public class BlockImpl extends AbstractScoresCache implements java.io.Serializable, Block, java.lang.Cloneable
Constructor and Description |
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BlockImpl(BlockImpl b)
Copy constructor.
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BlockImpl(BlockSet blockSet)
Constructor.
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Modifier and Type | Method and Description |
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void |
clear()
Resets all scores
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Block |
clone()
Creates and returns an identical copy of this block.
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java.util.List<java.util.List<java.lang.Integer>> |
getAlignRes()
Returns the double List containing the aligned residues for each structure.
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BlockSet |
getBlockSet()
Returns the parent BlockSet of the Block.
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int |
getCoreLength()
Returns the number of aligned positions (columns) without gaps in the Block.
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int |
length()
Returns the total number of aligned positions (columns) in the Block.
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void |
setAlignRes(java.util.List<java.util.List<java.lang.Integer>> alignRes)
Set the double List containing the aligned residues for each structure.
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void |
setBlockSet(BlockSet parent)
Set the back-reference to its parent BlockSet.
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int |
size()
Returns the number of aligned structures (rows) in the Block.
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java.lang.String |
toString() |
protected void |
updateCoreLength() |
clone, getScore, getScores, putScore
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
getScore, getScores, putScore
public BlockImpl(BlockSet blockSet)
blockSet
- the parent BlockSet of the BlockImpl instance.public BlockImpl(BlockImpl b)
b
- BlockImpl object to be copied.public Block clone()
Block
public void clear()
AbstractScoresCache
clear
in interface Block
clear
in class AbstractScoresCache
public java.lang.String toString()
toString
in class java.lang.Object
public void setBlockSet(BlockSet parent)
Block
setBlockSet
in interface Block
parent
- the parent BlockSet.Block.getBlockSet()
public BlockSet getBlockSet()
Block
getBlockSet
in interface Block
Block.setBlockSet(BlockSet)
public java.util.List<java.util.List<java.lang.Integer>> getAlignRes()
Block
getAlignRes
in interface Block
#setAlignRes()
public void setAlignRes(java.util.List<java.util.List<java.lang.Integer>> alignRes)
Block
setAlignRes
in interface Block
alignRes
- a double List of Integers with the aligned residues.Block.getAlignRes()
public int length()
Block
length
in interface Block
Block.getCoreLength();
,
Block.size()
public int size()
Block
size
in interface Block
Block.length()
,
Block.getCoreLength()
public int getCoreLength()
Block
getCoreLength
in interface Block
#updateCoreLength()
,
Block.length()
,
Block.size()
protected void updateCoreLength()