EditableAlignment (biojava-legacy 1.9.1 API)

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 and Description

static ChangeType GAPS

static ChangeType LOCATION

Fields
Modifier and Type	Field and Description
`static ChangeType`	`GAPS`
`static ChangeType`	`LOCATION`

Method Summary

Methods
Modifier and Type	Method and 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

Interface EditableAlignment

Field Summary

Method Summary

Field Detail

LOCATION

GAPS

Method Detail

edit

shiftAtAlignmentLoc

shiftAtSequenceLoc