Class CharactersBlock

    • Constructor Detail

      • CharactersBlock

        public CharactersBlock()
        Delegates to NexusBlock.Abstract constructor using CharactersBlock.CHARACTERS_BLOCK as the name.
      • CharactersBlock

        protected CharactersBlock​(java.lang.String replacementLabel)
        For the DATA block subclass.
        Parameters:
        replacementLabel - the different label to use.
    • Method Detail

      • setDimensionsNTax

        public void setDimensionsNTax​(int dimensionsNTax)
        Set the NTAX value.
        Parameters:
        dimensionsNTax - the NTAX value.
      • getDimensionsNTax

        public int getDimensionsNTax()
        Get the NTAX value.
        Returns:
        the NTAX value.
      • setDimensionsNChar

        public void setDimensionsNChar​(int dimensionsNChar)
        Set the NCHAR value.
        Parameters:
        dimensionsNChar - the NCHAR value.
      • getDimensionsNChar

        public int getDimensionsNChar()
        Get the NCHAR value.
        Returns:
        the NCHAR value.
      • setDataType

        public void setDataType​(java.lang.String dataType)
      • setRespectCase

        public void setRespectCase​(boolean respectCase)
      • setMissing

        public void setMissing​(java.lang.String missing)
      • getMissing

        public java.lang.String getMissing()
      • setGap

        public void setGap​(java.lang.String gap)
      • getGap

        public java.lang.String getGap()
      • addSymbol

        public void addSymbol​(java.lang.String symbol)
      • removeSymbol

        public void removeSymbol​(java.lang.String symbol)
      • addEquate

        public void addEquate​(java.lang.String symbol,
                              java.util.List symbols)
      • removeEquate

        public void removeEquate​(java.lang.String symbol)
      • setMatchChar

        public void setMatchChar​(java.lang.String matchChar)
      • setLabels

        public void setLabels​(boolean labels)
      • setTransposed

        public void setTransposed​(boolean transposed)
      • setInterleaved

        public void setInterleaved​(boolean interleaved)
      • addItem

        public void addItem​(java.lang.String item)
      • removeItem

        public void removeItem​(java.lang.String item)
      • getItems

        public java.util.List getItems()
      • setStatesFormat

        public void setStatesFormat​(java.lang.String statesFormat)
      • setTokens

        public void setTokens​(boolean tokens)
      • addTaxLabel

        public void addTaxLabel​(java.lang.String taxLabel)
                         throws ParseException
        Add a TAXLABEL. If it already exists, or is a number that refers to an index position that already exists, an exception is thrown.
        Parameters:
        taxLabel - the label to add.
        Throws:
        ParseException - if the label cannot be added.
      • removeTaxLabel

        public void removeTaxLabel​(java.lang.String taxLabel)
        Removes the given TAXLABEL.
        Parameters:
        taxLabel - the label to remove.
      • containsTaxLabel

        public boolean containsTaxLabel​(java.lang.String taxLabel)
        Checks to see if we contain the given TAXLABEL.
        Parameters:
        taxLabel - the label to check for.
        Returns:
        true if we already contain it.
      • getTaxLabels

        public java.util.List getTaxLabels()
        Get the TAXLABEL values added so far.
        Returns:
        this labels so far.
      • addCharState

        public void addCharState​(java.lang.String charState)
      • setCharStateLabel

        public void setCharStateLabel​(java.lang.String charState,
                                      java.lang.String label)
      • addCharStateKeyword

        public void addCharStateKeyword​(java.lang.String charState,
                                        java.lang.String keyword)
      • getCharStateLabel

        public java.lang.String getCharStateLabel​(java.lang.String charState)
      • removeCharState

        public void removeCharState​(java.lang.String charState)
      • addCharLabel

        public void addCharLabel​(java.lang.String charLabel)
      • removeCharLabel

        public void removeCharLabel​(java.lang.String charLabel)
      • containsCharLabel

        public boolean containsCharLabel​(java.lang.String charLabel)
      • addState

        public void addState​(java.lang.String state)
      • addStateLabel

        public void addStateLabel​(java.lang.String state,
                                  java.lang.String label)
      • getStateLabels

        public java.util.List getStateLabels​(java.lang.String state)
      • removeState

        public void removeState​(java.lang.String state)
      • addMatrixEntry

        public void addMatrixEntry​(java.lang.String taxa)
      • appendMatrixData

        public void appendMatrixData​(java.lang.String taxa,
                                     java.lang.Object data)
      • getMatrixData

        public java.util.List getMatrixData​(java.lang.String taxa)
      • addComment

        public void addComment​(NexusComment comment)
        Adds a comment.
        Parameters:
        comment - the comment to add.
      • removeComment

        public void removeComment​(NexusComment comment)
        Removes a comment.
        Parameters:
        comment - the comment to remove.
      • getComments

        public java.util.List getComments()
        Returns all comments.
        Returns:
        all the selected comments.
      • writeBlockContents

        protected void writeBlockContents​(java.io.Writer writer)
                                   throws java.io.IOException
        Description copied from class: NexusBlock.Abstract
        Implement this to write out block contents, not including the BEGIN and END tags.
        Specified by:
        writeBlockContents in class NexusBlock.Abstract
        Parameters:
        writer - the writer to write to.
        Throws:
        java.io.IOException - if writing failed.