A secondary parameters file with some Jalview friendly parameters

diff --git a/testsrc/testdata/RNAalifoldParameters.xml b/testsrc/testdata/RNAalifoldParameters.xml
new file mode 100644 (file)
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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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