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java.lang.Objectedu.unc.csbio.data.Feature
public abstract class Feature
The abstract class for all annotation features. Each feature belongs to only one chromosome, and it is in the region between its start position (inclusively) and end position(inclusively) in the chromosome. The unit of a position is a base pair. These properties are all valid for all inherited classes.
Field Summary | |
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protected java.lang.String |
chrom
The chromosome of the feature. |
protected int |
end
The end position of the feature. |
protected int |
start
The start position of the feature. |
Constructor Summary | |
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Feature()
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Method Summary | |
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int |
compareTo(Feature f)
A necessary method for the Comparable interface. |
java.lang.String |
getChromosome()
Get the chromosome |
int |
getEnd()
Get the offset of the end position from the beginning of the chromosome. |
int |
getLength()
Get the number of base pairs in the sequence related to this feature. |
int |
getRange()
Get the size of the spanning/effective range of this feature, from start position to end position in the reference coordinate. |
int |
getStart()
Get the offset of the start position from the beginning of the chromosome. |
abstract java.lang.String |
toString()
An abstract method of toString() |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected java.lang.String chrom
protected int start
protected int end
Constructor Detail |
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public Feature()
Method Detail |
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public int compareTo(Feature f)
Comparable
interface. Features
are ordered first by their chromosome alphabetically, then by start
position, and finally by end position. Two features are considered to be
the same only if their chromosome, start position and end position are
the same, which means they are totally overlapped.
compareTo
in interface java.lang.Comparable<Feature>
Comparable.compareTo(java.lang.Object)
public final java.lang.String getChromosome()
public final int getEnd()
public int getLength()
public final int getRange()
public final int getStart()
public abstract java.lang.String toString()
toString()
toString
in class java.lang.Object
Object.toString()
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