jprotein.data.dataformat.info
Class BlastSequenceInfo

java.lang.Object
  extended by java.util.AbstractCollection
      extended by java.util.AbstractList
          extended by java.util.Vector
              extended by jprotein.data.datatype.Sequence
                  extended by jprotein.data.dataformat.info.BlastSequenceInfo
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess
Direct Known Subclasses:
BlastPairwiseInfo

public class BlastSequenceInfo
extends Sequence

See Also:
Serialized Form

Constructor Summary
BlastSequenceInfo()
           
 
Method Summary
 boolean allPreliminaryChecked()
           
 boolean expectChecked()
           
 int getEndOverlap()
           
 double getEValue()
           
 int getIdentity()
           
 int getOverlapLength()
           
 int getStartOverlap()
           
 boolean identityChecked()
           
 int overlaps(BlastSequenceInfo seq)
           
 boolean overlapStartChecked()
           
 void setEndOverlap(int end)
           
 void setEValue(double expect)
           
 void setIdentity(int identity)
           
 void setOverlapLength(int length)
           
 void setStartOverlap(int start)
           
 
Methods inherited from class jprotein.data.datatype.Sequence
equals, getNonGappedPosition, getNonGappedSequenceLength, getResidue, getSequence, getSequenceLength, getSequenceName, isIdentical, setSequence, setSequenceName, toFasta, toString
 
Methods inherited from class java.util.Vector
add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, firstElement, get, hashCode, indexOf, indexOf, insertElementAt, isEmpty, lastElement, lastIndexOf, lastIndexOf, remove, remove, removeAll, removeAllElements, removeElement, removeElementAt, retainAll, set, setElementAt, setSize, size, subList, toArray, toArray, trimToSize
 
Methods inherited from class java.util.AbstractList
iterator, listIterator, listIterator
 
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.util.List
iterator, listIterator, listIterator
 

Constructor Detail

BlastSequenceInfo

public BlastSequenceInfo()
Method Detail

setEndOverlap

public void setEndOverlap(int end)

getEndOverlap

public int getEndOverlap()

setOverlapLength

public void setOverlapLength(int length)

getOverlapLength

public int getOverlapLength()

setStartOverlap

public void setStartOverlap(int start)

getStartOverlap

public int getStartOverlap()

overlapStartChecked

public boolean overlapStartChecked()

setIdentity

public void setIdentity(int identity)

getIdentity

public int getIdentity()

identityChecked

public boolean identityChecked()

setEValue

public void setEValue(double expect)

getEValue

public double getEValue()

expectChecked

public boolean expectChecked()

allPreliminaryChecked

public boolean allPreliminaryChecked()

overlaps

public int overlaps(BlastSequenceInfo seq)