* \r
*/\r
@XmlAccessorType(XmlAccessType.FIELD)\r
-@Immutable\r
public final class JpredAlignment extends Alignment{\r
\r
- private AlignmentMetadata metadata;\r
- private List<FastaSequence> sequences;\r
- \r
- FastaSequence jnetpred;\r
- FastaSequence JNETCONF;\r
- FastaSequence JNETSOL25;\r
- FastaSequence JNETSOL5;\r
- FastaSequence JNETSOL0;\r
- FastaSequence JNETHMM;\r
- FastaSequence JNETPSSM;\r
- FastaSequence JNETJURY;\r
-\r
private JpredAlignment() {\r
// This has to has a default constructor for JaxB\r
}\r
* @param program\r
* @param gapchar\r
*/\r
- public JpredAlignment(List<FastaSequence> sequences, Program program,\r
- char gapchar) {\r
- DecomposeInitalJpredSeq(sequences);\r
- this.metadata = new AlignmentMetadata(Program.CLUSTAL, gapchar);\r
+ public JpredAlignment(List<FastaSequence> sequences, Program program, char gapchar) {\r
+ this.sequences = sequences;\r
+ this.metadata = new AlignmentMetadata(Program.Jpred, gapchar);\r
}\r
\r
/**\r
* @param metadata\r
*/\r
public JpredAlignment(List<FastaSequence> sequences, AlignmentMetadata metadata) {\r
- DecomposeInitalJpredSeq(sequences);\r
+ this.sequences = sequences;\r
this.metadata = metadata;\r
}\r
\r
- /**\r
- * \r
- * @param sequences\r
- */\r
- private void DecomposeInitalJpredSeq(List<FastaSequence> sequences) {\r
+ private List<FastaSequence> getRealSeqs() {\r
List<FastaSequence> realsequences = new ArrayList<FastaSequence>();\r
- for (FastaSequence s : sequences) {\r
- if (s.getId().equals("jnetpred")) {\r
- this.jnetpred = s;\r
- } else if (s.getId().equals("JNETCONF")) {\r
- this.JNETCONF = s;\r
- } else if (s.getId().equals("JNETSOL25")) {\r
- this.JNETSOL25 = s;\r
- } else if (s.getId().equals("JNETSOL5")) {\r
- this.JNETSOL5 = s;\r
- } else if (s.getId().equals("JNETSOL0")) {\r
- this.JNETSOL0 = s;\r
- } else if (s.getId().equals("JNETHMM")) {\r
- this.JNETSOL0 = s;\r
- } else if (s.getId().equals("JNETHMM")) {\r
- this.JNETHMM = s;\r
- } else if (s.getId().equals("JNETSOL0")) {\r
- this.JNETPSSM = s;\r
- } else if (s.getId().equals("JNETHMM")) {\r
- this.JNETJURY = s;\r
+ for (FastaSequence s : this.sequences) {\r
+ if (s.getId().equals("jnetpred") || \r
+ s.getId().equals("JNETCONF") ||\r
+ s.getId().equals("JNETSOL25") ||\r
+ s.getId().equals("JNETSOL5") ||\r
+ s.getId().equals("JNETSOL0") ||\r
+ s.getId().equals("JNETHMM") ||\r
+ s.getId().equals("JNETHMM") ||\r
+ s.getId().equals("JNETSOL0") ||\r
+ s.getId().equals("JNETHMM")) {\r
+ // do nothing;\r
} else {\r
realsequences.add(s);\r
}\r
}\r
- this.sequences = realsequences;\r
+ return realsequences;\r
}\r
\r
+\r
+ public List<FastaSequence> getJpredSequences() {\r
+ List<FastaSequence> realsequences = new ArrayList<FastaSequence>();\r
+ for (FastaSequence s : this.sequences) {\r
+ if (s.getId().equals("jnetpred") || \r
+ s.getId().equals("JNETCONF") ||\r
+ s.getId().equals("JNETSOL25") ||\r
+ s.getId().equals("JNETSOL5") ||\r
+ s.getId().equals("JNETSOL0") ||\r
+ s.getId().equals("JNETHMM") ||\r
+ s.getId().equals("JNETHMM") ||\r
+ s.getId().equals("JNETSOL0") ||\r
+ s.getId().equals("JNETSOL0") ||\r
+ s.getId().equals("QUERY")) {\r
+ realsequences.add(s);\r
+ }\r
+ }\r
+ return realsequences;\r
+ }\r
/**\r
* \r
* @return Jpred prediction \r
*/\r
public String getJpredPrediction() {\r
- return this.jnetpred.getSequence();\r
+ for (FastaSequence s : this.sequences) {\r
+ if (s.getId().equals("jnetpred")) {\r
+ return s.getSequence();\r
+ }\r
+ }\r
+ return new String("");\r
}\r
\r
/**\r
* @return Jpred JNETSOL25 line\r
*/\r
public String getJpredSOL25() {\r
- return this.JNETSOL25.getSequence();\r
+ for (FastaSequence s : this.sequences) {\r
+ if (s.getId().equals("JNETSOL25")) {\r
+ return s.getSequence();\r
+ }\r
+ }\r
+ return new String("");\r
}\r
\r
/**\r
* @return Jpred JNETSOL5 line\r
*/\r
public String getJpredSOL5() {\r
- return this.JNETSOL5.getSequence();\r
+ for (FastaSequence s : this.sequences) {\r
+ if (s.getId().equals("JNETSOL5")) {\r
+ return s.getSequence();\r
+ }\r
+ }\r
+ return new String("");\r
}\r
/**\r
* \r
* @return Jpred JNETSOL0 line\r
*/\r
public String getJpredSOL0() {\r
- return this.JNETSOL0.getSequence();\r
+ for (FastaSequence s : this.sequences) {\r
+ if (s.getId().equals("JNETSOL0")) {\r
+ return s.getSequence();\r
+ }\r
+ }\r
+ return new String("");\r
}\r
/**\r
* \r
* @return Jpred JNETCONF line\r
*/\r
public String getJpredJNETCONF() {\r
- return this.JNETCONF.getSequence();\r
+ for (FastaSequence s : this.sequences) {\r
+ if (s.getId().equals("JNETCONF")) {\r
+ return s.getSequence();\r
+ }\r
+ }\r
+ return new String("");\r
}\r
+\r
/**\r
* \r
* @return list of FastaSequence records\r
*/\r
+ @Override\r
public List<FastaSequence> getSequences() {\r
- return sequences;\r
+ return this.getRealSeqs();\r
}\r
\r
/**\r
* \r
* @return a number of sequence in the alignment\r
*/\r
- public int getSize() {\r
- return this.sequences.size();\r
- }\r
-\r
- /**\r
- * \r
- * @return AlignmentMetadata object\r
- */\r
- public AlignmentMetadata getMetadata() {\r
- return metadata;\r
- }\r
-\r
- @Override\r
- public String toString() {\r
- String sseq = "";\r
- for (FastaSequence fs : getSequences()) {\r
- sseq += fs.toString() + "\n";\r
- }\r
- return sseq;\r
- }\r
-\r
@Override\r
- public int hashCode() {\r
- final int prime = 31;\r
- int result = 1;\r
- result = prime * result\r
- + ((metadata == null) ? 0 : metadata.hashCode());\r
- result = prime * result\r
- + ((sequences == null) ? 0 : sequences.hashCode());\r
- return result;\r
+ public int getSize() {\r
+ return this.getRealSeqs().size();\r
}\r
\r
/**\r
if (obj == null) {\r
return false;\r
}\r
- if (!(obj instanceof Alignment)) {\r
+ if (!(obj instanceof JpredAlignment)) {\r
return false;\r
}\r
- Alignment al = (Alignment) obj;\r
+ JpredAlignment al = (JpredAlignment) obj;\r
if (this.getSize() != al.getSize()) {\r
return false;\r
}\r
return false;\r
}\r
}\r
-\r
return true;\r
}\r
\r
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.OutputStream;\r
import java.io.PrintWriter;\r
import java.io.Writer;\r
import java.net.ConnectException;\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
* command line options\r
* @throws IOException\r
*/\r
+ @SuppressWarnings("unchecked")\r
<T> Jws2Client(String[] cmd) throws IOException {\r
\r
\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 = new JpredAlignment(alignment.getSequences(), alignment.getMetadata());\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
}\r
- writer.close();\r
}\r
\r
if (CmdHelper.listParameters(cmd)) {\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
git://source.jalview.org / jabaws.git / commitdiff