Package org.moltools.design.data

Examples of org.moltools.design.data.PropertyAcceptorNucleotideSequence

75
76
77
78
79
80
81
82
83
84
85
86
87
88
    task.run();
   
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
   
    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
    PropertyAcceptorNucleotideSequence tss3 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_THREE_PRIME);
   
    String seq5 = tss5.seqString();
    String seq3 = tss3.seqString();
   
    assertTrue("5' arm sequence failed, expected '" + expect5 + "', got: '" + seq5 + "'", seq5.equals(expect5)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    assertTrue("3' arm sequence failed, expected '" + expect3 + "', got: '" + seq3 + "'", seq3.equals(expect3));        //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
  }
View Full Code Here
77
78
79
80
81
82
83
84
85
86
87
88
89
90
    task.run();
   
    Probe p = proj.getProbes().getSequenceAt(0);
    TSSPair pair = p.getTSSPair();
   
    PropertyAcceptorNucleotideSequence tss5 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_FIVE_PRIME);
    PropertyAcceptorNucleotideSequence tss3 = (PropertyAcceptorNucleotideSequence) pair.getSequence(TSSPair.KEY_THREE_PRIME);
   
    String seq5 = tss5.seqString();
    String seq3 = tss3.seqString();
   
    assertTrue("5' arm sequence failed, expected '" + expect5 + "', got: '" + seq5 + "'", seq5.equals(expect5)); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    assertTrue("3' arm sequence failed, expected '" + expect3 + "', got: '" + seq3 + "'", seq3.equals(expect3));        //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
  }
View Full Code Here
35
36
37
38
39
40
41
42
43
/**Factory class for creating certain kinds of ProbeMaker-specific sequence types*/
public class ProbeMakerSequenceFactory {
 
  public static PropertyAcceptorNucleotideSequence createTSS(NucleotideSequence seq, String targetID) {
    PropertyAcceptorNucleotideSequence tss = new DefaultChangeablePropertyNucleotideSequence(seq.getID(),seq.seqString(),seq.getType());       
    tss.getMutablePropertySet().setProperty(new SimpleProperty(Targetted.KEY_TARGET_ID,targetID,false));
    return tss;
  }
View Full Code Here
91
92
93
94
95
96
97
98
99
100
101
102
    html.append(SwingUIMessages.getString("ProbeSummaryViewFactory.TEXT_HEADER_QUALITY")); //$NON-NLS-1$
    html.append("</TH>\n</TR>\n"); //$NON-NLS-1$
    //Each row
    for (Iterator<? extends Probe> i = probes.iterator(); i.hasNext(); ) {
      Probe p = i.next();
      PropertyAcceptorNucleotideSequence fivePrime;
      PropertyAcceptorNucleotideSequence threePrime;
      try {
        fivePrime = (PropertyAcceptorNucleotideSequence) p.getTSSPair().getSequence(TSSPair.KEY_FIVE_PRIME);
      }
      catch (ClusterException e) {
        fivePrime = null;
View Full Code Here
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
        List<SimpleChangeableNucleotideSequence> tags = new ArrayList<SimpleChangeableNucleotideSequence>();
        StringTokenizer st = new StringTokenizer(seqstr, "|"); //$NON-NLS-1$
        while (st.hasMoreTokens()) {
          l.add(st.nextToken());
        }
        PropertyAcceptorNucleotideSequence tss5 = ProbeMakerSequenceFactory.createTSS(new SimpleChangeableNucleotideSequence("5' TSS", l.get(0),NucleotideSequence.DNA, "5' TSS"),null); //$NON-NLS-1$
        for (int i = 1; i < l.size() - 1; i++) {
          tags.add(new SimpleChangeableNucleotideSequence(id+"|Tag " + i,  //$NON-NLS-1$
              l.get(i), NucleotideSequence.DNA,  "Tag " + i)); //$NON-NLS-1$
        }
        PropertyAcceptorNucleotideSequence tss3 = ProbeMakerSequenceFactory.createTSS(new SimpleChangeableNucleotideSequence("3' TSS", l.get(l.size() - 1), NucleotideSequence.DNA,"3' TSS"),null); //$NON-NLS-1$
        Probe p = new DefaultProbe(ProbeMakerSequenceFactory.createTSSPair(tss5, tss3, null),0,0,NucleotideSequence.DNA);
        for (int i = 0;i<tags.size();i++) {
          p.addTagAt(tags.get(i),i); 
        }
       
View Full Code Here
117
118
119
120
121
122
123
124
125
126
127
128
129
    byte probeAcidType = Byte.parseByte(parameters.get(ProbeDesigner.PROP_PROBE_ACID_TYPE));
   
//  Generate the 5' TSS
    setStatus("Constructing 5' TSS"); //$NON-NLS-1$
    PropertyAcceptorNucleotideSequence tss5 = tssConstructor.get5PrimeTSS(target, probeAcidType);
//  Generate the 3' TSS
    setStatus("Constructing 3' TSS"); //$NON-NLS-1$
    PropertyAcceptorNucleotideSequence tss3 = tssConstructor.get3PrimeTSS(target, probeAcidType);
   
//  Build the pair
    return ProbeMakerSequenceFactory.createTSSPair(tss5,tss3,target);    
  }
View Full Code Here
35
36
37
38
39
40
41
42
43
/**Factory class for creating certain kinds of ProbeMaker-specific sequence types*/
public class ProbeMakerSequenceFactory {
 
  public static PropertyAcceptorNucleotideSequence createTSS(NucleotideSequence seq, String targetID) {
    PropertyAcceptorNucleotideSequence tss = new DefaultChangeablePropertyNucleotideSequence(seq.getID(),seq.seqString(),seq.getType());       
    tss.getMutablePropertySet().setProperty(new SimpleProperty(Targetted.KEY_TARGET_ID,targetID,false));
    return tss;
  }
View Full Code Here
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
    tssPairE.setAttribute(TARGET_ID, targetID == null ? "" : targetID ,ns); //$NON-NLS-1$
    Collection<String> tssIDs = new HashSet<String>();
    for (Iterator<String> i2 = tssPair.getKeys().iterator();i2.hasNext();) {
      String key = i2.next();               
      try {
        PropertyAcceptorNucleotideSequence tss = (PropertyAcceptorNucleotideSequence) tssPair.getSequence(key);
        if (tss != null) {
          Element seqE = new Element(TSS,ns);
          seqE.setAttribute("key",key,ns); //$NON-NLS-1$
          seqE.setAttribute(ID,tss.getID(),ns);
          tssIDs.add(tss.getID());
          seqE.addContent(new Element(TYPE,ns).addContent(String.valueOf(tss.getType())));
          seqE.addContent(new Element(SEQUENCE,ns).addContent(tss.seqString()));
          seqE.addContent(new Element(TM,ns).addContent(String.valueOf(ProbeMakerPropertyUtils.getHybridizationTemp(tss))));
          seqE.addContent(getMessageListElement(ProbeMakerPropertyUtils.getAllMessages(tss)));                   
          tssPairE.addContent(seqE);
        }         
      }
View Full Code Here
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
        String key = tssE.getAttributeValue("key",ns);         //$NON-NLS-1$
        String tssID = tssE.getAttributeValue(ID,ns);
        String tssTypeStr = tssE.getChildText(TYPE,ns);
        String tssSeqStr = tssE.getChildText(SEQUENCE,ns);
        String tmStr = tssE.getChildText(TM,ns);
        PropertyAcceptorNucleotideSequence tss = ProbeMakerSequenceFactory.createTSS(
            new SimpleNucleotideSequence(tssID, tssSeqStr, Byte.parseByte(tssTypeStr)),
            targetID);
        ProbeMakerPropertyUtils.setHybridizationTemp(tss,Float.parseFloat(tmStr));       
        addMessagesFromElement(tss,tssE.getChild("messageList",ns)); //$NON-NLS-1$
        tssMap.put(key,tss);       
      } 

      PropertyAcceptorNucleotideSequence five = null;
      PropertyAcceptorNucleotideSequence three = null;
      five = tssMap.get(TSSPair.KEY_FIVE_PRIME);
      three = tssMap.get(TSSPair.KEY_THREE_PRIME);     
      TSSPair tssP = ProbeMakerSequenceFactory.createTSSPair(five,three,target);
      addMessagesFromElement(tssP,tssPairE.getChild("messageList",ns)); //$NON-NLS-1$
View Full Code Here
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
        List<SimpleChangeableNucleotideSequence> tags = new ArrayList<SimpleChangeableNucleotideSequence>();
        StringTokenizer st = new StringTokenizer(seqstr, "|"); //$NON-NLS-1$
        while (st.hasMoreTokens()) {
          l.add(st.nextToken());
        }
        PropertyAcceptorNucleotideSequence tss5 = ProbeMakerSequenceFactory.createTSS(new SimpleChangeableNucleotideSequence("5' TSS", l.get(0),NucleotideSequence.DNA, "5' TSS"),null); //$NON-NLS-1$
        for (int i = 1; i < l.size() - 1; i++) {
          tags.add(new SimpleChangeableNucleotideSequence(id+"|Tag " + i,  //$NON-NLS-1$
              l.get(i), NucleotideSequence.DNA,  "Tag " + i)); //$NON-NLS-1$
        }
        PropertyAcceptorNucleotideSequence tss3 = ProbeMakerSequenceFactory.createTSS(new SimpleChangeableNucleotideSequence("3' TSS", l.get(l.size() - 1), NucleotideSequence.DNA,"3' TSS"),null); //$NON-NLS-1$
        Probe p = new DefaultProbe(ProbeMakerSequenceFactory.createTSSPair(tss5, tss3, null),0,0,NucleotideSequence.DNA);
        for (int i = 0;i<tags.size();i++) {
          p.addTagAt(tags.get(i),i); 
        }
       
View Full Code Here
TOP

Related Classes of org.moltools.design.data.PropertyAcceptorNucleotideSequence

  • org.moltools.apps.probemaker.design.Analyzer
  • org.moltools.apps.probemaker.design.DefaultTSSPairDesigner
  • org.moltools.apps.probemaker.ext.mod.DefaultHybInterferenceModule
  • org.moltools.apps.probemaker.ext.pof.HTMLOutputFormat
  • org.moltools.apps.probemaker.ext.tc.DefaultTSSConstructor
  • org.moltools.apps.probemaker.project.ProjectIOTask
  • org.moltools.apps.probemaker.project.ProjectXMLIOTask
  • org.moltools.apps.probemaker.seq.impl.DefaultProbe
  • org.moltools.apps.probemaker.seq.ProbeMakerSequenceFactory
  • org.moltools.apps.probemaker.swingui.ProbeSummaryViewFactory
    • 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.