JWS-50 refactored the valid AACon method parameters as a series of options in the...

diff --git a/conf/settings/AAConParameters.xml b/conf/settings/AAConParameters.xml
index ac75e6b..6ebcad4 100644 (file)
--- a/conf/settings/AAConParameters.xml
+++ b/conf/settings/AAConParameters.xml
@@ -1,74 +1,74 @@
 <?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
+  <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
-       <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
+  </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
-       </parameters>\r
+  </parameters>\r
+\r
 </runnerConfig>\r

diff --git a/conf/settings/AAConPresets.xml b/conf/settings/AAConPresets.xml
index cdf8d37..f2e3cde 100644 (file)
--- a/conf/settings/AAConPresets.xml
+++ b/conf/settings/AAConPresets.xml
@@ -1,30 +1,25 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <presets>\r
- <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
+<runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
        <preset>\r
                <name>Quick conservation</name>\r
                <description>Collection of fast conservation methods</description>\r
                <optlist>\r
-                       <option>-m=KABAT,JORES,SCHNEIDER,SHENKIN,GERSTEIN,TAYLOR_GAPS,TAYLOR_NO_GAPS,ZVELIBIL,ARMON,THOMPSON,NOT_LANCET,MIRNY,WILLIAMSON</option>\r
+                       <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option>\r
                </optlist>\r
        </preset>\r
        <preset>\r
                <name>Slow conservation</name>\r
                <description>Collection of most expensive (slow) conservation methods</description>\r
                <optlist>\r
-                       <option>-m=LANDGRAF,KARLIN,SANDER,VALDAR,SMERFS</option>\r
+                       <option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
                </optlist>\r
        </preset>\r
        <preset>\r
                <name>Complete conservation</name>\r
                <description>Calculate conservation with all supported methods</description>\r
                <optlist>\r
-                       <option>-m=KABAT,JORES,SCHNEIDER,SHENKIN,GERSTEIN,TAYLOR_GAPS,TAYLOR_NO_GAPS,ZVELIBIL,ARMON,THOMPSON,NOT_LANCET,MIRNY,WILLIAMSON,LANDGRAF,KARLIN,SANDER,VALDAR,SMERFS</option>\r
+                       <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option><option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
                </optlist>\r
        </preset>\r
 </presets>\r
-\r
-\r
-\r
- \r
-\r