Merge branch 'JABAWS_Release_2_5' into develop

[jabaws.git] / conf / settings / ProbconsParameters.xml

diff --git a/conf/settings/ProbconsParameters.xml b/conf/settings/ProbconsParameters.xml
index ddd2605..c66cdcb 100644 (file)
--- a/conf/settings/ProbconsParameters.xml
+++ b/conf/settings/ProbconsParameters.xml
@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <runnerConfig>\r
- <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
+    <runnerClassName>compbio.runner.msa.Probcons</runnerClassName>\r
+\r
     <!-- This is requires training -t, but training output probabil file instead of the alignment   \r
     <options>\r
         <name>Reestimate EP</name>\r
@@ -9,14 +10,19 @@
         <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
     </options>\r
     -->\r
+\r
     <options>\r
         <name>Output aligned</name>\r
-        <description>Output sequences in alignment order rather than input order</description>\r
+        <description>\r
+            Output sequences in alignment order rather than input order\r
+        </description>\r
         <optionNames>-a</optionNames>\r
         <furtherDetails>prog_docs/probcons.pdf</furtherDetails>\r
     </options>\r
+\r
     <prmSeparator> </prmSeparator>\r
-       <!-- unsupported in practice \r
+\r
+<!-- unsupported in practice \r
        <parameters>\r
         <name>MATRIX</name>\r
         <description>Protein weight matrix. Specifies the emission probabilities that are to be used for scoring alignments.</description>\r
@@ -96,13 +102,16 @@
                <possibleValues>PAM80</possibleValues>\r
                <possibleValues>PAM90</possibleValues>\r
        </parameters>\r
-        -->\r
+-->\r
+\r
     <parameters>\r
         <name>Rounds of pre-training before aligning the sequences</name>\r
-        <description>This specifies the number of rounds of EM to be applied on the set of sequences being\r
-aligned. This option is used in case the default parameters are not appropriate for the\r
-particular sequences being aligned; in general, this option is not recommended as it may\r
-lead to unstable alignment parameters.</description>\r
+        <description>\r
+            This specifies the number of rounds of EM to be applied on the set of sequences being\r
+            aligned. This option is used in case the default parameters are not appropriate for the\r
+            particular sequences being aligned; in general, this option is not recommended as it may\r
+            lead to unstable alignment parameters.\r
+       </description>\r
         <optionNames>-pre</optionNames>\r
         <furtherDetails>prog_docs/probcons.pdf</furtherDetails>\r
         <defaultValue>0</defaultValue>\r