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Uses of Class
org.biojava.bio.symbol.Edit

Packages that use Edit
org.biojava.bio.alignment Classes to generate and describe sequence alignments. 
org.biojava.bio.dp HMM and Dynamic Programming Algorithms. 
org.biojava.bio.program.das Development client for the Distributed Annotation System. 
org.biojava.bio.seq Classes and interfaces for defining biological sequences and informatics objects. 
org.biojava.bio.seq.homol The classes and interfaces for defining sequence similarity and honology. 
org.biojava.bio.seq.impl Standard in-memory implementations of Sequence and Feature. 
org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. 
org.biojavax.bio.db.biosql   
org.biojavax.bio.seq Rich implementations of Sequences, Locations and Features. 
 

Uses of Edit in org.biojava.bio.alignment
 

Methods in org.biojava.bio.alignment with parameters of type Edit
 void FlexibleAlignment.edit(Object label, Edit edit)
           
 void EditableAlignment.edit(Object label, Edit edit)
           edit() allows edits on an individual sequence, they should be reflected back to the underlying SymbolList.
 

Uses of Edit in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp with parameters of type Edit
 void SimpleStatePath.edit(Edit edit)
           
 

Uses of Edit in org.biojava.bio.program.das
 

Methods in org.biojava.bio.program.das with parameters of type Edit
 void DASSequence.edit(Edit e)
           
 

Uses of Edit in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq with parameters of type Edit
 void SimpleAssembly.edit(Edit e)
           
 void NewSimpleAssembly.edit(Edit e)
           
 

Uses of Edit in org.biojava.bio.seq.homol
 

Methods in org.biojava.bio.seq.homol with parameters of type Edit
 void SimilarityPairFeature.EmptyPairwiseAlignment.edit(Edit edit)
           
 

Uses of Edit in org.biojava.bio.seq.impl
 

Methods in org.biojava.bio.seq.impl with parameters of type Edit
 void RevCompSequence.edit(Edit e)
          edit() will try to edit the underlying Sequence.
 void SimpleSequence.edit(Edit edit)
           
 void DummySequence.edit(Edit edit)
           
 void ViewSequence.edit(Edit edit)
           
 void SubSequence.edit(Edit edit)
           
 

Uses of Edit in org.biojava.bio.symbol
 

Methods in org.biojava.bio.symbol with parameters of type Edit
 void AbstractSymbolList.edit(Edit edit)
           
 void RelabeledAlignment.edit(Edit edit)
           
 void SymbolList.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void SimpleSymbolList.edit(Edit edit)
          Apply and edit to the SymbolList as specified by Edit.
 

Uses of Edit in org.biojavax.bio.db.biosql
 

Methods in org.biojavax.bio.db.biosql with parameters of type Edit
 void BioSQLRichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence 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

 RichSequence seq = //code to initialize RichSequence
 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());
 

Uses of Edit in org.biojavax.bio.seq
 

Methods in org.biojavax.bio.seq with parameters of type Edit
 void ThinRichSequence.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object.
 void InfinitelyAmbiguousSymbolList.edit(Edit edit)
          Apply an edit to the SymbolList as specified by the edit object. IGNORED
 void RichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
 void DummyRichSequenceHandler.edit(RichSequence seq, Edit edit)
          Apply an edit to the Sequence as specified by the edit object.
 

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