X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=conf%2Fsettings%2FAAConParameters.xml;fp=conf%2Fsettings%2FAAConParameters.xml;h=2274cd3045078fbf19390d52ba93528212c03c1e;hb=eee7bbead2d812ef1aa67389ae2d1c4884c47458;hp=9f5da9f7c58f272d61567702d1870f1df31bd7b8;hpb=6adca61e46b4daf4136621f942f313c74e44e61d;p=jabaws.git

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