Commit ea856e45 authored by Denis Shirshov's avatar Denis Shirshov

11

parent 832603a0
......@@ -16,11 +16,9 @@
(define (test-xml xml-file)
(let* (
(sbgn_ml (read-file xml-file))
; (sbgn_ml (bytes->string/utf-8 sbgn_ml))
(af-xml (sbgn-ml->af-xml sbgn_ml))
)
(write-file "../html/generated/result.sbgn" af-xml)
))
(test-xml "../examples/metabolismregulation.org_refined/F003-mevalonate-V002-SBGNv02.sbgn")
; (test-xml "../examples/logical-combination.sbgn")
(test-xml "../knowledge/sbgn-examples/metabolismregulation.org/MR015-tag.sbgn")
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph compartmentOrder="-11.0" id="glyph1" class="compartment">
<label text="CompartmentA">
<bbox y="252.0" x="759.0" h="16.0" w="92.0"/>
</label>
<bbox y="190.0" x="605.0" h="140.0" w="400.0"/>
</glyph>
<glyph id="M1" class="simple chemical">
<label text="M1"/>
<bbox y="530.0" x="160.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="M2" class="simple chemical">
<label text="M2"/>
<bbox y="530.0" x="360.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="p1" class="process">
<bbox y="538.0" x="288.0" h="24.0" w="24.0"/>
<port y="550.0" x="283.0" id="p1.1"/>
<port y="550.0" x="317.0" id="p1.2"/>
</glyph>
<glyph id="A" class="macromolecule">
<label text="A"/>
<bbox y="75.0" x="190.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="not-41" orientation="vertical" class="not">
<bbox y="227.0" x="327.0" h="25.0" w="25.0"/>
<port y="264.5" x="339.5" id="not-41.2"/>
<port y="214.5" x="339.5" id="not-41.1"/>
</glyph>
<glyph id="C" class="macromolecule">
<label text="C"/>
<bbox y="75.0" x="330.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="B" class="macromolecule">
<label text="B"/>
<bbox y="80.0" x="455.0" h="40.0" w="80.0"/>
</glyph>
<glyph id="or-42" orientation="vertical" class="or">
<bbox y="165.0" x="427.0" h="25.0" w="25.0"/>
<port y="152.5" x="439.5" id="or-42.1"/>
</glyph>
<glyph compartmentRef="glyph1" id="glyph2" class="macromolecule">
<label text="D"/>
<bbox y="210.0" x="871.0" h="60.0" w="108.0"/>
</glyph>
<glyph id="or-37" orientation="vertical" class="or">
<bbox y="307.0" x="262.0" h="25.0" w="25.0"/>
<port y="344.5" x="274.5" id="or-37.2"/>
<port y="294.5" x="274.5" id="or-37.1"/>
</glyph>
<arc target="p1.1" source="M1" id="consumption-35" class="consumption">
<start y="550.0" x="240.0"/>
<end y="550.0" x="283.0"/>
</arc>
<arc target="M2" source="p1.2" id="production-36" class="production">
<start y="550.0" x="317.0"/>
<end y="550.0" x="360.0"/>
</arc>
<arc target="p1" source="or-37.2" id="catalysis-49" class="catalysis">
<start y="344.5" x="274.5"/>
<end y="538.0" x="298.67245"/>
</arc>
<arc target="or-37.1" source="A" id="logic-arc-46" class="logic arc">
<start y="115.0" x="234.46115"/>
<end y="294.5" x="274.5"/>
</arc>
<arc target="or-37.1" source="not-41.2" id="logic-arc-48" class="logic arc">
<start y="264.5" x="339.5"/>
<end y="294.5" x="274.5"/>
</arc>
<arc target="not-41.1" source="or-42" id="logic-arc-45" class="logic arc">
<start y="195.0" x="439.5"/>
<next y="202.5" x="439.5"/>
<end y="214.5" x="339.5"/>
</arc>
<arc target="or-42.1" source="C" id="logic-arc-43" class="logic arc">
<start y="115.0" x="394.17392"/>
<end y="152.5" x="439.5"/>
</arc>
<arc target="or-42.1" source="B" id="logic-arc-44" class="logic arc">
<start y="120.0" x="495.0"/>
<end y="152.5" x="439.5"/>
</arc>
<arc target="or-37.1" source="glyph2" id="arc1" class="logic arc">
<start y="244.52422" x="871.0"/>
<end y="294.5" x="274.5"/>
</arc>
</map>
</sbgn>
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph class="simple chemical" id="glyph_n0">
<label text="Phosphatidylcholine"/>
<bbox w="140.0" h="30.0" x="768.41876" y="275.0"/>
</glyph>
<glyph class="process" orientation="vertical" id="glyph_n1">
<clone/>
<bbox w="18.0" h="18.0" x="829.41876" y="335.0"/>
<port id="glyph_n1_port_n1.1" x="838.41876" y="362.0"/>
<port id="glyph_n1_port_n1.2" x="838.41876" y="326.0"/>
</glyph>
<glyph class="macromolecule" id="glyph_n2">
<label text="cPLA2"/>
<bbox w="80.0" h="40.0" x="688.41876" y="324.0"/>
<glyph class="state variable" id="glyph_n2_1">
<state value="P" variable=""/>
<bbox w="18.0" h="18.0" x="703.2681" y="356.32703"/>
</glyph>
<glyph class="state variable" id="glyph_n2_2">
<state value="P" variable=""/>
<bbox w="18.0" h="18.0" x="739.2681" y="356.32703"/>
</glyph>
</glyph>
<glyph class="simple chemical" id="glyph_n3">
<label text="Arachidonic acid"/>
<bbox w="140.0" h="30.0" x="768.41876" y="383.0"/>
</glyph>
<glyph class="simple chemical" id="glyph_n4">
<label text="PGG2"/>
<bbox w="140.0" h="30.0" x="768.41876" y="491.0"/>
</glyph>
<glyph class="process" orientation="vertical" id="glyph_n5">
<clone/>
<bbox w="18.0" h="18.0" x="829.41876" y="443.0"/>
<port id="glyph_n5_port_n5.1" x="838.41876" y="470.0"/>
<port id="glyph_n5_port_n5.2" x="838.41876" y="434.0"/>
</glyph>
<glyph class="macromolecule" id="glyph_n6">
<label text="COX1/2"/>
<bbox w="80.0" h="40.0" x="693.41876" y="432.0"/>
</glyph>
<glyph class="macromolecule" id="glyph_n7">
<label text="cPLA2"/>
<bbox w="80.0" h="40.0" x="523.15063" y="324.0"/>
<glyph class="state variable" id="glyph_n7_3">
<bbox w="18.0" h="18.0" x="538.0" y="356.39343"/>
</glyph>
<glyph class="state variable" id="glyph_n7_4">
<state value="P" variable=""/>
<bbox w="18.0" h="18.0" x="574.0" y="356.32703"/>
</glyph>
</glyph>
<glyph class="macromolecule" id="glyph_n8">
<label text="ERK1/2"/>
<bbox w="80.0" h="40.0" x="440.51657" y="216.0"/>
<glyph class="state variable" id="glyph_n8_5">
<bbox w="18.0" h="18.0" x="455.36594" y="248.39343"/>
</glyph>
<glyph class="state variable" id="glyph_n8_6">
<bbox w="18.0" h="18.0" x="491.36594" y="248.39343"/>
</glyph>
</glyph>
<glyph class="macromolecule" id="glyph_n9">
<label text="MEK1/2"/>
<bbox w="80.0" h="40.0" x="523.15063" y="108.0"/>
<glyph class="state variable" id="glyph_n9_7">
<state value="P" variable=""/>
<bbox w="18.0" h="18.0" x="574.0" y="140.32703"/>
</glyph>
</glyph>
<glyph class="macromolecule" id="glyph_n10">
<label text="MEK1/2"/>
<bbox w="80.0" h="40.0" x="357.8825" y="108.0"/>
<glyph class="state variable" id="glyph_n10_8">
<bbox w="18.0" h="18.0" x="408.73187" y="140.39343"/>
</glyph>
</glyph>
<glyph class="process" orientation="horizontal" id="glyph_n11">
<clone/>
<bbox w="18.0" h="18.0" x="636.78467" y="335.0"/>
<port id="glyph_n11_port_n11.1" x="627.78467" y="344.0"/>
<port id="glyph_n11_port_n11.2" x="663.78467" y="344.0"/>
</glyph>
<glyph class="macromolecule" id="glyph_n12">
<label text="ERK1/2"/>
<bbox w="80.0" h="40.0" x="605.78467" y="216.0"/>
<glyph class="state variable" id="glyph_n12_9">
<state value="P" variable=""/>
<bbox w="18.0" h="18.0" x="620.63403" y="248.32703"/>
</glyph>
<glyph class="state variable" id="glyph_n12_10">
<state value="P" variable=""/>
<bbox w="18.0" h="18.0" x="656.63403" y="248.32703"/>
</glyph>
</glyph>
<glyph class="process" orientation="horizontal" id="glyph_n13">
<clone/>
<bbox w="18.0" h="18.0" x="554.15063" y="227.0"/>
<port id="glyph_n13_port_n13.1" x="545.15063" y="236.0"/>
<port id="glyph_n13_port_n13.2" x="581.15063" y="236.0"/>
</glyph>
<glyph class="process" orientation="horizontal" id="glyph_n14">
<clone/>
<bbox w="18.0" h="18.0" x="471.51657" y="119.0"/>
<port id="glyph_n14_port_n14.1" x="462.51657" y="128.0"/>
<port id="glyph_n14_port_n14.2" x="498.51657" y="128.0"/>
</glyph>
<glyph class="macromolecule" id="glyph_n15">
<label text="RAF1"/>
<bbox w="80.0" h="40.0" x="440.51657" y="0.0"/>
<glyph class="state variable" id="glyph_n15_11">
<state value="P" variable=""/>
<bbox w="18.0" h="18.0" x="491.36594" y="32.327026"/>
</glyph>
</glyph>
<glyph class="macromolecule" id="glyph_n16">
<label text="RAF1"/>
<bbox w="80.0" h="40.0" x="275.24847" y="0.0"/>
<glyph class="state variable" id="glyph_n16_12">
<bbox w="18.0" h="18.0" x="326.09784" y="32.393433"/>
</glyph>
</glyph>
<glyph class="process" orientation="horizontal" id="glyph_n17">
<clone/>
<bbox w="18.0" h="18.0" x="388.8825" y="11.0"/>
<port id="glyph_n17_port_n17.1" x="379.8825" y="20.0"/>
<port id="glyph_n17_port_n17.2" x="415.8825" y="20.0"/>
</glyph>
<arc class="production" id="arc_e0" source="glyph_n1_port_n1.1" target="glyph_n3">
<start x="838.41876" y="362.0"/>
<end x="838.41876" y="398.0"/>
</arc>
<arc class="consumption" id="arc_e1" source="glyph_n0" target="glyph_n1_port_n1.2">
<start x="838.41876" y="290.0"/>
<end x="838.41876" y="326.0"/>
</arc>
<arc class="consumption" id="arc_e2" source="glyph_n3" target="glyph_n5_port_n5.2">
<start x="838.41876" y="398.0"/>
<end x="838.41876" y="434.0"/>
</arc>
<arc class="production" id="arc_e3" source="glyph_n5_port_n5.1" target="glyph_n4">
<start x="838.41876" y="470.0"/>
<end x="838.41876" y="506.0"/>
</arc>
<arc class="catalysis" id="arc_e4" source="glyph_n6" target="glyph_n5">
<start x="733.41876" y="452.0"/>
<end x="826.41876" y="452.0"/>
</arc>
<arc class="production" id="arc_e5" source="glyph_n11_port_n11.2" target="glyph_n2">
<start x="663.78467" y="344.0"/>
<end x="728.41876" y="344.0"/>
</arc>
<arc class="consumption" id="arc_e6" source="glyph_n7" target="glyph_n11_port_n11.1">
<start x="563.15063" y="344.0"/>
<end x="627.78467" y="344.0"/>
</arc>
<arc class="catalysis" id="arc_e7" source="glyph_n2" target="glyph_n1">
<start x="728.41876" y="344.0"/>
<end x="826.41876" y="344.0"/>
</arc>
<arc class="catalysis" id="arc_e8" source="glyph_n12" target="glyph_n11">
<start x="645.78467" y="236.0"/>
<end x="645.78467" y="332.0"/>
</arc>
<arc class="production" id="arc_e9" source="glyph_n13_port_n13.2" target="glyph_n12">
<start x="581.15063" y="236.0"/>
<end x="645.78467" y="236.0"/>
</arc>
<arc class="consumption" id="arc_e10" source="glyph_n8" target="glyph_n13_port_n13.1">
<start x="480.51657" y="236.0"/>
<end x="545.15063" y="236.0"/>
</arc>
<arc class="consumption" id="arc_e11" source="glyph_n10" target="glyph_n14_port_n14.1">
<start x="397.8825" y="128.0"/>
<end x="462.51657" y="128.0"/>
</arc>
<arc class="production" id="arc_e12" source="glyph_n14_port_n14.2" target="glyph_n9">
<start x="498.51657" y="128.0"/>
<end x="563.15063" y="128.0"/>
</arc>
<arc class="catalysis" id="arc_e13" source="glyph_n9" target="glyph_n13">
<start x="563.15063" y="128.0"/>
<end x="563.15063" y="224.0"/>
</arc>
<arc class="consumption" id="arc_e14" source="glyph_n16" target="glyph_n17_port_n17.1">
<start x="315.24847" y="20.0"/>
<end x="379.8825" y="20.0"/>
</arc>
<arc class="production" id="arc_e15" source="glyph_n17_port_n17.2" target="glyph_n15">
<start x="415.8825" y="20.0"/>
<end x="480.51657" y="20.0"/>
</arc>
<arc class="catalysis" id="arc_e16" source="glyph_n15" target="glyph_n14">
<start x="480.51657" y="20.0"/>
<end x="480.51657" y="116.0"/>
</arc>
</map>
</sbgn>
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<extension>
<renderInformation xmlns="http://www.sbml.org/sbml/level3/version1/render/version1" backgroundColor="#ffffff" id="renderInformation" programName="graphml2sbgn" programVersion="0.1">
<listOfColorDefinitions>
<colorDefinition id="color_1" value="#E2ACA3"/>
<colorDefinition id="color_2" value="#C8D8EB"/>
<colorDefinition id="color_3" value="#DBEBDB"/>
<colorDefinition id="color_4" value="#FFFFFF"/>
<colorDefinition id="color_5" value="#000000"/>
</listOfColorDefinitions>
<listOfStyles>
<style id="style_1.0FFFFFF14.0000000" idList="n14 n0 n16 n1 n3 n4 n5 n7">
<g fill="color_4" fontSize="14.0" stroke="color_5" strokeWidth="1.0"/>
</style>
<style id="style_1.0DBEBDB14.0000000" idList="n15 n17 n9 n10 n12 n11">
<g fill="color_3" fontSize="14.0" stroke="color_5" strokeWidth="1.0"/>
</style>
<style id="style_1.0C8D8EB14.0000000" idList="n6 n8">
<g fill="color_2" fontSize="14.0" stroke="color_5" strokeWidth="1.0"/>
</style>
<style id="style_1.0E2ACA314.0000000" idList="n13 n2">
<g fill="color_1" fontSize="14.0" stroke="color_5" strokeWidth="1.0"/>
</style>
<style id="style_1.0000000" idList="e11 e10 e13 e12 e15 e14 e0 e16 e1 e2 e3 e4 e5 e6 e7 e8 e9">
<g fill="color_5" fontSize="10.0" stroke="color_5" strokeWidth="1.0"/>
</style>
</listOfStyles>
</renderInformation>
</extension>
<glyph class="source and sink" id="n0">
<clone/>
<bbox w="36.0" h="36.0" x="137.0" y="17.0"/>
</glyph>
<glyph class="source and sink" id="n1">
<clone/>
<bbox w="36.0" h="36.0" x="327.0" y="112.0"/>
</glyph>
<glyph class="macromolecule" id="n2">
<label text="GAC"/>
<bbox w="80.0" h="40.0" x="175.0" y="370.0"/>
<glyph class="state variable" id="1">
<state value="" variable="S314"/>
<bbox w="48.0" h="18.0" x="191.0" y="401.0"/>
</glyph>
</glyph>
<glyph class="nucleic acid feature" id="n3">
<label text="PKCε"/>
<bbox w="80.0" h="40.0" x="220.0" y="90.0"/>
<glyph class="unit of information" id="2">
<label text="ct:gene"/>
<bbox w="48.0" h="18.0" x="236.0" y="81.0"/>
</glyph>
</glyph>
<glyph class="nucleic acid feature" id="n4">
<label text="PKCε"/>
<bbox w="80.0" h="40.0" x="115.0" y="185.0"/>
<glyph class="unit of information" id="3">
<label text="ct:mRNA"/>
<bbox w="48.0" h="18.0" x="131.0" y="176.0"/>
</glyph>
</glyph>
<glyph class="process" orientation="vertical" id="n5">
<clone/>
<bbox w="18.0" h="18.0" x="336.0" y="196.0"/>
<port id="n5.1" x="345.0" y="223.0"/>
<port id="n5.2" x="345.0" y="187.0"/>
</glyph>
<glyph class="macromolecule" id="n6">
<label text="NF-κB"/>
<bbox w="80.0" h="40.0" x="10.0" y="90.0"/>
</glyph>
<glyph class="process" orientation="vertical" id="n7">
<clone/>
<bbox w="18.0" h="18.0" x="146.0" y="101.0"/>
<port id="n7.1" x="155.0" y="128.0"/>
<port id="n7.2" x="155.0" y="92.0"/>
</glyph>
<glyph class="macromolecule" id="n8">
<label text="PKCε"/>
<bbox w="80.0" h="40.0" x="305.0" y="265.0"/>
</glyph>
<glyph class="simple chemical" id="n9">
<label text="glutamine"/>
<bbox w="90.0" h="36.0" x="350.0" y="457.0"/>
</glyph>
<glyph class="simple chemical" id="n10">
<label text="H2O"/>
<bbox w="60.0" h="36.0" x="405.0" y="532.0"/>
</glyph>
<glyph class="simple chemical" id="n11">
<label text="glutamate"/>
<bbox w="90.0" h="36.0" x="580.0" y="457.0"/>
</glyph>
<glyph class="simple chemical" id="n12">
<label text="NH3"/>
<bbox w="60.0" h="36.0" x="550.0" y="532.0"/>
</glyph>
<glyph class="macromolecule" id="n13">
<label text="GAC"/>
<bbox w="80.0" h="40.0" x="460.0" y="370.0"/>
<glyph class="state variable" id="4">
<state value="P" variable="S314"/>
<bbox w="48.0" h="18.0" x="476.0" y="401.0"/>
</glyph>
</glyph>
<glyph class="process" orientation="horizontal" id="n14">
<clone/>
<bbox w="18.0" h="18.0" x="491.0" y="466.0"/>
<port id="n14.1" x="482.0" y="475.0"/>
<port id="n14.2" x="518.0" y="475.0"/>
</glyph>
<glyph class="simple chemical" id="n15">
<label text="ATP"/>
<bbox w="60.0" h="30.0" x="255.0" y="325.0"/>
</glyph>
<glyph class="process" orientation="horizontal" id="n16">
<clone/>
<bbox w="18.0" h="18.0" x="336.0" y="381.0"/>
<port id="n16.1" x="327.0" y="390.0"/>
<port id="n16.2" x="363.0" y="390.0"/>
</glyph>
<glyph class="simple chemical" id="n17">
<label text="ADP"/>
<bbox w="60.0" h="30.0" x="380.0" y="325.0"/>
</glyph>
<arc class="consumption" id="e0" source="n0" target="n7.2">
<start x="155.0" y="35.0"/>
<end x="155.0" y="92.0"/>
</arc>
<arc class="consumption" id="e1" source="n1" target="n5.2">
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<end x="345.0" y="187.0"/>
</arc>
<arc class="consumption" id="e2" source="n2" target="n16.1">
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<end x="327.0" y="390.0"/>
</arc>
<arc class="production" id="e3" source="n7.1" target="n4">
<start x="155.0" y="128.0"/>
<end x="155.0" y="176.07452"/>
</arc>
<arc class="production" id="e4" source="n5.1" target="n8">
<start x="345.0" y="223.0"/>
<end x="345.0" y="285.0"/>
</arc>
<arc class="production" id="e5" source="n16.2" target="n13">
<start x="363.0" y="390.0"/>
<end x="500.0" y="390.0"/>
</arc>
<arc class="necessary stimulation" id="e6" source="n3" target="n7">
<start x="260.0" y="110.0"/>
<end x="155.0" y="110.0"/>
</arc>
<arc class="necessary stimulation" id="e7" source="n4" target="n5">
<start x="155.0" y="205.0"/>
<end x="345.0" y="205.0"/>
</arc>
<arc class="stimulation" id="e8" source="n6" target="n7">
<start x="50.0" y="110.0"/>
<end x="155.0" y="110.0"/>
</arc>
<arc class="stimulation" id="e9" source="n8" target="n16">
<start x="345.0" y="285.0"/>
<end x="345.0" y="390.0"/>
</arc>
<arc class="consumption" id="e10" source="n9" target="n14.1">
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</arc>
<arc class="consumption" id="e11" source="n10" target="n14.1">
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<end x="482.0" y="475.0"/>
</arc>
<arc class="production" id="e12" source="n14.2" target="n11">
<start x="518.0" y="475.0"/>
<end x="625.0" y="475.0"/>
</arc>
<arc class="production" id="e13" source="n14.2" target="n12">
<start x="518.0" y="475.0"/>
<next x="524.0" y="475.0"/>
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