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Clean-up, refactoring, commenting. Parameters file containts only options since Jalvi...
[jabaws.git]
/
conf
/
settings
/
RNAalifoldParameters.xml
diff --git
a/conf/settings/RNAalifoldParameters.xml
b/conf/settings/RNAalifoldParameters.xml
index
a730f64
..
e79c44c
100644
(file)
--- a/
conf/settings/RNAalifoldParameters.xml
+++ b/
conf/settings/RNAalifoldParameters.xml
@@
-70,7
+70,7
@@
<optionNames>--MEA</optionNames>
</options>
<optionNames>--MEA</optionNames>
</options>
- <prmSeparator> </prmSeparator>
+ <prmSeparator> </prmSeparator>
<parameters isRequired='false'>
<name>scaling factor</name>
<parameters isRequired='false'>
<name>scaling factor</name>
@@
-96,7
+96,7
@@
</parameters>
<parameters isRequired='false'>
<name>Temperature</name>
</parameters>
<parameters isRequired='false'>
<name>Temperature</name>
- <description>Rescale Energy parameters to Temperature</description>
+ <description>Rescale Energy parameterss to Temperature</description>
<optionNames>-T</optionNames>
<defaultValue>37</defaultValue>
<validValue>
<optionNames>-T</optionNames>
<defaultValue>37</defaultValue>
<validValue>
@@
-105,6
+105,7
@@
<max>1000000</max>
</validValue>
</parameters>
<max>1000000</max>
</validValue>
</parameters>
+
<parameters isRequired='false'>
<name>cfactor</name>
<description>weight of covariance term</description>
<parameters isRequired='false'>
<name>cfactor</name>
<description>weight of covariance term</description>