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titleheader.xml
Code Block
<?xml version="1.0" encoding="ISO-8859-1"?>
<cgview backboneRadius="600" backboneColor="rgb(102,102,102)" backboneThickness="8" featureSlotSpacing="small" labelLineLength="100" labelP\
lacementQuality="good" labelLineThickness="2" rulerPadding="10" tickThickness="6" arrowheadLength="6" rulerFont="SansSerif, plain, 20" rule\
rFontColor="rgb(0,0,0)" labelFont="SansSerif, plain, 15" isLinear="true" minimumFeatureLength="0.2" sequenceLength="1255523" height="3000" \
width="3000" globalLabel="true" moveInnerLabelsToOuter="false" featureThickness="30" tickLength="15" useInnerLabels="true" shortTickColor="\
rgb(0,51,0)" longTickColor="rgb(0,51,0)" zeroTickColor="rgb(0,51,0)" showBorder="true" borderColor="black" backgroundColor="white" tickDens\
ity="0.166666666666667">




<!-- title -->
<legend position="lower-center" backgroundOpacity="0.8">
<legendItem textAlignment="center" font="SansSerif, plain, 60" text="IgH Locus (from chr14:106032563-107288085)" />
</legend>





<!-- details legend -->
<legend position="upper-left" font="SansSerif, plain, 20" backgroundOpacity="0.8">
<legendItem text="Accession: NC_000014" />
<legendItem text="Length: 1,255,523 bp" />
<legendItem text="Topology: linear" />
</legend>





<!-- legend -->
<legend position="upper-right" textAlignment="left" backgroundOpacity="0.8" font="SansSerif, plain, 20">
<legendItem text="CDS" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(0,0,153)" />
<legendItem text="tRNA" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(153,0,0)" />
<legendItem text="rRNA" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(153,0,153)" />
<legendItem text="Other" drawSwatch="true" swatchOpacity="0.5" swatchColor="rgb(51,51,51)" />
<legendItem text="Chr3 TLs" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(102,255,51)" />
<legendItem text="Chr5 TLs" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(102,51,255)" />
<legendItem text="Chr8 TLs" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(204,51,255)" />
<legendItem text="Chr16 TLs" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(255,51,102)" />
<legendItem text="Chr17 TLs" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(255,51,204)" />
<legendItem text="Chr18 TLs" drawSwatch="true" swatchOpacity="1.0" swatchColor="rgb(51,102,255)" />
</legend>
Code Block
titleUsing makeMap.sh

makeMap.sh FeatureA.xml FeatureB.xml

generates the graph as map.jpg, with Feature A and Feature B as separate tracks, where (for example) FeatureA.xml and FeatureB.xml are files of the form

Code Block
titleFeatureA

<featureSlot showShading="false" strand="direct">
<feature color="green" decoration="arc" >
<featureRange start="1" stop="1184" />
<featureRange start="1198" stop="1367" />
<featureRange start="1416" stop="1607" />
<featureRange start="1614" stop="1853" />
</feature>
</featureSlot>

Note that the input files here aren't technically XML files themselves, since they don't begin with an XML declaration, but this is a minor technical point.