Clean-up, refactoring, commenting. Parameters file containts only options since Jalvi...

[jabaws.git] / webservices / compbio / ws / client / Jws2Client.java

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index 888ec5f..7b781a2 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -43,16 +43,13 @@ import javax.xml.ws.Service;
 import javax.xml.ws.WebServiceException;\r
 \r
 import compbio.data.msa.JABAService;\r
-import compbio.data.msa.FoldWS;\r
 import compbio.data.msa.Metadata;\r
 import compbio.data.msa.MsaWS;\r
 import compbio.data.msa.RegistryWS;\r
 import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.RNAstruct;\r
 import compbio.data.sequence.ScoreManager;\r
-import compbio.data.sequence.ClustalAlignmentUtil;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.metadata.JobSubmissionException;\r
@@ -150,7 +147,6 @@ public class Jws2Client {
                String presetName = CmdHelper.getPresetName(cmd);\r
 \r
                Metadata<T> msaws = (Metadata<T>) connect(hostname, service);\r
-               Metadata<T> foldws = (Metadata<T>) connect(hostname, service);\r
                Preset<T> preset = null;\r
                if (presetName != null) {\r
                        preset = MetadataHelper.getPreset(msaws, presetName);\r
@@ -161,8 +157,9 @@ public class Jws2Client {
                        customOptions = MetadataHelper.processParameters(prms,\r
                                        msaws.getRunnerOptions());\r
                }\r
+//             System.out.println("The Options read from the command line: " + customOptions);\r
+               \r
                Alignment alignment = null;\r
-               RNAstruct rnastruct = null;\r
                if (inputFile != null) {\r
                        Writer writer = null;\r
                        if (outFile != null) {\r
@@ -176,17 +173,14 @@ public class Jws2Client {
                                ScoreManager result = analize(inputFile,\r
                                                ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 \r
+                               // A System.out.println just for testing!\r
+                               System.out.println(result.toString());\r
+                               \r
                                IOHelper.writeOut(writer, result);\r
                        } else if (service.getServiceType() == MsaWS.class) {\r
                                alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
                                                customOptions);\r
                                IOHelper.writeOut(writer, alignment);\r
-                       } else if (service.getServiceType() == FoldWS.class) {\r
-                               rnastruct = fold(inputFile, (FoldWS<T>) foldws, preset, customOptions);\r
-                               // No IOHelper method for rnastruct/String yet\r
-                               if (writer != null) {\r
-                                       writer.write(rnastruct.toString());\r
-                               }\r
                        }\r
                        writer.close();\r
                }\r
@@ -520,78 +514,6 @@ public class Jws2Client {
        }\r
        \r
        /**\r
-        * Return RNA secondary structure from a file using FoldWS\r
-        * \r
-        * @param <T>\r
-        *            web service type e.g. Clustal\r
-        * @param file\r
-        *            to read the results from\r
-        * @param foldws\r
-        *            FoldWS required\r
-        * @param preset\r
-        *            Preset to use optional\r
-        * @param customOptions\r
-        *            file which contains new line separated list of options\r
-        * @return RNAstruct\r
-        */\r
-       \r
-       static <T> RNAstruct fold(File file, FoldWS<T> foldws, Preset<T> preset,\r
-                       List<Option<T>> customOptions) {\r
-               FileInputStream instream = null;\r
-               Alignment alignment = null;\r
-               RNAstruct rnastruct = null;\r
-               try {\r
-                       instream = new FileInputStream(file);\r
-                       alignment = ClustalAlignmentUtil.readClustalFile(instream);\r
-                       instream.close();\r
-                       String jobId = null;\r
-                       if (customOptions != null && preset != null) {\r
-                               System.out.println("WARN: Parameters (-f) are defined together"\r
-                                               + "with a preset (-r), ignoring preset! ");\r
-                       }\r
-                       if (customOptions != null) {\r
-                               jobId = foldws.customFold(alignment, customOptions);\r
-                       } else if (preset != null) {\r
-                               jobId = foldws.presetFold(alignment, preset);\r
-                       } else {\r
-                               jobId = foldws.fold(alignment);\r
-                       }\r
-                       System.out.println("\n\ncalling fold.........");\r
-                       Thread.sleep(1000);\r
-                       rnastruct = foldws.getResult(jobId);\r
-                       log.info("log test print results:\n" + rnastruct.toString());\r
-                       System.out.println("print test results:\n " + rnastruct.toString());\r
-                               \r
-               } catch (IOException e) {\r
-                       System.err.println("Exception while reading the input file. Exception details: ");\r
-                       e.printStackTrace();\r
-               } catch (UnknownFileFormatException e) {\r
-                       System.err.println("Exception while reading input file. Doesnt look like a Clustal format file");\r
-                       e.printStackTrace();\r
-               } catch (JobSubmissionException e) {\r
-                       System.err.println("Exception while submitting job to the web server. ");\r
-                       e.printStackTrace();\r
-               } catch (ResultNotAvailableException e) {\r
-                       System.err.println("Exception while waiting for results. Exception details: ");\r
-                       e.printStackTrace();\r
-               } catch (InterruptedException ignored) {\r
-                       // ignore and propagate an interruption\r
-                       Thread.currentThread().interrupt();\r
-               } catch (WrongParameterException e) {\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 rnastruct;\r
-       }\r
-               \r
-       /**\r
         * Prints Jws2Client usage information to standard out\r
         * \r
         * @param exitStatus\r