compbio.ws.client

Class IOHelper

java.lang.Object

compbio.ws.client.IOHelper

public class IOHelper
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
IOHelper()

Method Summary

Modifier and Type	Method and Description
(package private) static java.io.File	getFile(java.lang.String[] cmd, java.lang.String key, boolean mustExist) Checks -i options and return the File if one was provided, null otherwise
(package private) static java.io.Writer	getWriter(java.io.File file)
(package private) static java.util.List<java.lang.String>	loadParameters(java.io.File paramsfile) Load parameters from file
(package private) static void	writeOut(java.io.Writer writer, Alignment align) Outputs clustal formatted alignment into the file represented by the outStream
(package private) static void	writeOut(java.io.Writer writer, ScoreManager results) Outputs AAcon results into the file represented by the outStream

Methods inherited from class java.lang.Object

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

Constructor Detail

IOHelper

public IOHelper()

Method Detail

getFile

static java.io.File getFile(java.lang.String[] cmd,
                            java.lang.String key,
                            boolean mustExist)
                     throws java.io.IOException

Checks -i options and return the File if one was provided, null otherwise

Parameters:

cmd -

key -

mustExist -

Returns:

Throws:

java.io.IOException

loadParameters

static java.util.List<java.lang.String> loadParameters(java.io.File paramsfile)
                                                throws java.io.IOException

Load parameters from file

Throws:

java.io.IOException

getWriter

static java.io.Writer getWriter(java.io.File file)
                         throws java.io.IOException

Throws:

java.io.IOException

writeOut

static void writeOut(java.io.Writer writer,
                     Alignment align)

Outputs clustal formatted alignment into the file represented by the outStream

Parameters:

outStream -

align - the alignment to output

writeOut

static void writeOut(java.io.Writer writer,
                     ScoreManager results)

Outputs AAcon results into the file represented by the outStream

Parameters:

outStream -

result - the AACon scores to output