Package org.nexml.model

Examples of org.nexml.model.CharacterState

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    Set<CharacterState> xmlMissingStates = new HashSet<CharacterState>();
    for ( Character symbol : stateForSymbol.keySet() ) {
      char sym = symbol.charValue();     
      if ( sym != '-' && sym != '?' ) {
        String symString = symbol.toString();
        CharacterState xmlState = xmlStateSet.createCharacterState(symString);
        xmlMissingStates.add(xmlState);
        DiscreteCharState tbState = stateForSymbol.get(symbol);
        xmlState.setLabel(symString);
        attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);       
      }       
    }
   
    // the missing symbol ("?") includes all others, including gap ("-")
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    // lookup the equivalent state in tb and attach identifiers
    for(StateSet tbStateSet : tbMatrix.getStateSets() ) {
      for (DiscreteCharState tbState : tbStateSet.getStates() ) {
        String tbSymbol = tbState.getSymbol().toString().toUpperCase();
        CharacterState xmlState = xmlStateSet.lookupCharacterStateBySymbol(tbSymbol);
        if ( null == xmlState ) {
          xmlState = xmlStateSet.createCharacterState(tbSymbol);
        }
        attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
      }
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    for ( MatrixColumn tbColumn : ((CharacterMatrix)tbMatrix).getColumns() ) {
     
      org.nexml.model.Character xmlCharacter = xmlCharacterList.get(charIndex);
      MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);
      String value = "" + seq.charAt(charIndex);
      CharacterState xmlState = xmlMatrix.parseSymbol(value);
      xmlCell.setValue(xmlState);
      attachTreeBaseID ((Annotatable) xmlCell,  tbColumn , DiscreteMatrixElement.class);
     
      for ( RowSegment tbSegment : tbSegments ) {
        if ( tbSegment.getStartIndex() <= charIndex && charIndex <= tbSegment.getEndIndex() ) {
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Related Classes of org.nexml.model.CharacterState

  • org.cipres.treebase.domain.nexus.nexml.NexmlMatrixWriter
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