meshi.applications.prediction
Class PredictionSequenceAlignment

java.lang.Object
  java.util.AbstractCollection<E>
      java.util.AbstractList<E>
          java.util.ArrayList<SequenceAlignmentColumn>
              meshi.sequences.SequenceAlignment
                  meshi.applications.prediction.PredictionSequenceAlignment

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Iterable<SequenceAlignmentColumn>, java.util.Collection<SequenceAlignmentColumn>, java.util.List<SequenceAlignmentColumn>, java.util.RandomAccess

public class PredictionSequenceAlignment
extends SequenceAlignment

See Also:

Serialized Form

Nested Class Summary

private static class

PredictionSequenceAlignment.TemplateAlignmentException

Field Summary

private boolean

debug A sequenceAlignment is extracted from a file whose name is referred to by the command line starting with key.

Fields inherited from class meshi.sequences.SequenceAlignment

comments

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

PredictionSequenceAlignment(CommandList commands, Key key, Sequence reference)

PredictionSequenceAlignment(Sequence targetSequence, Protein template, SequenceList sequenceList)

Method Summary

Methods inherited from class meshi.sequences.SequenceAlignment

getColumn, identityAlignment, isExactMach, isExactMachWithGaps, print, score, setScore, toString

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode, iterator, listIterator, listIterator, subList

Methods inherited from class java.util.AbstractCollection

containsAll, removeAll, retainAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList

Field Detail

debug

private boolean debug

A sequenceAlignment is extracted from a file whose name is referred to by the command line starting with key. The first sequence of the alignment is assumed to be a subsequence of the reference sequence. The reference sequence is used to correct the start field of the aligned sequences. The reference itself is assummed to have correct start field (that is, it indicates the correct residue numbers).

Constructor Detail

PredictionSequenceAlignment

public PredictionSequenceAlignment(CommandList commands,
                                   Key key,
                                   Sequence reference)

PredictionSequenceAlignment

public PredictionSequenceAlignment(Sequence targetSequence,
                                   Protein template,
                                   SequenceList sequenceList)