-Alignment -

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- -compbio.data.sequence -
-Class Alignment

-java.lang.Object
-  compbio.data.sequence.Alignment
-

@Immutable -public final class Alignment
extends Object
extends Object

- - -

-Multiple sequence alignment. - - Does not give any guarantees on the content of individual FastaSequece - records. It does not guarantee neither the uniqueness of the names of - sequences nor it guarantees the uniqueness of the sequences. -

- -

Version:: 1.0 September 2009
Author:: pvtroshin
See Also:: FastaSequence, -AlignmentMetadata

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- - - - - - - - - - - - - - -
-Constructor Summary
Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata) - -
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Alignment(List<FastaSequence> sequences, - Program program, - char gapchar) - -
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
- boolean equals(Object obj) - -
-          Please note that this implementation does not take the order of sequences - into account!
- AlignmentMetadata getMetadata() - -
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- List<FastaSequence> getSequences() - -
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- int getSize() - -
-
- int hashCode() - -
-
- String toString() - -
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- - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
- -

-Constructor Summary
`Alignment(List<FastaSequence> sequences, - AlignmentMetadata metadata)` - - -
`Alignment(List<FastaSequence> sequences, - Program program, - char gapchar)` - - -

-Method Summary
- `boolean`	`equals(Object obj)` - - - Please note that this implementation does not take the order of sequences - into account!
- `AlignmentMetadata`	`getMetadata()` - - -
- `List<FastaSequence>`	`getSequences()` - - -
- `int`	`getSize()` - - -
- `int`	`hashCode()` - - -
- `String`	`toString()` - - -

Methods inherited from class java.lang.Object
`getClass, notify, notifyAll, wait, wait, wait`

- - - - - - - - -
-Constructor Detail
- -

-Alignment

-public Alignment(List<FastaSequence> sequences,
-                 Program program,
-                 char gapchar)

Parameters:: sequences -; program -; gapchar -

- -

-Alignment

-public Alignment(List<FastaSequence> sequences,
-                 AlignmentMetadata metadata)

Parameters:: sequences -; metadata -

- - - - - - - - - -

-Method Detail

- -

-getSequences

-public List<FastaSequence> getSequences()

Returns:: list of FastaSequence records

- -

-getSize

-public int getSize()

Returns:: a number of sequence in the alignment

- -

-getMetadata

-public AlignmentMetadata getMetadata()

Returns:: AlignmentMetadata object

- -

-toString

-public String toString()

Overrides:: toString in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

- -

-equals

-public boolean equals(Object obj)

Please note that this implementation does not take the order of sequences - into account! -

Overrides:: equals in class Object

- -

- - - - - - - - - - - - - - - - - - - -

- - - - - - - - - - - - -

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

- -

- PREV CLASS - NEXT CLASS

- FRAMES - NO FRAMES - - - - -

- SUMMARY: NESTED | FIELD | CONSTR | METHOD

-DETAIL: FIELD | CONSTR | METHOD

- - - -

- - -

- -compbio.data.sequence - -Class Alignment

-Alignment

-Alignment

-getSequences

-getSize

-getMetadata

-toString

-hashCode

-equals

- -compbio.data.sequence -
-Class Alignment