public interface GappedSymbolList extends SymbolList
You could make a SymbolList that contains gaps directly. However, this leaves you with a nasty problem if you wish to support gapedit operations. Also, the original SymbolList must either be coppied or lost.
GappedSymbolList solves these problems. It will maintain a datastructure that places gaps. You can add and remove the gaps by using the public API.
For gapinsert 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.
EDIT, EMPTY_LIST
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.

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.

edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
SymbolList getSourceSymbolList()
int viewToSource(int indx) throws IndexOutOfBoundsException
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).
indx
 the index to projectIndexOutOfBoundsException
 if indx is not a valid view indexint sourceToView(int indx) throws IndexOutOfBoundsException
indx
 the index to projectIndexOutOfBoundsException
 if indx is not a valid source indexvoid addGapInView(int pos) throws IndexOutOfBoundsException
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.
pos
 the position to add a gap beforeIndexOutOfBoundsException
 if pos is not within 1>length+1void addGapsInView(int pos, int length) throws IndexOutOfBoundsException
this.symbolAt(i) will then return gap for i = (pos .. pos+count1). Adding gaps at 1 will prepend gaps. Adding gaps at (length+1) will append gaps.
pos
 the position to add a gap beforelength
 the number of gaps to insertIndexOutOfBoundsException
 if pos is not within 1>length+1void addGapInSource(int pos) throws IndexOutOfBoundsException
pos
 where to add the gapIndexOutOfBoundsException
 if pos is not within 1>source.length()void addGapsInSource(int pos, int length) throws IndexOutOfBoundsException
pos
 where to add the gaplength
 how many gaps to addIndexOutOfBoundsException
 if pos is not within 1>source.length()void removeGap(int pos) throws IndexOutOfBoundsException, IllegalSymbolException
pos
 where to remove the gapIndexOutOfBoundsException
 if pos is not within 1..lengthIllegalSymbolException
 if the symbol at pos is not a gapvoid removeGaps(int pos, int length) throws IndexOutOfBoundsException, IllegalSymbolException
pos
 where to remove the gapslength
 how many to removeIndexOutOfBoundsException
 if pos is not within 1..length() or if some of the Symbols
within pos>(pos+length1) are not gap SymbolsIllegalSymbolException
 if the symbol at pos is not a gapint firstNonGap()
All symbols before firstNonGap are leading gaps. firstNonGap is effectively the index in the view of symbol 1 in the original sequence.
int lastNonGap()
All symbols after lastNonGap untill length are trailing gaps. lastNonGap is effectively the index in the view of symbol length in the original sequence.
Location getUngappedLocation()
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.
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