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## 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
`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.bio.symbol.SymbolList
`edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

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

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