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wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways
Apache License 2.0
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Missing arrowheads #47

Closed AlexanderPico closed 6 years ago

AlexanderPico commented 6 years ago

Some of the mim type interactions are missing in your Target Arrow Shape mapping. Here is the complete list from PathVisio-Java:

    ShapeRegistry.registerArrow (MIM_NECESSARY_STIMULATION.getName(), getMIMNecessary(), ArrowShape.FillType.OPEN, ARROWWIDTH);
    ShapeRegistry.registerArrow (MIM_BINDING.getName(), getMIMBinding(), ArrowShape.FillType.CLOSED);
    ShapeRegistry.registerArrow (MIM_CONVERSION.getName(), getMIMConversion(), ArrowShape.FillType.CLOSED, ARROWWIDTH);
    ShapeRegistry.registerArrow (MIM_STIMULATION.getName(), getMIMStimulation(), ArrowShape.FillType.OPEN, ARROWWIDTH);
    ShapeRegistry.registerArrow (MIM_MODIFICATION.getName(), getMIMBinding(), ArrowShape.FillType.CLOSED);
    ShapeRegistry.registerArrow (MIM_CATALYSIS.getName(), getMIMCatalysis(), ArrowShape.FillType.OPEN, CATALYSIS_DIAM + CATALYSIS_GAP);
    ShapeRegistry.registerArrow (MIM_CLEAVAGE.getName(), getMIMCleavage(), ArrowShape.FillType.WIRE,CLEAVAGE_FIRST);
    ShapeRegistry.registerArrow (MIM_BRANCHING_LEFT.getName(), getMIMBranching(LEFT), ArrowShape.FillType.OPEN, BRANCH_LOCATION);
    ShapeRegistry.registerArrow (MIM_BRANCHING_RIGHT.getName(), getMIMBranching(RIGHT), ArrowShape.FillType.OPEN, BRANCH_LOCATION);
    ShapeRegistry.registerArrow (MIM_INHIBITION.getName(), getMIMInhibition(),  ArrowShape.FillType.OPEN,TBARWIDTH + TBAR_GAP);
    ShapeRegistry.registerArrow (MIM_COVALENT_BOND.getName(), getMIMCovalentBond(), ArrowShape.FillType.OPEN);
    ShapeRegistry.registerArrow (MIM_TRANSLATION.getName(), getMIMTranslation(), ArrowShape.FillType.WIRE, ARROWWIDTH + ARROWHEIGHT);

ShapeRegistry.registerArrow (MIM_GAP.getName(), getMIMGap(), ArrowShape.FillType.OPEN, 10);

AlexanderPico commented 6 years ago

Clarification my request for new arrowheads… I’m not asking for new arrowhead shapes to be added for those mim interactions, I’m asking that those mim-interactions map to something :) Just pick existing filled/open arrowheads that closest approximate the originals. Otherwise, they render without any arrowhead. IOW, the style mapper for Target Arrow Type should never have an empty entry. Any empty mapping is a "bug".

AdamStuart commented 6 years ago

all mim types are now mapped in GpmlToPathway.PV_ARROW_MAP