Examples of org.moltools.apps.probemaker.design.SpacerLibrary

Package org.moltools.apps.probemaker.design

Examples of org.moltools.apps.probemaker.design.SpacerLibrary

org.moltools.apps.probemaker.design.SpacerLibrary
A SpacerLibrary is a special extension of a TagLibrary to be used for spacer tags. It is allways in USE_SAME_TAG mode to appear not to be variable, but calling its getNext() method will always return a new spacer Tag, not previously tested.
@author Johan Stenberg @version 1.0

        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;


      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);


      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.

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            }
            spacer = new SimpleNucleotideSequence("Spacer " + temp, temp, p.getType()); //$NON-NLS-1$
          }
          else {
            //Create a new spacer lib for the spacer position and get the first tag
            taglibraries[spacerPosition] = new SpacerLibrary(spacerLength,
                p.getType());
            spacer = ((SpacerLibrary) taglibraries[spacerPosition]).getNext();
          }
          p.addTagAt(spacer, spacerPosition);
        }

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        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;


      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);


      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.

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            }
            spacer = new SimpleNucleotideSequence("Spacer " + temp, temp, p.getType()); //$NON-NLS-1$
          }
          else {
            //Create a new spacer lib for the spacer position and get the first tag
            taglibraries[spacerPosition] = new SpacerLibrary(spacerLength,
                p.getType());
            spacer = ((SpacerLibrary) taglibraries[spacerPosition]).getNext();
          }
          p.addTagAt(spacer, spacerPosition);
        }

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        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;


      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);


      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.

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            }
            spacer = new SimpleNucleotideSequence("Spacer " + temp, temp, p.getType()); //$NON-NLS-1$
          }
          else {
            //Create a new spacer lib for the spacer position and get the first tag
            taglibraries[spacerPosition] = new SpacerLibrary(spacerLength,
                p.getType());
            spacer = ((SpacerLibrary) taglibraries[spacerPosition]).getNext();
          }
          p.addTagAt(spacer, spacerPosition);
        }

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        throw new IllegalArgumentException("Invalid spacer position"); //$NON-NLS-1$
      }
      spacerPosition = spacerPos;


      //Create and set up a spacer library
      TagLibrary spacerLib = new SpacerLibrary(0, NucleotideSequence.DNA);


      //parse the spacer string and check that its valid
      spacerSequence = ""; //$NON-NLS-1$
      for (int i = 0; i < spacerString.length(); i++) {
        Nucleotide nt = NucleotideSequenceHandler.getNucleotide(spacerString.

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            }
            spacer = new SimpleNucleotideSequence("Spacer " + temp, temp, p.getType()); //$NON-NLS-1$
          }
          else {
            //Create a new spacer lib for the spacer position and get the first tag
            taglibraries[spacerPosition] = new SpacerLibrary(spacerLength,
                p.getType());
            spacer = ((SpacerLibrary) taglibraries[spacerPosition]).getNext();
          }
          p.addTagAt(spacer, spacerPosition);
        }

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Related Classes of org.moltools.apps.probemaker.design.SpacerLibrary

org.moltools.apps.probemaker.ext.ta.GreedyTagAllocator

org.moltools.lib.seq.impl.SimpleChangeableNucleotideSequence

org.moltools.lib.seq.impl.SimpleNucleotideSequence

org.moltools.lib.seq.NucleotideSequence

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