merge JABAWS_Release_2_1 into develop

diff --cc conf/settings/AAConParameters.xml
index ac75e6b,6ebcad4..bdc1ef7
--- 1/conf/settings/AAConParameters.xml
--- 2/conf/settings/AAConParameters.xml
+++ b/conf/settings/AAConParameters.xml
@@@ -1,72 -1,71 +1,71 @@@
  <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
  <runnerConfig>\r
-       <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
-       <options>\r
-               <name>Normalize</name>\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
-               <defaultValue>-n</defaultValue>\r
-               <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
-       </options>\r
-             <options><name>KABAT</name><description></description><optionNames>-m=KABAT</optionNames><furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails></options>\r
-         <options><name>JORES</name><description></description><optionNames>-m=JORES</optionNames><furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails></options>\r
-     <options><name>SCHNEIDER</name><description></description><optionNames>-m=SCHNEIDER</optionNames><furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails></options>\r
-     <options><name>SHENKIN</name><description></description><optionNames>-m=SHENKIN</optionNames><furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails><defaultValue>-m=SHENKIN</defaultValue></options>\r
-     <options><name>GERSTEIN</name><description></description><optionNames>-m=GERSTEIN</optionNames><furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails></options>\r
-     <options><name>TAYLOR_GAPS</name><description></description><optionNames>-m=TAYLOR_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails></options>\r
-     <options><name>TAYLOR_NO_GAPS</name><description></description><optionNames>-m=TAYLOR_NO_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails></options> \r
-         <options><name>ZVELIBIL</name><description></description><optionNames>-m=ZVELIBIL</optionNames><furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails></options>\r
-         <options><name>KARLIN</name><description></description><optionNames>-m=KARLIN</optionNames><furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails></options>\r
-     <options><name>ARMON</name><description></description><optionNames>-m=ARMON</optionNames><furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails></options>\r
-     <options><name>THOMPSON</name><description></description><optionNames>-m=THOMPSON</optionNames><furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails></options>\r
-     <options><name>NOT_LANCET</name><description></description><optionNames>-m=NOT_LANCET</optionNames><furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails></options>\r
-     <options><name>MIRNY</name><description></description><optionNames>-m=MIRNY</optionNames><furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails></options>\r
-     <options><name>WILLIAMSON</name><description></description><optionNames>-m=WILLIAMSON</optionNames><furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails></options> \r
-         <options><name>LANDGRAF</name><description></description><optionNames>-m=LANDGRAF</optionNames><furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails></options>\r
-         <options><name>SANDER</name><description></description><optionNames>-m=SANDER</optionNames><furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails></options>\r
-         <options><name>VALDAR</name><description></description><optionNames>-m=VALDAR</optionNames><furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails></options>\r
-         <options><name>SMERFS</name><description></description><optionNames>-m=SMERFS</optionNames><furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails></options>\r
-       \r
-       <prmSeparator>=</prmSeparator>\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>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>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>prog_docs/aacon.txt</furtherDetails>\r
-               <defaultValue>0.1</defaultValue>\r
-               <validValue>\r
-               <type>Float</type>\r
+   <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
+   <options>\r
+     <name>Normalize</name>\r
+     <description>\r
+     Normalize the results. Normalized results have values between 0 and 1. Please note however, \r
+     that some results cannot be normalized. In such a case, the system returns not \r
+     normalized value. The following formula is used for normalization n = (d - dmin)/(dmax - dmin)\r
+     Negative results first converted to positive by adding a greatest absolute result value.\r
+     </description>\r
+     <optionNames>-n</optionNames>\r
+     <defaultValue>-n</defaultValue>\r
+     <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
+   </options>\r
+   <options><name>KABAT</name><description></description><optionNames>-m=KABAT</optionNames><furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails></options>\r
+   <options><name>JORES</name><description></description><optionNames>-m=JORES</optionNames><furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails></options>\r
+   <options><name>SCHNEIDER</name><description></description><optionNames>-m=SCHNEIDER</optionNames><furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails></options>\r
+   <options><name>SHENKIN</name><description></description><optionNames>-m=SHENKIN</optionNames><furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails><defaultValue>-m=SHENKIN</defaultValue></options>\r
+   <options><name>GERSTEIN</name><description></description><optionNames>-m=GERSTEIN</optionNames><furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails></options>\r
+   <options><name>TAYLOR_GAPS</name><description></description><optionNames>-m=TAYLOR_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails></options>\r
+   <options><name>TAYLOR_NO_GAPS</name><description></description><optionNames>-m=TAYLOR_NO_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails></options> \r
+   <options><name>ZVELIBIL</name><description></description><optionNames>-m=ZVELIBIL</optionNames><furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails></options>\r
+   <options><name>KARLIN</name><description></description><optionNames>-m=KARLIN</optionNames><furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails></options>\r
+   <options><name>ARMON</name><description></description><optionNames>-m=ARMON</optionNames><furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails></options>\r
+   <options><name>THOMPSON</name><description></description><optionNames>-m=THOMPSON</optionNames><furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails></options>\r
+   <options><name>NOT_LANCET</name><description></description><optionNames>-m=NOT_LANCET</optionNames><furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails></options>\r
+   <options><name>MIRNY</name><description></description><optionNames>-m=MIRNY</optionNames><furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails></options>\r
+   <options><name>WILLIAMSON</name><description></description><optionNames>-m=WILLIAMSON</optionNames><furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails></options> \r
+   <options><name>LANDGRAF</name><description></description><optionNames>-m=LANDGRAF</optionNames><furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails></options>\r
+   <options><name>SANDER</name><description></description><optionNames>-m=SANDER</optionNames><furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails></options>\r
+   <options><name>VALDAR</name><description></description><optionNames>-m=VALDAR</optionNames><furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails></options>\r
+   <options><name>SMERFS</name><description></description><optionNames>-m=SMERFS</optionNames><furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails></options>\r
+ \r
+   <prmSeparator>=</prmSeparator>\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>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
+ \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: MID_SCORE - gives the window score to the middle column\r
+           MAX_SCORE - gives the column the highest score of all the windows it belongs to. Optional defaults to MID_SCORE. </description>\r
+     <optionNames>-smerfsCS</optionNames>\r
+     <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
+     <defaultValue>MID_SCORE</defaultValue>\r
+     <possibleValues>MAX_SCORE</possibleValues>\r
 -        <possibleValues>MID_SCORE</possibleValues>\r
++    <possibleValues>MID_SCORE</possibleValues>\r
+   </parameters>\r
+ \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>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