Package org.moltools.apps.probemaker.design

Examples of org.moltools.apps.probemaker.design.ProbeDesigner

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        TSSConstructor tsc = (TSSConstructor) ProbeMakerPlugIn.defaultTSSConstructorClass.newInstance();

        ta.addParameters(s.getDesignParameters());
        tsc.addParameters(s.getDesignParameters());

        ProbeDesigner pd = new DefaultProbeDesigner(ta);
        TSSPairDesigner td = new DefaultTSSPairDesigner(tsc);
        NamingScheme namer = new DefaultNamingScheme();
        DesignLogWriter log = new TextDesignLogWriter(new FileWriter(new File(logPath, p.getName() + ".designlog")));

        ProbeDesignTask runner = pm.getProbeDesignTask(append,false,log,namer,acceptor,selector,pd, td, callback);
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      if (platform.getUI().inputData((ParameterPlugIn) ta,CoreMessages.getString("ProbeMakerPlugIn.TITLE_TAGALLOC_SETTINGS"))) { //$NON-NLS-1$
        return;
      }
    }

    final ProbeDesigner designer = new DefaultProbeDesigner(ta);

    //TODO reimplement uselog
    final boolean useLog = true;
    final ProbeDesignTask designTask = getProbeDesignTask(append, resetTags.booleanValue(), useLog, acceptor, selector, designer, con, platform);
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        TSSConstructor tsc = (TSSConstructor) ProbeMakerPlugIn.defaultTSSConstructorClass.newInstance();

        ta.addParameters(s.getDesignParameters());
        tsc.addParameters(s.getDesignParameters());

        ProbeDesigner pd = new DefaultProbeDesigner(ta);

        ProbeDesignTask runner = pm.getProbeDesignTask(append,false,true,acceptor,selector,pd, tsc, callback);
        runner.timing = true;
        runner.verbose = true;
        System.out.println("Starting design of " + runner.getMaxProgress() + " probe groups"); //$NON-NLS-1$ //$NON-NLS-2$
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    tl.setMode(TagLibrary.USE_UNIQUE_TAG);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl}));
   
    //Design
    ProbeDesigner pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false, null, new DefaultNamingScheme(), new AllAcceptor(),new NoSelector(), pd, new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true)).run();
       
//  Store to project file
    File f = new File("temp.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
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    pm.setProject(proj);
  }
  
 
  protected void doTest(TSSConstructor tsc, String expect5, String expect3) throws ClusterException {
    ProbeDesigner pd = new DefaultProbeDesigner(new GreedyTagAllocator());
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, false, new GoodAcceptor(), new NoSelector(), pd, tsc, new StreamErrorHandler(System.out,true));
    task.run();
   
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
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    pm.setProject(proj);
  }
  
 
  protected void doTest(TSSConstructor tsc, String expect5, String expect3) throws ClusterException {
    ProbeDesigner pd = new DefaultProbeDesigner(new GreedyTagAllocator());
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), pd, new DefaultTSSPairDesigner(tsc), new StreamErrorHandler(System.out,true));
    task.run();
   
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
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      if (platform.getUI().inputData((ParameterPlugIn) ta,CoreMessages.getString("ProbeMakerPlugIn.TITLE_TAGALLOC_SETTINGS"))) { //$NON-NLS-1$
        return;
      }
    }

    final ProbeDesigner designer = new DefaultProbeDesigner(ta);

    //TODO reimplement uselog
    final boolean useLog = true;
    final ProbeDesignTask designTask = getProbeDesignTask(append, resetTags.booleanValue(), useLog, acceptor, selector, designer, con, platform);
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      if (platform.getUI().inputData((ParameterPlugIn) ta,CoreMessages.getString("ProbeMakerPlugIn.TITLE_TAGALLOC_SETTINGS"))) { //$NON-NLS-1$
        return;
      }
    }

    final ProbeDesigner designer = new DefaultProbeDesigner(ta);

    //TODO reimplement uselog
    final boolean useLog = true;
    final ProbeDesignTask designTask = getProbeDesignTask(append, resetTags.booleanValue(), useLog, acceptor, selector, designer, con, platform);
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    tl.setMode(TagLibrary.USE_UNIQUE_TAG);
   
    pm.getProject().setTagSettings(new DefaultTagSettings(new TagLibrary[] {tl}));
   
    //Design
    ProbeDesigner pd = new DefaultProbeDesigner(new PairwiseTagAllocator());
    pm.getProbeDesignTask(false, false, true, new AllAcceptor(),new NoSelector(), pd, new DefaultTSSConstructor(), new StreamErrorHandler(System.out,true)).run();
       
//  Store to project file
    File f = new File("temp.pmp"); //$NON-NLS-1$
    f.deleteOnExit();
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      if (platform.getUI().inputData((ParameterPlugIn) ta,CoreMessages.getString("ProbeMakerPlugIn.TITLE_TAGALLOC_SETTINGS"))) { //$NON-NLS-1$
        return;
      }
    }

    final ProbeDesigner designer = new DefaultProbeDesigner(ta);
    TSSPairDesigner td = new DefaultTSSPairDesigner(con);
    NamingScheme namer = new DefaultNamingScheme();   
   
    String date = SimpleDateFormat.getDateTimeInstance(DateFormat.SHORT, DateFormat.SHORT).format(new Date());
   
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Related Classes of org.moltools.apps.probemaker.design.ProbeDesigner

  • org.moltools.apps.probemaker.ProbeMakerLauncher
  • org.moltools.apps.probemaker.ProbeMakerPlugIn
  • org.moltools.apps.probemaker.test.ProjectIOTest
  • org.moltools.apps.probemaker.test.TSSConstructionTest
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