SimpleAlignedSequence

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

org.biojava3.alignment
Class SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>

java.lang.Object
  org.biojava3.alignment.SimpleAlignedSequence<S,C>


Type Parameters:: C - each element of the Sequence is a Compound of type C

All Implemented Interfaces:: Iterable<C>, AlignedSequence<S,C>, Accessioned, Sequence<C>

public class SimpleAlignedSequence<S extends Sequence<C>,C extends Compound>
extends Object
implements AlignedSequence<S,C>
extends Object
implements AlignedSequence<S,C>

Implements a data structure for a Sequence within an alignment.

Author:: Mark Chapman

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava3.alignment.template.AlignedSequence
`AlignedSequence.Step`

Constructor Summary
`SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps)` Creates a new `AlignedSequence` for the given `AlignedSequence` in a global alignment.
`SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps, int numBefore, int numAfter)` Creates a new `AlignedSequence` for the given `AlignedSequence` in a local alignment.
`SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps)` Creates an `AlignedSequence` for the given `Sequence` in a global alignment.
`SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps, int numBefore, int numAfter)` Creates an `AlignedSequence` for the given `Sequence` in a local alignment.

Method Summary
`void`	`clearCache()` Nullifies cached arrays/objects.
`int`	`countCompounds(C... compounds)` Returns the number of times we found a compound in the Sequence
`AccessionID`	`getAccession()` Returns the AccessionID this location is currently bound with
`int`	`getAlignmentIndexAt(int sequenceIndex)` Returns the column index within an alignment corresponding to the given index in the original `Sequence`.
`List<C>`	`getAsList()` Returns the Sequence as a List of compounds
`C`	`getCompoundAt(int alignmentIndex)` Returns the Compound at the given biological index
`CompoundSet<C>`	`getCompoundSet()` Gets the compound set used to back this Sequence
`Point`	`getEnd()` Returns the `Point` within an alignment of the last element of the original `Sequence`.
`int`	`getIndexOf(C compound)` Scans through the Sequence looking for the first occurrence of the given compound
`SequenceView<C>`	`getInverse()` Does the right thing to get the inverse of the current Sequence.
`int`	`getLastIndexOf(C compound)` Scans through the Sequence looking for the last occurrence of the given compound
`int`	`getLength()` Returns the length of the Sequence
`Location`	`getLocationInAlignment()` Returns the `Location` of the original `Sequence` within an alignment.
`int`	`getNumGaps()` Returns number of gaps in the sequence.
`S`	`getOriginalSequence()` Returns the original `Sequence` before alignment.
`int`	`getOverlapCount()` Returns the maximum number of elements contributed to a column of an alignment by this `Sequence`.
`String`	`getSequenceAsString()` Returns the String representation of the Sequence
`int`	`getSequenceIndexAt(int alignmentIndex)` Returns the index in the original `Sequence` corresponding to the given index within an alignment.
`Point`	`getStart()` Returns the `Point` within an alignment of the first element of the original `Sequence`.
`SequenceView<C>`	`getSubSequence(Integer start, Integer end)` Returns a portion of the sequence from the different positions.
`boolean`	`isCircular()` Returns true if this `Sequence` wraps around from the last alignment column back to the first.
`boolean`	`isGap(int alignmentIndex)` Returns true if this `Sequence` has a gap at a particular alignment column.
`Iterator<C>`	`iterator()`
`String`	`toString()` Provides standard Java language access to results of `getSequenceAsString()`.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Constructor Detail

SimpleAlignedSequence

public SimpleAlignedSequence(S original,
                             List<AlignedSequence.Step> steps)

Creates an AlignedSequence for the given Sequence in a global alignment.

Parameters:: original - the original Sequence before alignment; steps - lists whether the sequence aligns a Compound or gap at each index of the alignment
Throws:: IllegalArgumentException - if given sequence does not fit in alignment

SimpleAlignedSequence

public SimpleAlignedSequence(S original,
                             List<AlignedSequence.Step> steps,
                             int numBefore,
                             int numAfter)

Creates an AlignedSequence for the given Sequence in a local alignment.

Parameters:: original - the original Sequence before alignment; steps - lists whether the sequence aligns a Compound or gap at each index of the alignment; numBefore - number of Compounds before a local alignment; numAfter - number of Compounds after a local alignment
Throws:: IllegalArgumentException - if given sequence does not fit in alignment

SimpleAlignedSequence

public SimpleAlignedSequence(AlignedSequence<S,C> prev,
                             List<AlignedSequence.Step> steps)

Creates a new AlignedSequence for the given AlignedSequence in a global alignment.

Parameters:: prev - the previous AlignedSequence before this alignment; steps - lists whether the sequence aligns a Compound or gap at each index of the alignment
Throws:: IllegalArgumentException - if given sequence does not fit in alignment

SimpleAlignedSequence

public SimpleAlignedSequence(AlignedSequence<S,C> prev,
                             List<AlignedSequence.Step> steps,
                             int numBefore,
                             int numAfter)

Creates a new AlignedSequence for the given AlignedSequence in a local alignment.

Parameters:: prev - the previous AlignedSequence before this alignment; steps - lists whether the sequence aligns a Compound or gap at each index of the alignment; numBefore - number of Compounds before a local alignment; numAfter - number of Compounds after a local alignment
Throws:: IllegalArgumentException - if given sequence does not fit in alignment

Method Detail