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java.lang.Objectutil.Alignment
public class Alignment
This class does a simple alignment by using a dot plot matrix for the PDB and the given alignment sequence. It follow the assumption of a correctly selected PDB sequence. Main goal is to provide a mapping from the alignment AA position to the PDB sequence position.
Constructor Summary | |
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Alignment(java.lang.String alignSequence,
java.lang.String pdbSequence)
Constructor of the DotPlotMatrix |
Method Summary | |
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void |
alignSequenceToStructure()
Initializes the alignment by the condition of matching the first four amino acids and aligns the two sequences by starting at the first four matching positions and going diagonal (down-to-the-right) in the matrix. |
void |
checkAlignment()
Checks sequence converage and shows a warning if it is under the specified threshold |
java.util.HashMap<java.lang.Integer,java.lang.Integer> |
getAlign2PDBPositionMap()
Returns the alignment to PDB position hash map. |
int |
getAlignPos(int pdbPos)
Receives an aminoacid position on the pdb chain and returns its position on the alignment sequence |
int |
getNumCols()
Returns the number of columns of the matrix; |
int |
getNumRows()
Returns the number of rows of the matrix; |
java.util.HashMap<java.lang.Integer,java.lang.Integer> |
getPdb2alignPositionMap()
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int |
getPDBPos(int alignPos)
Receives an aminoacid position on the alignment sequence chain and returns its position on the pdb chain |
void |
showAlignment()
Shows a a window with the alignment data |
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 Alignment(java.lang.String alignSequence, java.lang.String pdbSequence)
alignSequence
- pdbSequence
- Method Detail |
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public int getNumCols()
public int getNumRows()
public void alignSequenceToStructure()
public java.util.HashMap<java.lang.Integer,java.lang.Integer> getAlign2PDBPositionMap()
public java.util.HashMap<java.lang.Integer,java.lang.Integer> getPdb2alignPositionMap()
public void checkAlignment()
public void showAlignment()
public int getAlignPos(int pdbPos)
pbdPos
- Position of an aminoacid in the pdb chain
public int getPDBPos(int alignPos)
alignPos
- Position of given aminoacid in the alignment sequence
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