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Autolayout with only a species results in zero-size layout #29

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luciansmith opened this issue Dec 16, 2024 · 3 comments
Open

Autolayout with only a species results in zero-size layout #29

luciansmith opened this issue Dec 16, 2024 · 3 comments

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@luciansmith
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If I run autolayout with a model with one species and no reactions, I get the following, which doesn't actually display the species:

<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v3.0.0 with libSBML version 5.20.4. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1" level="3" version="2" layout:required="false" render:required="false">
  <model metaid="__main" id="__main">
    <listOfCompartments>
      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="S1" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
      <layout:layout layout:id="libSBMLNetwork_Layout">
        <layout:dimensions layout:width="0" layout:height="0"/>
        <layout:listOfCompartmentGlyphs>
          <layout:compartmentGlyph layout:id="default_compartment_Glyph_0" layout:compartment="default_compartment">
            <layout:boundingBox layout:id="default_compartment_Glyph_0_bb">
              <layout:position layout:x="0" layout:y="0"/>
              <layout:dimensions layout:width="0" layout:height="0"/>
            </layout:boundingBox>
          </layout:compartmentGlyph>
        </layout:listOfCompartmentGlyphs>
        <layout:listOfTextGlyphs>
          <layout:textGlyph layout:id="default_compartment_Glyph_0_TextGlyph_0" layout:originOfText="default_compartment" layout:graphicalObject="default_compartment_Glyph_0">
            <layout:boundingBox layout:id="default_compartment_Glyph_0_TextGlyph_0_bb">
              <layout:position layout:x="0" layout:y="0"/>
              <layout:dimensions layout:width="0" layout:height="0"/>
            </layout:boundingBox>
          </layout:textGlyph>
        </layout:listOfTextGlyphs>
        <render:listOfRenderInformation xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
          <render:renderInformation render:id="libSBMLNetwork_Local_Render" render:referenceRenderInformation="libSBMLNetwork_Global_Render" render:backgroundColor="#FFFFFFFF"/>
        </render:listOfRenderInformation>
      </layout:layout>
      <render:listOfGlobalRenderInformation xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
        <render:renderInformation render:id="libSBMLNetwork_Global_Render" render:backgroundColor="white">
          <render:listOfColorDefinitions>
            <render:colorDefinition render:id="white" render:value="#ffffff"/>
            <render:colorDefinition render:id="black" render:value="#000000"/>
            <render:colorDefinition render:id="lightgray" render:value="#d3d3d3"/>
            <render:colorDefinition render:id="darkslategray" render:value="#2f4f4f"/>
            <render:colorDefinition render:id="darkcyan" render:value="#008b8b"/>
            <render:colorDefinition render:id="teal" render:value="#008080"/>
            <render:colorDefinition render:id="silver" render:value="#c0c0c0"/>
          </render:listOfColorDefinitions>
          <render:listOfLineEndings>
            <render:lineEnding render:id="productHead">
              <layout:boundingBox layout:id="productHead_bb">
                <layout:position layout:x="-12" layout:y="-6"/>
                <layout:dimensions layout:width="12" layout:height="12"/>
              </layout:boundingBox>
              <render:g>
                <render:polygon render:stroke="black" render:stroke-width="2" render:fill="black">
                  <render:listOfElements>
                    <render:element xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RenderPoint" render:x="0" render:y="0"/>
                    <render:element xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RenderPoint" render:x="100%" render:y="50%"/>
                    <render:element xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RenderPoint" render:x="0" render:y="100%"/>
                  </render:listOfElements>
                </render:polygon>
              </render:g>
            </render:lineEnding>
            <render:lineEnding render:id="modifierHead">
              <layout:boundingBox layout:id="modifierHead_bb">
                <layout:position layout:x="-12" layout:y="-6"/>
                <layout:dimensions layout:width="12" layout:height="12"/>
              </layout:boundingBox>
              <render:g>
                <render:ellipse render:stroke="black" render:stroke-width="2" render:fill="white" render:cx="50%" render:cy="50%" render:rx="50%"/>
              </render:g>
            </render:lineEnding>
            <render:lineEnding render:id="activatorHead">
              <layout:boundingBox layout:id="activatorHead_bb">
                <layout:position layout:x="-12" layout:y="-6"/>
                <layout:dimensions layout:width="12" layout:height="12"/>
              </layout:boundingBox>
              <render:g>
                <render:polygon render:stroke="black" render:stroke-width="2" render:fill="white">
                  <render:listOfElements>
                    <render:element xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RenderPoint" render:x="0" render:y="50%"/>
                    <render:element xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RenderPoint" render:x="50%" render:y="0"/>
                    <render:element xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RenderPoint" render:x="100%" render:y="50%"/>
                    <render:element xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="RenderPoint" render:x="50%" render:y="100%"/>
                  </render:listOfElements>
                </render:polygon>
              </render:g>
            </render:lineEnding>
            <render:lineEnding render:id="inhibitorHead">
              <layout:boundingBox layout:id="inhibitorHead_bb">
                <layout:position layout:x="-12" layout:y="-6"/>
                <layout:dimensions layout:width="12" layout:height="12"/>
              </layout:boundingBox>
              <render:g>
                <render:rectangle render:stroke="black" render:stroke-width="2" render:fill="white" render:x="80%" render:y="0" render:width="20%" render:height="100%"/>
              </render:g>
            </render:lineEnding>
          </render:listOfLineEndings>
          <render:listOfStyles>
            <render:style render:id="COMPARTMENTGLYPH_style_0" render:typeList="COMPARTMENTGLYPH">
              <render:g render:stroke="darkcyan" render:font-family="sans-serif" render:font-weight="normal" render:font-style="normal" render:text-anchor="middle" render:vtext-anchor="bottom" render:font-size="10">
                <render:rectangle render:stroke="darkcyan" render:stroke-width="2" render:fill="lightgray" render:x="0" render:y="0" render:width="100%" render:height="100%" render:rx="25" render:ry="25"/>
              </render:g>
            </render:style>
            <render:style render:id="SPECIESGLYPH_style_0" render:typeList="SPECIESGLYPH">
              <render:g render:stroke="black" render:font-family="sans-serif" render:font-weight="normal" render:font-style="normal" render:text-anchor="middle" render:vtext-anchor="middle" render:font-size="24">
                <render:rectangle render:stroke="black" render:stroke-width="2" render:fill="white" render:x="0" render:y="0" render:width="100%" render:height="100%" render:rx="6" render:ry="3.6"/>
              </render:g>
            </render:style>
            <render:style render:id="REACTIONGLYPH_style_0" render:typeList="REACTIONGLYPH">
              <render:g render:stroke="darkslategray" render:font-family="sans-serif" render:font-weight="normal" render:font-style="normal" render:text-anchor="middle" render:vtext-anchor="middle" render:font-size="12">
                <render:ellipse render:stroke="black" render:stroke-width="2" render:fill="white" render:cx="50%" render:cy="50%" render:rx="50%"/>
              </render:g>
            </render:style>
            <render:style render:id="substrate_style_0" render:roleList="substrate">
              <render:g render:stroke="black" render:stroke-width="2"/>
            </render:style>
            <render:style render:id="sidesubstrate_style_0" render:roleList="sidesubstrate">
              <render:g render:stroke="black" render:stroke-width="2"/>
            </render:style>
            <render:style render:id="product_style_0" render:roleList="product">
              <render:g render:stroke="black" render:stroke-width="2" render:endHead="productHead"/>
            </render:style>
            <render:style render:id="sideproduct_style_0" render:roleList="sideproduct">
              <render:g render:stroke="black" render:stroke-width="2" render:endHead="productHead"/>
            </render:style>
            <render:style render:id="modifier_style_0" render:roleList="modifier">
              <render:g render:stroke="black" render:stroke-width="2" render:endHead="modifierHead"/>
            </render:style>
            <render:style render:id="activator_style_0" render:roleList="activator">
              <render:g render:stroke="black" render:stroke-width="2" render:endHead="activatorHead"/>
            </render:style>
            <render:style render:id="inhibitor_style_0" render:roleList="inhibitor">
              <render:g render:stroke="black" render:stroke-width="2" render:endHead="inhibitorHead"/>
            </render:style>
            <render:style render:id="EMPTY_SPECIESGLYPH_style_0" render:typeList="EMPTY_SPECIESGLYPH">
              <render:g>
                <render:ellipse render:stroke="black" render:stroke-width="2" render:fill="white" render:cx="50%" render:cy="50%" render:rx="50%"/>
              </render:g>
            </render:style>
            <render:style render:id="COMPARTMENTGLYPH_TEXTGLYPH_style_0" render:typeList="COMPARTMENTGLYPH_TEXTGLYPH">
              <render:g render:stroke="darkcyan" render:font-family="sans-serif" render:font-weight="normal" render:font-style="normal" render:text-anchor="middle" render:vtext-anchor="bottom" render:font-size="10"/>
            </render:style>
            <render:style render:id="SPECIESGLYPH_TEXTGLYPH_style_0" render:typeList="SPECIESGLYPH_TEXTGLYPH">
              <render:g render:stroke="black" render:font-family="sans-serif" render:font-weight="normal" render:font-style="normal" render:text-anchor="middle" render:vtext-anchor="middle" render:font-size="24"/>
            </render:style>
            <render:style render:id="REACTIONGLYPH_TEXTGLYPH_style_0" render:typeList="REACTIONGLYPH_TEXTGLYPH">
              <render:g render:stroke="darkslategray" render:font-family="sans-serif" render:font-weight="normal" render:font-style="normal" render:text-anchor="middle" render:vtext-anchor="middle" render:font-size="12"/>
            </render:style>
            <render:style render:id="GRAPHICALOBJECT_style_0" render:typeList="GRAPHICALOBJECT">
              <render:g render:stroke="black" render:font-family="sans-serif" render:font-weight="normal" render:font-style="normal" render:text-anchor="middle" render:vtext-anchor="middle" render:font-size="24">
                <render:rectangle render:stroke="black" render:stroke-width="2" render:fill="white" render:x="0" render:y="0" render:width="100%" render:height="100%" render:rx="6" render:ry="3.6"/>
              </render:g>
            </render:style>
          </render:listOfStyles>
        </render:renderInformation>
      </render:listOfGlobalRenderInformation>
    </layout:listOfLayouts>
  </model>
</sbml>
@adelhpour
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Currently, the autolayout fist creates the Reactions, and then the Species, which are the participants of those reactions. So, if a Species is not part of a reaction, its graphical representation (SpeciesGlyph) is not created. I'm not sure what having a Species which is not part of any reactions mean from a modeling point of view, so maybe we can talk more about it!

@luciansmith
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It just means that it's a model of stuff in a compartment, that might change due to rate rules or assignment rules, or might just stay constant. It's perfectly reasonable to visualize it, though.

@adelhpour
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Nice! So I will add visualizing them in my list. Thank you!

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@luciansmith @adelhpour