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java.lang.Objectprocope.data.purifications.PurificationDataReader
public class PurificationDataReader
Contains static methods to read purification data from a file. Each line of the input data contains one bait-prey interaction. The following tab-separated fields are assumed (adapted from the purification data provided by The Krogan Lab Interactome Database):
Currently this reader only uses the purification name, bait
and prey information. All bait-prey interactions with the same
purification name (which of course should also all have the same bait) will
be combined into one PurificationExperiment
.
Multiple preys
Multiple occurences of preys in the same experiment (e.g. due to
different mass spectrometry methods) can be counted multiple times
or just once. All methods provide signatures which allow the setting
of a multiplePreys
flag.
Constructor Summary | |
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PurificationDataReader()
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Method Summary | |
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static PurificationData |
readPurifications(File file)
Read purification data from a given file. |
static PurificationData |
readPurifications(File file,
boolean multiplyPreys)
Read purification data from a given file. |
static PurificationData |
readPurifications(InputStream input)
Read purification data from a given input stream. |
static PurificationData |
readPurifications(InputStream input,
boolean multiplePreys)
Read purification data from a given input stream. |
static PurificationData |
readPurifications(String file)
Read purification data from a given file. |
static PurificationData |
readPurifications(String file,
boolean multiplyPreys)
Read purification data 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 |
Constructor Detail |
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public PurificationDataReader()
Method Detail |
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public static PurificationData readPurifications(String file) throws IOException
above
).
file
- file from which the purification data will be read
IOException
- if the file could not be readpublic static PurificationData readPurifications(String file, boolean multiplyPreys) throws IOException
file
- file from which the purification data will be readmultiplyPreys
- true
: count multiple preys, see above
IOException
- if the file could not be readpublic static PurificationData readPurifications(File file) throws IOException
above
).
file
- file from which the purification data will be read
IOException
- if the file could not be readpublic static PurificationData readPurifications(File file, boolean multiplyPreys) throws IOException
file
- file from which the purification data will be readmultiplyPreys
- true
: count multiple preys, see above
IOException
- if the file could not be readpublic static PurificationData readPurifications(InputStream input)
above
).
input
- inputstream from which the data will be read
public static PurificationData readPurifications(InputStream input, boolean multiplePreys)
input
- inputstream from which the data will be readmultiplePreys
- true
: count multiple preys, see above
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