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java.lang.Object | +--uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment | +--uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment
DefaultSequenceAlignment.java A class to model the multiple sequence alignment. NB: Sequence numbering starts at 1 NOT 0. Created: Mon Feb 21 13:51:11 2000
Constructor Summary | |
DefaultSequenceAlignment(Element[][] seqs,
SequenceType type)
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DefaultSequenceAlignment(GappedSequence[] seqs,
SequenceType type)
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DefaultSequenceAlignment(GappedSequence[] seqs,
SequenceType type,
int[] inset)
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DefaultSequenceAlignment(GappedSequence[] seqs,
SequenceType type,
int[] inset,
Identifier ident)
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DefaultSequenceAlignment(SequenceAlignment msa,
SequenceType type)
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DefaultSequenceAlignment(SequenceType type)
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DefaultSequenceAlignment(SequenceType type,
Identifier ident)
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Method Summary | |
protected void |
addSequenceQuietly(GappedSequence seq,
int inset)
Adds a sequence quietly to the alignment (i.e., without notifying listeners - it should really only be done from it's parent procedure addSequence). |
Identifier |
getIdentifier()
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int |
getInset(int seqIndex)
Returns the inset of a particular sequence in the alignment. |
int |
getLength()
Returns the length of the multiple sequence alignment. |
int |
getNumberSequences()
Returns the total number of sequences in the multiple sequence alignment. |
GappedSequence |
getSequenceAt(int index)
Returns the sequence, given a specific location in the MSA. |
int |
getSequenceIndex(GappedSequence seq)
Returns the location of a sequence, in the multiple sequence alignment. |
SequenceType |
getSequenceType()
Returns the sequence type for the alignment (e.g: Protien Sequence). |
SequenceAlignment |
getSubAlignment(int startPos,
int length,
int startSeq,
int numSeqs)
Returns a sub-alignment, given the exact location in this alignment. |
protected void |
init(GappedSequence[] seqs,
SequenceType type,
int[] inset,
Identifier ident)
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protected GappedSequence |
removeSequenceQuietly(int seqIndex)
Removes a sequence from the alignment, quietly, i.e., without notifying any listeners. |
protected void |
setInsetQuietly(int seqIndex,
int inset)
Sets the inset (or preceeding number of gaps) for a sequence in the alignment. |
protected void |
setLengthQuietly(int length)
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Methods inherited from class uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment |
addAlignmentListener, addSequence, addSequence, addSequenceListener, addVetoableAlignmentListener, addVetoableSequenceListener, changeOccurred, fireAlignmentEvent, fireVetoableAlignmentEvent, getSubAlignment, removeAlignmentListener, removeSequence, removeSequenceListener, removeVetoableAlignmentListener, removeVetoableSequenceListener, setInset, vetoableChangeOccurred |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public DefaultSequenceAlignment(SequenceType type)
public DefaultSequenceAlignment(SequenceType type, Identifier ident)
public DefaultSequenceAlignment(Element[][] seqs, SequenceType type)
public DefaultSequenceAlignment(GappedSequence[] seqs, SequenceType type, int[] inset, Identifier ident)
public DefaultSequenceAlignment(GappedSequence[] seqs, SequenceType type, int[] inset)
public DefaultSequenceAlignment(GappedSequence[] seqs, SequenceType type)
public DefaultSequenceAlignment(SequenceAlignment msa, SequenceType type)
Method Detail |
protected void init(GappedSequence[] seqs, SequenceType type, int[] inset, Identifier ident)
public SequenceAlignment getSubAlignment(int startPos, int length, int startSeq, int numSeqs)
startPos
- the start position for the sub-alignment (i.e: x1)length
- the length of the sub-alignmentstartSeq
- the first sequence in the current alignment to be
included in the sub-alignment (i.e: y1)numSeqs
- the number of sequences to be included in the
sub-alignment
public SequenceType getSequenceType()
public GappedSequence getSequenceAt(int index)
index
- the location in the MSA of the target sequence
public int getSequenceIndex(GappedSequence seq)
seq
- the sequence of interest
protected void setLengthQuietly(int length)
setLengthQuietly
in class AbstractSequenceAlignment
protected void addSequenceQuietly(GappedSequence seq, int inset)
addSequenceQuietly
in class AbstractSequenceAlignment
seq
- the sequenceinset
- the sequence inset in the alignmentprotected GappedSequence removeSequenceQuietly(int seqIndex)
removeSequenceQuietly
in class AbstractSequenceAlignment
seqIndex
- the sequence index
protected void setInsetQuietly(int seqIndex, int inset)
setInsetQuietly
in class AbstractSequenceAlignment
seqIndex
- the sequence index for the inset to be added toinset
- the insetpublic int getInset(int seqIndex)
seqIndex
- the sequence index
public int getNumberSequences()
public int getLength()
public Identifier getIdentifier()
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