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Merge branch 'JABAWS_Release_2_5' into develop
[jabaws.git] / conf / settings / AAConParameters.xml
diff --git a/conf/settings/AAConParameters.xml b/conf/settings/AAConParameters.xml
index bdc1ef7..5530ebb 100644 (file)
--- a/conf/settings/AAConParameters.xml
+++ b/conf/settings/AAConParameters.xml
@@ -1,74 +1,191 @@
 <?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>\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
-  </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
+    <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
+\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
+\r
+    <options>\r
+        <name>SHENKIN</name>\r
+        <description></description>\r
+        <optionNames>-m=SHENKIN</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails>\r
+        <defaultValue>-m=SHENKIN</defaultValue>\r
+    </options>\r
+\r
+    <options>\r
+        <name>KABAT</name>\r
+        <description></description>\r
+        <optionNames>-m=KABAT</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>JORES</name>\r
+        <description></description>\r
+        <optionNames>-m=JORES</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>SCHNEIDER</name>\r
+        <description></description>\r
+        <optionNames>-m=SCHNEIDER</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>GERSTEIN</name>\r
+        <description></description>\r
+        <optionNames>-m=GERSTEIN</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>TAYLOR_GAPS</name>\r
+        <description></description>\r
+        <optionNames>-m=TAYLOR_GAPS</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>TAYLOR_NO_GAPS</name>\r
+        <description></description>\r
+        <optionNames>-m=TAYLOR_NO_GAPS</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails>\r
+    </options> \r
+    <options>\r
+        <name>ZVELIBIL</name>\r
+        <description></description>\r
+        <optionNames>-m=ZVELIBIL</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>KARLIN</name>\r
+        <description></description>\r
+        <optionNames>-m=KARLIN</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>ARMON</name>\r
+        <description></description>\r
+        <optionNames>-m=ARMON</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>THOMPSON</name>\r
+        <description></description>\r
+        <optionNames>-m=THOMPSON</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>NOT_LANCET</name>\r
+        <description></description>\r
+        <optionNames>-m=NOT_LANCET</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>MIRNY</name>\r
+        <description></description>\r
+        <optionNames>-m=MIRNY</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>WILLIAMSON</name>\r
+        <description></description>\r
+        <optionNames>-m=WILLIAMSON</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails>\r
+    </options> \r
+    <options>\r
+        <name>LANDGRAF</name>\r
+        <description></description>\r
+        <optionNames>-m=LANDGRAF</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>SANDER</name>\r
+        <description></description>\r
+        <optionNames>-m=SANDER</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>VALDAR</name>\r
+        <description></description>\r
+        <optionNames>-m=VALDAR</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails>\r
+    </options>\r
+\r
+    <options>\r
+        <name>SMERFS</name>\r
+        <description></description>\r
+        <optionNames>-m=SMERFS</optionNames>\r
+        <furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails>\r
+    </options>\r
+\r
+    <prmSeparator>=</prmSeparator>\r
+\r
+    <parameters>\r
+        <name>SMERFS Window Width</name>\r
+        <description>\r
+            The width of the window for SMERFS. Optional, defaults to 7\r
+        </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>\r
+            SMERFS Column Score algorithm defines the window scores to columns allocation, \r
+            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. \r
+            Optional defaults to MID_SCORE.\r
+        </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
+\r
+    <parameters>\r
+        <name>SMERFS Gap Threshhold</name>\r
+        <description>\r
+            a gap percentage cutoff - a float greater than 0 and smaller or equal 1.\r
+            Optional defaults to 0.1\r
+        </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
-  </parameters>\r
+    </parameters>\r
 \r
 </runnerConfig>\r