Package org.biojava.nbio.structure.align

Class MultiThreadedDBSearch

  • public class MultiThreadedDBSearch
extends java.lang.Object
    Performs a multi threaded database search for an input protein structure
    Author:
    Andreas Prlic

    • Constructor Detail

      • MultiThreadedDBSearch

        public MultiThreadedDBSearch​(java.lang.String name,
                             Structure structure,
                             java.lang.String outFile,
                             StructureAlignment algorithm,
                             int nrCPUs,
                             boolean domainSplit)

    • Method Detail

      • getCustomFile1

        public java.lang.String getCustomFile1()

      • setCustomFile1

        public void setCustomFile1​(java.lang.String customFile1)
        set the file path for a custom, user provided file, not a standard PDB file.
        Parameters:
        customFile1 -

      • getCustomChain1

        public java.lang.String getCustomChain1()

      • setCustomChain1

        public void setCustomChain1​(java.lang.String customChain1)
        sets a chain in a custom, user provided file
        Parameters:
        customChain1 -

      • getAtomCache

        public AtomCache getAtomCache()

      • setAtomCache

        public void setAtomCache​(AtomCache cache)

      • getOutFile

        public java.lang.String getOutFile()

      • setOutFile

        public void setOutFile​(java.lang.String outFile)

      • getLegend

        public static java.lang.String getLegend​(java.lang.String algorithmName)

      • getResultFile

        public java.io.File getResultFile()

      • setResultFile

        public void setResultFile​(java.io.File resultList)

      • run

        public void run()

      • interrupt

        public void interrupt()
        stops what is currently happening and does not continue

      • cleanup

        public void cleanup()