X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Ftestdata%2FRNAalifoldParameters.xml;fp=testsrc%2Ftestdata%2FRNAalifoldParameters.xml;h=7cae87059f4bd2ca130e3c910169d0d816932a31;hb=babb6decd107f2769f1fbcce00afcda16bd07110;hp=0000000000000000000000000000000000000000;hpb=8bb35115758f447219bef40d3e7c1f1ac9ba3ed6;p=proteocache.git

diff --git a/testsrc/testdata/RNAalifoldParameters.xml b/testsrc/testdata/RNAalifoldParameters.xml
new file mode 100644
index 0000000..7cae870
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+++ b/testsrc/testdata/RNAalifoldParameters.xml
@@ -0,0 +1,134 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+
+<runnerConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema.dtd"
+			xsi:noNamespaceSchemaLocation="RunnerConfigSchema.xsd">
+	<runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
+	<options isRequired='false'>
+		<name>Endgaps</name>
+		<description>Score pairs with endgaps same as gap-gap pairs</description>
+		<optionNames>-E</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>Most Informative Sequence</name>
+		<description>Ouput Set of nucleotides with frequency > average</description>
+		<optionNames>--mis</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>Partition Function</name>
+		<description>Output partition function and probability matrix</description>
+		<optionNames>-p</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>Circular</name>
+		<description>Assume circular RNA molecule</description>
+		<optionNames>-c</optionNames>
+	</options>
+	<!--  Not Currently available with circular structures (-c) -->
+	<options isRequired='false'>
+		<name>G-Quadruplex</name>
+		<description>Incorporate G-Quadruplex formation into prediction algorithm</description>
+		<optionNames>-g</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>d2</name>
+		<description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
+		<optionNames>-d2</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>No LP</name>
+		<description>Produce Structures without lonely pairs</description>
+		<optionNames>--noLP</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>No GU</name>
+		<description>Do not allow GU pairs</description>
+		<optionNames>--noGU</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>No Closing GU</name>
+		<description>Do not allow GU pairs at the end of sequences</description>
+		<optionNames>--noClosingGU</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>old</name>
+		<description>Use old energy evaluation, treating gaps as characters</description>
+		<optionNames>--old</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>Ribosum Scoring</name>
+		<description>Use Ribosum Scoring Matrix</description>
+		<optionNames>-r</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>d2</name>
+		<description>
+		Dangling energies are added for the bases adjacent to a helix on both sides
+		</description>
+		<optionNames>-d2</optionNames>
+	</options>
+	<options isRequired='false'>
+		<name>MEA Structure</name>
+		<description>Maximum Expected Accuracy Structure</description>
+		<optionNames>--MEA</optionNames>
+	</options>
+	
+	<prmSeparator> </prmSeparator>	
+	
+	<parameters isRequired='false'>
+		<name>scaling factor</name>
+		<description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
+		<optionNames>-S</optionNames>
+		<defaultValue>1.07</defaultValue>
+		<validValue>
+			<type>Float</type>
+			<min>0</min>
+			<max>100</max>
+		</validValue>
+	</parameters>
+	<parameters isRequired='false'>
+		<name>bppmThreshold</name>
+		<description>Threshold for base pair probabilities</description>
+		<optionNames>--bppmThreshold</optionNames>
+		<defaultValue>0.000001</defaultValue>
+		<validValue>
+			<type>Float</type>
+			<min>0.0000000000001</min>
+			<max>1.0</max>
+		</validValue>
+	</parameters>
+	<parameters isRequired='false'>
+		<name>Temperature</name>
+		<description>Rescale Energy parameterss to Temperature</description>
+		<optionNames>-T</optionNames>
+		<defaultValue>37</defaultValue>
+		<validValue>
+			<type>Float</type>
+			<min>-274</min>
+			<max>1000000</max>
+		</validValue>
+	</parameters>
+	
+	<parameters isRequired='false'>
+		<name>cfactor</name>
+		<description>weight of covariance term</description>
+		<optionNames>--cfactor</optionNames>
+		<defaultValue>1.0</defaultValue>
+		<validValue>
+			<type>Float</type>
+			<min>0</min>
+			<max>100000</max>
+		</validValue>
+	</parameters>
+	<parameters isRequired='false'>
+		<name>nfactor</name>
+		<description>penalty for non-compatible sequences in covariance term</description>	
+		<optionNames>--nfactor</optionNames>
+		<defaultValue>1.0</defaultValue>
+		<validValue>
+			<type>Float</type>
+			<min>0</min>
+			<max>100000</max>
+		</validValue>
+	</parameters>
+	
+</runnerConfig>
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