel="group_abc" .../> <Group elementId="d4107" style="Complex".../>

Example for nested Group with Aliases:

<DataNode elementId="n1" groupRef="abc" textLabel="DataNode;" type="GeneProduct" .../> <DataNode elementId="n2" groupRef="efg" textLabel="DataNode;" type="GeneProduct" .../> <Label elementId="n3" groupRef="abc" textLabel="group_abc" .../> <Label elementId="n4" groupRef="efg" textLabel="group_efg".../>

commit 67de54a closes #51 and older issue #16.