-FastaSequence -

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- -compbio.data.sequence -
-Class FastaSequence

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

@Immutable -public class FastaSequence
extends Object
extends Object

- - -

-A FASTA formatted sequence. Please note that this class does not make any - assumptions as to what sequence it stores e.g. it could be nucleotide, - protein or even gapped alignment sequence! The only guarantee it makes is - that the sequence does not contain white space characters e.g. spaces, new - lines etc -

- -

Version:: 1.0 September 2009
Author:: pvtroshin

- -

- - - - - - - - - - - -
-Constructor Summary
FastaSequence(String id, - String sequence) - -
-          Upon construction the any whitespace characters are removed from the - sequence
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-Method Summary
-static int countMatchesInSequence(String theString, - String theRegExp) - -
-
- boolean equals(Object obj) - -
-
- String getFormatedSequence(int width) - -
-          Format sequence per width letter in one string.
- String getFormattedFasta() - -
-
- String getId() - -
-          Gets the value of id
- int getLength() - -
-
- String getOnelineFasta() - -
-
- String getSequence() - -
-          Gets the value of sequence
- int hashCode() - -
-
- String toString() - -
-          Same as oneLineFasta
- - - - - - - - -
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
- -

-Constructor Summary
`FastaSequence(String id, - String sequence)` - - - Upon construction the any whitespace characters are removed from the - sequence

-Method Summary
-`static int`	`countMatchesInSequence(String theString, - String theRegExp)` - - -
- `boolean`	`equals(Object obj)` - - -
- `String`	`getFormatedSequence(int width)` - - - Format sequence per width letter in one string.
- `String`	`getFormattedFasta()` - - -
- `String`	`getId()` - - - Gets the value of id
- `int`	`getLength()` - - -
- `String`	`getOnelineFasta()` - - -
- `String`	`getSequence()` - - - Gets the value of sequence
- `int`	`hashCode()` - - -
- `String`	`toString()` - - - Same as oneLineFasta

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

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

-FastaSequence

-public FastaSequence(String id,
-                     String sequence)

Upon construction the any whitespace characters are removed from the - sequence -

Parameters:: id -; sequence -

- - - - - - - - -

-Method Detail

- -

-getId

-public String getId()

Gets the value of id -

Returns:: the value of id

- -

-getSequence

-public String getSequence()

Gets the value of sequence -

Returns:: the value of sequence

- -

-countMatchesInSequence

-public static int countMatchesInSequence(String theString,
-                                         String theRegExp)

- -

-getFormattedFasta

-public String getFormattedFasta()

- -

-getOnelineFasta

-public String getOnelineFasta()

Returns:: one line name, next line sequence, no matter what the sequence - length is

- -

-getFormatedSequence

-public String getFormatedSequence(int width)

Format sequence per width letter in one string. Without spaces. -

Returns:: multiple line formated sequence, one line width letters length

- -

-getLength

-public int getLength()

Returns:: sequence length

- -

-toString

-public String toString()

Same as oneLineFasta -

Overrides:: toString in class Object

- -

-hashCode

-public int hashCode()

Overrides:: hashCode in class Object

- -

-equals

-public boolean equals(Object obj)

Overrides:: equals in class Object

- -