List of addSpan() Examples

Examples of addSpan()

Examples of com.affymetrix.genometryImpl.symmetry.SimpleSymWithProps.addSpan()

      throw new NullPointerException("Conflict with start and end in processCDS.");
    }


        result = new SimpleSymWithProps();


        result.addSpan(gend_point);
        SeqUtils.transformSymmetry((MutableSeqSymmetry) result, m2gPath);
        SeqSpan mend_point = result.getSpan(mrna);


    if(mend_point == null) {
      throw new NullPointerException("Conflict with start and end in processCDS.");

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Examples of com.affymetrix.genometryImpl.symmetry.TypeContainerAnnot.addSpan()

        hitSym.setProperty("num_spans", prop);
        hitSym.setProperty(TYPESTR, "simHit");
    hitSym.setProperty(AA_START, String.valueOf(aa_start));
    hitSym.setProperty(AA_END, String.valueOf(aa_end));
    hitSym.setProperty(AA_LENGTH, String.valueOf(aa_end - aa_start));
        hitSym.addSpan(hitSpan);
        hitSym.setID("");
        query_seq.addAnnotation(hitSym);
    }


    /**

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Examples of com.affymetrix.genometryImpl.symmetry.TypeContainerAnnot.addSpan()

        }
        NodeList children = elem.getChildNodes();
        SeqSpan span = new SimpleSeqSpan(start, end, genomic);


        TypeContainerAnnot m2gSym = new TypeContainerAnnot(elem.getAttribute("method"));
        m2gSym.addSpan(span);
        addDescriptors(elem, m2gSym);
        m2gSym.setProperty(TYPESTR, "mRNA");
        boolean forward = (span.isForward());

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Examples of com.affymetrix.genometryImpl.symmetry.TypeContainerAnnot.addSpan()

        prot_hash.put(protein_id, protein);
        SeqSpan pspan = new SimpleSeqSpan(protein.getMin(), protein.getMax(), protein); 
        if (DEBUG) {
            System.err.println("protein: length = " + pspan.getLength());
        }
        m2pSym.addSpan(mspan);
        m2pSym.addSpan(pspan);


        m2pSym.setID("");
        protein.addAnnotation(m2pSym);
        mrna.addAnnotation(m2pSym);

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Examples of com.affymetrix.genometryImpl.symmetry.TypeContainerAnnot.addSpan()

        SeqSpan pspan = new SimpleSeqSpan(protein.getMin(), protein.getMax(), protein); 
        if (DEBUG) {
            System.err.println("protein: length = " + pspan.getLength());
        }
        m2pSym.addSpan(mspan);
        m2pSym.addSpan(pspan);


        m2pSym.setID("");
        protein.addAnnotation(m2pSym);
        mrna.addAnnotation(m2pSym);

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Examples of edu.stanford.nlp.sempre.LanguageInfo.addSpan()

      nextNodes.add(nextTrie);
  }


  private RuleApplication generateApplications(LanguageInfo antecedent, int i, int j, List<WordInfo> rhsMatch, SubstitutableSyntacticRule rule) {
    LanguageInfo consequent = new LanguageInfo();
    consequent.addSpan(antecedent, 0, i);
    consequent.addWordInfos(rhsMatch);
    consequent.addSpan(antecedent, j, antecedent.numTokens());
    RuleApplication application = new RuleApplication(antecedent, consequent, new ApplicationInfo(SYNT_SUBST, rule.toString()));
    FeatureVector fv = new FeatureVector();
    fv.add(SYNT_SUBST, rule.toString());

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Examples of edu.stanford.nlp.sempre.LanguageInfo.addSpan()


  private RuleApplication generateApplications(LanguageInfo antecedent, int i, int j, List<WordInfo> rhsMatch, SubstitutableSyntacticRule rule) {
    LanguageInfo consequent = new LanguageInfo();
    consequent.addSpan(antecedent, 0, i);
    consequent.addWordInfos(rhsMatch);
    consequent.addSpan(antecedent, j, antecedent.numTokens());
    RuleApplication application = new RuleApplication(antecedent, consequent, new ApplicationInfo(SYNT_SUBST, rule.toString()));
    FeatureVector fv = new FeatureVector();
    fv.add(SYNT_SUBST, rule.toString());
    fv.add(SYNT_SUBST, "score" ,rule.count);
    application.addFeatures(fv);

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Examples of edu.stanford.nlp.sempre.LanguageInfo.addSpan()

      if(obj instanceof WordInfo) {
        res.addWordInfo(((WordInfo) obj));
      }
      else if(obj instanceof Integer) {
        Interval matchingInterval = match.get(((Integer) obj));
        res.addSpan(antecedent, matchingInterval.start, matchingInterval.end);
      }
      else
        throw new RuntimeException("Rhs should be a list of wordinfo or integer keys to intervals only");
    }
    RuleApplication application = new RuleApplication(antecedent, res, new ApplicationInfo(RULE,""));

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Examples of edu.stanford.nlp.sempre.LanguageInfo.addSpan()

      if(obj instanceof WordInfo) {
        res.addWordInfo(((WordInfo) obj));
      }
      else if(obj instanceof Integer) {
        Interval matchingInterval = match.get(((Integer) obj));
        res.addSpan(antecedent, matchingInterval.start, matchingInterval.end);
      }
      else
        throw new RuntimeException("Rhs should be a list of wordinfo or integer keys to intervals only");
    }
    RuleApplication application = new RuleApplication(antecedent, res,new ApplicationInfo(DELETE,

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Examples of edu.stanford.nlp.sempre.LanguageInfo.addSpan()

    for(Interval targetInterval: targetIntervals) {
      LanguageInfo consequent = new LanguageInfo();
      for(int i = 0; i < 3; ++i) {
        if(i==0 || i==2) {
          Interval matchingInterval = match.get(i);
          consequent.addSpan(antecedent, matchingInterval.start, matchingInterval.end);
        }
        else { //i==1
          consequent.addSpan(target, targetInterval.start, targetInterval.end);
        }
      }

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