public class NewSimpleAssembly extends AbstractChangeable implements Sequence, RealizingFeatureHolder
The class has been extended to handle overlapping component sequences. It is assumed that the overlaps are consistent between components: this will not be checked.
There is still some potential for optimising SymbolList operations on this class.
Annotatable.AnnotationForwarderFeatureHolder.EmptyFeatureHolder| Modifier and Type | Field and Description |
|---|---|
protected ChangeForwarder |
annotationForwarder |
EDIT, EMPTY_LISTANNOTATIONEMPTY_FEATURE_HOLDER, FEATURES, SCHEMA| Constructor and Description |
|---|
NewSimpleAssembly(int length,
String name,
String uri)
Construct a new SimpleAssembly using the DNA alphabet.
|
NewSimpleAssembly(String name,
String uri)
Construct a new NewSimpleAssembly using the DNA alphabet.
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
containsFeature(Feature f)
Check if the feature is present in this holder.
|
int |
countFeatures()
Count how many features are contained.
|
Feature |
createFeature(Feature.Template temp)
Create a new Feature, and add it to this FeatureHolder.
|
void |
edit(Edit e)
Apply an edit to the SymbolList as specified by the edit object.
|
Iterator |
features()
Iterate over the features in no well defined order.
|
FeatureHolder |
filter(FeatureFilter ff)
Query this set of features using a supplied
FeatureFilter. |
FeatureHolder |
filter(FeatureFilter ff,
boolean recurse)
Return a new FeatureHolder that contains all of the children of this one
that passed the filter fc.
|
Alphabet |
getAlphabet()
The alphabet that this SymbolList is over.
|
Annotation |
getAnnotation()
Should return the associated annotation object.
|
protected ChangeSupport |
getChangeSupport(ChangeType ct)
Called to retrieve the ChangeSupport for this object.
|
String |
getName()
The name of this sequence.
|
FeatureFilter |
getSchema()
Return a schema-filter for this
FeatureHolder. |
String |
getURN()
A Uniform
Resource Identifier (URI) which identifies the sequence
represented by this object.
|
Iterator |
iterator()
An Iterator over all Symbols in this SymbolList.
|
int |
length()
The number of symbols in this SymbolList.
|
Feature |
realizeFeature(FeatureHolder fh,
Feature.Template temp)
Realize a feature template.
|
void |
removeFeature(Feature f)
Remove a feature from this FeatureHolder.
|
String |
seqString()
Stringify this symbol list.
|
SymbolList |
subList(int start,
int end)
Return a new SymbolList for the symbols start to end inclusive.
|
String |
subStr(int start,
int end)
Return a region of this symbol list as a String.
|
Symbol |
symbolAt(int pos)
Return the symbol at index, counting from 1.
|
List |
toList()
Returns a List of symbols.
|
addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerprotected transient ChangeForwarder annotationForwarder
public NewSimpleAssembly(int length, String name, String uri)
length - The length of the sequencename - The name of the sequence (returned by getName())uri - The identifier of the sequence (returned by getURN());public NewSimpleAssembly(String name, String uri)
name - The name of the sequence (returned by getName())uri - The identifier of the sequence (returned by getURN());public Alphabet getAlphabet()
SymbolList
Every symbol within this SymbolList is a member of this alphabet.
alphabet.contains(symbol) == true
for each symbol that is within this sequence.
getAlphabet in interface SymbolListpublic int length()
SymbolListlength in interface SymbolListpublic Symbol symbolAt(int pos)
SymbolListsymbolAt in interface SymbolListpos - the offset into this SymbolListpublic SymbolList subList(int start, int end)
SymbolListThe resulting SymbolList will count from 1 to (end-start + 1) inclusive, and refer to the symbols start to end of the original sequence.
subList in interface SymbolListstart - the first symbol of the new SymbolListend - the last symbol (inclusive) of the new SymbolListpublic String seqString()
SymbolListIt 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.
seqString in interface SymbolListpublic String subStr(int start, int end)
SymbolListThis should use the same rules as seqString.
subStr in interface SymbolListstart - the first symbol to includeend - the last symbol to includepublic Iterator iterator()
SymbolListThis is an ordered iterator over the Symbols. It cannot be used to edit the underlying symbols.
iterator in interface SymbolListpublic List toList()
SymbolListThis is an immutable list of symbols. Do not edit it.
toList in interface SymbolListpublic void edit(Edit e) throws IllegalAlphabetException, ChangeVetoException
SymbolListAll 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:
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());
edit in interface SymbolListe - the Edit to performIllegalAlphabetException - if the SymbolList to insert has an
incompatible alphabetChangeVetoException - if either the SymboList does not support the
edit, or if the change was vetoedpublic String getName()
SequenceThe name may contain spaces or odd characters.
public String getURN()
Sequenceurn:sequence/embl:AL121903It 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
public Annotation getAnnotation()
AnnotatablegetAnnotation in interface Annotatablepublic Iterator features()
FeatureHolderfeatures in interface FeatureHolderpublic int countFeatures()
FeatureHoldercountFeatures in interface FeatureHolderpublic FeatureHolder filter(FeatureFilter ff, boolean recurse)
FeatureHolderfilter in interface FeatureHolderff - the FeatureFilter to applyrecurse - 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.public FeatureHolder filter(FeatureFilter ff)
FeatureHolderFeatureFilter.filter in interface FeatureHolderff - the FeatureFilter to apply.filter.public boolean containsFeature(Feature f)
FeatureHoldercontainsFeature in interface FeatureHolderf - the Feature to checkpublic Feature createFeature(Feature.Template temp) throws BioException, ChangeVetoException
FeatureHoldercreateFeature in interface FeatureHolderBioException - if something went wrong during creating the featureChangeVetoException - if this FeatureHolder does not support
creation of new features, or if the change was vetoedpublic void removeFeature(Feature f) throws ChangeVetoException
FeatureHolderremoveFeature in interface FeatureHolderChangeVetoException - if this FeatureHolder does not support
feature removal or if the change was vetoedpublic Feature realizeFeature(FeatureHolder fh, Feature.Template temp) throws BioException
RealizingFeatureHoldercreateFeature method of either
this FeatureHolder or one of our child Features.realizeFeature in interface RealizingFeatureHolderBioExceptionprotected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
Your implementation of this method should have the following structure:
ChangeSupport cs = super.getChangeSupport(ct);
if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
someForwarder = new ChangeForwarder(...
this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
}
return cs;
getChangeSupport in class AbstractChangeablepublic FeatureFilter getSchema()
FeatureHolderFeatureHolder. 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)).
getSchema in interface FeatureHolderCopyright © 2014 BioJava. All rights reserved.