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java.lang.Objectedu.upenn.gloDB.FeatureUtils
public class FeatureUtils
FeatureUtils. Miscellaneous functions that act on Features and Sets of Features.
Constructor Summary | |
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FeatureUtils()
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Method Summary | |
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static java.util.TreeSet |
cluster(Track track,
int maxSpace,
int threshold)
Deprecated. replaced with cluster.py |
static int |
compareFeatures(Feature featureA,
Feature featureB)
Compares two Features for order. |
static Feature |
contained(Feature feature,
int minB,
int maxB)
Returns a new Feature containing the region in 'feature' that is bounded by minB/maxB. |
static boolean |
contains(Feature featureA,
Feature featureB)
Returns 'true' if the second Feature ('featureB') is contained in the first Feature ('featureA'). |
static int |
contains(Feature feature,
int pos)
Returns '-1' if 'feature' exists after the integer 'pos', returns '0' if 'pos' is contained in 'feature', and '1' if 'pos' occurs after 'feature'. |
static boolean |
isContiguous(java.util.TreeSet features)
Returns 'true' if the set of Features does not contain gaps between Features. |
static java.util.TreeSet |
mergeContiguous(Track track)
This will merge all overlapping Features in the track, creating new Feature objects as necessary. |
static Feature |
overlap(Feature featureA,
Feature featureB)
Returns the overlapping region between the two Features. |
static boolean |
overlaps(Feature featureA,
Feature featureB)
Returns 'true' if the Features have overlapping positions. |
static boolean |
overlaps(Feature featureA,
Track track)
Returns 'true' if the Feature and Track overlap. |
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 FeatureUtils()
Method Detail |
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public static Feature contained(Feature feature, int minB, int maxB)
public static int contains(Feature feature, int pos)
public static boolean contains(Feature featureA, Feature featureB)
public static boolean overlaps(Feature featureA, Track track)
public static boolean overlaps(Feature featureA, Feature featureB)
public static Feature overlap(Feature featureA, Feature featureB)
public static int compareFeatures(Feature featureA, Feature featureB)
public static boolean isContiguous(java.util.TreeSet features)
public static java.util.TreeSet cluster(Track track, int maxSpace, int threshold)
public static java.util.TreeSet mergeContiguous(Track track)
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