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java.lang.Object | +--uk.ac.man.bioinf.sequence.Sequences
Sequences.java Created: Tue Mar 14 13:43:59 2000
Method Summary | |
static int |
chompLeadingGaps(GappedSequence seq)
This removes all of the leading gaps from a gapped sequence, and then returns the number of gaps removed. |
static int |
chompTrailingGaps(GappedSequence seq)
Removes and returns the number of trailing gaps off a gapped sequence. |
static String |
getComplexSequenceAsString(ComplexSequence seq)
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static GappedSequence |
getElementsAsGappedSequence(Element[] elements,
SequenceType type)
Returns a GappedSequence with the Elements in the array, which can included gaps. |
static GappedSequence |
getElementsAsGappedSequence(Element[] elements,
SequenceType type,
Identifier ident)
Returns a GappedSequence with the Elements in the array, which can included gaps. |
static Sequence |
getElementsAsSequence(Element[] elements,
SequenceType type)
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static Sequence |
getElementsAsSequence(Element[] elements,
SequenceType type,
Identifier ident)
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static String |
getElementsAsString(Element[] elem)
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static String |
getGappedSequenceAsString(GappedSequence seq)
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static String |
getGappedSubSequenceAsString(GappedSequence seq,
int start,
int length)
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static int |
getNumberGapsDownstreamFrom(int index,
GappedSequence seq)
Returns the number of gaps downstream from a given index in the given sequence. |
static int |
getNumberGapsUpstreamFrom(int index,
GappedSequence seq)
Returns the number of gaps upstream from a given index in the given sequence. |
static ComplexElement[] |
getResiduesAsComplexElements(Residue[] elements)
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static String |
getSequenceAsString(Sequence seq)
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static String |
getSubSequenceAsString(Sequence seq,
int start,
int length)
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static void |
printAlignment(SequenceAlignment align)
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static void |
printElements(Element[] elem)
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static void |
printSequence(ComplexSequence seq)
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static void |
printSequence(GappedComplexSequence seq)
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static void |
printSequence(GappedSequence seq)
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static void |
printSequence(Sequence seq)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
public static GappedSequence getElementsAsGappedSequence(Element[] elements, SequenceType type)
elements
- the elementstype
- the sequence type
public static GappedSequence getElementsAsGappedSequence(Element[] elements, SequenceType type, Identifier ident)
elements
- the elementstype
- the sequence type
public static Sequence getElementsAsSequence(Element[] elements, SequenceType type)
public static Sequence getElementsAsSequence(Element[] elements, SequenceType type, Identifier ident)
public static int chompLeadingGaps(GappedSequence seq) throws SequenceVetoException
seq
- the sequence to chomp
SequenceVetoException
public static int chompTrailingGaps(GappedSequence seq) throws SequenceVetoException
seq
- the sequence
SequenceVetoException
public static int getNumberGapsUpstreamFrom(int index, GappedSequence seq)
index
- the location in the sequence to start counting
upstream fromseq
- the sequence
public static int getNumberGapsDownstreamFrom(int index, GappedSequence seq)
index
- the location in the sequence to start counting
downstream fromseq
- the sequence
public static String getSequenceAsString(Sequence seq)
public static String getSubSequenceAsString(Sequence seq, int start, int length)
public static String getGappedSequenceAsString(GappedSequence seq)
public static String getGappedSubSequenceAsString(GappedSequence seq, int start, int length)
public static String getElementsAsString(Element[] elem)
public static String getComplexSequenceAsString(ComplexSequence seq)
public static ComplexElement[] getResiduesAsComplexElements(Residue[] elements)
public static void printAlignment(SequenceAlignment align)
public static void printSequence(GappedSequence seq)
public static void printSequence(ComplexSequence seq)
public static void printSequence(GappedComplexSequence seq)
public static void printSequence(Sequence seq)
public static void printElements(Element[] elem)
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