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java.lang.Objectpal.alignment.SimpleCharacterAlignment
public class SimpleCharacterAlignment
This provides a basic implementation of CharacterAlignment. This class holds quantitative character states. Each trait (a quantitative character) has two sets of labels. One is the traitName, and the second is the environmentName. Obviously any descriptor could be placed in these two labels, however for printing purposes traitName is printed first. Double.NaN is assumed to be the missing value.
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 java.lang.String[] |
environmentNames
names of the traits |
protected IdGroup |
idGroup
sequence identifiers |
protected int |
numSeqs
number of sequences |
protected int |
numTraits
number of traits |
protected java.lang.String[] |
traitNames
names of the traits |
protected double[][] |
traitValues
trait values |
Fields inherited from interface pal.alignment.CharacterAlignment |
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MISSING |
Constructor Summary | |
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SimpleCharacterAlignment()
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SimpleCharacterAlignment(Identifier[] ids,
double[][] traitValues,
java.lang.String[] traitNames)
Constructor for SimpleCharacterAlignment. |
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SimpleCharacterAlignment(IdGroup group,
double[][] traitValues,
java.lang.String[] traitNames)
Constructor for SimpleCharacterAlignment. |
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SimpleCharacterAlignment(IdGroup group,
double[][] traitValues,
java.lang.String[] traitNames,
java.lang.String[] environNames)
Constructor for SimpleCharacterAlignment |
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SimpleCharacterAlignment(IdGroup group,
double[] traitValue,
java.lang.String traitName)
Constructor for SimpleCharacterAlignment when there is only a single trait. |
Method Summary | |
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java.lang.String |
getEnvironmentName(int trait)
Return name of the environments for this trait number |
int |
getIdCount()
Returns the number of identifiers in this group |
Identifier |
getIdentifier(int i)
Returns the ith identifier. |
int |
getLength()
Return number of traits in this alignment |
int |
getSequenceCount()
Return number of taxa or sequences in this alignment |
java.lang.Object[] |
getTableColumnNames()
Return column names for the table |
java.lang.Object[][] |
getTableData()
Return data for the table |
java.lang.String |
getTableTitle()
Return the name for the title of the ANOVA |
double |
getTrait(int seq,
int trait)
Return the trait value for a given sequence (taxon) and trait number |
int |
getTraitCount()
Return number of trait for each taxon in this alignment |
java.lang.String |
getTraitName(int trait)
Return name of the trait for this trait number |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
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 double[][] traitValues
protected java.lang.String[] traitNames
protected java.lang.String[] environmentNames
protected int numSeqs
protected int numTraits
protected IdGroup idGroup
Constructor Detail |
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public SimpleCharacterAlignment()
public SimpleCharacterAlignment(Identifier[] ids, double[][] traitValues, java.lang.String[] traitNames)
group
- array of taxa identifierstraitValues
- matrix of trait valuestraitNames
- array of trait namespublic SimpleCharacterAlignment(IdGroup group, double[][] traitValues, java.lang.String[] traitNames)
group
- taxa namestraitValues
- matrix of trait valuestraitNames
- array of trait namespublic SimpleCharacterAlignment(IdGroup group, double[][] traitValues, java.lang.String[] traitNames, java.lang.String[] environNames)
group
- taxa namestraitValues
- matrix of trait valuestraitNames
- array of trait namesenvironNames
- array of environment namespublic SimpleCharacterAlignment(IdGroup group, double[] traitValue, java.lang.String traitName)
group
- holds taxa namestraitValue
- array of trait valuestraitName
- trait nameMethod Detail |
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public double getTrait(int seq, int trait)
getTrait
in interface CharacterAlignment
public final int getLength()
public final int getSequenceCount()
getSequenceCount
in interface CharacterAlignment
public final int getTraitCount()
getTraitCount
in interface CharacterAlignment
public java.lang.String getTraitName(int trait)
getTraitName
in interface CharacterAlignment
public java.lang.String getEnvironmentName(int trait)
getEnvironmentName
in interface CharacterAlignment
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
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 java.lang.Object[] getTableColumnNames()
getTableColumnNames
in interface TableReport
public java.lang.Object[][] getTableData()
getTableData
in interface TableReport
public java.lang.String getTableTitle()
getTableTitle
in interface TableReport
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