Package org.moltools.apps.probemaker

Examples of org.moltools.apps.probemaker.ProbeDesignTask

186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
     
     
    //New design, with accept OK pairs. Expected to generate candidates, but fail.     
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"false");
      ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
      task.run();
      long candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
     
      assertEquals("Tag allocation should have failed", 0, p.getTags().size());    //$NON-NLS-1$
      assertEquals("Candidates expected", libraries1_1[0].size() , candCount);
      assertEquals("Quality expected to be bad", ProbeMakerConstants.BAD_QUALITY, ProbeMakerPropertyUtils.getRank(p));     
     
    //New design, with accept OK pairs AND candidates. Expected to generate candidates, and find candidate with warning.     
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"true");
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_CANDIDATES,"true");
      task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodFairAcceptor(), new BestQualitySelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
      task.run();
      candCount = task.getCandidatesGenerated();
      p = proj.getProbes().getSequenceAt(0);
      System.out.println("Probe");
      for (Iterator<KeyValue> i = p.getPropertySet().getKeyValueIterator();i.hasNext();) {
        System.out.println(i.next());
      }
View Full Code Here
258
259
260
261
262
263
264
265
266
267
268
269
270
271
    pm.setProject(proj);
   
    dummy.setData(DummyModule.KEY_WARNING_CHANCE, new Integer(100));
    proj.getSettings().addCandidateModuleStage1(dummy);

    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();

    //Check the number of candidates tested
    long candCount = task.getCandidatesGenerated();  
    assertTrue("Tag selection, 10 candidates expected, " + candCount + " generated.",candCount==10); //$NON-NLS-1$ //$NON-NLS-2$

    proj.getSettings().getCandidateModulesStage1().clear();   
  }
View Full Code Here
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_PREFERRED_LENGTH,String.valueOf(61));
    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_SPACER_SEQUENCE,"CT");     //$NON-NLS-1$
    pm.setProject(proj);

    GreedyTagAllocator ta = new GreedyTagAllocator();          
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    //task.addListener(new TaskListener());
    task.run();

    long candCount = task.getCandidatesGenerated();

    //Check the number of candidates tested
    assertEquals("Constant spacer, 10 candidates expected, " + candCount + " generated.", candCount, 10); //$NON-NLS-1$ //$NON-NLS-2$

    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_SPACER_SEQUENCE,""); //$NON-NLS-1$

    ta = new GreedyTagAllocator();
    //ta.setDebug(3,System.out);

    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(), new NoSelector(), new DefaultProbeDesigner(ta), new DefaultTSSPairDesigner(new DefaultTSSConstructor()) ,new StreamErrorHandler(System.out,true));
    //task.addListener(new TaskListener());
    task.run();

    //Check the number of candidates tested
    candCount = task.getCandidatesGenerated();

    assertTrue("Variable spacer, 40 candidates expected, " + candCount + " generated.", candCount==40); //$NON-NLS-1$ //$NON-NLS-2$

    proj.getSettings().getDesignParameters().put(TagAllocator.PROP_USE_SPACER,"FALSE"); //$NON-NLS-1$
    proj.getSettings().getCandidateModulesStage1().clear();   
View Full Code Here
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
    proj.getTargets().addSequence(t1);   
    proj.getSettings().addCandidateModuleStage1(dummy);
    pm.setProject(proj);

    //Run test to fail all    
    ProbeDesignTask task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));

    task.run();
    long candCount = task.getCandidatesGenerated();

    assertTrue("Pairwise allocation (Stage 1 module), 10 candidates expected, " + candCount + " generated.",candCount == 10); //$NON-NLS-1$ //$NON-NLS-2$

    //Move dummy to arm stage, check that there are no candidates generated
    proj.getSettings().getCandidateModulesStage1().clear();
    proj.getSettings().getArmModules().add(dummy);

    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new PairwiseTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();   
    candCount = task.getCandidatesGenerated();

    assertTrue("Pairwise allocation (TSS module), 0 candidates expected, " + candCount + " generated.",candCount==0); //$NON-NLS-1$ //$NON-NLS-2$

//  Expand target and test use unique mode, 2 candidates expected
    TargetHandler.expandTargets(pm.getProject().getTargets());
    proj.getSettings().getArmModules().clear();   

    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    candCount = task.getCandidatesGenerated();
    Probe p1 = pm.getProject().getProbes().getSequenceAt(0);
    Probe p2 = pm.getProject().getProbes().getSequenceAt(1);

    assertTrue("2 candidates expected, " + candCount + " generated.",candCount == 2); //$NON-NLS-1$ //$NON-NLS-2$
    assertTrue("Same tags allocated in unique mode!",p1.getTagAt(0)!=p2.getTagAt(0)); //$NON-NLS-1$

//  Expand target and test use per group, no modules, 2 candidates expected       
    libraries1_10[0].setMode(TagLibrary.USE_PER_GROUP);          

    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
    candCount = task.getCandidatesGenerated();
    p1 = pm.getProject().getProbes().getSequenceAt(0);
    p2 = pm.getProject().getProbes().getSequenceAt(1);

    assertTrue("2 candidates expected, " + candCount + " generated.",candCount == 2); //$NON-NLS-1$ //$NON-NLS-2$
    assertTrue("Different tags allocated in group mode!",p1.getTagAt(0)==p2.getTagAt(0)); //$NON-NLS-1$

//  Still expanded targets, per group mode, greedy allocator, dummy module in stage 1.
    //Expect 20 candidates generated
    libraries1_10[0].setMode(TagLibrary.USE_PER_GROUP);          
    proj.getSettings().getCandidateModulesStage1().add(dummy);   
      
    task = pm.getProbeDesignTask(false, true, null, new DefaultNamingScheme(), new GoodAcceptor(),
        new NoSelector(), new DefaultProbeDesigner(new GreedyTagAllocator()), new DefaultTSSPairDesigner(new DefaultTSSConstructor()), new StreamErrorHandler(System.out,true));
    task.run();
   
    candCount = task.getCandidatesGenerated();   
    assertTrue("20 candidates expected, " + candCount + " generated.",candCount == 20);      //$NON-NLS-1$ //$NON-NLS-2$
  }
View Full Code Here
TOP

Related Classes of org.moltools.apps.probemaker.ProbeDesignTask

  • net.sf.apptools.utils.HTMLLogWriter
  • org.moltools.apps.probemaker.design.Analyzer
  • org.moltools.apps.probemaker.design.DefaultNamingScheme
  • org.moltools.apps.probemaker.seq.Probe
  • org.moltools.apps.probemaker.test.TagAllocationTest
  • org.moltools.apps.probemaker.test.TSSConstructionTest
  • org.moltools.design.data.Target
  • org.moltools.design.data.ValidatingTarget
  • java.io.File
  • java.io.FileOutputStream
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.