Package org.moltools.apps.probemaker.messages

Examples of org.moltools.apps.probemaker.messages.MessageType

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  /**(Re)calculate the Tm values of the TSSs of this pair*/
  public static void calculateArmTemperatures(TSSPair p, MeltingPointCalculator defaultMpc, MeltingPointCalculator backupMpc) {
    MessageType mt = new MessageType("TEMPERATUR_CALCULATION", //$NON-NLS-1$
    "Temperature calculation"); //$NON-NLS-1$
    ProbeMakerTarget t = null;
    try {
      t = (ProbeMakerTarget) p.getTarget();     
      if (p.getTarget() == null) {
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  public void testTargetSpecificSequence() {
    PropertyAcceptorNucleotideSequence tss = ProbeMakerSequenceFactory.createTSS(seq,target.getID());
   
    ProbeMakerPropertyUtils.setHybridizationTemp(tss, 10f);
    ProbeMakerPropertyUtils.addMessage(tss, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    assertTrue("Incorrect target ID", target.getID().equals(DesignUtils.getTargetID(tss))); //$NON-NLS-1$
    assertTrue("Incorrect temp", 10f == ProbeMakerPropertyUtils.getHybridizationTemp(tss)); //$NON-NLS-1$
    assertTrue("Incorrect message count", 1 == ProbeMakerPropertyUtils.getAllMessages(tss).size()); //$NON-NLS-1$
 
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  }

  public void testTSSPair() {
    PropertyAcceptorNucleotideSequence tss5 = ProbeMakerSequenceFactory.createTSS(seq,target.getID());   
    ProbeMakerPropertyUtils.addMessage(tss5, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR));     //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    TSSPair pair = new TSSPair(tss5,null,target);
    ProbeMakerPropertyUtils.setRank(pair, ProbeMakerConstants.BAD_QUALITY);
   
    assertTrue("Incorrect rank", ProbeMakerConstants.BAD_QUALITY == ProbeMakerPropertyUtils.getRank(pair)); //$NON-NLS-1$
    assertTrue("Incorrect target ID", target.getID().equals(DesignUtils.getTargetID(pair))); //$NON-NLS-1$
    assertTrue("Incorrect message count", 1 == ProbeMakerPropertyUtils.getAllMessages(pair).size()); //$NON-NLS-1$
   
    ProbeMakerPropertyUtils.addMessage(pair, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    assertTrue("Incorrect message count", 2 == ProbeMakerPropertyUtils.getAllMessages(pair).size()); //$NON-NLS-1$
 
  }
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  }

  public void testProbe() {
    PropertyAcceptorNucleotideSequence tss5 = ProbeMakerSequenceFactory.createTSS(seq,target.getID());   
    ProbeMakerPropertyUtils.addMessage(tss5, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR));     //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    TSSPair pair = new TSSPair(tss5,null,target);
    ProbeMakerPropertyUtils.addMessage(pair, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$

    Probe probe = new DefaultProbe(pair,0,0,NucleotideSequence.DNA);

    ProbeMakerPropertyUtils.setRank(probe, ProbeMakerConstants.BAD_QUALITY);
   
    assertTrue("Incorrect rank", ProbeMakerConstants.BAD_QUALITY == ProbeMakerPropertyUtils.getRank(probe)); //$NON-NLS-1$
   
    assertTrue("Incorrect target ID", target.getID().equals(DesignUtils.getTargetID(probe))); //$NON-NLS-1$
    assertTrue("Incorrect target", target.equals(pair.getTarget())); //$NON-NLS-1$
    assertTrue("Incorrect target", target.equals(probe.getTarget())); //$NON-NLS-1$
    assertTrue("Incorrect message count", 2 == ProbeMakerPropertyUtils.getAllMessages(probe).size()); //$NON-NLS-1$
    assertTrue("Wrong tss pair",pair == probe.getTSSPair()); //$NON-NLS-1$
   
    ProbeMakerPropertyUtils.addMessage(probe, new Message("Test",new MessageType("test_type","Test type"),Message.ERROR)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
   
    assertTrue("Incorrect message count", 3 == ProbeMakerPropertyUtils.getAllMessages(probe).size()); //$NON-NLS-1$
   
  }
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      public void doAnalysis(Probe p, TagAllocator pd,
          DefiniteSequenceDB<? extends Probe> otherProbes) {
        ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(
            "Dummy", //$NON-NLS-1$
            new MessageType("DUMMY", "Dummy"),
            Message.WARNING));
   
      }   
    });
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"false");
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    for (Iterator<? extends Probe> i = probes.iterator();i.hasNext();) {
      Probe p = i.next();
      for (Iterator<Message> mi = ProbeMakerPropertyUtils.getAllMessages(p).iterator();mi.hasNext();) {
        Message m = mi.next();
        MessageType t = m.getType();
        int s = m.getSeverity();
        boolean found = false;
        for (Iterator<MessageSummaryEntry> ei = l.iterator();ei.hasNext();) {
          MessageSummaryEntry mse = ei.next();
          if (mse.isMatch(t,s)) {
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      public void doAnalysis(Probe p, TagAllocator pd,
          DefiniteSequenceDB<? extends Probe> otherProbes) {
        ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(
            "Dummy", //$NON-NLS-1$
            new MessageType("DUMMY", "Dummy"),
            Message.WARNING));
   
      }   
    });
      proj.getSettings().getDesignParameters().put(Analyzer.PROP_ACCEPT_OK_ARMS,"false");
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    for (Iterator<?> i = messageListElement.getChildren(MESSAGE,ns).iterator();i.hasNext();) {
      Element messE = (Element) i.next();

      String type = messE.getAttributeValue(MESSAGE_TYPE_NAME,ns);
      String desc = messE.getAttributeValue(DESCRIPTION,ns);
      MessageType mt = new MessageType(type,desc);
      byte severity = Byte.parseByte(messE.getAttributeValue(SEVERITY,ns));     
      String messageStr = messE.getText();
      Message m = new Message(messageStr,mt,severity);
      ProbeMakerPropertyUtils.addMessage(mh,m);
    }   
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  protected Element getMessageListElement(Collection<? extends Message> messages) {
    Element messageList = new Element("messageList",ns); //$NON-NLS-1$
    for (Iterator<? extends Message> i = messages.iterator();i.hasNext();) {
      Message m = i.next();
      MessageType mt = m.getType();

      Element me = new Element(MESSAGE,ns);          
      me.setAttribute(MESSAGE_TYPE_NAME,mt.getType(),ns);
      me.setAttribute(DESCRIPTION,mt.getDescription(),ns);
      me.setAttribute(SEVERITY,String.valueOf(m.getSeverity()),ns);
      me.addContent(m.getMessage());           
      messageList.addContent(me);
    }
    return messageList;
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      p.println(outStr);

      if (fivePrime != null) {
        for (Iterator<Message> mi = ProbeMakerPropertyUtils.getAllMessages(fivePrime).iterator();mi.hasNext();) {
          Message m = mi.next();
          MessageType mt = m.getType();
          p.println(tio.getOutString(new String[] {mt.getType(),mt.getDescription(),m.getMessage(),String.valueOf(m.getSeverity())}));
        }
      }
      if (threePrime != null) {
        for (Iterator<Message> mi = ProbeMakerPropertyUtils.getAllMessages(threePrime).iterator();mi.hasNext();) {
          Message m = mi.next();
          MessageType mt = m.getType();
          p.println(tio.getOutString(new String[] {mt.getType(),mt.getDescription(),m.getMessage(),String.valueOf(m.getSeverity())}));
        }
      }
      for (Iterator<Message> mi = ProbeMakerPropertyUtils.getOwnMessages(pr.getTSSPair()).iterator();mi.hasNext();) {
        Message m = mi.next();
        MessageType mt = m.getType();
        p.println(tio.getOutString(new String[] {mt.getType(),mt.getDescription(),m.getMessage(),String.valueOf(m.getSeverity())}));
      }
      for (Iterator<Message> mi = ProbeMakerPropertyUtils.getOwnMessages(pr).iterator();mi.hasNext();) {
        Message m = mi.next();
        MessageType mt = m.getType();
        p.println(tio.getOutString(new String[] {mt.getType(),mt.getDescription(),m.getMessage(),String.valueOf(m.getSeverity())}));
      }
    }
    p.println(TITLE_DESCRIPTOR + LISTEND);

    increaseProgress();
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Related Classes of org.moltools.apps.probemaker.messages.MessageType

  • org.moltools.apps.probemaker.design.Analyzer
  • org.moltools.apps.probemaker.ProbeSummarizer
  • org.moltools.apps.probemaker.project.ProjectIOTask
  • org.moltools.apps.probemaker.project.ProjectXMLIOTask
  • org.moltools.apps.probemaker.test.DataStructureTest
  • org.moltools.apps.probemaker.test.TagAllocationTest
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