X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FJws2Client.java;h=ae38d9f7771360f81f582b2f82409751a283aab7;hb=7522ace91fc0804a9719dbac9f68bc8154da3132;hp=a06a6fa35b6aebed0f154019e9b9e977de7c8b21;hpb=9072bd850138bedbd005509e5b14bb5e104574b4;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index a06a6fa..ae38d9f 100644
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -50,7 +50,6 @@ import compbio.data.msa.RegistryWS;
 import compbio.data.msa.SequenceAnnotation;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
-import compbio.data.sequence.RNAstruct;
 import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.SequenceUtil;
@@ -150,7 +149,6 @@ public class Jws2Client {
 		String presetName = CmdHelper.getPresetName(cmd);
 
 		Metadata<T> msaws = (Metadata<T>) connect(hostname, service);
-		Metadata<T> foldws = (Metadata<T>) connect(hostname, service);
 		Preset<T> preset = null;
 		if (presetName != null) {
 			preset = MetadataHelper.getPreset(msaws, presetName);
@@ -164,7 +162,6 @@ public class Jws2Client {
 //		System.out.println("The Options read from the command line: " + customOptions);
 		
 		Alignment alignment = null;
-		String rnastruct = null;
 		if (inputFile != null) {
 			Writer writer = null;
 			if (outFile != null) {
@@ -178,17 +175,14 @@ public class Jws2Client {
 				ScoreManager result = analize(inputFile,
 						((SequenceAnnotation<T>) msaws), preset, customOptions);
 
+				// A System.out.println just for testing!
+				System.out.println(result.toString());
+				
 				IOHelper.writeOut(writer, result);
 			} else if (service.getServiceType() == MsaWS.class) {
 				alignment = align(inputFile, (MsaWS<T>) msaws, preset,
 						customOptions);
 				IOHelper.writeOut(writer, alignment);
-			} else if (service.getServiceType() == FoldWS.class) {
-				rnastruct = fold(inputFile, (FoldWS<T>) foldws, preset, customOptions);
-				// No IOHelper method for rnastruct/String yet
-				if (writer != null) {
-					writer.write(rnastruct);
-				}
 			}
 			writer.close();
 		}
@@ -537,60 +531,60 @@ public class Jws2Client {
 	 * @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;
-	}
-		
+//	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
 	 *