Package org.biojava.bio.symbol

Interface GappedSymbolList

All Superinterfaces:

Changeable, SymbolList

All Known Subinterfaces:

GappedSequence

All Known Implementing Classes:

SimpleGappedSequence, SimpleGappedSymbolList

public interface GappedSymbolList
extends SymbolList

This extends SymbolList with API for manipulating, inserting and deleting gaps.

You could make a SymbolList that contains gaps directly. However, this leaves you with a nasty problem if you wish to support gap-edit operations. Also, the original SymbolList must either be coppied or lost.

GappedSymbolList solves these problems. It will maintain a data-structure that places gaps. You can add and remove the gaps by using the public API.

For gap-insert operations, the insert index is the position that will become a gap. The symbol currently there will move to a higher index. To insert leading gaps, add gaps at index 1. To insert trailing gaps, add gaps at index length+1.

Since:

1.3

Author:

Matthew Pocock

Field Summary

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Method Summary

Modifier and Type	Method	Description
void	addGapInSource(int pos)	Add a gap at pos within the source coordinates.
void	addGapInView(int pos)	Add a single gap at pos within the view coordintates.
void	addGapsInSource(int pos, int length)	Add length gaps at pos within the source coordinates.
void	addGapsInView(int pos, int length)	Add length gaps at pos within the view coordinates.
int	firstNonGap()	Return the index of the first Symbol that is not a Gap character.
SymbolList	getSourceSymbolList()	Return the underlying (ungapped) SymbolList.
Location	getUngappedLocation()	Get a Location that contains exactly those positions that are not gaps.
int	lastNonGap()	Return the index of the last Symbol that is not a Gap character.
void	removeGap(int pos)	Remove a single gap at position pos in this GappedSymbolList.
void	removeGaps(int pos, int length)	Remove some gaps at position pos in this GappedSymbolList.
int	sourceToView(int indx)	Coordinate conversion from source to view.
int	viewToSource(int indx)	Coordinate conversion from view to source.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.symbol.SymbolList

edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList

Method Detail

getSourceSymbolList

SymbolList getSourceSymbolList()

Return the underlying (ungapped) SymbolList.

Since:

1.4

viewToSource

int viewToSource(int indx)
          throws IndexOutOfBoundsException

Coordinate conversion from view to source.

If the index can be projected onto the source, the index it projects onto is returned. If it falls within a gap, then the index of the first symbol after the run of gaps is negated and returned. If the index is after the last block of symbols (and therefore in the trailing list of gaps), then it returns -(length + 1).

Parameters:

indx - the index to project

Returns:

the position of indx projected from view to source

Throws:

IndexOutOfBoundsException - if indx is not a valid view index

sourceToView

int sourceToView(int indx)
          throws IndexOutOfBoundsException

Coordinate conversion from source to view.

Parameters:

indx - the index to project

Returns:

the position of indx projected from source to view

Throws:

IndexOutOfBoundsException - if indx is not a valid source index

addGapInView

void addGapInView(int pos)
           throws IndexOutOfBoundsException

Add a single gap at pos within the view coordintates.

this.symbolAt(pos) will then return gap. Adding a gap at 1 will prepend gaps. Adding a gap at (length+1) will append a gap.

Parameters:

pos - the position to add a gap before

Throws:

IndexOutOfBoundsException - if pos is not within 1->length+1

addGapsInView

void addGapsInView(int pos,
                   int length)
            throws IndexOutOfBoundsException

Add length gaps at pos within the view coordinates.

this.symbolAt(i) will then return gap for i = (pos .. pos+count-1). Adding gaps at 1 will prepend gaps. Adding gaps at (length+1) will append gaps.

Parameters:

pos - the position to add a gap before

length - the number of gaps to insert

Throws:

IndexOutOfBoundsException - if pos is not within 1->length+1

addGapInSource

void addGapInSource(int pos)
             throws IndexOutOfBoundsException

Add a gap at pos within the source coordinates.

Parameters:

pos - where to add the gap

Throws:

IndexOutOfBoundsException - if pos is not within 1->source.length()

addGapsInSource

void addGapsInSource(int pos,
                     int length)
              throws IndexOutOfBoundsException

Add length gaps at pos within the source coordinates.

Parameters:

pos - where to add the gap

length - how many gaps to add

Throws:

IndexOutOfBoundsException - if pos is not within 1->source.length()

removeGap

void removeGap(int pos)
        throws IndexOutOfBoundsException,
               IllegalSymbolException

Remove a single gap at position pos in this GappedSymbolList.

Parameters:

pos - where to remove the gap

Throws:

IndexOutOfBoundsException - if pos is not within 1..length

IllegalSymbolException - if the symbol at pos is not a gap

removeGaps

void removeGaps(int pos,
                int length)
         throws IndexOutOfBoundsException,
                IllegalSymbolException

Remove some gaps at position pos in this GappedSymbolList.

Parameters:

pos - where to remove the gaps

length - how many to remove

Throws:

IndexOutOfBoundsException - if pos is not within 1..length() or if some of the Symbols within pos->(pos+length-1) are not gap Symbols

IllegalSymbolException - if the symbol at pos is not a gap

firstNonGap

int firstNonGap()

Return the index of the first Symbol that is not a Gap character.

All symbols before firstNonGap are leading gaps. firstNonGap is effectively the index in the view of symbol 1 in the original sequence.

Returns:

the index of the first character not to be a gap

lastNonGap

int lastNonGap()

Return the index of the last Symbol that is not a Gap character.

All symbols after lastNonGap untill length are trailing gaps. lastNonGap is effectively the index in the view of symbol length in the original sequence.

Returns:

the index of the last character not to be a gap

getUngappedLocation

Location getUngappedLocation()

Get a Location that contains exactly those positions that are not gaps.

This will be a Location that contains every symbol in the underlying ungapped sequence. Every symbol not in the Location is not from the underlying sequence and is a gap.

Returns:

a new Location that contains all non-gap symbols