compbio.conservation

Class ConservationFormatter

java.lang.Object

compbio.conservation.ConservationFormatter

public final class ConservationFormatter
extends java.lang.Object

Conservation calculation results writer. A helper class for outputting the conservation results.

Author:

Agnieszka Golicz & Peter Troshin

Constructor Summary

Constructors

Constructor and Description
ConservationFormatter()

Method Summary

Modifier and Type	Method and Description
static void	formatResults(java.util.Map<compbio.data.sequence.ConservationMethod,double[]> scores, java.io.OutputStream outStream) Use this method to save the conservation results into a file.
static void	formatResults(java.util.Map<compbio.data.sequence.ConservationMethod,double[]> scores, java.lang.String outFilePath, Format format, java.util.List<compbio.data.sequence.FastaSequence> alignment) Formats and prints results.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ConservationFormatter

public ConservationFormatter()

Method Detail

formatResults

public static void formatResults(java.util.Map<compbio.data.sequence.ConservationMethod,double[]> scores,
                                 java.lang.String outFilePath,
                                 Format format,
                                 java.util.List<compbio.data.sequence.FastaSequence> alignment)
                          throws java.io.IOException

Formats and prints results. If you do not need to output the alignment please use the other method formatResults(Map, OutputStream)

Parameters:

scores - the results on the calculation, the Map with Method keys and double[] values.

outFilePath - the path to the output file. Optional. If null System.out is used.

format - the output format. Optional. Defaults to Format.RESULT_NO_ALIGNMENT

alignment - the alignment for which score was calculated

Throws:

java.io.IOException - if the file cannot be written/created for whatever reason.

java.lang.NullPointerException - if the alignment is null

formatResults

public static void formatResults(java.util.Map<compbio.data.sequence.ConservationMethod,double[]> scores,
                                 java.io.OutputStream outStream)

Use this method to save the conservation results into a file. The call to this method produce the same results as formatResults(Map, String, Format, List) where the first parameter is scores, the second is a name of the file, third if Format.RESULT_NO_ALIGNMENT and the fourth is null.

Parameters:

scores - the results of the calculation - the Map

outStream - the stream to write the results to. Please note that the method leaves this stream open. It is up to the caller to close it!