org.biojava.bio.symbol

Class SimpleGappedSymbolList

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.AbstractSymbolList

org.biojava.bio.symbol.SimpleGappedSymbolList

All Implemented Interfaces:

Serializable, GappedSymbolList, SymbolList, Changeable

Direct Known Subclasses:

SimpleGappedSequence

public class SimpleGappedSymbolList
extends AbstractSymbolList
implements GappedSymbolList, Serializable

This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps. Please note that this is a view onto another SymbolList. Gaps created and removed are only in the view not the underlying original. This means that any gaps present in the original cannot be manipulated in this view. To manipulate the original you would need to use Edit objects.

Since:

1.3

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	SimpleGappedSymbolList.Block An aligned block.

Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList

AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater

Field Summary

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

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Constructor and Description
SimpleGappedSymbolList(Alphabet alpha)
SimpleGappedSymbolList(GappedSymbolList gappedSource) Create a new SimpleGappedSymbolList that will view source, inheriting all existing gaps.
SimpleGappedSymbolList(SymbolList source) Create a new SimpleGappedSymbolList that will view source.

Method Summary

Modifier and Type	Method and 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.
List<SimpleGappedSymbolList.Block>	BlockIterator() Get list of the un-gapped region of the SymbolList.
void	dumpBlocks() Debugging method
protected int	findSourceBlock(int indx) Finds the index of the block containing the source coordinate indx.
protected int	findSourceGap(int indx) Finds the index of the Block before the gap at indx within the following gap.
protected int	findViewBlock(int indx) Finds the index of the Block containing indx within the view ranges.
protected int	findViewGap(int indx) Finds the index of the Block before the gap at indx within the view range.
int	firstNonGap() Return the index of the first Symbol that is not a Gap character.
Location	gappedToLocation(Location l) Translates a Location from the gapped view into the underlying sequence.
Alphabet	getAlphabet() The alphabet that this SymbolList is over.
SymbolList	getSourceSymbolList() Return the underlying (ungapped) SymbolList.
Location	getUngappedLocation() Get a Location that contains exactly those positions that are not gaps.
protected boolean	isSane()
int	lastNonGap() Return the index of the last Symbol that is not a Gap character.
int	length() The number of symbols in this SymbolList.
Location	locationToGapped(Location l) Translate a Location onto the gapped view, splitting blocks if necessary
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.
protected void	renumber(int i, int delta) Renumber the view indexes from block, adding delta to each offset.
int	sourceToView(int indx) Coordinate conversion from source to view.
protected int	sourceToView(SimpleGappedSymbolList.Block b, int indx) Coordinate conversion from source to view.
Symbol	symbolAt(int indx) Return the symbol at index, counting from 1.
int	viewToSource(int indx) Coordinate conversion from view to source.
protected int	viewToSource(SimpleGappedSymbolList.Block b, int indx) Coordinate conversion from view to source.

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList

edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

edit, iterator, seqString, subList, subStr, toList

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

SimpleGappedSymbolList

public SimpleGappedSymbolList(GappedSymbolList gappedSource)

Create a new SimpleGappedSymbolList that will view source, inheriting all existing gaps.

Parameters:

gappedSource - the underlying sequence

SimpleGappedSymbolList

public SimpleGappedSymbolList(SymbolList source)

Create a new SimpleGappedSymbolList that will view source.

Parameters:

source - the underlying sequence

SimpleGappedSymbolList

public SimpleGappedSymbolList(Alphabet alpha)

Method Detail

addGapInSource

public void addGapInSource(int pos)
                    throws IndexOutOfBoundsException

Description copied from interface: GappedSymbolList

Add a gap at pos within the source coordinates.

Specified by:

addGapInSource in interface GappedSymbolList

Parameters:

pos - where to add the gap

Throws:

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

addGapInView

public void addGapInView(int pos)
                  throws IndexOutOfBoundsException

Description copied from interface: GappedSymbolList

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.

Specified by:

addGapInView in interface GappedSymbolList

Parameters:

pos - the position to add a gap before

Throws:

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

addGapsInSource

public void addGapsInSource(int pos,
                            int length)

Description copied from interface: GappedSymbolList

Add length gaps at pos within the source coordinates.

Specified by:

addGapsInSource in interface GappedSymbolList

Parameters:

pos - where to add the gap

length - how many gaps to add

addGapsInView

public void addGapsInView(int pos,
                          int length)
                   throws IndexOutOfBoundsException

Description copied from interface: GappedSymbolList

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.

Specified by:

addGapsInView in interface GappedSymbolList

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

BlockIterator

public List<SimpleGappedSymbolList.Block> BlockIterator()

Get list of the un-gapped region of the SymbolList.

The gapped symbol list can be represented as a list of ungapped regions. Given a list of start-stop pairs in the ungapped coordinate system each with a corresponding pair of start-stop pairs in the gapped view, the entire gapped list can be reconstructed.

Returns:

a List of Block instances

dumpBlocks

public void dumpBlocks()

Debugging method

firstNonGap

public int firstNonGap()

Description copied from interface: GappedSymbolList

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.

Specified by:

firstNonGap in interface GappedSymbolList

Returns:

the index of the first character not to be a gap

gappedToLocation

public Location gappedToLocation(Location l)

Translates a Location from the gapped view into the underlying sequence. End points that are in gaps are moved 'inwards' to shorten the location.

Since:

1.3

getAlphabet

public Alphabet getAlphabet()

Description copied from interface: SymbolList

The alphabet that this SymbolList is over.

Every symbol within this SymbolList is a member of this alphabet. alphabet.contains(symbol) == true for each symbol that is within this sequence.

Specified by:

getAlphabet in interface SymbolList

Returns:

the alphabet

getSourceSymbolList

public SymbolList getSourceSymbolList()

Description copied from interface: GappedSymbolList

Return the underlying (ungapped) SymbolList.

Specified by:

getSourceSymbolList in interface GappedSymbolList

getUngappedLocation

public Location getUngappedLocation()

Description copied from interface: GappedSymbolList

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.

Specified by:

getUngappedLocation in interface GappedSymbolList

Returns:

a new Location that contains all non-gap symbols

lastNonGap

public int lastNonGap()

Description copied from interface: GappedSymbolList

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.

Specified by:

lastNonGap in interface GappedSymbolList

Returns:

the index of the last character not to be a gap

length

public int length()

Description copied from interface: SymbolList

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Returns:

the length

locationToGapped

public Location locationToGapped(Location l)

Translate a Location onto the gapped view, splitting blocks if necessary

Since:

1.3

removeGap

public void removeGap(int pos)
               throws IndexOutOfBoundsException,
                      IllegalSymbolException

Description copied from interface: GappedSymbolList

Remove a single gap at position pos in this GappedSymbolList.

Specified by:

removeGap in interface 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

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

Description copied from interface: GappedSymbolList

Remove some gaps at position pos in this GappedSymbolList.

Specified by:

removeGaps in interface 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

sourceToView

public final int sourceToView(int indx)
                       throws IndexOutOfBoundsException

Description copied from interface: GappedSymbolList

Coordinate conversion from source to view.

Specified by:

sourceToView in interface GappedSymbolList

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

symbolAt

public Symbol symbolAt(int indx)
                throws IndexOutOfBoundsException

Description copied from interface: SymbolList

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface SymbolList

Parameters:

indx - the offset into this SymbolList

Returns:

the Symbol at that index

Throws:

IndexOutOfBoundsException - if index is less than 1, or greater than the length of the symbol list

viewToSource

public final int viewToSource(int indx)
                       throws IndexOutOfBoundsException

Description copied from interface: GappedSymbolList

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).

Specified by:

viewToSource in interface GappedSymbolList

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

findSourceBlock

protected final int findSourceBlock(int indx)

Finds the index of the block containing the source coordinate indx.

Parameters:

indx - the index to find

Returns:

the index of the Block containing indx

findSourceGap

protected final int findSourceGap(int indx)

Finds the index of the Block before the gap at indx within the following gap.

Parameters:

indx - the index to find within a gap

Returns:

the index of the block with indx in the gap

findViewBlock

protected final int findViewBlock(int indx)

Finds the index of the Block containing indx within the view ranges.

If indx is not within a view block, then it is the index of a gap. The method will return -(indx+1) where indx is the block emediately following the gap.

Parameters:

indx - the index to find within a view range.

Returns:

the index of the block containing index or one less than the negative of the index of the block following the gap

findViewGap

protected final int findViewGap(int indx)

Finds the index of the Block before the gap at indx within the view range.

If indx is in-fact a real symbol, then there will be no Block before it. In this case, the method returns -2. It returns -1 if indx is within the leading gaps and blocks.size()-1 if it is within the trailing gaps.

Parameters:

indx - the index to find within a view range

Returns:

the index of the block with indx in the following gap

isSane

protected boolean isSane()

renumber

protected final void renumber(int i,
                              int delta)

Renumber the view indexes from block, adding delta to each offset.

This adjusts viewStart and viewEnd to be += delta for each block i->blocks.size(), and sets the total length to += delta.

Parameters:

i - the first

sourceToView

protected final int sourceToView(SimpleGappedSymbolList.Block b,
                                 int indx)

Coordinate conversion from source to view.

Parameters:

b - the block containing indx

indx - the index to project

Returns:

the position of indx projected from source to view

viewToSource

protected final int viewToSource(SimpleGappedSymbolList.Block b,
                                 int indx)

Coordinate conversion from view to source.

Parameters:

b - the block containing indx

indx - the index to project

Returns:

the position of indx projected from view to source