Package 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:

  • Constructor Details

  • Method Details

    • 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