Package org.biojava.bio.alignment

Interface EditableAlignment

All Known Implementing Classes:

FlexibleAlignment

public interface EditableAlignment

EditableAlignment is an interface that defines methods for shifting bases within an Alignment.

Shift should work as follows. Bases within a sequence can be shifted to the right with offset > 1 to the left with offset < 1. Shifting bases will be allowed if:

1: Shift would remove only gaps on one side, they will be replace with gaps on the other. 2: Shift is at the end of a sequence. It will add gaps if the range location is less than the whole sequence. Shifts that would delete bases will throw a IllegalEditException

If the Alignment is an UnequalLengthAlignment it should be acceptable to shift bases in such a way as to increase (or decrease) the size of the overall length of the alignment, i.e. shift them over the edge.

Author:

David Waring

Field Summary

Fields

Modifier and Type	Field	Description
static ChangeType	GAPS
static ChangeType	LOCATION

Method Summary

Modifier and Type	Method	Description
void	edit(Object label, Edit edit)	edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
void	shiftAtAlignmentLoc(Object label, Location loc, int offset)	loc in this case is the Alignment Location
void	shiftAtSequenceLoc(Object label, Location loc, int offset)	loc in this case is the SymbolList Location

Field Detail

LOCATION

static final ChangeType LOCATION

GAPS

static final ChangeType GAPS

Method Detail

edit

void edit(Object label,
          Edit edit)
   throws ChangeVetoException

edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.

Throws:

ChangeVetoException

shiftAtAlignmentLoc

void shiftAtAlignmentLoc(Object label,
                         Location loc,
                         int offset)
                  throws ChangeVetoException,
                         IllegalAlignmentEditException,
                         IndexOutOfBoundsException

loc in this case is the Alignment Location

Throws:

ChangeVetoException

IllegalAlignmentEditException

IndexOutOfBoundsException

shiftAtSequenceLoc

void shiftAtSequenceLoc(Object label,
                        Location loc,
                        int offset)
                 throws ChangeVetoException,
                        IllegalAlignmentEditException,
                        IndexOutOfBoundsException

loc in this case is the SymbolList Location

Throws:

ChangeVetoException

IllegalAlignmentEditException

IndexOutOfBoundsException