Class PdbBlock

java.lang.Object
com.compomics.util.pdbfinder.pdb.PdbBlock

public class PdbBlock
extends Object
PdbBlock.
Author:
Niklaas Colaert
  • Constructor Details

    • 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 block
      aStart_protein - the protein start position
      aEnd_protein - the protein end position
      aStart_block - the block start position
      aEnd_block - the block end position
  • Method Details

    • getBlock

      public String getBlock()
      Returns the block.
      Returns:
      block
    • setBlock

      public void setBlock​(String aBlock)
      Sets the block.
      Parameters:
      aBlock - the block
    • getStartProtein

      public int getStartProtein()
      Returns the protein start.
      Returns:
      the protein start
    • setStartProtein

      public void setStartProtein​(int aStartProtein)
      Set the protein start.
      Parameters:
      aStartProtein - the protein start
    • getEndProtein

      public int getEndProtein()
      Returns the protein end.
      Returns:
      the protein end
    • setEndProtein

      public void setEndProtein​(int aEndProtein)
      Set the protein end.
      Parameters:
      aEndProtein - the protein end
    • getStartBlock

      public int getStartBlock()
      Returns the block start.
      Returns:
      the block start
    • setStartBlock

      public void setStartBlock​(int aStartBlock)
      Set the block start.
      Parameters:
      aStartBlock - the start block
    • getEndBlock

      public int getEndBlock()
      Returns the block end.
      Returns:
      the block end
    • setEndBlock

      public void setEndBlock​(int aEndBlock)
      Set the block end.
      Parameters:
      aEndBlock - the end block
    • getDifference

      public int getDifference()
      Returns the difference.
      Returns:
      the difference
    • getSelection

      public boolean getSelection()
      Returns true if there is a selection.
      Returns:
      true if there is a selection.
    • getSelectedPositions

      public Integer[] getSelectedPositions()
      Returns the selected positions.
      Returns:
      the selected positions
    • setSelectedPositions

      public void setSelectedPositions​(Integer[] aSelectedPositions)
      Set the selected positions.
      Parameters:
      aSelectedPositions - the selected positions
    • getBlockSequence

      public String getBlockSequence​(String aPdbAccession)
      Get the blocked sequence.
      Parameters:
      aPdbAccession - the PDB accession
      Returns:
      the blocked sequence
    • readUrl

      public String readUrl​(String aUrl, String aPdbAccession)
      Read a URL.
      Parameters:
      aUrl - the URL
      aPdbAccession - the PDB accession
      Returns:
      the sequence
    • readFasta

      public String readFasta​(String lFasta, String aPdbAccession)
      Read a FASTA.
      Parameters:
      lFasta - the FASTA entry
      aPdbAccession - the PDB accession
      Returns:
      the sequence