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java.lang.Objectjava.util.AbstractCollection
java.util.AbstractList
java.util.Vector
jprotein.tree.tools.DistanceMatrix
public class DistanceMatrix
Constructor Summary | |
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DistanceMatrix(MultiAlignment multiAlignment,
SubstitutionMatrix sm)
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Method Summary | |
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java.util.Vector |
getDistantCouple()
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Leaf |
getLeaf(int index)
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java.lang.Double |
getLowerLimitScore(int i,
int j)
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int |
getNonGappedAlignedLength(int i,
int j)
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double |
getUpperLimitScore(int i,
int j)
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boolean |
isExtension(int i,
int j,
int k)
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boolean |
isGapped(int i,
int j,
int k)
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void |
setDistantCouple(Sequence seq1,
Sequence seq2)
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void |
setMultipleAlignment(MultiAlignment multiAlignment)
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void |
setSubstitutionMatrix(SubstitutionMatrix sm)
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java.lang.String |
toString()
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Methods inherited from class java.util.Vector |
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add, add, addAll, addAll, addElement, capacity, clear, clone, contains, containsAll, copyInto, elementAt, elements, ensureCapacity, equals, 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 |
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iterator, listIterator, listIterator |
Methods inherited from class java.lang.Object |
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getClass, notify, notifyAll, wait, wait, wait |
Methods inherited from interface java.util.List |
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iterator, listIterator, listIterator |
Constructor Detail |
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public DistanceMatrix(MultiAlignment multiAlignment, SubstitutionMatrix sm) throws java.lang.Exception
java.lang.Exception
Method Detail |
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public Leaf getLeaf(int index)
public void setSubstitutionMatrix(SubstitutionMatrix sm)
public void setMultipleAlignment(MultiAlignment multiAlignment)
public java.lang.String toString()
toString
in class java.util.Vector
public boolean isGapped(int i, int j, int k)
public boolean isExtension(int i, int j, int k)
public double getUpperLimitScore(int i, int j)
public java.lang.Double getLowerLimitScore(int i, int j)
public int getNonGappedAlignedLength(int i, int j)
public void setDistantCouple(Sequence seq1, Sequence seq2)
public java.util.Vector getDistantCouple()
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