merged conf/Executable.properties

diff --git a/conf/Executable.properties b/conf/Executable.properties
index 28b9f66..3f2cbbb 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -200,7 +200,7 @@ aacon.presets.file=conf/settings/AAConPresets.xml
 local.rnaalifold.bin.windows=binaries/windows/ViennaRNA/RNAalifold.exe\r
 local.rnaalifold.bin=binaries/src/ViennaRNA/Progs/RNAalifold\r
 #cluster.rnaalifold.bin=/homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/ViennaRNA/Progs/RNAalifold\r
-rnaalifold.parameters.file=conf/settings/RNAalifoldOptionsOnly.xml\r
+rnaalifold.parameters.file=conf/settings/RNAalifoldParameters.xml\r
 rnaalifold.limits.file=conf/settings/RNAalifoldLimits.xml\r
 rnaalifold.cluster.settings=-P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
 \r

diff --git a/conf/settings/RNAalifoldParameters.xml b/conf/settings/RNAalifoldParameters.xml
index e79c44c..a234019 100644 (file)
--- a/conf/settings/RNAalifoldParameters.xml
+++ b/conf/settings/RNAalifoldParameters.xml
@@ -80,7 +80,7 @@
                <validValue>
                        <type>Float</type>
                        <min>0</min>
-                       <max>100</max>
+                       <max>10</max>
                </validValue>
        </parameters>
        <parameters isRequired='false'>
@@ -90,7 +90,7 @@
                <defaultValue>0.000001</defaultValue>
                <validValue>
                        <type>Float</type>
-                       <min>0.0000000000001</min>
+                       <min>0.00000001</min>
                        <max>1.0</max>
                </validValue>
        </parameters>
@@ -102,7 +102,7 @@
                <validValue>
                        <type>Float</type>
                        <min>-274</min>
-                       <max>1000000</max>
+                       <max>5000</max>
                </validValue>
        </parameters>
        
@@ -114,7 +114,7 @@
                <validValue>
                        <type>Float</type>
                        <min>0</min>
-                       <max>100000</max>
+                       <max>100</max>
                </validValue>
        </parameters>
        <parameters isRequired='false'>
@@ -125,7 +125,7 @@
                <validValue>
                        <type>Float</type>
                        <min>0</min>
-                       <max>100000</max>
+                       <max>100</max>
                </validValue>
        </parameters>
        

diff --git a/conf/settings/RNAalifoldOptionsOnly.xml b/testsrc/testdata/RNAalifoldParameters.xml
similarity index 59%
rename from conf/settings/RNAalifoldOptionsOnly.xml
rename to testsrc/testdata/RNAalifoldParameters.xml
index 7f8ef44..7cae870 100644 (file)
--- a/conf/settings/RNAalifoldOptionsOnly.xml
+++ b/testsrc/testdata/RNAalifoldParameters.xml
@@ -1,5 +1,7 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
-<runnerConfig>
+
+<runnerConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema.dtd"
+                       xsi:noNamespaceSchemaLocation="RunnerConfigSchema.xsd">
        <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
        <options isRequired='false'>
                <name>Endgaps</name>
@@ -70,6 +72,63 @@
                <optionNames>--MEA</optionNames>
        </options>
        
+       <prmSeparator> </prmSeparator>  
        
+       <parameters isRequired='false'>
+               <name>scaling factor</name>
+               <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
+               <optionNames>-S</optionNames>
+               <defaultValue>1.07</defaultValue>
+               <validValue>
+                       <type>Float</type>
+                       <min>0</min>
+                       <max>100</max>
+               </validValue>
+       </parameters>
+       <parameters isRequired='false'>
+               <name>bppmThreshold</name>
+               <description>Threshold for base pair probabilities</description>
+               <optionNames>--bppmThreshold</optionNames>
+               <defaultValue>0.000001</defaultValue>
+               <validValue>
+                       <type>Float</type>
+                       <min>0.0000000000001</min>
+                       <max>1.0</max>
+               </validValue>
+       </parameters>
+       <parameters isRequired='false'>
+               <name>Temperature</name>
+               <description>Rescale Energy parameterss to Temperature</description>
+               <optionNames>-T</optionNames>
+               <defaultValue>37</defaultValue>
+               <validValue>
+                       <type>Float</type>
+                       <min>-274</min>
+                       <max>1000000</max>
+               </validValue>
+       </parameters>
+       
+       <parameters isRequired='false'>
+               <name>cfactor</name>
+               <description>weight of covariance term</description>
+               <optionNames>--cfactor</optionNames>
+               <defaultValue>1.0</defaultValue>
+               <validValue>
+                       <type>Float</type>
+                       <min>0</min>
+                       <max>100000</max>
+               </validValue>
+       </parameters>
+       <parameters isRequired='false'>
+               <name>nfactor</name>
+               <description>penalty for non-compatible sequences in covariance term</description>      
+               <optionNames>--nfactor</optionNames>
+               <defaultValue>1.0</defaultValue>
+               <validValue>
+                       <type>Float</type>
+                       <min>0</min>
+                       <max>100000</max>
+               </validValue>
+       </parameters>
        
 </runnerConfig>
\ No newline at end of file

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 7b781a2..5a72802 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -173,9 +173,6 @@ public class Jws2Client {
                                ScoreManager result = analize(inputFile,\r
                                                ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 \r
-                               // A System.out.println just for testing!\r
-                               System.out.println(result.toString());\r
-                               \r
                                IOHelper.writeOut(writer, result);\r
                        } else if (service.getServiceType() == MsaWS.class) {\r
                                alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index 91081c4..33208a0 100644 (file)
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -53,7 +53,7 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
                ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
                \r
                List<String> params = WSUtil.getCommands(options,\r
-                               AACon.KEY_VALUE_SEPARATOR);\r
+                               RNAalifold.KEY_VALUE_SEPARATOR);\r
                confRNAalifold.addParameters(params);\r
                return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize",\r
                                getLimit(""));\r

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index e46c2d9..da4182c 100644 (file)
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -150,8 +150,6 @@ public final class WSUtil {
                // This line is different from the above method\r
                compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
                AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
-               System.out.println("Job Command: + " \r
-                               + confExec.getParameters());\r
                String jobId = engine.submitJob(confExec);\r
                reportUsage(confExec, log);\r
                return jobId;\r