X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=eda6533fc8d2d02ed04fd7a52724f729c66b1b89;hb=3644426ec0e9e9ceb798bd426085d8d9dd8dbb56;hp=5c7a879cae518e987f2352c9f683bda54cb837ec;hpb=6e1c873d0879f462b1fb1a1efa444cf993a9e76a;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 5c7a879..eda6533 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -47,9 +47,12 @@ import javax.xml.ws.WebServiceException;
 import compbio.data.msa.JABAService;
 import compbio.data.msa.Metadata;
 import compbio.data.msa.MsaWS;
+import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
+import compbio.data.sequence.UnknownFileFormatException;
 import compbio.metadata.JobSubmissionException;
 import compbio.metadata.Option;
 import compbio.metadata.Preset;
@@ -147,23 +150,25 @@ public class Jws2Client {
 		}
 		Alignment alignment = null;
 		if (inputFile != null) {
-			if (service == Services.AAConWS) {
-				System.out.println("calc conserv!");
+			OutputStream outStream = null;
+			if (outFile != null) {
+				outStream = IOHelper.getOutStream(outFile);
 			} else {
+				// this stream is going to be closed later which is fine as
+				// std.out will not be
+				outStream = System.out;
+			}
+			if (service.getServiceType() == SequenceAnnotation.class) {
+				ScoreManager result = analize(inputFile,
+						((SequenceAnnotation<T>) msaws), preset, customOptions);
 
+				IOHelper.writeOut(outStream, result);
+			} else {
 				alignment = align(inputFile, (MsaWS<T>) msaws, preset,
 						customOptions);
-				OutputStream outStream = null;
-				if (outFile != null) {
-					outStream = IOHelper.getOutStream(outFile);
-				} else {
-					// this stream is going to be closed later which is fine as
-					// std.out will not be
-					outStream = System.out;
-				}
 				IOHelper.writeOut(outStream, alignment);
-				// stream is closed in the method no need to close it here
 			}
+			outStream.close();
 		}
 
 		boolean listParameters = CmdHelper.listParameters(cmd);
@@ -182,11 +187,83 @@ public class Jws2Client {
 		((Closeable) msaws).close();
 		log.fine("Disconnected successfully!");
 	}
+	/**
+	 * Calculate conservation for sequences loaded from the file
+	 * 
+	 * @param wsproxy
+	 *            a web service proxy
+	 * @param file
+	 *            the file to read the results from
+	 * @param preset
+	 *            Preset to use optional
+	 * @param customOptions
+	 *            the list of options
+	 * @return Set<Score> the conservation scores
+	 * @throws UnknownFileFormatException
+	 */
+	<T> ScoreManager analize(File file, SequenceAnnotation<T> wsproxy,
+			Preset<T> preset, List<Option<T>> customOptions) {
+
+		List<FastaSequence> fastalist = null;
+		ScoreManager scores = null;
+		try {
+			fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());
+			assert !fastalist.isEmpty() : "Input is empty!";
+
+			String jobId = null;
+			if (customOptions != null && preset != null) {
+				System.out
+						.println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");
+			}
+			if (customOptions != null) {
+				jobId = wsproxy.customAnalize(fastalist, customOptions);
+			} else if (preset != null) {
+				jobId = wsproxy.presetAnalize(fastalist, preset);
+			} else {
+				System.out.println("\n\ncalling analise.........");
+				jobId = wsproxy.analize(fastalist);
+			}
+			Thread.sleep(2000);
+
+			scores = wsproxy.getAnnotation(jobId);
+
+		} catch (IOException e) {
+			System.err
+					.println("Exception while reading the input file. "
+							+ "Check that the input file contains a list of fasta formatted sequences! "
+							+ "Exception details are below:");
+			e.printStackTrace();
+		} catch (JobSubmissionException e) {
+			System.err
+					.println("Exception while submitting job to a web server. "
+							+ "Exception details are below:");
+			e.printStackTrace();
+		} catch (ResultNotAvailableException e) {
+			System.err.println("Exception while waiting for results. "
+					+ "Exception details are below:");
+			e.printStackTrace();
+		} catch (InterruptedException ignored) {
+			// ignore and propagate an interruption
+			Thread.currentThread().interrupt();
+		} catch (WrongParameterException e) {
+			System.err
+					.println("Exception while parsing the web method input parameters. "
+							+ "Exception details are below:");
+			e.printStackTrace();
+		} catch (UnknownFileFormatException e) {
+			System.err
+					.println("Exception while attempting to read the input file "
+							+ "Exception details are below:");
+			System.out.println(e.getMessage());
+			e.printStackTrace();
+		}
+		return scores;
+	}
 
 	/**
 	 * Connects to a web service by the host and the service name
 	 * 
-	 * @param <T>
+	 * @param T
 	 *            web service type
 	 * @param host
 	 * @param service
@@ -212,8 +289,13 @@ public class Jws2Client {
 				serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);
 			}
 		}
+		if (serv == null) {
+			System.err.println("Could not connect to " + url
+					+ " the server is down?");
+			// FIXME
+		}
 		JABAService serviceIF = service.getInterface(serv);
-		log.log(Level.FINE, "Connected successfully!");
+		log.log(Level.INFO, "Connected successfully!");
 
 		return serviceIF;
 	}
@@ -351,7 +433,7 @@ public class Jws2Client {
 
 	/**
 	 * Starts command line client, if no parameter are supported print help. Two
-	 * parameters are required for successfull call the JWS2 host name and a
+	 * parameters are required for successful call the JWS2 host name and a
 	 * service name.
 	 * 
 	 * @param args