procope.evaluation.complexquality.go
Class GOAnnotationReader

java.lang.Object
  extended by procope.evaluation.complexquality.go.GOAnnotationReader

public class GOAnnotationReader
extends Object

Contains static methods to read annotations from a GO annotations file.

This class is not instantiatable.

Author:
Jan Krumsiek
See Also:
GOAnnotations

Method Summary
static GOAnnotations readAnnotations(File annotationFile)
          Reads annotations from a given annotations file.
static GOAnnotations readAnnotations(File annotationFile, int useColumn)
          Reads annotations from a given annotations file.
static GOAnnotations readAnnotations(InputStream annotation)
          Reads annotations from a given input stream.
static GOAnnotations readAnnotations(InputStream annotations, int useColumn)
          Reads annotations from a given input stream.
static GOAnnotations readAnnotations(String annotationFile)
          Reads annotations from a given annotations file.
static GOAnnotations readAnnotations(String annotationFile, int useColumn)
          Reads annotations from a given annotations file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Method Detail

readAnnotations

public static GOAnnotations readAnnotations(String annotationFile)
                                     throws IOException
Reads annotations from a given annotations file. The protein identifiers will be parsed from the second column of that tab-delimited file.

Parameters:
annotationFile - annotations file to be read
Returns:
the annotations read from the file
Throws:
IOException - if the file could not be read

readAnnotations

public static GOAnnotations readAnnotations(String annotationFile,
                                            int useColumn)
                                     throws IOException
Reads annotations from a given annotations file.

Parameters:
annotationFile - annotations file to be read
useColumn - read protein identifiers from this column, you might want to use regular expressions
Returns:
the annotations read from the file
Throws:
IOException - if the file could not be read

readAnnotations

public static GOAnnotations readAnnotations(File annotationFile)
                                     throws IOException
Reads annotations from a given annotations file. The protein identifiers will be parsed from the second column of that tab-delimited file.

Parameters:
annotationFile - annotations file to be read
Returns:
the annotations read from the file
Throws:
IOException - if the file could not be read

readAnnotations

public static GOAnnotations readAnnotations(File annotationFile,
                                            int useColumn)
                                     throws IOException
Reads annotations from a given annotations file.

Parameters:
annotationFile - annotations file to be read
useColumn - read protein identifiers from this column, you might want to use regular expressions
Returns:
the annotations read from the file
Throws:
IOException - if the file could not be read

readAnnotations

public static GOAnnotations readAnnotations(InputStream annotation)
Reads annotations from a given input stream. The protein identifiers will be parsed from the second column of the tab-delimited data.

Parameters:
annotation - input stream from which the annotation data will be read
Returns:
the annotations read from the stream

readAnnotations

public static GOAnnotations readAnnotations(InputStream annotations,
                                            int useColumn)
Reads annotations from a given input stream.

Parameters:
annotations - input stream from which the annotation data will be read
useColumn - read protein identifiers from this column, you might want to use regular expressions
Returns:
the annotations read from the stream