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

Package org.moltools.apps.probemaker.messages

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

org.moltools.apps.probemaker.messages.Message
Description: A class that represents a message appended to a MessageHolder. A message specifies a message type, a severity, and contains a message string @author Johan Stenberg @version 1.0

      
      float percentGC = ((Float) prop.getValue()).floatValue();
      
      if (percentGC > maxGC) {
        
          ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(
            "%GC content in target is too high, " + Math.round(percentGC) + "% (Max set to " + maxGC + "%)", //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
            GC_CONTENT, Message.ERROR));
        
      } else if (percentGC < minGC) {
        
          ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(
            "%GC content in target is too low, " + Math.round(percentGC) + "%  (Min set to " + minGC + "%)", //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
            GC_CONTENT, Message.ERROR));
      }
    }
  }

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  }


  public void doAnalysis(Probe p, TagAllocator pd, DefiniteSequenceDB<? extends Probe> probes) {
    if (tests[0].perform()) {
      if (p.getTags().size() < pd.getTagLibraries().length) {
        ProbeMakerPropertyUtils.addMessage(p,new Message(
            "Probe does not contain all tags", //$NON-NLS-1$
            TagAllocator.TAG_ALLOCATION,
            Message.FATAL));
      }
    }

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        Probe other = i.next();
        //If other is not yet allocated, this will be found when checking other's arms
        if (other != p && other.tagsAllocated()) {
          boolean dimer = dimer(p,other);
          if (dimer)
            ProbeMakerPropertyUtils.addMessage(other,new Message("High risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                PROBE_HETERODIMER_FORMATION, Message.ERROR));
          /*else if (dimer == RISK) 
            other.addMessage(new Message("Risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                 PROBE_HETERODIMER_FORMATION, Message.WARNING));*/
          Analyzer.calculateAndSetQuality(other);

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        Probe other = probeit.next();
        //Don't do anything if other is same as probe being analysed
        if (other != p && other.tagsAllocated()) {
          boolean dimer = dimer(p,other);
          if (dimer)
            ProbeMakerPropertyUtils.addMessage(p,new Message("High risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                PROBE_HETERODIMER_FORMATION, Message.ERROR));
          /*else if (dimer == RISK) 
            p.addMessage(new Message("Risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                 PROBE_HETERODIMER_FORMATION, Message.WARNING));
           */

View Full Code Here

      root.addContent(CoreMessages.getString("ProbeMakerHTMLRenderer.TEXT_NO_MESSAGES"));  //$NON-NLS-1$
    }
    else {                      
      Element list = new Element(HTMLWriter.UL.getTag());    
      for (Iterator<Message> i = messages.iterator(); i.hasNext(); ) {
        Message m = i.next();
        Element li = new Element(HTMLWriter.LI.getTag());
        Element font = new Element(HTMLWriter.FONT.getTag());
        font.setAttribute(HTMLWriter.COLOR.getTag(),fontColorStrings[m.getSeverity()]);
        font.addContent(Message.messageSeverityDescriptions[m.getSeverity()]);
        li.addContent(font);
        li.addContent(": " + m.getMessage()); //$NON-NLS-1$
        list.addContent(li);
      }
      
      root.addContent(list);
    }

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      for (Iterator<? extends Probe> i = probes.iterator(); i.hasNext(); ) {
        Probe other = i.next();
        //If other is not yet allocated, this will be found when checking other's arms
        if (other != p && other.tagsAllocated()) {
          if (ltc.isLigationTemplate(p, other, true, false) != null) {
            ProbeMakerPropertyUtils.addMessage(other,new Message("May be templated by " + //$NON-NLS-1$
                p.getName(),
                PadlockLigationCalculator.
                OTHER_PROBE_IS_TEMPLATE,
                Message.ERROR));
            Analyzer.calculateAndSetQuality(other);

View Full Code Here

        Probe other = probeit.next();
        //Don't do anything if other is same as probe being analysed
        if (!other.equals(p) && other.tagsAllocated()) {
          byte dimer = compare(p,other);
          if (dimer == HI_RISK)
            ProbeMakerPropertyUtils.addMessage(p,new Message("High risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                PROBE_DIMER_FORMATION, Message.ERROR));
          else if (dimer == RISK) 
            ProbeMakerPropertyUtils.addMessage(p,new Message("Risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                 PROBE_DIMER_FORMATION, Message.WARNING));


        }
      }      
    }
    if (tests[1].perform()) {
      byte dimer = compare(p,p);
      if (dimer == HI_RISK)
        ProbeMakerPropertyUtils.addMessage(p,new Message("High risk of homo-dimer formation", //$NON-NLS-1$
            PROBE_DIMER_FORMATION, Message.ERROR));
      else if (dimer == RISK) 
        ProbeMakerPropertyUtils.addMessage(p,new Message("Risk of homo-dimer formation", //$NON-NLS-1$
            PROBE_DIMER_FORMATION, Message.WARNING));                 
    }    
  }

View Full Code Here

        Probe other = i.next();
        //If other is not yet allocated, this will be found when checking other's arms
        if (!other.equals(p) && other.tagsAllocated()) {
          byte dimer = compare(p,other);
          if (dimer == HI_RISK)
            ProbeMakerPropertyUtils.addMessage(other,new Message("High risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                PROBE_DIMER_FORMATION, Message.ERROR));
          else if (dimer == RISK) 
            ProbeMakerPropertyUtils.addMessage(other,new Message("Risk of hetero-dimer formation with " + other.getName(), //$NON-NLS-1$
                 PROBE_DIMER_FORMATION, Message.WARNING));
          Analyzer.calculateAndSetQuality(other);          
        }
      }
    }

View Full Code Here

      }
    }
    else { //TSS pair not accepted
      log.info("TSS pair not accepted"); //$NON-NLS-1$


      ProbeMakerPropertyUtils.addMessage(p,new Message(
          "Skipped probe because of problems with TSS pair",  //$NON-NLS-1$
          TAG_ALLOCATION, Message.FATAL));
      htmllog.printLine("TSS pair not accepted - Skipping probe"); //$NON-NLS-1$
      htmllog.printList(ProbeMakerPropertyUtils.getAllMessages(p));
      ProbeMakerPropertyUtils.setRank(p, BAD_QUALITY);

View Full Code Here


  /**Called when all variations of a probe have been tested. Clears the tags of the probe,
   * adds a fatal internal message and calculates the quality*/
  protected void badProbe(Probe p) {
    clear(p);
    ProbeMakerPropertyUtils.addMessage(p,new Message("Tested all variations, none accepted", //$NON-NLS-1$
        TAG_ALLOCATION, Message.FATAL));
    ProbeMakerPropertyUtils.setRank(p, BAD_QUALITY);
  }

View Full Code Here

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Related Classes of org.moltools.apps.probemaker.messages.Message

org.moltools.apps.probemaker.calculators.GapLigationCalculator

org.moltools.apps.probemaker.calculators.PadlockLigationCalculator

org.moltools.apps.probemaker.design.Analyzer

org.moltools.apps.probemaker.ext.mod.DefaultHybInterferenceModule

org.moltools.apps.probemaker.ext.mod.DefaultTagOccurrenceModule

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

org.moltools.apps.probemaker.ext.mod.DummyModule

org.moltools.apps.probemaker.ext.mod.FalsePrimingModule

org.moltools.apps.probemaker.ext.mod.GapFillPadlockLigationModule

org.moltools.apps.probemaker.ext.mod.GCContentModule

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