Package org.moltools.apps.probemaker.messages

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

64
65
66
67
68
69
70
71
72
73
74
  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()); //$NON-NLS-1$
View Full Code Here
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
  }

  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()); //$NON-NLS-1$

  }
View Full Code Here
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
  }

  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()); //$NON-NLS-1$

  }
View Full Code Here
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
      //UITexts for 5' TSS
      for (int mess = 0;mess < messageCount5;mess++) {
        String[] messageLine = tio.getInStrings(r.readLine());
        if (messageLine.length != 4)
          throw new UnsupportedOperationException("Error parsing message line: " + messageLine); //$NON-NLS-1$
        MessageType mt = new MessageType(messageLine[0],messageLine[1]);
        ProbeMakerPropertyUtils.addMessage(tss5,new Message(messageLine[2],mt,Byte.parseByte(messageLine[3])));
      }

      //UITexts for 3' TSS
      for (int mess = 0;mess < messageCount3;mess++) {
        String[] messageLine = tio.getInStrings(r.readLine());
        if (messageLine.length != 4)
          throw new UnsupportedOperationException("Error parsing message line: " + messageLine); //$NON-NLS-1$
        MessageType mt = new MessageType(messageLine[0],messageLine[1]);
        ProbeMakerPropertyUtils.addMessage(tss3,new Message(messageLine[2],mt,Byte.parseByte(messageLine[3])));
      }

      //UITexts for TSS Pair
      for (int mess = 0;mess < messageCountTSS;mess++) {
        String[] messageLine = tio.getInStrings(r.readLine());
        if (messageLine.length != 4)
          throw new UnsupportedOperationException("Error parsing message line: " + messageLine); //$NON-NLS-1$
        MessageType mt = new MessageType(messageLine[0],messageLine[1]);
        ProbeMakerPropertyUtils.addMessage(p.getTSSPair(),new Message(messageLine[2],mt,Byte.parseByte(messageLine[3])));
      }

      //UITexts for Probe
      for (int mess = 0;mess < messageCountProbe;mess++) {
        String[] messageLine = tio.getInStrings(r.readLine());
        if (messageLine.length != 4)
          throw new UnsupportedOperationException("Error parsing message line: " + messageLine); //$NON-NLS-1$
        MessageType mt = new MessageType(messageLine[0],messageLine[1]);
        ProbeMakerPropertyUtils.addMessage(p,new Message(messageLine[2],mt,Byte.parseByte(messageLine[3])));
      }

      proj.getProbes().addSequence(p);
    }
View Full Code Here
361
362
363
364
365
366
367
368
369
370
371


  /**(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) {
View Full Code Here
TOP

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
    • 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.