org.biojavax.bio.db.biosql
Class BioSQLRichSequenceHandler

java.lang.Object
  org.biojavax.bio.seq.DummyRichSequenceHandler
      org.biojavax.bio.db.biosql.BioSQLRichSequenceHandler

All Implemented Interfaces:

RichSequenceHandler

public class BioSQLRichSequenceHandler
extends DummyRichSequenceHandler

A handler which loads sequence data from a BioSQL database, caching it where possible. Note that this data is read-only. If you want to modify it permanently, you must use BioSQLRichSequenceDB.getRichSequence() to convert the original sequence into a proper SimpleRichSequence.

Since:

1.5

Author:

Richard Holland, David Scott

Constructor Summary

BioSQLRichSequenceHandler(Object session)
Requires a Hibernate session to work correctly.

Method Summary

void	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());
Iterator	iterator(RichSequence seq) 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.
String	seqString(RichSequence seq) Stringify this Sequences. 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.
SymbolList	subList(RichSequence seq, int start, int end) 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.
String	subStr(RichSequence seq, int start, int end) Return a region of this sequence as a String. This should use the same rules as seqString.
Symbol	symbolAt(RichSequence seq, int index) Return the symbol at index, counting from 1.
List	toList(RichSequence seq) Returns a List of symbols. This should be an immutable list of symbols or a copy.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioSQLRichSequenceHandler

public BioSQLRichSequenceHandler(Object session)

Requires a Hibernate session to work correctly. The session parameter is a Hibernate Session object and must not be null. It is this session that database objects will be retrieved from/persisted to.

See Also:

org.hibernate.Session

Method Detail

edit

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

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());
 

Specified by:

edit in interface RichSequenceHandler

Overrides:

edit in class DummyRichSequenceHandler

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(RichSequence seq,
                       int index)
                throws IndexOutOfBoundsException

Return the symbol at index, counting from 1.

Specified by:

symbolAt in interface RichSequenceHandler

Overrides:

symbolAt in class DummyRichSequenceHandler

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(RichSequence seq)

Returns a List of symbols.

This should be an immutable list of symbols or a copy.

Specified by:

toList in interface RichSequenceHandler

Overrides:

toList in class DummyRichSequenceHandler

Returns:

a List of Symbols

subStr

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

Return a region of this sequence as a String.

This should use the same rules as seqString.

Specified by:

subStr in interface RichSequenceHandler

Overrides:

subStr in class DummyRichSequenceHandler

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(RichSequence seq,
                          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 RichSequenceHandler

Overrides:

subList in class DummyRichSequenceHandler

start - the first symbol of the new SymbolList

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

Throws:

IndexOutOfBoundsException

seqString

public String seqString(RichSequence seq)

Stringify this Sequences.

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 RichSequenceHandler

Overrides:

seqString in class DummyRichSequenceHandler

Returns:

a string representation of the symbol list

iterator

public Iterator iterator(RichSequence seq)

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 RichSequenceHandler

Overrides:

iterator in class DummyRichSequenceHandler

Returns:

an iterator