Parameter bug fixed, Jalview will now run some parameters

diff --git a/conf/Executable.properties b/conf/Executable.properties
index ba9b4a7..333477e 100644 (file)
--- a/conf/Executable.properties
+++ b/conf/Executable.properties
@@ -199,5 +199,5 @@ aacon.presets.file=conf/settings/AAConPresets.xml
 #####                                  RNAALIFOLD CONFIGURATION                         ######\r
 local.rnaalifold.bin.windows=binaries/windows/ViennaRNA/RNAalifold.exe\r
 local.rnaalifold.bin=binaries/src/ViennaRNA/Progs/RNAalifold\r
-rnaalifold.parameters.file=conf/settings/RNAalifoldOptionsOnly.xml\r
+rnaalifold.parameters.file=conf/settings/RNAalifoldParameters.xml\r
 \r

diff --git a/conf/settings/RNAalifoldOptionsOnly.xml b/conf/settings/RNAalifoldOptionsOnly.xml
deleted file mode 100644 (file)
index 7f8ef44..0000000
--- a/conf/settings/RNAalifoldOptionsOnly.xml
+++ /dev/null
@@ -1,75 +0,0 @@
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
-<runnerConfig>
-       <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
-       <options isRequired='false'>
-               <name>Endgaps</name>
-               <description>Score pairs with endgaps same as gap-gap pairs</description>
-               <optionNames>-E</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>Most Informative Sequence</name>
-               <description>Ouput Set of nucleotides with frequency > average</description>
-               <optionNames>--mis</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>Partition Function</name>
-               <description>Output partition function and probability matrix</description>
-               <optionNames>-p</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>Circular</name>
-               <description>Assume circular RNA molecule</description>
-               <optionNames>-c</optionNames>
-       </options>
-       <!--  Not Currently available with circular structures (-c) -->
-       <options isRequired='false'>
-               <name>G-Quadruplex</name>
-               <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
-               <optionNames>-g</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>d2</name>
-               <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
-               <optionNames>-d2</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>No LP</name>
-               <description>Produce Structures without lonely pairs</description>
-               <optionNames>--noLP</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>No GU</name>
-               <description>Do not allow GU pairs</description>
-               <optionNames>--noGU</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>No Closing GU</name>
-               <description>Do not allow GU pairs at the end of sequences</description>
-               <optionNames>--noClosingGU</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>old</name>
-               <description>Use old energy evaluation, treating gaps as characters</description>
-               <optionNames>--old</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>Ribosum Scoring</name>
-               <description>Use Ribosum Scoring Matrix</description>
-               <optionNames>-r</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>d2</name>
-               <description>
-               Dangling energies are added for the bases adjacent to a helix on both sides
-               </description>
-               <optionNames>-d2</optionNames>
-       </options>
-       <options isRequired='false'>
-               <name>MEA Structure</name>
-               <description>Maximum Expected Accuracy Structure</description>
-               <optionNames>--MEA</optionNames>
-       </options>
-       
-       
-       
-</runnerConfig>
\ No newline at end of file

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/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