##### 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/RNAalifoldParameters.xml\r
+rnaalifold.parameters.file=conf/settings/RNAalifoldOptionsOnly.xml\r
\r
--- /dev/null
+<?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
<optionNames>--MEA</optionNames>
</options>
- <prmSeparator> </prmSeparator>
+ <prmSeparator> </prmSeparator>
<parameters isRequired='false'>
<name>scaling factor</name>
</parameters>
<parameters isRequired='false'>
<name>Temperature</name>
- <description>Rescale Energy parameters to Temperature</description>
+ <description>Rescale Energy parameterss to Temperature</description>
<optionNames>-T</optionNames>
<defaultValue>37</defaultValue>
<validValue>
<max>1000000</max>
</validValue>
</parameters>
+
<parameters isRequired='false'>
<name>cfactor</name>
<description>weight of covariance term</description>
this.seqScores = seqScores;\r
}\r
\r
- // I put this in purely because it mirrors a method in ScoreManager, not because I need it \r
public static RNAStructScoreManager newInstance(List<String> structs, List<TreeSet<Score>> data) {\r
return new RNAStructScoreManager(structs, data);\r
}\r
return data;\r
\r
}\r
+ \r
+ /*\r
+ * I want to be able to get the information in a ScoreHolder Object by\r
+ * \r
+ */\r
\r
// Send this data Structure back to something approximating the stdoutFile\r
// with extra information from alifold.out\r
Score s = iScores.next();\r
Range r = s.getRanges().first();\r
Float score = s.getScores().get(0);\r
- out += String.format("%4d %4d %.1f%n", r.getFrom(), r.getTo(),\r
+ out += String.format("%4d %4d %.1f%n", r.from, r.to,\r
score);\r
}\r
}\r
this.to = Integer.parseInt(twoElementAr[1].trim());\r
}\r
\r
- // Daniel Check these get methods are ok with Jim\r
- public int getFrom() { return from; }\r
- public int getTo() { return to; }\r
- \r
- \r
@Override\r
public String toString() {\r
return from + "-" + to;\r
return true;\r
}\r
\r
- // daniel wants to mess with method. this is how it was\r
+ /*\r
+ * Daniel messed with this method.\r
+ * It now compares Ranges based on \r
+ */\r
+ \r
// @Override\r
// public int compareTo(Range o) {\r
// if (o == null)\r
writer.flush();\r
}\r
\r
+ // Old compareTo method\r
// @Override\r
// public int compareTo(Score o) {\r
// return this.method.compareTo(o.method);\r
// }\r
\r
- /* daniel wants to mess with this method and, while preserving the \r
- * ordering when the method Enumerations are different, add additional\r
- * constraints on how equal Score objects must be to be considered equal\r
+ /* daniel messed with this method. While preserving the original\r
+ * ordering when the method Enumerations are different, additional\r
+ * constraints have been added on how equal Score objects must be \r
+ * to be considered equal.\r
* \r
* It is necessary to distinguish Score objects by their ranges in order\r
* to use a Set of Score objects to represent the alifold.out information\r
* \r
- * It is necessary to distinguish Score objects by their scores in order\r
- * to return Stochastic Backtrack information reliably\r
+ * Distinguishing score objects by their Scores has the result of ordering\r
+ * the base pair contacts so into descending probability.\r
+ * \r
+ * Should this be in a new extended Score class?\r
*/\r
\r
- \r
-\r
- \r
@Override\r
public int compareTo(Score o) {\r
if (this.method.compareTo(o.method) != 0) {\r
\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
-import java.util.Arrays;\r
-import java.util.List;\r
-\r
-\r
-\r
-\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.RNAStructScoreManager;\r
-import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.engine.client.PipedExecutable;\r
import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.runner.Util;\r
\r
-\r
-import compbio.engine.client.CommandBuilder;\r
-\r
public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
implements PipedExecutable<RNAalifold> {\r
\r
\r
// May not be necessary as defult is "<space>" but still dont know\r
// How to deal with different key value separators for different params\r
- public static final String KEY_VALUE_SEPARATOR = " ";\r
+ public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
\r
public RNAalifold() {\r
super(KEY_VALUE_SEPARATOR);\r
package compbio.ws.client;
-import compbio.metadata.AllTestSuit;
-import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.fail;
-import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
-import java.io.Writer;
import java.io.OutputStreamWriter;
+import java.io.Writer;
import java.net.ConnectException;
import java.util.ArrayList;
import java.util.List;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
-import compbio.data.msa.FoldWS;
import compbio.data.msa.JABAService;
import compbio.data.msa.SequenceAnnotation;
import compbio.data.sequence.Alignment;
import compbio.data.sequence.ClustalAlignmentUtil;
-import compbio.data.sequence.ConservationMethod;
import compbio.data.sequence.FastaSequence;
import compbio.data.sequence.RNAStructScoreManager;
-import compbio.data.sequence.ScoreManager;
-import compbio.data.sequence.SequenceUtil;
import compbio.data.sequence.UnknownFileFormatException;
import compbio.metadata.AllTestSuit;
import compbio.metadata.JobSubmissionException;
import compbio.metadata.LimitExceededException;
import compbio.metadata.Option;
-import compbio.metadata.PresetManager;
import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
import compbio.metadata.UnsupportedRuntimeException;
import compbio.metadata.WrongParameterException;
-import compbio.runner.conservation.AACon;
-import compbio.runner.structure.RNAalifold;
-import compbio.util.SysPrefs;
import compbio.ws.server.RNAalifoldWS;
public void testFold() throws FileNotFoundException, IOException,
UnknownFileFormatException {
-
-// String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
-// + File.separator;
-
Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
AllTestSuit.test_input_aln));
System.out.println("J: " + jobId);
RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
-
- // standard and RNAStruct specific ways of formatting scoremanager
- System.out.println("fold results: \n" + result.toString());
-
Writer writer = new OutputStreamWriter(System.out);
result.writeOut(writer);
+++ /dev/null
-<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
-<runnerConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:noNamespaceSchemaLocation="RunnerConfigSchema.xsd">
- <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>
- <optionNames>--endgaps</optionNames>
- <defaultValue>-E</defaultValue>
- </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>
- <optionNames>--partfunc</optionNames>
- <defaultValue>-p</defaultValue>
- </options>
- <options isRequired='false'>
- <name>p0</name>
- <description>deactivates the calculation of the pair probabilities</description>
- <optionNames>-p0</optionNames>
- </options>
- <options isRequired='false'>
- <name>color</name>
- <description>Consensus structure plot is colored</description>
- <optionNames>--color</optionNames>
- </options>
- <options isRequired='false'>
- <name>Alignment</name>
- <description>Output structure annotated alignment</description>
- <optionNames>--aln</optionNames>
- </options>
- <options isRequired='false'>
- <name>No Postscript</name>
- <description>Do not produce postscript output</description>
- <optionNames>--noPS</optionNames>
- </options>
- <options isRequired='false'>
- <name>Circular</name>
- <description>Assume circular RNA molecule</description>
- <optionNames>-c</optionNames>
- <optionNames>--circ</optionNames>
- <defaultValue>-c</defaultValue>
- </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>
- <optionNames>--gquad</optionNames>
- <defaultValue>-g</defaultValue>
- </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>
- <optionNames>--ribosum_scoring</optionNames>
- <defaultValue>-r</defaultValue>
- </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>
-<!-- Constraints are entered on the command line followed by the input .aln file
- Causing problems for a batch RNAalifold execution system -->
-<!--
- <option isRequired='false'>
- <name>Constraints</name>
- <description>Structures calculated subject to constraints</description>
- <optionNames>-C</optionNames>
- <validValue>
- <type>String</type>
- </validValue>
- </option> -->
-
- <prmSeparator> </prmSeparator>
- <parameters isRequired='false'>
- <name>Stochastic Backtrack</name>
- <description>Compute a number of random structures</description>
- <optionNames>-s</optionNames>
-<!-- Having multiple optionNames requires a default value but -->
-<!-- in a parameter defaultValue refers to the argument -->
-<!-- <optionNames>-stochBT</optionNames> -->
- <defaultValue>5</defaultValue>
- <validValue>
- <type>Integer</type>
- <min>1</min>
- <max>100000</max>
- </validValue>
- </parameters>
- <parameters isRequired='false'>
- <name>stochBT_en</name>
- <description>Print Backtrack structures</description>
- <optionNames>--stochBT_en</optionNames>
- <defaultValue>5</defaultValue> <!-- arbitrary -->
- <validValue>
- <type>Integer</type>
- <min>1</min>
- <max>100000</max>
- </validValue>
- </parameters>
- <parameters isRequired='false'>
- <name>scaling factor</name>
- <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
- <optionNames>-S</optionNames>
-<!-- <optionNames>-pfScale</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>
-<!-- <optionNames>-temp</optionNames> -->
- <defaultValue>37</defaultValue>
- <validValue>
- <type>Float</type>
- <min>-274</min>
- <max>1000000</max>
- </validValue>
- </parameters>
- <parameters isRequired='false'>
- <name>Dangling End</name>
- <description>How to treat Dangling End energies for bases adjacent to helices</description>
- <optionNames>-d</optionNames>
-<!-- <optionNames>-dangles</optionNames> -->
- <defaultValue>2</defaultValue>
- <validValue>
- <type>Integer</type>
- <min>0</min>
- <max>100000</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>
-
-<!-- How to deal with default/possible values for parameter files? -->
-<!-- <parameters isRequired='false'> -->
-<!-- <name>Ribosum File</name> -->
-<!-- <description>Use Specified Ribosum Matrix</description> -->
-<!-- <optionNames>-R</optionNames> -->
-<!-- <optionNames>-ribosum_file</optionNames> -->
-<!-- </parameters> -->
-<!-- <parameters isRequired='false'> -->
-<!-- <name>Paramfile</name> -->
-<!-- <description>Use Energy parameters from a file</description> -->
-<!-- <optionNames>-P</optionNames> -->
-<!-- <optionNames>-paramFile</optionNames> -->
-<!-- <validValue> -->
-<!-- <type>String</type> -->
-<!-- </validValue> -->
-<!-- </parameters> -->
-
- <!-- The values of this parameter are in the form of a comma separated
- list of allowed pairs. This makes a complete parameter list
- too large to be represented as a list of possible values
- How to deal with this? -->
- <!-- just support the most biologically viable pairs? -->
-
- <parameters isRequired='false'>
- <name>Allow Pairs</name>
- <description>allow pairs in addition to AU, GC and GU</description>
- <optionNames>--nsp</optionNames>
- <defaultValue>-GA</defaultValue>
- <possibleValues>-GA</possibleValues>
- <possibleValues>-AG</possibleValues>
- </parameters>
- <!-- Is dependant on -p (partfunc) -->
- <parameters isRequired='false'>
- <name>betaScale</name>
- <description>Set scaling of Boltzmann factors</description>
- <optionNames>--betaScale</optionNames>
- <defaultValue>1.0</defaultValue>
- <validValue>
- <type>Float</type>
- <min>0</min>
- <max>100000</max>
- </validValue>
- </parameters>
-</runnerConfig>
\ No newline at end of file
+++ /dev/null
-package compbio.data.msa;
-
-import java.security.InvalidParameterException;
-import java.util.List;
-
-import javax.jws.WebMethod;
-import javax.jws.WebParam;
-import javax.jws.WebService;
-import javax.naming.ldap.UnsolicitedNotificationEvent;
-
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.RNAStruct;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.LimitExceededException;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.UnsupportedRuntimeException;
-import compbio.metadata.WrongParameterException;
-
-/*
- * Interface for tools that results RNA secondary structure information
- *
- * Still Unsure whether It would be better to use just the aligned fastaList
- * or the Alignment object
- */
-
-// effect of a different targetNamespace?
-@WebService(targetNamespace = "http://msa.data.compbio/01/01/2010/")
-public interface FoldWS<T>
- extends
- JABAService,
- JManagement,
- Metadata<T> {
-
-
- // Is Alignment object JaxB compatible?
-
- String fold(
- @WebParam(name = "alignment") Alignment alignment)
- throws UnsupportedRuntimeException, LimitExceededException,
- JobSubmissionException;
-
- String customFold(
- @WebParam(name = "alignment") Alignment alignment,
- @WebParam(name = "options") List<Option<T>> options)
- throws UnsupportedRuntimeException, LimitExceededException,
- JobSubmissionException, WrongParameterException;
-
- String presetFold(
- @WebParam(name = "alignment") Alignment alignment,
- @WebParam(name = "preset") Preset<T> preset)
- throws UnsupportedRuntimeException, LimitExceededException,
- JobSubmissionException, WrongParameterException;
-
- String getResult(@WebParam(name = "jobId") String jobId)
- throws ResultNotAvailableException;
-
-}
import javax.xml.ws.WebServiceException;\r
\r
import compbio.data.msa.JABAService;\r
-import compbio.data.msa.FoldWS;\r
import compbio.data.msa.Metadata;\r
import compbio.data.msa.MsaWS;\r
import compbio.data.msa.RegistryWS;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.sequence.ScoreManager;\r
-import compbio.data.sequence.ClustalAlignmentUtil;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
}\r
\r
/**\r
- * Return RNA secondary structure from a file using FoldWS\r
- * \r
- * @param <T>\r
- * web service type e.g. Clustal\r
- * @param file\r
- * to read the results from\r
- * @param foldws\r
- * FoldWS required\r
- * @param preset\r
- * Preset to use optional\r
- * @param customOptions\r
- * file which contains new line separated list of options\r
- * @return String\r
- */\r
- \r
-// static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,\r
-// List<Option<T>> customOptions) {\r
-// FileInputStream instream = null;\r
-// Alignment alignment = null;\r
-// String rnastruct = null;\r
-// try {\r
-// instream = new FileInputStream(file);\r
-// alignment = ClustalAlignmentUtil.readClustalFile(instream);\r
-// instream.close();\r
-// String jobId = null;\r
-// if (customOptions != null && preset != null) {\r
-// System.out.println("WARN: Parameters (-f) are defined together"\r
-// + "with a preset (-r), ignoring preset! ");\r
-// }\r
-// if (customOptions != null) {\r
-// jobId = foldws.customFold(alignment, customOptions);\r
-// } else if (preset != null) {\r
-// jobId = foldws.presetFold(alignment, preset);\r
-// } else {\r
-// jobId = foldws.fold(alignment);\r
-// }\r
-// System.out.println("\n\ncalling fold.........");\r
-// Thread.sleep(1000);\r
-// rnastruct = foldws.getResult(jobId);\r
-// \r
-// } catch (IOException e) {\r
-// System.err.println("Exception while reading the input file. Exception details: ");\r
-// e.printStackTrace();\r
-// } catch (UnknownFileFormatException e) {\r
-// System.err.println("Exception while reading input file. Doesnt look like a Clustal format file");\r
-// e.printStackTrace();\r
-// } catch (JobSubmissionException e) {\r
-// System.err.println("Exception while submitting job to the web server. ");\r
-// e.printStackTrace();\r
-// } catch (ResultNotAvailableException e) {\r
-// System.err.println("Exception while waiting for results. Exception details: ");\r
-// e.printStackTrace();\r
-// } catch (InterruptedException ignored) {\r
-// // ignore and propagate an interruption\r
-// Thread.currentThread().interrupt();\r
-// } catch (WrongParameterException e) {\r
-// e.printStackTrace();\r
-// } finally {\r
-// if (instream != null) {\r
-// try {\r
-// instream.close();\r
-// } catch (IOException ignored) {\r
-// // ignore\r
-// }\r
-// }\r
-// }\r
-// return rnastruct;\r
-// }\r
-// \r
- /**\r
* Prints Jws2Client usage information to standard out\r
* \r
* @param exitStatus\r
import javax.xml.namespace.QName;\r
import javax.xml.ws.Service;\r
\r
-import compbio.data.msa.FoldWS;\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.MsaWS;\r
import compbio.data.msa.SequenceAnnotation;\r
* Make sure this class has NO references to runners or engines as it is a\r
* part of minimal client package. Such things should go into ServicesUtil\r
*/\r
- MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, RNAalifoldWS;\r
+ MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS,\r
+ JronnWS, DisemblWS, GlobPlotWS, IUPredWS, RNAalifoldWS;\r
\r
public static Services getService(String servName) {\r
servName = servName.trim().toLowerCase();\r
// TODO reference\r
public static final String RNAALIFOLD_INFO = new ServiceInfo(\r
RNAalifoldWS,\r
- "Reference to come", "2.1.2",\r
- "http://www.tbi.univie.ac.at/RNA/").toString();;\r
+ "Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler 'Secondary Structure Prediction"\r
+ + " for Aligned RNA Sequences'. J.Mol.Biol. 319: 1059-1066, 2002. Stephan H. Bernhart,"\r
+ + " Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler. "\r
+ + "'RNAalifold: Improved consensus structure prediction for RNA alignments'. BMC Bioinformatics, 9:474, 2008.\r\n",\r
+ "2.1.2", "http://www.tbi.univie.ac.at/RNA/").toString();;\r
\r
@XmlAccessorType(XmlAccessType.FIELD)\r
static class ServiceInfo {\r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.Metadata;\r
import compbio.data.msa.MsaWS;\r
-import compbio.data.msa.FoldWS;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.Program;\r
import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.metadata.JobStatus;\r
return succeed;\r
}\r
\r
- private <T> boolean testFoldWS(FoldWS<T> foldws) throws Exception {\r
- assert foldws != null;\r
- \r
- boolean succeed = testDefaultFold(foldws);\r
- \r
- // testMetadata(foldws);\r
- return succeed;\r
- }\r
/**\r
* Call most of web services functions and check the output\r
* \r
} else if (wservice instanceof SequenceAnnotation) {\r
return testSequenceAnnotationWS(\r
(SequenceAnnotation<T>) wservice, service);\r
- } else if (wservice instanceof FoldWS) {\r
- return testFoldWS( (FoldWS<T>) wservice);\r
} else {\r
throw new UnsupportedOperationException("The service: "\r
+ wservice.getClass() + " is not supported! ");\r
return succeed;\r
}\r
\r
- /**\r
- * Fold using default settings\r
- * \r
- * @param <T>\r
- * @param foldws\r
- * @throws UnsupportedRuntimeException\r
- */\r
\r
- private <T> boolean testDefaultFold(FoldWS<T> foldws) throws Exception {\r
- writer.print("Testing fold with default parameters:");\r
- // load the input from the aligned fasta string at the top of the file\r
- Alignment al = new Alignment(loadAlignment(), Program.CLUSTAL, '-');\r
- String rs = null;\r
- boolean succeed = false;\r
- \r
- String taskId = foldws.fold(al);\r
- writer.print("\nQuerying job status...");\r
- JobStatus status = foldws.getJobStatus(taskId);\r
- while (status != JobStatus.FINISHED) {\r
- Thread.sleep(1000);\r
- status = foldws.getJobStatus(taskId);\r
- }\r
- writer.println(OK);\r
- writer.print("Retrieving results...");\r
- rs = foldws.getResult(taskId);\r
- succeed = true;\r
- if (rs != null) {\r
- writer.println(OK);\r
- }\r
- return succeed;\r
- }\r
/**\r
* Test JWS2 web services\r
* \r
import compbio.data.msa.JABAService;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.RNAStructScoreManager;\r
import compbio.engine.client.ConfiguredExecutable;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.LimitExceededException;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
-import compbio.metadata.ResultNotAvailableException;\r
import compbio.metadata.UnsupportedRuntimeException;\r
import compbio.metadata.WrongParameterException;\r
import compbio.runner.conservation.AACon;\r
}\r
\r
// Only purpose is to replace "analize" with "fold" method \r
- // so that a clustal input file and not fasta will be generated\r
+ // so that a clustal input file and not fasta will be generated\r
@Override\r
public String customAnalize(List<FastaSequence> sequences,\r
List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.RNAStructScoreManager;\r
import compbio.data.sequence.ScoreManager;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
return jobId;\r
}\r
\r
- // Hardcoded gapchar '-' in this method\r
- \r
-// public static <T> String fold(Alignment alignment,\r
-// ConfiguredExecutable<T> confExec, Logger logger,\r
-// String callingMethod, Limit<T> limit)\r
-// throws LimitExceededException, JobSubmissionException {\r
-// \r
-// List<FastaSequence> sequences = alignment.getSequences();\r
-// if (limit != null && limit.isExceeded(sequences)) {\r
-// throw LimitExceededException.newLimitExceeded(limit, sequences);\r
-// }\r
-// compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
-// System.out.println("WSUtil-fold: Writing the clustal input file on the server: to file: "\r
-// + confExec.getInput());\r
-// System.out.println("WSUtil-fold: The executable is configured with parameters: " \r
-// + confExec.getParameters());\r
-//// System.out.println("WSUTil-fold: Dump the configured executable:\n" \r
-//// + confExec.toString());\r
-// AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
-// String jobId = engine.submitJob(confExec);\r
-// reportUsage(confExec, logger);\r
-// return jobId;\r
-// }\r
\r
static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
if (GAUtils.IS_GA_ENABLED) {\r
}\r
\r
// Same as analize but Alifold takes clustal input not fasta\r
+ // An if condition in the above method might be a better solution but \r
+ // you need a way of finding out the type of confExec at runtime\r
\r
public static <T> String fold(List<FastaSequence> sequences,\r
ConfiguredExecutable<T> confExec, Logger log, String method,\r
// 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
git://source.jalview.org / jabaws.git / commitdiff