assert spacePos > 0 : "Space is expected as delimited between method "\r
+ "name and values!";\r
String methodLine = line.substring(0, spacePos);\r
- ConservationMethod method = ConservationMethod.getMethod(methodLine);\r
+ ConservationMethod method = ConservationMethod\r
+ .getMethod(methodLine);\r
assert method != null : "Method " + methodLine\r
+ " is not recognized! ";\r
Scanner valuesScanner = new Scanner(line.substring(spacePos));\r
return annotations;\r
}\r
\r
+ /**\r
+ * Reads and parses Fasta or Clustal formatted file into a list of\r
+ * FastaSequence objects\r
+ * \r
+ * @param inFilePath\r
+ * the path to the input file\r
+ * @throws IOException\r
+ * if the file denoted by inFilePath cannot be read\r
+ * @throws UnknownFileFormatException\r
+ * if the inFilePath points to the file which format cannot be\r
+ * recognised\r
+ * @return the List of FastaSequence objects\r
+ * \r
+ */\r
+ public static List<FastaSequence> openInputStream(String inFilePath)\r
+ throws IOException, UnknownFileFormatException {\r
+\r
+ // This stream gets closed in isValidClustalFile method\r
+ InputStream inStrForValidation = new FileInputStream(inFilePath);\r
+ // This stream is closed in the calling methods\r
+ InputStream inStr = new FileInputStream(inFilePath);\r
+ List<FastaSequence> fastaSeqs = null;\r
+ if (ClustalAlignmentUtil.isValidClustalFile(inStrForValidation)) {\r
+ Alignment al = ClustalAlignmentUtil.readClustalFile(inStr);\r
+ // alignment cannot be null see\r
+ // ClustalAlignmentUtil.readClustalFile(inStr);\r
+ fastaSeqs = al.getSequences();\r
+ } else {\r
+ fastaSeqs = SequenceUtil.readFasta(inStr);\r
+ }\r
+ return fastaSeqs;\r
+ }\r
+\r
}\r
-/* Copyright (c) 2009 Peter Troshin\r
+/* Copyright (c) 2010 Peter Troshin\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
+ * Amino Acid Conservation Web Service client @version: 1.0 \r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
\r
import java.io.Closeable;\r
import java.io.File;\r
-import java.io.FileInputStream;\r
import java.io.IOException;\r
import java.io.OutputStream;\r
import java.net.MalformedURLException;\r
import java.net.URL;\r
-import java.util.Arrays;\r
import java.util.List;\r
import java.util.Set;\r
import java.util.logging.Level;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.sequence.Score;\r
import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
private static final Logger log = Logger.getLogger(AAConClient.class\r
.getCanonicalName());\r
\r
+ /**\r
+ * The fully qualified web service namespace\r
+ */\r
static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\r
\r
- // static final String hostname = "http://www.compbio.dundee.ac.uk/aacon";\r
- static final String hostname = "http://localhost:8080/jabaws";\r
-\r
- static final String serviceName = "AAConWS";\r
+ /**\r
+ * Web service host\r
+ */\r
+ static final String hostname = "http://www.compbio.dundee.ac.uk/aacon";\r
+ // static final String hostname = "http://localhost:8080/jabaws";\r
\r
/**\r
- * Attempt to construct the URL object from the string\r
- * \r
- * @param urlstr\r
- * @return true if it succeed false otherwise\r
+ * Web service name\r
*/\r
- public static boolean validURL(String urlstr) {\r
- try {\r
- if (urlstr == null || urlstr.trim().length() == 0) {\r
- return false;\r
- }\r
- new URL(urlstr);\r
- } catch (MalformedURLException e) {\r
- return false;\r
- }\r
- return true;\r
- }\r
+ static final String serviceName = "AAConWS";\r
\r
/**\r
* Connects to the service and do the job as requested, if something goes\r
* wrong reports or/and prints usage help.\r
* \r
- * @param <AAConWS>\r
- * web service type\r
* @param cmd\r
* command line options\r
* @throws IOException\r
+ * if the system cannot read/write from/into the file system\r
*/\r
@SuppressWarnings("unchecked")\r
AAConClient(String[] cmd) throws IOException {\r
\r
- Services service = Services.getService(serviceName);\r
- if (service == null) {\r
- System.out.println("Service " + serviceName\r
- + " is no supported! Valid values are: "\r
- + Arrays.toString(Services.values()));\r
- printUsage(1);\r
- }\r
File inputFile = IOHelper.getFile(cmd, inputkey, true);\r
File outFile = IOHelper.getFile(cmd, outputkey, false);\r
File parametersFile = IOHelper.getFile(cmd, paramFile, true);\r
String presetName = CmdHelper.getPresetName(cmd);\r
\r
- Annotation<AAConWS> msaws = connect(hostname, service);\r
+ Annotation<AAConWS> msaws = connect();\r
Preset<AAConWS> preset = null;\r
if (presetName != null) {\r
preset = MetadataHelper.getPreset(msaws, presetName);\r
}\r
Set<Score> result = null;\r
if (inputFile != null) {\r
- System.out.println("calc conserv!");\r
+ System.out.println("Calculating conservation...");\r
result = analize(inputFile, msaws, preset, customOptions);\r
OutputStream outStream = null;\r
if (outFile != null) {\r
}\r
\r
/**\r
- * Outputs clustal formatted alignment into the file represented by the\r
- * outStream\r
+ * Outputs AAcon results into the file represented by the outStream\r
* \r
* @param outStream\r
- * @param align\r
- * the alignment to output\r
+ * @param result\r
+ * the AACon scores to output\r
*/\r
static void writeOut(OutputStream outStream, Set<Score> result) {\r
try {\r
}\r
\r
/**\r
- * Connects to a web service by the host and the service name\r
+ * Connects to a AACon web service by the host and the service name\r
+ * \r
* \r
- * @param T\r
- * web service type\r
- * @param host\r
- * @param service\r
- * @return MsaWS<T>\r
+ * @return {@link Annotation}\r
* @throws WebServiceException\r
+ * if cannot connect to a web service\r
*/\r
- public static Annotation<AAConWS> connect(String host, Services service)\r
- throws WebServiceException {\r
+ public static Annotation<AAConWS> connect() throws WebServiceException {\r
URL url = null;\r
log.log(Level.FINE, "Attempting to connect...");\r
try {\r
- url = new URL(host + "/" + service.toString() + "?wsdl");\r
+ url = new URL(hostname + "/" + "AAConWS" + "?wsdl");\r
} catch (MalformedURLException e) {\r
e.printStackTrace();\r
// ignore as the host name is already verified\r
}\r
- Service serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
- @SuppressWarnings("unchecked")\r
+ QName qname = new QName(QUALIFIED_SERVICE_NAME, "AAConWS");\r
+ Service serv = Service.create(url, qname);\r
QName portName = new QName(QUALIFIED_SERVICE_NAME, "AAConWS" + "Port");\r
\r
+ @SuppressWarnings("unchecked")\r
Annotation<AAConWS> serviceIF = serv\r
.getPort(portName, Annotation.class);\r
\r
}\r
\r
/**\r
- * Align sequences from the file using MsaWS\r
+ * Calculate conservation for sequences loaded from the file\r
* \r
- * @param <T>\r
- * web service type e.g. Clustal\r
- * @param file\r
- * to write the resulting alignment to\r
* @param wsproxy\r
- * MsaWS required\r
+ * a web service proxy\r
+ * @param file\r
+ * the file to read the results from\r
* @param preset\r
* Preset to use optional\r
* @param customOptions\r
- * file which contains new line separated list of options\r
- * @return Alignment\r
+ * the list of options\r
+ * @return Set<Score> the conservation scores\r
+ * @throws UnknownFileFormatException\r
*/\r
- static <AAConWS> Set<Score> analize(File file, Annotation<AAConWS> wsproxy,\r
+ static Set<Score> analize(File file, Annotation<AAConWS> wsproxy,\r
Preset<AAConWS> preset, List<Option<AAConWS>> customOptions) {\r
- FileInputStream instream = null;\r
+\r
List<FastaSequence> fastalist = null;\r
Set<Score> scores = null;\r
try {\r
- instream = new FileInputStream(file);\r
- fastalist = SequenceUtil.readFasta(instream);\r
- instream.close();\r
+ fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
+\r
String jobId = null;\r
if (customOptions != null && preset != null) {\r
System.out\r
// ignore and propagate an interruption\r
Thread.currentThread().interrupt();\r
} catch (WrongParameterException e) {\r
+ System.err\r
+ .println("Exception while parsing the web method input parameters. "\r
+ + "Exception details are below:");\r
+ e.printStackTrace();\r
+ } catch (UnknownFileFormatException e) {\r
+ System.err\r
+ .println("Exception while attempting to read the input file "\r
+ + "Exception details are below:");\r
+ System.out.println(e.getMessage());\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 scores;\r
}\r
\r
/**\r
- * Prints Jws2Client usage information to standard out\r
+ * Prints AAConClient usage information to standard out\r
* \r
* @param exitStatus\r
*/\r
}\r
\r
/**\r
- * Starts command line client, if no parameter are supported print help. Two\r
- * parameters are required for successfull call the JWS2 host name and a\r
- * service name.\r
+ * Starts command line client, if no parameters are supplied prints help.\r
* \r
* @param args\r
* Usage: <Class or Jar file name> ACTION [OPTIONS]\r
git://source.jalview.org / jabaws.git / commitdiff