|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.gersteinlab.act.io.DataFilesReader
public abstract class DataFilesReader
This class defines a reader of data files.
Field Summary | |
---|---|
protected java.io.BufferedReader |
br
The input reader. |
Constructor Summary | |
---|---|
DataFilesReader(java.io.Reader rIn)
Create a new reader with source data from an input reader. |
Method Summary | |
---|---|
void |
close()
Close the reader. |
int |
countIntervals()
Get the total number of intervals. |
static DataFilesReader |
getReader(Config config,
java.io.File dataFile)
Get a data file reader for a data file. |
abstract Interval |
readInterval()
Read the next interval from the reader. |
void |
readIntervals(java.util.Collection<Interval> output)
Read all intervals into a collection. |
void |
readIntervals(java.util.Collection<Interval> output,
double value)
Read the intervals that contain a given value into a collection. |
void |
reset()
Reset the reader. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
protected java.io.BufferedReader br
Constructor Detail |
---|
public DataFilesReader(java.io.Reader rIn)
rIn
- The input readerMethod Detail |
---|
public static DataFilesReader getReader(Config config, java.io.File dataFile) throws java.lang.ClassNotFoundException, java.io.FileNotFoundException, java.lang.IllegalAccessException, java.lang.InstantiationException, java.lang.reflect.InvocationTargetException, java.lang.NoSuchMethodException
config
- ConfigurationsdataFile
- The data file
java.lang.ClassNotFoundException
java.io.FileNotFoundException
java.lang.IllegalAccessException
java.lang.InstantiationException
java.lang.reflect.InvocationTargetException
java.lang.NoSuchMethodException
public void reset() throws java.io.IOException
java.io.IOException
public void close() throws java.io.IOException
java.io.IOException
public abstract Interval readInterval() throws java.io.IOException
java.io.IOException
public void readIntervals(java.util.Collection<Interval> output) throws java.io.IOException
output
- Collection for storing the intervals
java.io.IOException
public void readIntervals(java.util.Collection<Interval> output, double value) throws java.io.IOException
output
- Collection for storing the intervalsvalue
- The value
java.io.IOException
public int countIntervals() throws java.io.IOException
java.io.IOException
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |