sbrt.kernel.fba.analysis
Class FluxIntervalAnalyzer

java.lang.Object
  extended by sbrt.kernel.fba.analysis.FluxIntervalAnalyzer

public class FluxIntervalAnalyzer
extends java.lang.Object

This class is used to analyze flux intervals.

The zeroCutoff arguments to each method must be:

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Constructor Summary
FluxIntervalAnalyzer()
           
 
Method Summary
 java.util.Set<java.lang.String> getAlwaysActive(java.util.Map<java.lang.String,Interval> fluxIntervals, double zeroCutoff)
          Returns the always-active fluxes in the provided map.
 java.util.Set<java.lang.String> getNeverActive(java.util.Map<java.lang.String,Interval> fluxIntervals, double zeroCutoff)
          Returns the never-active fluxes in the provided map.
 java.util.Set<java.lang.String> getPotentiallyActive(java.util.Map<java.lang.String,Interval> fluxIntervals, double zeroCutoff)
          Returns the potentially-active fluxes in the provided map.
 int lowerBoundsEqualZero(java.util.Collection<Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose lower bound equals zero.
 int lowerBoundsEqualZero(java.util.Map<?,Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose lower bound equals zero.
 int lowerBoundsGreaterThanZero(java.util.Collection<Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose lower bounds are greater than zero.
 int lowerBoundsGreaterThanZero(java.util.Map<?,Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose lower bounds are greater than zero.
 int rangesEqualZero(java.util.Collection<Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose ranges equal zero.
 int rangesEqualZero(java.util.Map<?,Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose ranges equal zero.
 int rangesGreaterThanZero(java.util.Collection<Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose ranges are greater than zero.
 int rangesGreaterThanZero(java.util.Map<?,Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose ranges are greater than zero.
 int upperBoundsEqualZero(java.util.Collection<Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose upper bounds equal zero.
 int upperBoundsEqualZero(java.util.Map<?,Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose upper bounds equal zero.
 int upperBoundsGreaterThanZero(java.util.Collection<Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose upper bounds are greater than zero.
 int upperBoundsGreaterThanZero(java.util.Map<?,Interval> intervals, double zeroCutoff)
          Returns the number of provided intervals whose upper bounds are greater than zero.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FluxIntervalAnalyzer

public FluxIntervalAnalyzer()
Method Detail

getAlwaysActive

public java.util.Set<java.lang.String> getAlwaysActive(java.util.Map<java.lang.String,Interval> fluxIntervals,
                                                       double zeroCutoff)
Returns the always-active fluxes in the provided map.

Parameters:
fluxIntervals - reaction names mapped to their corresponding flux interval.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the keys in the provided map whose corresponding interval has a lower bound greater than zero.

getPotentiallyActive

public java.util.Set<java.lang.String> getPotentiallyActive(java.util.Map<java.lang.String,Interval> fluxIntervals,
                                                            double zeroCutoff)
Returns the potentially-active fluxes in the provided map.

Parameters:
fluxIntervals - reaction names mapped to their corresponding flux interval.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the keys in the provided map whose corresponding interval has a lower bound equal to zero and an upper bound greater than zero.

getNeverActive

public java.util.Set<java.lang.String> getNeverActive(java.util.Map<java.lang.String,Interval> fluxIntervals,
                                                      double zeroCutoff)
Returns the never-active fluxes in the provided map.

Parameters:
fluxIntervals - reaction names mapped to their corresponding flux interval.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the keys in the provided map whose corresponding interval has lower and upper bounds equal to zero.

lowerBoundsEqualZero

public int lowerBoundsEqualZero(java.util.Map<?,Interval> intervals,
                                double zeroCutoff)
Returns the number of provided intervals whose lower bound equals zero.

Parameters:
intervals - a map whose values are intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose lower bound equals zero.

lowerBoundsEqualZero

public int lowerBoundsEqualZero(java.util.Collection<Interval> intervals,
                                double zeroCutoff)
Returns the number of provided intervals whose lower bound equals zero.

Parameters:
intervals - a collection of intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose lower bound equals zero.

lowerBoundsGreaterThanZero

public int lowerBoundsGreaterThanZero(java.util.Map<?,Interval> intervals,
                                      double zeroCutoff)
Returns the number of provided intervals whose lower bounds are greater than zero.

Parameters:
intervals - a map whose values are intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose lower bounds are greater than zero.

lowerBoundsGreaterThanZero

public int lowerBoundsGreaterThanZero(java.util.Collection<Interval> intervals,
                                      double zeroCutoff)
Returns the number of provided intervals whose lower bounds are greater than zero.

Parameters:
intervals - a collection of intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose lower bounds are greater than zero.

upperBoundsEqualZero

public int upperBoundsEqualZero(java.util.Map<?,Interval> intervals,
                                double zeroCutoff)
Returns the number of provided intervals whose upper bounds equal zero.

Parameters:
intervals - a map whose values are intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose upper bounds equal zero.

upperBoundsEqualZero

public int upperBoundsEqualZero(java.util.Collection<Interval> intervals,
                                double zeroCutoff)
Returns the number of provided intervals whose upper bounds equal zero.

Parameters:
intervals - a collection of intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose upper bounds equal zero.

upperBoundsGreaterThanZero

public int upperBoundsGreaterThanZero(java.util.Map<?,Interval> intervals,
                                      double zeroCutoff)
Returns the number of provided intervals whose upper bounds are greater than zero.

Parameters:
intervals - a map whose values are intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose upper bounds are greater than zero.

upperBoundsGreaterThanZero

public int upperBoundsGreaterThanZero(java.util.Collection<Interval> intervals,
                                      double zeroCutoff)
Returns the number of provided intervals whose upper bounds are greater than zero.

Parameters:
intervals - a collection of intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose upper bounds are greater than zero.

rangesEqualZero

public int rangesEqualZero(java.util.Map<?,Interval> intervals,
                           double zeroCutoff)
Returns the number of provided intervals whose ranges equal zero.

Parameters:
intervals - a map whose values are intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose ranges equal zero.

rangesEqualZero

public int rangesEqualZero(java.util.Collection<Interval> intervals,
                           double zeroCutoff)
Returns the number of provided intervals whose ranges equal zero.

Parameters:
intervals - a collection of intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose ranges equal zero.

rangesGreaterThanZero

public int rangesGreaterThanZero(java.util.Map<?,Interval> intervals,
                                 double zeroCutoff)
Returns the number of provided intervals whose ranges are greater than zero.

Parameters:
intervals - a map whose values are intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose ranges are greater than zero.

rangesGreaterThanZero

public int rangesGreaterThanZero(java.util.Collection<Interval> intervals,
                                 double zeroCutoff)
Returns the number of provided intervals whose ranges are greater than zero.

Parameters:
intervals - a collection of intervals.
zeroCutoff - the amount by which a value can differ from zero, but still be considered equal to zero.
Returns:
the number of provided intervals whose ranges are greater than zero.