statalign.io
Class RawSequences

java.lang.Object
  statalign.io.RawSequences

All Implemented Interfaces:

DataType

public class RawSequences
extends java.lang.Object
implements DataType

Dynamic array of raw sequence data. Sequences can be aligned, in which case the strings must be of equal length and the '-' character must represent the gaps.

Author:

novak, miklos, aszabo

Field Summary

java.lang.String

alphabet Sorted string of characters present in sequences.

Constructor Summary

RawSequences()

RawSequences(java.lang.String seq, java.lang.String name)

Method Summary

void	add(RawSequences more)
void	add(java.lang.String name, java.lang.String sequence) Add a name and a sequence, that belong together.
void	addOrReplace(java.lang.String name, java.lang.String sequence)
void	clear() Removes all sequences (and their names).
java.lang.String	getAlphabet()
int	getMaxNameLength()
java.lang.String	getSeqName(int i)
java.lang.String	getSeqNamePadded(int i)
java.util.List<java.lang.String>	getSeqnames()
RawSequences	getSeqs()
java.lang.String	getSequence(int i)
java.util.List<java.lang.String>	getSequences()
java.lang.String	getSummaryAssociatedWith(java.lang.String sequenceName)
boolean	isAligned()
boolean	isRNA()
int	len() Returns the common length of the aligned sequences or -1 if sequences are unaligned (have different length).
static void	main(java.lang.String[] args)
boolean	perSequenceData()
boolean	remove(int i) Removes a sequence and its name.
boolean	removeByName(java.lang.String name) Removes a sequence and its name (given by name).
void	removeDataAssociatedWith(java.lang.String sequenceName)
void	removeGaps() Removes all gaps from each sequence.
void	setSeqs(RawSequences rs)
int	size() Returns the number of sequences.
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

alphabet

public java.lang.String alphabet

Sorted string of characters present in sequences. Does not contain the gap '-'.

Constructor Detail

RawSequences

public RawSequences()

RawSequences

public RawSequences(java.lang.String seq,
                    java.lang.String name)

Method Detail

getSeqs

public RawSequences getSeqs()

Specified by:

getSeqs in interface DataType

setSeqs

public void setSeqs(RawSequences rs)

Specified by:

setSeqs in interface DataType

perSequenceData

public boolean perSequenceData()

Specified by:

perSequenceData in interface DataType

Returns:

true if the DataType contains a List of items, each of which is associated with one of the input sequences, for example protein structure coordinates.

getSummaryAssociatedWith

public java.lang.String getSummaryAssociatedWith(java.lang.String sequenceName)

Specified by:

getSummaryAssociatedWith in interface DataType

removeDataAssociatedWith

public void removeDataAssociatedWith(java.lang.String sequenceName)

Specified by:

removeDataAssociatedWith in interface DataType

isAligned

public boolean isAligned()

len

public int len()

Returns the common length of the aligned sequences or -1 if sequences are unaligned (have different length).

add

public void add(java.lang.String name,
                java.lang.String sequence)

Add a name and a sequence, that belong together. If another sequence with the same name is already added then it won't be added.

addOrReplace

public void addOrReplace(java.lang.String name,
                         java.lang.String sequence)

add

public void add(RawSequences more)

getMaxNameLength

public int getMaxNameLength()

getAlphabet

public java.lang.String getAlphabet()

size

public int size()

Returns the number of sequences.

getSeqName

public java.lang.String getSeqName(int i)

getSequence

public java.lang.String getSequence(int i)

getSeqnames

public java.util.List<java.lang.String> getSeqnames()

getSequences

public java.util.List<java.lang.String> getSequences()

getSeqNamePadded

public java.lang.String getSeqNamePadded(int i)

remove

public boolean remove(int i)

Removes a sequence and its name.

Returns:

true on success

removeByName

public boolean removeByName(java.lang.String name)

Removes a sequence and its name (given by name).

Returns:

true on success

clear

public void clear()

Removes all sequences (and their names).

removeGaps

public void removeGaps()

Removes all gaps from each sequence.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isRNA

public boolean isRNA()

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException

Throws:

java.io.IOException