Add testing dirs

[proteocache.git] / testsrc / testdata / ProbconsParameters.xml

diff --git a/testsrc/testdata/ProbconsParameters.xml b/testsrc/testdata/ProbconsParameters.xml
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+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<runnerConfig>\r
+ <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
+ <!-- \r
+    <options>\r
+        <name>Reestimate EP</name>\r
+        <description>Reestimate emission probabilities</description>\r
+        <optionNames>-e</optionNames>\r
+        <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
+    </options>\r
+     -->\r
+    <options>\r
+        <name>Output aligned</name>\r
+        <description>Output sequences in alignment order rather than input order</description>\r
+        <optionNames>-a</optionNames>\r
+        <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
+    </options>\r
+    <prmSeparator> </prmSeparator>\r
+       <!-- TODO This needs matrix file accessible to the program \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
+        <optionNames>-m</optionNames>\r
+        <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
+        <defaultValue>BLOSUM62</defaultValue>\r
+        <possibleValues>BLOSUM62</possibleValues>\r
+        <possibleValues>PAM</possibleValues>\r
+        <possibleValues>ID</possibleValues>\r
+        <possibleValues>GONNET</possibleValues>\r
+    </parameters>\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
+        <optionNames>-pre</optionNames>\r
+        <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
+        <defaultValue>0</defaultValue>\r
+         <validValue>\r
+               <type>Integer</type>\r
+            <min>0</min>\r
+            <max>20</max>\r
+        </validValue>\r
+    </parameters>\r
+    <parameters>\r
+        <name>Passes of iterative refinement</name>\r
+        <description>This specifies the number of iterations of iterative refinement to be performed. In each\r
+stage of iterative refinement, the set of sequences in the alignment is randomly\r
+partitioned into two groups. After projecting the alignments to these groups, the two\r
+groups are realigned, resulting in an alignment whose objective score is guaranteed to be\r
+at least that of the original alignment</description>\r
+        <optionNames>-ir</optionNames>\r
+        <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
+         <defaultValue>100</defaultValue>\r
+         <validValue>\r
+               <type>Integer</type>\r
+            <min>0</min>\r
+            <max>1000</max>\r
+        </validValue>\r
+    </parameters>\r
+    <parameters>\r
+        <name>Passes of consistency transformation</name>\r
+        <description>Each pass applies one round of the consistency transformation on the set of sequences.\r
+       The consistency transformation is described in detail in the mentioned papers. In each\r
+       round, the aligner computes the consistency transformation for each pair of sequences\r
+       using all other sequences. The aligner then updates the posterior probability matrices of\r
+       the pairwise alignments.</description>\r
+        <optionNames>-c</optionNames>\r
+        <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
+        <defaultValue>2</defaultValue>\r
+         <validValue>\r
+               <type>Integer</type>\r
+            <min>0</min>\r
+            <max>5</max>\r
+        </validValue>\r
+    </parameters>\r
+</runnerConfig>\r