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, Yehia Farag

  • 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