Alifold results are now parsed and stored in a ScoreManager object

[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 3c62c29..aa048b0 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -43,13 +43,16 @@ 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
@@ -103,6 +106,7 @@ public class Jws2Client {
         * @throws IOException\r
         */\r
        <T> Jws2Client(String[] cmd) throws IOException {\r
+               \r
 \r
                String hostname = CmdHelper.getHost(cmd);\r
                if (hostname == null) {\r
@@ -146,6 +150,7 @@ 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
@@ -156,7 +161,10 @@ 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
+               String rnastruct = null;\r
                if (inputFile != null) {\r
                        Writer writer = null;\r
                        if (outFile != null) {\r
@@ -171,10 +179,16 @@ public class Jws2Client {
                                                ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
 \r
                                IOHelper.writeOut(writer, result);\r
-                       } else {\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);\r
+                               }\r
                        }\r
                        writer.close();\r
                }\r
@@ -506,7 +520,77 @@ public class Jws2Client {
                }\r
                return alignment;\r
        }\r
-\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 String\r
+        */\r
+       \r
+       static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,\r
+                       List<Option<T>> customOptions) {\r
+               FileInputStream instream = null;\r
+               Alignment alignment = null;\r
+               String 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
+                               \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