X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=7b781a2c1ea00d75402d7798a0d9f31999018aa4;hb=c84ec6492607920b938cfa3645e1a92e15727dd1;hp=ae38d9f7771360f81f582b2f82409751a283aab7;hpb=c00a86ec130a4bf0bc9b8fc25bbbc7b2912bd62a;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index ae38d9f..7b781a2 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -43,7 +43,6 @@ import javax.xml.ws.Service;
 import javax.xml.ws.WebServiceException;
 
 import compbio.data.msa.JABAService;
-import compbio.data.msa.FoldWS;
 import compbio.data.msa.Metadata;
 import compbio.data.msa.MsaWS;
 import compbio.data.msa.RegistryWS;
@@ -51,7 +50,6 @@ import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
 import compbio.data.sequence.ScoreManager;
-import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
 import compbio.metadata.JobSubmissionException;
@@ -516,76 +514,6 @@ public class Jws2Client {
 	}
 	
 	/**
-	 * Return RNA secondary structure from a file using FoldWS
-	 * 
-	 * @param <T>
-	 *            web service type e.g. Clustal
-	 * @param file
-	 *            to read the results from
-	 * @param foldws
-	 *            FoldWS required
-	 * @param preset
-	 *            Preset to use optional
-	 * @param customOptions
-	 *            file which contains new line separated list of options
-	 * @return String
-	 */
-	
-//	static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,
-//			List<Option<T>> customOptions) {
-//		FileInputStream instream = null;
-//		Alignment alignment = null;
-//		String rnastruct = null;
-//		try {
-//			instream = new FileInputStream(file);
-//			alignment = ClustalAlignmentUtil.readClustalFile(instream);
-//			instream.close();
-//			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 = foldws.customFold(alignment, customOptions);
-//			} else if (preset != null) {
-//				jobId = foldws.presetFold(alignment, preset);
-//			} else {
-//				jobId = foldws.fold(alignment);
-//			}
-//			System.out.println("\n\ncalling fold.........");
-//			Thread.sleep(1000);
-//			rnastruct = foldws.getResult(jobId);
-//				
-//		} catch (IOException e) {
-//			System.err.println("Exception while reading the input file. Exception details: ");
-//			e.printStackTrace();
-//		} catch (UnknownFileFormatException e) {
-//			System.err.println("Exception while reading input file. Doesnt look like a Clustal format file");
-//			e.printStackTrace();
-//		} catch (JobSubmissionException e) {
-//			System.err.println("Exception while submitting job to the web server. ");
-//			e.printStackTrace();
-//		} catch (ResultNotAvailableException e) {
-//			System.err.println("Exception while waiting for results. Exception details: ");
-//			e.printStackTrace();
-//		} catch (InterruptedException ignored) {
-//			// ignore and propagate an interruption
-//			Thread.currentThread().interrupt();
-//		} catch (WrongParameterException e) {
-//			e.printStackTrace();
-//		} finally {
-//			if (instream != null) {
-//				try {
-//					instream.close();
-//				} catch (IOException ignored) {
-//					// ignore
-//				}
-//			}
-//		}
-//		return rnastruct;
-//	}
-//		
-	/**
 	 * Prints Jws2Client usage information to standard out
 	 * 
 	 * @param exitStatus