AAConWS further work

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

diff --git a/conf/settings/AAConParameters.xml b/conf/settings/AAConParameters.xml
index 9f5da9f..2274cd3 100644 (file)
--- a/conf/settings/AAConParameters.xml
+++ b/conf/settings/AAConParameters.xml
@@ -3,7 +3,13 @@
        <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
        <options>\r
                <name>Normalize</name>\r
-               <description>Normalize the results. The results of the calculation by different methods will all be scaled to the range between 0 and 1, so that they are comparable</description>\r
+               <description>Normalize the results.  \r
+               Normalized results have values between 0 and 1. Please note however, that \r
+        some results cannot be normalized. In such a case, the system returns not \r
+        normalized value. The following formula is used for normalization \r
+                               n = (d - dmin)/(dmax - dmin)\r
+               Negative results first converted to positive by adding a greatest absolute \r
+               result value.</description>\r
                <optionNames>-n</optionNames>\r
                <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
        </options>\r
@@ -33,4 +39,41 @@
         <possibleValues>VALDAR</possibleValues>\r
         <possibleValues>SMERFS</possibleValues>\r
        </parameters>\r
+       <parameters>\r
+               <name>SMERFS Window Width</name>\r
+               <description>The width of the window for SMERFS. Optional, defaults to 7</description>\r
+               <optionNames>-smerfsWW</optionNames>\r
+               <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
+               <defaultValue>7</defaultValue>\r
+               <validValue>\r
+               <type>Integer</type>\r
+            <min>3</min>\r
+            <max>100</max>\r
+        </validValue>\r
+       </parameters>\r
+       <parameters>\r
+               <name>SMERFS Column Scoring Method</name>\r
+               <description>SMERFS Column Score algorithm defines the window scores to \r
+                       columns allocation, two methods are possible:\r
+               MID_SCORE - gives the window score to the middle column\r
+               MAX_SCORE - gives the column the highest score of all the windows it \r
+               belongs to. Optional defaults to MID_SCORE. </description>\r
+               <optionNames>-smerfsCS</optionNames>\r
+               <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
+               <defaultValue>MID_SCORE</defaultValue>\r
+               <possibleValues>MAX_SCORE</possibleValues>\r
+        <possibleValues>MID_SCORE</possibleValues>\r
+       </parameters>\r
+       <parameters>\r
+               <name>SMERFS Gap Threshhold</name>\r
+               <description>a gap percentage cutoff - a float greater than 0 and smaller or equal 1. Optional defaults to 0.1</description>\r
+               <optionNames>-smerfsGT</optionNames>\r
+               <furtherDetails>http://www.compbio.dundee.ac.uk/jabaws/prog_docs/aacon.txt</furtherDetails>\r
+               <defaultValue>0.1</defaultValue>\r
+               <validValue>\r
+               <type>Float</type>\r
+            <min>0.001</min>\r
+            <max>1</max>\r
+        </validValue>\r
+       </parameters>\r
 </runnerConfig>\r