Examples of DINAMeltSecStructModule

org.moltools.apps.probemaker.ext.mod.DINAMeltSecStructModule
This AnalysisModule will connect to the DINAMelt web server and send a request to predict the secondary structure of a Probe.
Reference:
M. Zuker
Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acids Res. 31 (13), 3406-15, (2003)
@author Johan Stenberg

Examples of org.moltools.apps.probemaker.ext.mod.DINAMeltSecStructModule

  @Override
  protected void setUp() throws DuplicateIDException, FileNotFoundException, IOException, SequenceFormatException {
    pm = new ProbeMakerPlugIn();
    project = new Project("Mfold_test"); //$NON-NLS-1$
    pm.setProject(project);
    m = new DINAMeltSecStructModule();    
    project.getSettings().addCandidateModuleStage1(m);    
    Collection<Probe> seqs = SequenceIO.readSequences(new InputStreamReader(getClass().getResourceAsStream("mfold_test.lib")),new IDAndNameFastaFormatter<Probe>(),DefaultProbe.getSequenceBuilder()); //$NON-NLS-1$
    project.getProbes().addSequences(seqs);
  }

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Examples of org.moltools.apps.probemaker.ext.mod.DINAMeltSecStructModule

  @Override
  protected void setUp() throws DuplicateIDException, FileNotFoundException, IOException, SequenceFormatException {
    pm = new ProbeMakerPlugIn();
    project = new Project("Mfold_test"); //$NON-NLS-1$
    pm.setProject(project);
    m = new DINAMeltSecStructModule();    
    project.getSettings().addCandidateModuleStage1(m);    
    Collection<Probe> seqs = SequenceIO.readSequences(new InputStreamReader(getClass().getResourceAsStream("mfold_test.lib")),new IDAndNameFastaFormatter<Probe>(),DefaultProbe.getSequenceBuilder()); //$NON-NLS-1$
    project.getProbes().addSequences(seqs);
  }

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