client - 1 week\r
docs - 1 week\r
\r
-make sure that aacon checks its input (must be alignment) and log errors/throws\r
-exceptions if the input is not correct or absent! \r
-\r
Cluster stats: \r
+cancelled should not be reported as incomplete!\r
-Remove hyperlinks from tasks which workdirs were removed \r
import java.io.IOException;\r
import java.io.InputStream;\r
import java.io.InputStreamReader;\r
-import java.io.OutputStream;\r
-import java.io.OutputStreamWriter;\r
-import java.io.PrintWriter;\r
+import java.io.Writer;\r
import java.util.ArrayList;\r
import java.util.Arrays;\r
import java.util.HashMap;\r
* @param alignment\r
* @throws IOException\r
*/\r
- public static void writeClustalAlignment(final OutputStream outStream,\r
+ public static void writeClustalAlignment(final Writer out,\r
final Alignment alignment) throws IOException {\r
List<FastaSequence> seqs = alignment.getSequences();\r
\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(outStream));\r
-\r
out.write("CLUSTAL\n\n\n");\r
\r
int max = 0;\r
// display at most 30 characters in the name, keep the names\r
// 6 spaces away from the alignment for longest sequence names,\r
// and more than this for shorter names\r
- out.format(\r
+ out.write(String.format(\r
"%-" + maxidLength + "s" + spacer,\r
(name.length() > maxNameLength ? name.substring(0,\r
- maxidLength) : name));\r
+ maxidLength) : name)));\r
int start = i * oneLineAlignmentLength;\r
int end = start + oneLineAlignmentLength;\r
\r
\r
@Override\r
public String toString() {\r
- return "[" + from + ", " + to + "]";\r
+ return from + "-" + to;\r
}\r
\r
@Override\r
package compbio.data.sequence;\r
\r
-import java.io.BufferedWriter;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
-import java.io.OutputStreamWriter;\r
+import java.io.Writer;\r
import java.text.NumberFormat;\r
import java.util.ArrayList;\r
import java.util.Locale;\r
-import java.util.Set;\r
import java.util.TreeSet;\r
\r
import javax.xml.bind.annotation.XmlAccessType;\r
*/\r
@XmlAccessorType(XmlAccessType.FIELD)\r
@Immutable\r
-public class Score {\r
+public class Score implements Comparable<Score> {\r
\r
static final NumberFormat NUMBER_FORMAT = NumberFormat\r
.getNumberInstance(Locale.UK);\r
\r
private Score() {\r
// JaXB default constructor\r
- method = null;\r
+ method = "";\r
}\r
\r
/**\r
* @throws NullPointerException\r
* if the output stream is null\r
*/\r
- public static void write(Set<Score> scores, OutputStream output)\r
+ public static void write(TreeSet<Score> scores, Writer writer)\r
throws IOException {\r
- if (output == null) {\r
- throw new NullPointerException("OutputStream must be provided!");\r
+ if (writer == null) {\r
+ throw new NullPointerException("Writer must be provided!");\r
}\r
- BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
- output));\r
for (Score score : scores) {\r
writer.write("#" + score.method + " ");\r
- for (Float scoreVal : score.getScores()) {\r
+ int count = score.ranges.size();\r
+ for (Range range : score.ranges) {\r
+ count--;\r
+ writer.write(range.toString());\r
+ if (count != 0) {\r
+ writer.write(", ");\r
+ }\r
+ }\r
+ for (Float scoreVal : score.scores) {\r
writer.write(NUMBER_FORMAT.format(scoreVal) + " ");\r
}\r
writer.write("\n");\r
+ writer.flush();\r
}\r
writer.flush();\r
}\r
+\r
+ @Override\r
+ public int compareTo(Score o) {\r
+ return this.method.compareTo(o.method);\r
+ }\r
}\r
package compbio.data.sequence;\r
\r
-import java.io.BufferedWriter;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
-import java.io.OutputStreamWriter;\r
+import java.io.Writer;\r
import java.util.ArrayList;\r
-import java.util.HashMap;\r
-import java.util.HashSet;\r
import java.util.List;\r
import java.util.Map;\r
import java.util.Set;\r
+import java.util.TreeMap;\r
+import java.util.TreeSet;\r
\r
import javax.xml.bind.annotation.XmlAccessType;\r
import javax.xml.bind.annotation.XmlAccessorType;\r
\r
public static ScoreManager newInstanceSingleScore(\r
Map<String, Score> seqScoresMap) {\r
- Map<String, Set<Score>> multipleScoresMap = new HashMap<String, Set<Score>>();\r
+ Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
- Set<Score> scores = new HashSet<Score>();\r
+ Set<Score> scores = new TreeSet<Score>();\r
scores.add(seqScore.getValue());\r
multipleScoresMap.put(seqScore.getKey(), scores);\r
}\r
}\r
\r
public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
- return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY, data);\r
+ return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
+ new TreeSet(data));\r
}\r
\r
- public Map<String, Set<Score>> asMap() {\r
- Map<String, Set<Score>> seqScoresMap = new HashMap<String, Set<Score>>();\r
+ public Map<String, TreeSet<Score>> asMap() {\r
+ Map<String, TreeSet<Score>> seqScoresMap = new TreeMap<String, TreeSet<Score>>();\r
for (ScoreHolder sch : this.seqScores) {\r
- Set<Score> oldValue = seqScoresMap.put(sch.id, sch.scores);\r
+ TreeSet<Score> oldValue = seqScoresMap.put(sch.id, new TreeSet(\r
+ sch.scores));\r
if (oldValue != null) {\r
throw new IllegalStateException(\r
"Cannot represent this ScoreManager instance "\r
return null;\r
}\r
\r
- public void writeOut(OutputStream outStream) throws IOException {\r
- BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
- outStream));\r
+ public void writeOut(Writer outStream) throws IOException {\r
for (ScoreHolder oneSeqScores : seqScores) {\r
oneSeqScores.writeOut(outStream);\r
}\r
- writer.flush();\r
}\r
\r
@Override\r
public static class ScoreHolder {\r
\r
public String id;\r
- public HashSet<Score> scores;\r
+ public TreeSet<Score> scores;\r
\r
private ScoreHolder() {\r
// JAXB Default constructor should not be used otherwise\r
\r
ScoreHolder(String id, Set<Score> scores) {\r
this.id = id;\r
- this.scores = new HashSet<Score>(scores);\r
+ this.scores = new TreeSet<Score>(scores);\r
}\r
\r
- public void writeOut(OutputStream outStream) throws IOException {\r
- BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(\r
- outStream));\r
+ public void writeOut(Writer writer) throws IOException {\r
writer.write(">" + id + "\n");\r
- Score.write(scores, outStream);\r
+ Score.write(scores, writer);\r
}\r
\r
public Score getScoreByMethod(Enum<?> method) {\r
* Also possible FastaSequence fs = new FastaSequence(sequenceName,\r
* seqbuffer.toString());\r
*/\r
- HashSet<Score> scores = new HashSet<Score>();\r
+ Set<Score> scores = new TreeSet<Score>();\r
scores.add(new Score(GlobProtResult.Disorder, disorderR));\r
scores.add(new Score(GlobProtResult.GlobDoms, domsR));\r
scores.add(new Score(GlobProtResult.Dydx, dydxScore));\r
\r
import java.io.FileInputStream;\r
import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
+import java.io.FileWriter;\r
import java.io.IOException;\r
+import java.io.Writer;\r
\r
import org.testng.annotations.Test;\r
\r
\r
public class ClustalAlignmentUtilTester {\r
\r
- @Test()\r
- public void testReadClustalFile() {\r
- try {\r
- readWriteClustal("TO1381.aln");\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
+ @Test()\r
+ public void testReadClustalFile() {\r
+ try {\r
+ readWriteClustal("TO1381.aln");\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
}\r
- }\r
\r
- static void readWriteClustal(String fname) throws IOException,\r
- UnknownFileFormatException {\r
- FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
- + fname);\r
- Alignment seqAl = ClustalAlignmentUtil.readClustalFile(fio);\r
- assertTrue(seqAl != null);\r
- assertTrue(seqAl.getSize() == 3);\r
- assertNotNull(seqAl.getSequences());\r
- assertEquals(3, seqAl.getSequences().size());\r
+ static void readWriteClustal(String fname) throws IOException,\r
+ UnknownFileFormatException {\r
+ FileInputStream fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+ + fname);\r
+ Alignment seqAl = ClustalAlignmentUtil.readClustalFile(fio);\r
+ assertTrue(seqAl != null);\r
+ assertTrue(seqAl.getSize() == 3);\r
+ assertNotNull(seqAl.getSequences());\r
+ assertEquals(3, seqAl.getSequences().size());\r
\r
- // Now try to write the alignment read\r
- FileOutputStream os = new FileOutputStream(AllTestSuit.TEST_DATA_PATH\r
- + fname + ".written");\r
- ClustalAlignmentUtil.writeClustalAlignment(os, seqAl);\r
- fio.close();\r
- os.close();\r
+ // Now try to write the alignment read\r
+ Writer os = new FileWriter(AllTestSuit.TEST_DATA_PATH + fname\r
+ + ".written");\r
+ ClustalAlignmentUtil.writeClustalAlignment(os, seqAl);\r
+ fio.close();\r
+ os.close();\r
\r
- fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + fname\r
- + ".written");\r
- Alignment readseqs = ClustalAlignmentUtil.readClustalFile(fio);\r
- assertTrue(readseqs != null);\r
- assertTrue(readseqs.getSize() == 3);\r
- fio.close();\r
- }\r
+ fio = new FileInputStream(AllTestSuit.TEST_DATA_PATH + fname\r
+ + ".written");\r
+ Alignment readseqs = ClustalAlignmentUtil.readClustalFile(fio);\r
+ assertTrue(readseqs != null);\r
+ assertTrue(readseqs.getSize() == 3);\r
+ fio.close();\r
+ }\r
\r
- @Test()\r
- public void testReadClustalFileShortNames() {\r
- try {\r
- readWriteClustal("TO1381s.aln");\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
+ @Test()\r
+ public void testReadClustalFileShortNames() {\r
+ try {\r
+ readWriteClustal("TO1381s.aln");\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
}\r
- }\r
\r
- @Test()\r
- public void testReadClustalFileLongNames() {\r
- try {\r
- readWriteClustal("TO1381L.aln");\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- fail(e.getMessage());\r
+ @Test()\r
+ public void testReadClustalFileLongNames() {\r
+ try {\r
+ readWriteClustal("TO1381L.aln");\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
}\r
- }\r
\r
}\r
import java.io.FileOutputStream;\r
import java.io.IOException;\r
import java.io.InputStream;\r
+import java.io.PrintWriter;\r
import java.util.HashMap;\r
import java.util.HashSet;\r
import java.util.List;\r
Map<String, Set<Score>> aseqs = SequenceUtil.readDisembl(fio);\r
assertNotNull(aseqs);\r
assertEquals(aseqs.size(), 3);\r
- // System.out.println(aseqs);\r
+ ScoreManager sman = ScoreManager.newInstance(aseqs);\r
+\r
for (String fs : aseqs.keySet()) {\r
assertTrue(" Foobar_dundeefriends Foobar dundeefriends "\r
.contains(fs));\r
}\r
assertEquals(scores.size(), 5);\r
}\r
+\r
+ ScoreManager sm = ScoreManager.newInstanceSingleSequence(scores);\r
+ sm.writeOut(new PrintWriter(System.out, true));\r
+\r
for (Score score : scores) {\r
\r
if (score.getMethod()\r
import java.io.ByteArrayInputStream;\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
+import java.io.PrintWriter;\r
+import java.io.Writer;\r
import java.util.List;\r
\r
import compbio.data.msa.SequenceAnnotation;\r
// }\r
\r
/* Output the alignment to standard out */\r
- IOHelper.writeOut(System.out, result);\r
+ Writer writer = new PrintWriter(System.out, true);\r
+ IOHelper.writeOut(writer, result);\r
+ writer.close();\r
// Score.write(result, System.out);\r
\r
/* Alternatively, you can record retrieved alignment into the file */\r
import java.io.Closeable;\r
import java.io.File;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
+import java.io.PrintWriter;\r
+import java.io.Writer;\r
import java.net.MalformedURLException;\r
import java.net.URL;\r
import java.util.List;\r
if (inputFile != null) {\r
System.out.println("Calculating conservation...");\r
result = analize(inputFile, msaws, preset, customOptions);\r
- OutputStream outStream = null;\r
+ Writer outStream = null;\r
if (outFile != null) {\r
- outStream = IOHelper.getOutStream(outFile);\r
+ outStream = IOHelper.getWriter(outFile);\r
} else {\r
// this stream is going to be closed later which is fine as\r
// std.out will not be\r
- outStream = System.out;\r
+ outStream = new PrintWriter(System.out, true);\r
}\r
writeOut(outStream, result);\r
// stream is closed in the method no need to close it here\r
* @param result\r
* the AACon scores to output\r
*/\r
- static void writeOut(OutputStream outStream, ScoreManager result) {\r
+ static void writeOut(Writer writer, ScoreManager result) {\r
try {\r
- result.writeOut(outStream);\r
+ result.writeOut(writer);\r
} catch (IOException e) {\r
System.err\r
.println("Problems writing output file! Stack trace is below: ");\r
e.printStackTrace();\r
} finally {\r
- if (outStream != null) {\r
+ if (writer != null) {\r
try {\r
- outStream.close();\r
+ writer.close();\r
} catch (IOException ignored) {\r
// e.printStackTrace();\r
}\r
\r
import java.io.BufferedReader;\r
import java.io.File;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
import java.io.FileReader;\r
+import java.io.FileWriter;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
+import java.io.Writer;\r
import java.util.ArrayList;\r
import java.util.List;\r
\r
return params;\r
}\r
\r
- static OutputStream getOutStream(File file) {\r
+ static Writer getWriter(File file) throws IOException {\r
assert file != null && file.exists();\r
- try {\r
- return new FileOutputStream(file);\r
- } catch (FileNotFoundException e) {\r
- e.printStackTrace();\r
- }\r
- return null;\r
+ return new FileWriter(file);\r
}\r
\r
/**\r
* @param align\r
* the alignment to output\r
*/\r
- static void writeOut(OutputStream outStream, Alignment align) {\r
+ static void writeOut(Writer writer, Alignment align) {\r
try {\r
- ClustalAlignmentUtil.writeClustalAlignment(outStream, align);\r
+ ClustalAlignmentUtil.writeClustalAlignment(writer, align);\r
} catch (IOException e) {\r
System.err\r
.println("Problems writing output file! Stack trace is below: ");\r
e.printStackTrace();\r
} finally {\r
- if (outStream != null) {\r
+ if (writer != null) {\r
try {\r
- outStream.close();\r
+ writer.close();\r
} catch (IOException ignored) {\r
// e.printStackTrace();\r
}\r
* @param result\r
* the AACon scores to output\r
*/\r
- static void writeOut(OutputStream outStream, ScoreManager results) {\r
+ static void writeOut(Writer writer, ScoreManager results) {\r
try {\r
- results.writeOut(outStream);\r
+ results.writeOut(writer);\r
} catch (IOException e) {\r
System.err\r
.println("Problems writing output file! Stack trace is below: ");\r
e.printStackTrace();\r
} finally {\r
- if (outStream != null) {\r
+ if (writer != null) {\r
try {\r
- outStream.close();\r
+ writer.close();\r
} catch (IOException ignored) {\r
// e.printStackTrace();\r
}\r
import java.io.File;\r
import java.io.FileInputStream;\r
import java.io.IOException;\r
-import java.io.OutputStream;\r
+import java.io.PrintWriter;\r
+import java.io.Writer;\r
import java.net.MalformedURLException;\r
import java.net.URL;\r
import java.util.Arrays;\r
}\r
Alignment alignment = null;\r
if (inputFile != null) {\r
- OutputStream outStream = null;\r
+ Writer writer = null;\r
if (outFile != null) {\r
- outStream = IOHelper.getOutStream(outFile);\r
+ writer = IOHelper.getWriter(outFile);\r
} else {\r
// this stream is going to be closed later which is fine as\r
// std.out will not be\r
- outStream = System.out;\r
+ writer = new PrintWriter(System.out, true);\r
}\r
if (service.getServiceType() == SequenceAnnotation.class) {\r
ScoreManager result = analize(inputFile,\r
((SequenceAnnotation<T>) msaws), preset, customOptions);\r
\r
- IOHelper.writeOut(outStream, result);\r
+ IOHelper.writeOut(writer, result);\r
} else {\r
alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
customOptions);\r
- IOHelper.writeOut(outStream, alignment);\r
+ IOHelper.writeOut(writer, alignment);\r
}\r
- outStream.close();\r
+ writer.close();\r
}\r
\r
boolean listParameters = CmdHelper.listParameters(cmd);\r
return aaconOptions;\r
}\r
\r
- String analize(List<FastaSequence> sequences,\r
+ private String analize(List<FastaSequence> sequences,\r
ConfiguredExecutable<AACon> confExec, Logger log, String method,\r
Limit<AACon> limit) throws JobSubmissionException {\r
if (limit != null && limit.isExceeded(sequences)) {\r
public String analize(List<FastaSequence> sequences)\r
throws UnsupportedRuntimeException, LimitExceededException,\r
JobSubmissionException {\r
- WSUtil.validateFastaInput(sequences);\r
+\r
+ WSUtil.validateAAConInput(sequences);\r
ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
\r
// set default conservation method to fastest - SHENKIN\r
List<Option<AACon>> options) throws UnsupportedRuntimeException,\r
LimitExceededException, JobSubmissionException,\r
WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
+ WSUtil.validateAAConInput(sequences);\r
ConfiguredExecutable<AACon> confAACon = init(sequences);\r
// Could not do that! Space separated values\r
// will all be treated as keys! thus duplicates removed\r
Preset<AACon> preset) throws UnsupportedRuntimeException,\r
LimitExceededException, JobSubmissionException,\r
WrongParameterException {\r
- WSUtil.validateFastaInput(sequences);\r
+ WSUtil.validateAAConInput(sequences);\r
if (preset == null) {\r
throw new WrongParameterException("Preset must be provided!");\r
}\r
}\r
\r
public static final void validateFastaInput(List<FastaSequence> sequences)\r
- throws InvalidParameterException {\r
+ throws JobSubmissionException {\r
if (sequences == null || sequences.isEmpty()) {\r
- throw new InvalidParameterException(\r
+ throw new JobSubmissionException(\r
"List of fasta sequences required but not provided! ");\r
}\r
+ for (FastaSequence fs : sequences) {\r
+ if (fs.getLength() == 0) {\r
+ throw new JobSubmissionException(\r
+ "Sequence must not be empty! Sequence: " + fs.getId()\r
+ + " was empty");\r
+ }\r
+ }\r
}\r
\r
public static JobStatus getJobStatus(String jobId) {\r
return oList;\r
}\r
\r
+ public static void validateAAConInput(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ validateFastaInput(sequences);\r
+ int len = 0;\r
+ for (FastaSequence fs : sequences) {\r
+ if (len == 0) {\r
+ len = fs.getLength();\r
+ continue;\r
+ }\r
+ if (fs.getLength() != len) {\r
+ throw new JobSubmissionException(\r
+ "All sequences must be of the same length. Please align "\r
+ + "the sequences prior to submission! The first sequence length is : "\r
+ + len + " but the sequence '" + fs.getId()\r
+ + "' length is " + fs.getLength());\r
+ }\r
+ }\r
+ }\r
+\r
/*\r
* UNUSED\r
* \r
<message name="ResultNotAvailableException">
<part name="fault" element="tns:ResultNotAvailableException"/>
</message>
- <message name="presetAlign">
- <part name="parameters" element="tns:presetAlign"/>
+ <message name="customAlign">
+ <part name="parameters" element="tns:customAlign"/>
</message>
- <message name="presetAlignResponse">
- <part name="parameters" element="tns:presetAlignResponse"/>
+ <message name="customAlignResponse">
+ <part name="parameters" element="tns:customAlignResponse"/>
</message>
<message name="UnsupportedRuntimeException">
<part name="fault" element="tns:UnsupportedRuntimeException"/>
<message name="WrongParameterException">
<part name="fault" element="tns:WrongParameterException"/>
</message>
- <message name="customAlign">
- <part name="parameters" element="tns:customAlign"/>
+ <message name="presetAlign">
+ <part name="parameters" element="tns:presetAlign"/>
</message>
- <message name="customAlignResponse">
- <part name="parameters" element="tns:customAlignResponse"/>
+ <message name="presetAlignResponse">
+ <part name="parameters" element="tns:presetAlignResponse"/>
</message>
<message name="align">
<part name="parameters" element="tns:align"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
<fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
- <operation name="presetAlign">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
- <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
- </operation>
<operation name="customAlign">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
+ <operation name="presetAlign">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
+ <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
+ </operation>
<operation name="align">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
<soap:fault name="ResultNotAvailableException" use="literal"/>
</fault>
</operation>
- <operation name="presetAlign">
+ <operation name="customAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="customAlign">
+ <operation name="presetAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
git://source.jalview.org / jabaws.git / commitdiff