Class ThinRichSequence

Method Details

• getSeqVersion

  public Double getSeqVersion()

  The version of the associated symbol list. Note the use of an object for the value means that it can be nulled.

  Specified by:

  getSeqVersion in interface RichSequence

  Returns:

  the version

• setSeqVersion

  public void setSeqVersion(Double seqVersion) throws ChangeVetoException

  Sets the version of the associated symbol list. Note the use of an object for the value means that it can be nulled.

  Specified by:

  setSeqVersion in interface RichSequence

  Parameters:

  seqVersion - the version to set.

  Throws:

  ChangeVetoException - if it doesn't want to change.

• setCircular

  public void setCircular(boolean circular) throws ChangeVetoException

  Circularises the Sequence. The circular length can then be said to be the length of the sequence itself.

  Specified by:

  setCircular in interface RichSequence

  Parameters:

  circular - set to true if you want it to be circular

  Throws:

  ChangeVetoException - if the change is blocked. Some implementations may choose not to support circularisation and should throw an exception here. Some implementations may only support this method for certain Alphabets.

• getCircular

  public boolean getCircular()

  Is the sequence circular? Circularity has implications for work with locations and any coordinate work eg symbolAt(int i). Classes that allow it should test this method when working with coordinates or locations / features.

  Specified by:

  getCircular in interface RichSequence

  Returns:

  true if the this is circular else false.

• edit

  public void edit(Edit edit) throws IndexOutOfBoundsException, IllegalAlphabetException, ChangeVetoException

  Apply an edit to the SymbolList as specified by the edit object.

  Description

  All edits can be broken down into a series of operations that change contiguous blocks of the sequence. This represent a one of those operations.

  When applied, this Edit will replace 'length' number of symbols starting a position 'pos' by the SymbolList 'replacement'. This allow to do insertions (length=0), deletions (replacement=SymbolList.EMPTY_LIST) and replacements (length>=1 and replacement.length()>=1).

  The pos and pos+length should always be valid positions on the SymbolList to:

  • be edited (between 0 and symL.length()+1).
  • To append to a sequence, pos=symL.length()+1, pos=0.
  • To insert something at the beginning of the sequence, set pos=1 and length=0.

  Examples

   SymbolList seq = DNATools.createDNA("atcaaaaacgctagc");
   System.out.println(seq.seqString());
  
   // delete 5 bases from position 4
   Edit ed = new Edit(4, 5, SymbolList.EMPTY_LIST);
   seq.edit(ed);
   System.out.println(seq.seqString());
  
   // delete one base from the start
   ed = new Edit(1, 1, SymbolList.EMPTY_LIST);
   seq.edit(ed);
  
   // delete one base from the end
   ed = new Edit(seq.length(), 1, SymbolList.EMPTY_LIST);
   seq.edit(ed);
   System.out.println(seq.seqString());
  
   // overwrite 2 bases from position 3 with "tt"
   ed = new Edit(3, 2, DNATools.createDNA("tt"));
   seq.edit(ed);
   System.out.println(seq.seqString());
  
   // add 6 bases to the start
   ed = new Edit(1, 0, DNATools.createDNA("aattgg");
   seq.edit(ed);
   System.out.println(seq.seqString());
  
   // add 4 bases to the end
   ed = new Edit(seq.length() + 1, 0, DNATools.createDNA("tttt"));
   seq.edit(ed);
   System.out.println(seq.seqString());
  
   // full edit
   ed = new Edit(3, 2, DNATools.createDNA("aatagaa");
   seq.edit(ed);
   System.out.println(seq.seqString());
   

  Specified by:

  edit in interface SymbolList

  Parameters:

  edit - the Edit to perform

  Throws:

  IndexOutOfBoundsException - if the edit does not lie within the SymbolList

  IllegalAlphabetException - if the SymbolList to insert has an incompatible alphabet

  ChangeVetoException - if either the SymboList does not support the edit, or if the change was vetoed

• symbolAt

  public Symbol symbolAt(int index) throws IndexOutOfBoundsException

  Return the symbol at index, counting from 1.

  Specified by:

  symbolAt in interface SymbolList

  Parameters:

  index - 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

• toList

  public List toList()

  Returns a List of symbols.

  This is an immutable list of symbols. Do not edit it.

  Specified by:

  toList in interface SymbolList

  Returns:

  a List of Symbols

• subStr

  public String subStr(int start, int end) throws IndexOutOfBoundsException

  Return a region of this symbol list as a String.

  This should use the same rules as seqString.

  Specified by:

  subStr in interface SymbolList

  Parameters:

  start - the first symbol to include

  end - the last symbol to include

  Returns:

  the string representation

  Throws:

  IndexOutOfBoundsException - if either start or end are not within the SymbolList

• subList

  public SymbolList subList(int start, int end) throws IndexOutOfBoundsException

  Return a new SymbolList for the symbols start to end inclusive.

  The resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.

  Specified by:

  subList in interface SymbolList

  Parameters:

  start - the first symbol of the new SymbolList

  end - the last symbol (inclusive) of the new SymbolList

  Throws:

  IndexOutOfBoundsException

• seqString

  public String seqString()

  Stringify this symbol list.

  It is expected that this will use the symbol's token to render each symbol. It should be parsable back into a SymbolList using the default token parser for this alphabet.

  Specified by:

  seqString in interface SymbolList

  Returns:

  a string representation of the symbol list

• length

  public int length()

  The number of symbols in this SymbolList.

  Specified by:

  length in interface SymbolList

  Returns:

  the length

• iterator

  public Iterator iterator()

  An Iterator over all Symbols in this SymbolList.

  This is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.

  Specified by:

  iterator in interface SymbolList

  Returns:

  an iterator

• getAlphabet

  public Alphabet getAlphabet()

  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

• setAlphabetName

  protected void setAlphabetName(String alphaname) throws IllegalSymbolException, BioException

  Throws:

  IllegalSymbolException

  BioException

• getAlphabetName

  protected String getAlphabetName()

• setSequenceLength

  protected void setSequenceLength(int length)

• getSequenceLength

  protected int getSequenceLength()

• getURN

  public String getURN()

  A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g.

   urn:sequence/embl:AL121903
   

  It may also be a URL identifying a specific resource, either locally or over the network

   file:///home/thomas/myseq.fa|seq22
   http://www.mysequences.net/chr22.seq
   

  Specified by:

  getURN in interface Sequence

  Returns:

  the URI as a String

• filter

  public FeatureHolder filter(FeatureFilter fc, boolean recurse)

  Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.

  Specified by:

  filter in interface FeatureHolder

  Parameters:

  fc - the FeatureFilter to apply

  recurse - true if all features-of-features should be scanned, and a single flat collection of features returned, or false if just immediate children should be filtered.

• createFeature

  public Feature createFeature(Feature.Template ft) throws BioException, ChangeVetoException

  Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.

  Specified by:

  createFeature in interface FeatureHolder

  Throws:

  BioException - if something went wrong during creating the feature

  ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

• removeFeature

  public void removeFeature(Feature f) throws ChangeVetoException, BioException

  Remove a feature from this FeatureHolder.

  Specified by:

  removeFeature in interface FeatureHolder

  Throws:

  ChangeVetoException - if this FeatureHolder does not support feature removal or if the change was vetoed

  BioException - if there was an error removing the feature

• containsFeature

  public boolean containsFeature(Feature f)

  Check if the feature is present in this holder.

  Specified by:

  containsFeature in interface FeatureHolder

  Parameters:

  f - the Feature to check

  Returns:

  true if f is in this set

• filter

  public FeatureHolder filter(FeatureFilter filter)

  Query this set of features using a supplied FeatureFilter.

  Specified by:

  filter in interface FeatureHolder

  Parameters:

  filter - the FeatureFilter to apply.

  Returns:

  all features in this container which match filter.

• getFeatureSet

  public Set<Feature> getFeatureSet()

  The features for this sequence. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:

  getFeatureSet in interface RichSequence

  Returns:

  a set of RichFeature objects.

• setFeatureSet

  public void setFeatureSet(Set<Feature> features) throws ChangeVetoException

  Sets the features of this sequence. Note that it is not checked to see if the features actually belong to this sequence, you'd best check that yourself and make changes using feature.setParent() if necessary. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:

  setFeatureSet in interface RichSequence

  Parameters:

  features - the features to assign to this sequence, replacing all others. Must be a set of RichFeature objects.

  Throws:

  ChangeVetoException - if they could not be assigned.

• getSchema

  public FeatureFilter getSchema()

  Return a schema-filter for this FeatureHolder. This is a filter which all Features immediately contained by this FeatureHolder will match. It need not directly match their child features, but it can (and should!) provide information about them using FeatureFilter.OnlyChildren filters. In cases where there is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in the schema filter.

  For the truly non-informative case, it is possible to return FeatureFilter.all. However, it is almost always possible to provide slightly more information that this. For example, Sequence objects should, at a minimum, return FeatureFilter.top_level. Feature objects should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).

  Specified by:

  getSchema in interface FeatureHolder

  Returns:

  the schema filter

• features

  public Iterator<Feature> features()

  Iterate over the features in no well defined order. Warning this method gives access to the original Collection not a copy. This is required by Hibernate. If you modify the object directly the behaviour may be unpredictable.

  Specified by:

  features in interface FeatureHolder

  Returns:

  an Iterator

• countFeatures

  public int countFeatures()

  Count how many features are contained.

  Specified by:

  countFeatures in interface FeatureHolder

  Returns:

  a positive integer or zero, equal to the number of features contained

• getInternalSymbolList

  public SymbolList getInternalSymbolList()

  A special function that returns the SymbolList that this RichSequence is based around. This should _not_ be the RichSequence object itself, as this function is used to perform actions on the symbol list without referring to the RichSequence object directly.

  Specified by:

  getInternalSymbolList in interface RichSequence

  Returns:

  the internal SymbolList of the RichSequence, NOT the RichSequence object itself.