From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Mon, 29 Jul 2013 12:58:12 +0000 (+0100)
Subject: merge JABAWS_Release_2_1 into develop
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=00a2b15acef8866a404db64381d7dfeb93bf7ad9;p=jabaws.git

merge JABAWS_Release_2_1 into develop
---

00a2b15acef8866a404db64381d7dfeb93bf7ad9
diff --cc conf/settings/AAConParameters.xml
index ac75e6b,6ebcad4..bdc1ef7
--- a/conf/settings/AAConParameters.xml
+++ b/conf/settings/AAConParameters.xml
@@@ -1,72 -1,71 +1,71 @@@
  <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
  <runnerConfig>
- 	<runnerClassName>compbio.runner.conservation.AACon</runnerClassName>
- 	<options>
- 		<name>Normalize</name>
- 		<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>
- 		<defaultValue>-n</defaultValue>
- 		<furtherDetails>prog_docs/aacon.txt</furtherDetails>
- 	</options>
- 	      <options><name>KABAT</name><description></description><optionNames>-m=KABAT</optionNames><furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails></options>
-         <options><name>JORES</name><description></description><optionNames>-m=JORES</optionNames><furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails></options>
-     <options><name>SCHNEIDER</name><description></description><optionNames>-m=SCHNEIDER</optionNames><furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails></options>
-     <options><name>SHENKIN</name><description></description><optionNames>-m=SHENKIN</optionNames><furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails><defaultValue>-m=SHENKIN</defaultValue></options>
-     <options><name>GERSTEIN</name><description></description><optionNames>-m=GERSTEIN</optionNames><furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails></options>
-     <options><name>TAYLOR_GAPS</name><description></description><optionNames>-m=TAYLOR_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails></options>
-     <options><name>TAYLOR_NO_GAPS</name><description></description><optionNames>-m=TAYLOR_NO_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails></options> 
-         <options><name>ZVELIBIL</name><description></description><optionNames>-m=ZVELIBIL</optionNames><furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails></options>
-         <options><name>KARLIN</name><description></description><optionNames>-m=KARLIN</optionNames><furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails></options>
-     <options><name>ARMON</name><description></description><optionNames>-m=ARMON</optionNames><furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails></options>
-     <options><name>THOMPSON</name><description></description><optionNames>-m=THOMPSON</optionNames><furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails></options>
-     <options><name>NOT_LANCET</name><description></description><optionNames>-m=NOT_LANCET</optionNames><furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails></options>
-     <options><name>MIRNY</name><description></description><optionNames>-m=MIRNY</optionNames><furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails></options>
-     <options><name>WILLIAMSON</name><description></description><optionNames>-m=WILLIAMSON</optionNames><furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails></options> 
-         <options><name>LANDGRAF</name><description></description><optionNames>-m=LANDGRAF</optionNames><furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails></options>
-         <options><name>SANDER</name><description></description><optionNames>-m=SANDER</optionNames><furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails></options>
-         <options><name>VALDAR</name><description></description><optionNames>-m=VALDAR</optionNames><furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails></options>
-         <options><name>SMERFS</name><description></description><optionNames>-m=SMERFS</optionNames><furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails></options>
-   	
- 	<prmSeparator>=</prmSeparator>
- 	<parameters>
- 		<name>SMERFS Window Width</name>
- 		<description>The width of the window for SMERFS. Optional, defaults to 7</description>
- 		<optionNames>-smerfsWW</optionNames>
- 		<furtherDetails>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>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>prog_docs/aacon.txt</furtherDetails>
- 		<defaultValue>0.1</defaultValue>
- 		<validValue>
-         	<type>Float</type>
+   <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>
+   <options>
+     <name>Normalize</name>
+     <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>
+     <defaultValue>-n</defaultValue>
+     <furtherDetails>prog_docs/aacon.txt</furtherDetails>
+   </options>
+   <options><name>KABAT</name><description></description><optionNames>-m=KABAT</optionNames><furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails></options>
+   <options><name>JORES</name><description></description><optionNames>-m=JORES</optionNames><furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails></options>
+   <options><name>SCHNEIDER</name><description></description><optionNames>-m=SCHNEIDER</optionNames><furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails></options>
+   <options><name>SHENKIN</name><description></description><optionNames>-m=SHENKIN</optionNames><furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails><defaultValue>-m=SHENKIN</defaultValue></options>
+   <options><name>GERSTEIN</name><description></description><optionNames>-m=GERSTEIN</optionNames><furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails></options>
+   <options><name>TAYLOR_GAPS</name><description></description><optionNames>-m=TAYLOR_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails></options>
+   <options><name>TAYLOR_NO_GAPS</name><description></description><optionNames>-m=TAYLOR_NO_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails></options> 
+   <options><name>ZVELIBIL</name><description></description><optionNames>-m=ZVELIBIL</optionNames><furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails></options>
+   <options><name>KARLIN</name><description></description><optionNames>-m=KARLIN</optionNames><furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails></options>
+   <options><name>ARMON</name><description></description><optionNames>-m=ARMON</optionNames><furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails></options>
+   <options><name>THOMPSON</name><description></description><optionNames>-m=THOMPSON</optionNames><furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails></options>
+   <options><name>NOT_LANCET</name><description></description><optionNames>-m=NOT_LANCET</optionNames><furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails></options>
+   <options><name>MIRNY</name><description></description><optionNames>-m=MIRNY</optionNames><furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails></options>
+   <options><name>WILLIAMSON</name><description></description><optionNames>-m=WILLIAMSON</optionNames><furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails></options> 
+   <options><name>LANDGRAF</name><description></description><optionNames>-m=LANDGRAF</optionNames><furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails></options>
+   <options><name>SANDER</name><description></description><optionNames>-m=SANDER</optionNames><furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails></options>
+   <options><name>VALDAR</name><description></description><optionNames>-m=VALDAR</optionNames><furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails></options>
+   <options><name>SMERFS</name><description></description><optionNames>-m=SMERFS</optionNames><furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails></options>
+ 
+   <prmSeparator>=</prmSeparator>
+   <parameters>
+     <name>SMERFS Window Width</name>
+     <description>The width of the window for SMERFS. Optional, defaults to 7</description>
+     <optionNames>-smerfsWW</optionNames>
+     <furtherDetails>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>prog_docs/aacon.txt</furtherDetails>
+     <defaultValue>MID_SCORE</defaultValue>
+     <possibleValues>MAX_SCORE</possibleValues>
 -        <possibleValues>MID_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>prog_docs/aacon.txt</furtherDetails>
+     <defaultValue>0.1</defaultValue>
+     <validValue>
+           <type>Float</type>
              <min>0.001</min>
              <max>1</max>
          </validValue>