Package org.moltools.lib.seq.impl

Examples of org.moltools.lib.seq.impl.SimpleChangeableNucleotideSequence

340
341
342
343
344
345
346
347
348
349
350
    }

    if (tp == null || fp == null) throw new UnsupportedOperationException("Can't perform ligation calculations with missing TSSs"); //$NON-NLS-1$

    int[] results = isLigationTemplate(
        new SimpleChangeableNucleotideSequence(
            "TSS|"+p.getName(), //$NON-NLS-1$
            tp.seqString() + fp.seqString(),
            p.getType()
            ), p, false, false);
    if (results != 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
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
59
60
61
62
63
64
65
66
67
    super(new ListSequenceDB<NucleotideSequence>(), "Spacers"); //$NON-NLS-1$
    //The mode is set to be SAME so that the library look non-variable although it actually is,
    mode = TagLibrary.USE_SAME_TAG;
    nextIndices = new int[length];
    type = acidType;
    NucleotideSequence proto = new SimpleChangeableNucleotideSequence("Spacer","",NucleotideSequence.DNA); //$NON-NLS-1$ //$NON-NLS-2$

    addSequence(proto);
  }
View Full Code Here
341
342
343
344
345
346
347
348
349
350
351
    }
   
    if (tp == null || fp == null) throw new UnsupportedOperationException("Can't perform ligation calculations with missing TSSs"); //$NON-NLS-1$
   
    int[] results = isLigationTemplate(
        new SimpleChangeableNucleotideSequence(
            "TSS|"+p.getName(), //$NON-NLS-1$
            tp.seqString() + fp.seqString(),
            p.getType()
        ), p, false, false);
    if (results != null) {
View Full Code Here
TOP

Related Classes of org.moltools.lib.seq.impl.SimpleChangeableNucleotideSequence

  • org.moltools.apps.probemaker.calculators.PadlockLigationCalculator
  • org.moltools.apps.probemaker.design.SpacerLibrary
  • org.moltools.apps.probemaker.seq.impl.DefaultProbe
    • 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.