import java.io.Closeable;\r
import java.io.File;\r
import java.io.FileInputStream;\r
+import java.io.FileOutputStream;\r
import java.io.IOException;\r
import java.io.PrintWriter;\r
import java.io.Writer;\r
import compbio.data.msa.RegistryWS;\r
import compbio.data.msa.SequenceAnnotation;\r
import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.AlignmentMetadata;\r
+import compbio.data.sequence.JpredAlignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.SequenceUtil;\r
*/\r
public class Jws2Client {\r
\r
- /*\r
+ /**\r
* Use java.util.Logger instead of log4j logger to reduce the size of the client package\r
*/\r
private static final Logger log = Logger.getLogger(Jws2Client.class.getCanonicalName());\r
* command line options\r
* @throws IOException\r
*/\r
+ @SuppressWarnings("unchecked")\r
<T> Jws2Client(String[] cmd) throws IOException {\r
+ \r
\r
String hostname = CmdHelper.getHost(cmd);\r
if (hostname == null) {\r
if (outfile != null) {\r
writer = IOHelper.getWriter(outfile);\r
} else {\r
- // this stream is going to be closed later which is fine as std.out will not be\r
writer = new PrintWriter(System.out, true);\r
}\r
if (service.getServiceType() == SequenceAnnotation.class) {\r
ScoreManager result = analize(infile, ((SequenceAnnotation<T>) thews), preset, customOptions);\r
IOHelper.writeOut(writer, result);\r
+ writer.close();\r
} else if (service.getServiceType() == MsaWS.class) {\r
Alignment alignment = align(infile, (MsaWS<T>) thews, preset, customOptions);\r
- IOHelper.writeOut(writer, alignment);\r
+ if (serviceName.equalsIgnoreCase("JpredWS")) {\r
+ writer.close();\r
+ JpredAlignment jpred = (JpredAlignment)alignment;\r
+ if (outfile != null) {\r
+ FileOutputStream fout = new FileOutputStream(outfile);\r
+ SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);\r
+ fout.close();\r
+ } else {\r
+ SequenceUtil.writeFasta(System.out, jpred.getJpredSequences());\r
+ }\r
+ } else {\r
+ IOHelper.writeOut(writer, alignment);\r
+ writer.close();\r
+ }\r
+ AlignmentMetadata md = alignment.getMetadata();\r
+ System.out.println("Output has been prepared with " + md.getProgram());\r
}\r
- writer.close();\r
}\r
\r
if (CmdHelper.listParameters(cmd)) {\r
return;\r
}\r
if (!func_services.isEmpty()) {\r
- String mess = "\n\rAvailable services: ";\r
+ System.out.println("There are " + func_services.size() + " services at " + hostname + ":");\r
+ String mess = "\n\rThe list:\n";\r
System.out.println(mess + Services.toString(func_services));\r
}\r
if (!nonfunc_services.isEmpty()) {\r
- String mess = "Non-available services (internal tests failed): ";\r
+ System.out.println("There are " + nonfunc_services.size() + " non-available services at " + hostname + ":");\r
+ String mess = "The list (internal tests failed): ";\r
System.out.println(mess + Services.toString(nonfunc_services));\r
}\r
}\r
static <T> Alignment align(File file, MsaWS<T> msaws, Preset<T> preset,\r
List<Option<T>> customOptions) {\r
FileInputStream instream = null;\r
- List<FastaSequence> fastalist = null;\r
Alignment alignment = null;\r
try {\r
instream = new FileInputStream(file);\r
- fastalist = SequenceUtil.readFasta(instream);\r
+ List<FastaSequence> fastalist = SequenceUtil.readFasta(instream);\r
instream.close();\r
String jobId = null;\r
if (customOptions != null && preset != null) {\r
} else {\r
jobId = msaws.align(fastalist);\r
}\r
- System.out.println("\ncalling aligner.........");\r
- Thread.sleep(1000);\r
+ System.out.println("\ncalling program.........");\r
+ Thread.sleep(100);\r
alignment = msaws.getResult(jobId);\r
-\r
} catch (IOException e) {\r
- System.err.println("Exception while reading the input file. "\r
- + "Check that the input file contains a list of fasta formatted sequences! "\r
+ System.err.println("Exception while reading the input file. Check that the input file is a FASTA file! "\r
+ "Exception details are below:");\r
e.printStackTrace();\r
} catch (JobSubmissionException e) {\r
- System.err.println("Exception while submitting job to a web server. "\r
- + "Exception details are below:");\r
+ System.err.println("Exception while submitting job to a web server. 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
+ System.err.println("Exception while waiting for results. Exception details are below:");\r
e.printStackTrace();\r
} catch (InterruptedException ignored) {\r
// ignore and propagate an interruption\r
}\r
return alignment;\r
}\r
-\r
+ \r
/**\r
* Starts command line client, if no parameter are supported print help. Two\r
* parameters are required for successful call the JWS2 host name and a\r
* \r
*/\r
public static void main(String[] args) {\r
-\r
if (args == null) {\r
System.out.println(Constraints.help_text);\r
System.exit(1);\r
System.out.println(Constraints.help_text);\r
System.exit(1);\r
}\r
-\r
try {\r
new Jws2Client(args);\r
} catch (IOException e) {\r
git://source.jalview.org / jabaws.git / blobdiff