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java.lang.Objectpal.alignment.AbstractAlignment
public abstract class AbstractAlignment
abstract base class for any alignment data.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary | |
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protected IdGroup |
idGroup
sequence identifiers |
protected int |
numSeqs
number of sequences |
protected int |
numSites
length of each sequence |
Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
Constructor Summary | |
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AbstractAlignment()
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Method Summary | |
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java.lang.String |
getAlignedSequenceString(int seq)
Returns a string representing a single sequence (including gaps) from this alignment. |
protected char |
getChar(int state)
Same as getDataType().getChar(state) |
abstract char |
getData(int seq,
int site)
sequence alignment at (sequence, site) |
DataType |
getDataType()
Returns the datatype of this alignment |
int |
getIdCount()
Returns the number of identifiers in this group |
Identifier |
getIdentifier(int i)
Returns the ith identifier. |
int |
getLength()
Return number of sites in this alignment |
int |
getSequenceCount()
Return number of sequences in this alignment |
int |
getSiteCount()
Return number of sites for each sequence in this alignment |
protected int |
getState(char c)
Same as getDataType().getState(char) |
int[][] |
getStates()
Fills a [numsequences][length] matrix with indices. |
void |
guessDataType()
Guess data type |
boolean |
isGap(int seq,
int site)
returns true if there is a gap in the give position. |
protected boolean |
isUnknownState(int state)
Same as getDataType().isUnknownState(state) |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
setDataType(DataType d)
Sets the datatype of this alignment |
void |
setIdentifier(int i,
Identifier ident)
Sets the ith identifier. |
java.lang.String |
toString()
returns representation of this alignment as a string |
int |
whichIdNumber(java.lang.String name)
returns the index of the identifier with the given name. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected int numSeqs
protected int numSites
protected IdGroup idGroup
Constructor Detail |
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public AbstractAlignment()
Method Detail |
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public abstract char getData(int seq, int site)
getData
in interface Alignment
public boolean isGap(int seq, int site)
public void guessDataType()
protected final char getChar(int state)
protected final int getState(char c)
protected final boolean isUnknownState(int state)
public final DataType getDataType()
getDataType
in interface Alignment
public final void setDataType(DataType d)
public java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output streampublic int[][] getStates()
public final int getLength()
public final int getSequenceCount()
getSequenceCount
in interface Alignment
public final int getSiteCount()
getSiteCount
in interface Alignment
public java.lang.String getAlignedSequenceString(int seq)
getAlignedSequenceString
in interface Alignment
public Identifier getIdentifier(int i)
IdGroup
getIdentifier
in interface IdGroup
public void setIdentifier(int i, Identifier ident)
IdGroup
setIdentifier
in interface IdGroup
public int getIdCount()
IdGroup
getIdCount
in interface IdGroup
public int whichIdNumber(java.lang.String name)
IdGroup
whichIdNumber
in interface IdGroup
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