Disembl and Jronn web services work. Modified to produce raw scores Globplot script...

[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 9da8abe..62aa383 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -37,7 +37,9 @@ import java.io.OutputStream;
 import java.net.MalformedURLException;\r
 import java.net.URL;\r
 import java.util.Arrays;\r
+import java.util.HashSet;\r
 import java.util.List;\r
+import java.util.Map;\r
 import java.util.logging.Level;\r
 import java.util.logging.Logger;\r
 \r
@@ -47,9 +49,12 @@ import javax.xml.ws.WebServiceException;
 import compbio.data.msa.JABAService;\r
 import compbio.data.msa.Metadata;\r
 import compbio.data.msa.MsaWS;\r
+import compbio.data.msa.SequenceAnnotation;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
 import compbio.data.sequence.SequenceUtil;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.metadata.JobSubmissionException;\r
 import compbio.metadata.Option;\r
 import compbio.metadata.Preset;\r
@@ -147,23 +152,25 @@ public class Jws2Client {
                }\r
                Alignment alignment = null;\r
                if (inputFile != null) {\r
+                       OutputStream outStream = null;\r
+                       if (outFile != null) {\r
+                               outStream = IOHelper.getOutStream(outFile);\r
+                       } else {\r
+                               // this stream is going to be closed later which is fine as\r
+                               // std.out will not be\r
+                               outStream = System.out;\r
+                       }\r
                        if (service == Services.AAConWS) {\r
-                               System.out.println("calc conserv!");\r
+                               Map<String, HashSet<Score>> result = analize(inputFile,\r
+                                               ((SequenceAnnotation<T>) msaws), preset, customOptions);\r
+                               IOHelper.writeOut(outStream, result);\r
                        } else {\r
-\r
                                alignment = align(inputFile, (MsaWS<T>) msaws, preset,\r
                                                customOptions);\r
-                               OutputStream outStream = null;\r
-                               if (outFile != null) {\r
-                                       outStream = IOHelper.getOutStream(outFile);\r
-                               } else {\r
-                                       // this stream is going to be closed later which is fine as\r
-                                       // std.out will not be\r
-                                       outStream = System.out;\r
-                               }\r
                                IOHelper.writeOut(outStream, alignment);\r
-                               // stream is closed in the method no need to close it here\r
                        }\r
+\r
+                       // stream is closed in the method no need to close it here\r
                }\r
 \r
                boolean listParameters = CmdHelper.listParameters(cmd);\r
@@ -182,6 +189,76 @@ public class Jws2Client {
                ((Closeable) msaws).close();\r
                log.fine("Disconnected successfully!");\r
        }\r
+       /**\r
+        * Calculate conservation for sequences loaded from the file\r
+        * \r
+        * @param wsproxy\r
+        *            a web service proxy\r
+        * @param file\r
+        *            the file to read the results from\r
+        * @param preset\r
+        *            Preset to use optional\r
+        * @param customOptions\r
+        *            the list of options\r
+        * @return Set<Score> the conservation scores\r
+        * @throws UnknownFileFormatException\r
+        */\r
+       <T> Map<String, HashSet<Score>> analize(File file,\r
+                       SequenceAnnotation<T> wsproxy, Preset<T> preset,\r
+                       List<Option<T>> customOptions) {\r
+\r
+               List<FastaSequence> fastalist = null;\r
+               Map<String, HashSet<Score>> scores = null;\r
+               try {\r
+                       fastalist = SequenceUtil.openInputStream(file.getAbsolutePath());\r
+\r
+                       String jobId = null;\r
+                       if (customOptions != null && preset != null) {\r
+                               System.out\r
+                                               .println("WARN: Parameters (-f) are defined together with a preset (-r) ignoring preset!");\r
+                       }\r
+                       if (customOptions != null) {\r
+                               jobId = wsproxy.customAnalize(fastalist, customOptions);\r
+                       } else if (preset != null) {\r
+                               jobId = wsproxy.presetAnalize(fastalist, preset);\r
+                       } else {\r
+                               jobId = wsproxy.analize(fastalist);\r
+                       }\r
+                       Thread.sleep(1000);\r
+                       scores = wsproxy.getAnnotation(jobId);\r
+\r
+               } catch (IOException e) {\r
+                       System.err\r
+                                       .println("Exception while reading the input file. "\r
+                                                       + "Check that the input file contains a list of fasta formatted sequences! "\r
+                                                       + "Exception details are below:");\r
+                       e.printStackTrace();\r
+               } catch (JobSubmissionException e) {\r
+                       System.err\r
+                                       .println("Exception while submitting job to a web server. "\r
+                                                       + "Exception details are below:");\r
+                       e.printStackTrace();\r
+               } catch (ResultNotAvailableException e) {\r
+                       System.err.println("Exception while waiting for results. "\r
+                                       + "Exception details are below:");\r
+                       e.printStackTrace();\r
+               } catch (InterruptedException ignored) {\r
+                       // ignore and propagate an interruption\r
+                       Thread.currentThread().interrupt();\r
+               } catch (WrongParameterException e) {\r
+                       System.err\r
+                                       .println("Exception while parsing the web method input parameters. "\r
+                                                       + "Exception details are below:");\r
+                       e.printStackTrace();\r
+               } catch (UnknownFileFormatException e) {\r
+                       System.err\r
+                                       .println("Exception while attempting to read the input file "\r
+                                                       + "Exception details are below:");\r
+                       System.out.println(e.getMessage());\r
+                       e.printStackTrace();\r
+               }\r
+               return scores;\r
+       }\r
 \r
        /**\r
         * Connects to a web service by the host and the service name\r