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java.lang.Objectprocope.data.complexes.ComplexSetReader
public class ComplexSetReader
This class contains static methods to read complexes from files or streams. It is not instantiatable.
A complex set file contains one complex per line. Each complex consists
of a list of proteins seperated by a separator character. Protein
identifiers will be mapped to internal integer IDs (see also:
ProteinManager
)
Complex
,
ComplexSet
Field Summary | |
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static String |
DEFAULT_SEPARATOR
Default separator which seperates the proteins of a complex: TAB |
Method Summary | |
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static ComplexSet |
readComplexes(File file)
Reads complexes from a given file. |
static ComplexSet |
readComplexes(File file,
String separator)
Reads complexes from a given file. |
static ComplexSet |
readComplexes(InputStream input)
Reads complexes from a given InputStream. |
static ComplexSet |
readComplexes(InputStream input,
String separator)
Reads complexes from a given InputStream. |
static ComplexSet |
readComplexes(String file)
Reads complexes from a given file. |
static ComplexSet |
readComplexes(String file,
String separator)
Reads complexes from a given file. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String DEFAULT_SEPARATOR
Method Detail |
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public static ComplexSet readComplexes(String file) throws IOException, ProCopeException
file
- path to the file which contains the complexes
IOException
- on input/output errors
ProCopeException
- if the file could not be parsedpublic static ComplexSet readComplexes(String file, String separator) throws IOException, ProCopeException
file
- path to the file which contains the complexesseparator
- seperator character between proteins in a complex
IOException
- on input/output errors
ProCopeException
- if the file could not be parsedpublic static ComplexSet readComplexes(File file) throws IOException, ProCopeException
file
- path to the file which contains the complexes
IOException
- on input/output errors
ProCopeException
- if the file could not be parsedpublic static ComplexSet readComplexes(File file, String separator) throws IOException, ProCopeException
file
- path to the file which contains the complexesseparator
- seperator character between proteins in a complex
IOException
- on input/output errors
ProCopeException
- if the file could not be parsedpublic static ComplexSet readComplexes(InputStream input) throws IOException, ProCopeException
input
- input stream from which complex data will be read
IOException
- on input/output errors
ProCopeException
- if the file could not be parsedpublic static ComplexSet readComplexes(InputStream input, String separator) throws IOException, ProCopeException
input
- input stream from which complex data will be read
IOException
- on input/output errors
ProCopeException
- if the file could not be parsed
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