Class MultipleAlignmentImpl

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void clear()
      Clear the cached scores.
      MultipleAlignmentImpl clone()
      Creates and returns an identical copy of this alignment, including a deep copy of all constituent BlockSets.
      java.util.List<java.lang.Integer> getAlignResCounts()
      Returns the number of non null positions (residues) of each structure in the alignment.
      java.util.List<Atom[]> getAtomArrays()
      Returns the array of Atoms for each structure from its parent Ensemble.
      Block getBlock​(int index)
      Returns the Block with the specified index of the MultipleAlignment.
      java.util.List<Block> getBlocks()
      Convenience method to get a List of all Blocks from all BlockSets.
      BlockSet getBlockSet​(int index)
      Returns the BlockSet with the specified index of the MultipleAlignment.
      java.util.List<BlockSet> getBlockSets()
      Returns the BlockSet List of the multiple structure alignment.
      int getCoreLength()
      Returns the number of aligned residues (columns) without gaps in the alignment: the sum of all BlockSet core lengths.
      java.util.List<java.lang.Double> getCoverages()
      Returns the coverage of the alignment for each structure in the alignment as a fraction between 0.0 and 1.0.
      MultipleAlignmentEnsemble getEnsemble()
      Returns the parent Ensemble of the MultipleAlignment.
      StructureIdentifier getStructureIdentifier​(int index)
      Returns the StructureIdentifier associated with the structure index from its parent Ensemble.
      int length()
      Returns the total number of aligned residues (columns) in the multiple alignment: the sum of all BlockSet lengths.
      void setBlockSets​(java.util.List<BlockSet> blockSets)
      Sets the List of BlockSet List of the specified alignment.
      void setEnsemble​(MultipleAlignmentEnsemble parent)
      Set the back-reference to its parent Ensemble.
      int size()
      Returns the number of aligned structures in the MultipleAlignment.
      java.lang.String toString()
      Return a summary of the MultipleAlignment, containing the structures, the lengths and the cached scores.
      protected void updateCache()
      Updates all cached properties
      protected void updateCoreLength()
      Force recalculation of the core length (ungapped columns) based on the BlockSet core lengths.
      protected void updateLength()
      Force recalculation of the length (aligned columns) based on the BlockSet lengths.
      • Methods inherited from class java.lang.Object

        equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Constructor Detail

      • MultipleAlignmentImpl

        public MultipleAlignmentImpl()
        Default Constructor. Empty alignment. No structures assigned.
      • MultipleAlignmentImpl

        public MultipleAlignmentImpl​(MultipleAlignmentEnsemble ensemble)
        Constructor linking to an existing ensemble. Automatically adds this alignment to the parent ensemble.
        Parameters:
        ensemble - parent MultipleAlignmentEnsemble.
      • MultipleAlignmentImpl

        public MultipleAlignmentImpl​(MultipleAlignmentImpl ma)
        Copy constructor. Recursively copies member BlockSets.
        Parameters:
        ma - MultipleAlignmentImpl to copy.