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java.lang.Objectedu.upenn.gloDB.AbstractFeature
edu.upenn.gloDB.FuzzyFeature
public class FuzzyFeature
These objects code Features that don't have definite boundaries. It's not clear whether it's more advantagous to have separate class definitions: FuzzyFeature - make abstract class BetweenFeature - same fields as below AfterFeature - no stop -> stop = sequence length; stopExtension = 0 BeforeFeature - no start -> start = 0; startExtension = 0
Field Summary | |
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private int |
start
The initial position defining this Feature. |
private int |
startExt
The number of the positions defining the start position. |
private int |
stop
The last position defining this Feature. |
private int |
stopExt
The number of the positions defining the stop position. |
Fields inherited from class edu.upenn.gloDB.AbstractFeature |
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attributes, source |
Constructor Summary | |
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FuzzyFeature(int start,
int startExt,
int stop,
int stopExt,
Sequence source)
Create a new FuzzyFeature object and add it to the set of Feature objects. |
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FuzzyFeature(int start,
int startExt,
int stop,
int stopExt,
Sequence source,
boolean addToPool)
Create a new FuzzyFeature object and add the newly created FuzzyFeature object to the set of Feature objects if addToPool is true. |
Method Summary | |
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int |
compareTo(java.lang.Object o)
Compares this object with the specified object for order. |
boolean |
contains(Feature feature)
Returns 'true' if the Feature 'feature' is contained in this Feature. |
int |
contains(int pos)
Returns '-1' if this Feature exists after the integer 'pos', returns '0' if 'pos' is contained in this Feature, and '1' if 'pos' occurs after this Feature. |
boolean |
equals(java.lang.Object o)
This will return true if the features are equal and the sources are the same. |
Feature |
flip()
Inverts the positions, returning a new Feature object. |
java.lang.String |
getData()
Returns the Sequence data from start to stopExt. |
java.lang.String |
getDataFormatted()
Returns the Sequence data from start to stopExt, with "\n" inserted every 80 characters. |
int |
getMax()
Returns the maximum position of the Feature. |
int |
getMin()
Returns the initial position of the Feature. |
int |
getStart()
Returns the start position. |
int |
getStartExt()
Returns the startExt position. |
int |
getStop()
Returns the stop position. |
int |
getStopExt()
Returns the stopExt. |
int |
length()
Returns the maximum number of positions contained in the Feature (((stop + stopExt) - start) + 1). |
int |
maxLength()
This is the same as length() . |
int |
minLength()
Returns the minimum number of positions contained in the Feature ((stop - start) + 1). |
Feature |
overlap(Feature feature)
Returns the overlapping region between the two Features. |
boolean |
overlaps(Feature feature)
Returns 'true' if the feature 'featCk' has positions that overlap positions in this feature. |
java.lang.String |
toString()
Only returns basic Feature information. |
java.lang.String |
toStringFull()
Returns all Feature information. |
java.lang.String |
toStringMin()
Only returns start/stop position information. |
Methods inherited from class edu.upenn.gloDB.AbstractFeature |
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addAttribute, addAttribute, containsAttribute, delAttribute, getAttribute, getAttributes, getAttributesMap, getSource, getSourceID, getType, setAttributes, setAttributes |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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private int start
private int startExt
private int stop
private int stopExt
Constructor Detail |
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public FuzzyFeature(int start, int startExt, int stop, int stopExt, Sequence source)
public FuzzyFeature(int start, int startExt, int stop, int stopExt, Sequence source, boolean addToPool)
Method Detail |
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public int getStart()
public int getStartExt()
public int getStop()
public int getStopExt()
public java.lang.String getData()
public java.lang.String getDataFormatted()
public int length()
public int getMin()
public int getMax()
public int minLength()
public int maxLength()
length()
.
public Feature flip()
public int contains(int pos)
public boolean contains(Feature feature)
public boolean overlaps(Feature feature)
public Feature overlap(Feature feature)
public int compareTo(java.lang.Object o) throws java.lang.ClassCastException
java.lang.ClassCastException
public boolean equals(java.lang.Object o) throws java.lang.ClassCastException
equals
in interface Feature
equals
in class java.lang.Object
java.lang.ClassCastException
public java.lang.String toString()
toString
in interface Feature
toString
in class AbstractFeature
public java.lang.String toStringMin()
public java.lang.String toStringFull()
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