Class NCBIQBlastOutputProperties

    • Constructor Detail

      • NCBIQBlastOutputProperties

        public NCBIQBlastOutputProperties()
        This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:
         FORMAT_TYPE = XML;
         ALIGNMENT_VIEW = Pairwise;
         DESCRIPTIONS = 100;
         ALIGNMENTS = 100;
         
    • Method Detail

      • getOutputOption

        public java.lang.String getOutputOption​(BlastOutputParameterEnum key)
        Gets the value of specified parameter or null if it is not set
      • setOutputOption

        public void setOutputOption​(BlastOutputParameterEnum key,
                                    java.lang.String value)
        Sets the value of specified output parameter
      • getOutputOptions

        public java.util.Set<java.lang.String> getOutputOptions()
        Gets output parameters, which are currently set
        Specified by:
        getOutputOptions in interface RemotePairwiseAlignmentOutputProperties
        Returns:
        a Set with all keys held in this instance of the object
      • getOutputFormat

        public java.lang.String getOutputFormat()
        Returns:
        stream output format - a String with the value of key FORMAT_TYPE
      • setOutputFormat

        public void setOutputFormat​(BlastOutputFormatEnum formatType)
        Sets the stream output format to get from the QBlast service

        If HTML format is selected, also adds the following parameters (which are removed if another output format is chosen):

         NOHEADER = true;
         SHOW_OVERVIEW = false;
         SHOW_LINKOUT = false;
         
        Parameters:
        formatType - : one of the output format types defined in enum
      • getAlignmentOutputFormat

        public java.lang.String getAlignmentOutputFormat()
        Returns:
        alignment output format - a String with the value of key ALIGNMENT_VIEW
      • setAlignmentOutputFormat

        public void setAlignmentOutputFormat​(BlastOutputAlignmentFormatEnum alignmentFormat)
        Sets the alignment output format to get from the QBlast service
        Parameters:
        alignmentFormat - : one of available alignment types
      • getDescriptionNumber

        public int getDescriptionNumber()
        Returns:
        number of descriptions fetched - an int with the value of the key DESCRIPTIONS
      • setDescriptionNumber

        public void setDescriptionNumber​(int number)
        Sets the number of descriptions to fetch
        Parameters:
        number - : an int with the required number of descriptions to fetch
      • getAlignmentNumber

        public int getAlignmentNumber()
        Returns:
        number of alignments fetched - an int with the value of the key ALIGNMENTS
      • setAlignmentNumber

        public void setAlignmentNumber​(int number)
        Set the number of alignments to fetch
        Parameters:
        number - : an int with the required number of alignments to fetch