Package com.compomics.util.pdbfinder.pdb
Class PdbBlock
java.lang.Object
com.compomics.util.pdbfinder.pdb.PdbBlock
public class PdbBlock extends Object
PdbBlock.
- Author:
- Niklaas Colaert
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Constructor Summary
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Method Summary
Modifier and Type Method Description String
getBlock()
Returns the block.String
getBlockSequence(String aPdbAccession)
Get the blocked sequence.int
getDifference()
Returns the difference.int
getEndBlock()
Returns the block end.int
getEndProtein()
Returns the protein end.Integer[]
getSelectedPositions()
Returns the selected positions.boolean
getSelection()
Returns true if there is a selection.int
getStartBlock()
Returns the block start.int
getStartProtein()
Returns the protein start.String
readFasta(String lFasta, String aPdbAccession)
Read a FASTA.String
readUrl(String aUrl, String aPdbAccession)
Read a URL.void
setBlock(String aBlock)
Sets the block.void
setEndBlock(int aEndBlock)
Set the block end.void
setEndProtein(int aEndProtein)
Set the protein end.void
setSelectedPositions(Integer[] aSelectedPositions)
Set the selected positions.void
setStartBlock(int aStartBlock)
Set the block start.void
setStartProtein(int aStartProtein)
Set the protein start.
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Constructor Details
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PdbBlock
public PdbBlock()Empty default constructor -
PdbBlock
public PdbBlock(String aBlock, int aStart_protein, int aEnd_protein, int aStart_block, int aEnd_block)Constructor.- Parameters:
aBlock
- the blockaStart_protein
- the protein start positionaEnd_protein
- the protein end positionaStart_block
- the block start positionaEnd_block
- the block end position
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Method Details
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getBlock
Returns the block.- Returns:
- block
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setBlock
Sets the block.- Parameters:
aBlock
- the block
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getStartProtein
public int getStartProtein()Returns the protein start.- Returns:
- the protein start
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setStartProtein
public void setStartProtein(int aStartProtein)Set the protein start.- Parameters:
aStartProtein
- the protein start
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getEndProtein
public int getEndProtein()Returns the protein end.- Returns:
- the protein end
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setEndProtein
public void setEndProtein(int aEndProtein)Set the protein end.- Parameters:
aEndProtein
- the protein end
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getStartBlock
public int getStartBlock()Returns the block start.- Returns:
- the block start
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setStartBlock
public void setStartBlock(int aStartBlock)Set the block start.- Parameters:
aStartBlock
- the start block
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getEndBlock
public int getEndBlock()Returns the block end.- Returns:
- the block end
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setEndBlock
public void setEndBlock(int aEndBlock)Set the block end.- Parameters:
aEndBlock
- the end block
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getDifference
public int getDifference()Returns the difference.- Returns:
- the difference
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getSelection
public boolean getSelection()Returns true if there is a selection.- Returns:
- true if there is a selection.
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getSelectedPositions
Returns the selected positions.- Returns:
- the selected positions
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setSelectedPositions
Set the selected positions.- Parameters:
aSelectedPositions
- the selected positions
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getBlockSequence
Get the blocked sequence.- Parameters:
aPdbAccession
- the PDB accession- Returns:
- the blocked sequence
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readUrl
Read a URL.- Parameters:
aUrl
- the URLaPdbAccession
- the PDB accession- Returns:
- the sequence
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readFasta
Read a FASTA.- Parameters:
lFasta
- the FASTA entryaPdbAccession
- the PDB accession- Returns:
- the sequence
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