java.lang.Object
- com.biomatters.geneious.publicapi.plugin.SequenceViewerExtension.StatisticsSection

Enclosing class:

SequenceViewerExtension
```
public static class SequenceViewerExtension.StatisticsSection
extends java.lang.Object
```
One or more lines of statistics that show up in the statistics section of the sequence viewer.

Since:

API 4.700 (Geneious 7.0.0)

Field Summary

Fields
Modifier and Type	Field	Description
`static double`	`POSITION_AMINO_ACID_TRANSLATION_FREQUENCIES`	The value that amino acid translation frequencies returns from `getVerticalPosition()`
`static double`	`POSITION_CODON_FREQUENCIES`	The value that codon frequencies returns from `getVerticalPosition()`
`static double`	`POSITION_COVERAGE`	The value that the read length distributions returns from `getVerticalPosition()`
`static double`	`POSITION_EXPECTED_ERRORS`	The value that the expected errors returns from `getVerticalPosition()`
`static double`	`POSITION_FREQUENCIES`	The value that the frequencies of nucleotides or amino acids in the sequence returns from `getVerticalPosition()`
`static double`	`POSITION_IDENTICAL_SITES`	The value that the number of identical sites returns from `getVerticalPosition()`
`static double`	`POSITION_MEAN_CONFIDENCE`	The value that the mean confidence returns from `getVerticalPosition()`
`static double`	`POSITION_NUMBER_OF_SEQUENCES`	The value that the number of sequences returns from `getVerticalPosition()`
`static double`	`POSITION_PERCENTAGE_PAIRWISE_IDENTITY`	The value that the percentage pairwise identity returns from `getVerticalPosition()`
`static double`	`POSITION_PROTEIN_EXTINCTION_COEFFICIENT`	The value that the protein molecular weight returns from `getVerticalPosition()`
`static double`	`POSITION_PROTEIN_ISOELECTRIC_POINT`	The value that the protein molecular weight returns from `getVerticalPosition()`
`static double`	`POSITION_PROTEIN_MOLECULAR_WEIGHT`	The value that the protein molecular weight returns from `getVerticalPosition()`
`static double`	`POSITION_QUALITY_THRESHOLD_COUNTS`	The value that the quality threshold counts (e.g.
`static double`	`POSITION_READ_LENGTHS`	The value that the read length distributions returns from `getVerticalPosition()`
`static double`	`POSITION_SEQUENCE_LENGTH`	The value that the sequence length returns from `getVerticalPosition()`
`static double`	`POSITION_STATISTICS_HEADER`	The value that the statistics header returns from `getVerticalPosition()`
`static double`	`RELATIVE_POSITION_BELOW`	Added to the position of a statistic to position it below the other statistic.
`static double`	`RELATIVE_POSITION_DIRECTLY_BELOW`	Added to the position of a statistic to position it directly below the other statistic.

Constructor Summary

Constructors
Constructor	Description
`StatisticsSection(java.lang.String name, java.lang.Number numericValue, java.lang.String nicelyFormattedNameAndValue, double verticalPosition)`	Equivalent to `(StatisticsSection(name, numericValue, nicelyFormattedNameAndValue, verticalPosition, Collections.emptyList()`
`StatisticsSection(java.lang.String name, java.lang.Number numericValue, java.lang.String nicelyFormattedNameAndValue, double verticalPosition, java.util.List<DocumentFieldAndValue> documentFieldsAndValues)`	Creates a new statistics section

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.util.List<DocumentFieldAndValue>`	`getDocumentFieldsAndValues()`
`java.lang.String`	`getName()`
`java.lang.String`	`getNicelyFormattedNameAndValue()`
`java.lang.Number`	`getNumericValue()`
`double`	`getVerticalPosition()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - POSITION_STATISTICS_HEADER
```
public static final double POSITION_STATISTICS_HEADER
```
    The value that the statistics header returns from getVerticalPosition()
    
    Since:
    
    API 4.201904 (Geneious 2019.0.4)
    
    See Also:
    
    Constant Field Values
  - POSITION_SEQUENCE_LENGTH
```
public static final double POSITION_SEQUENCE_LENGTH
```
    The value that the sequence length returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_NUMBER_OF_SEQUENCES
```
public static final double POSITION_NUMBER_OF_SEQUENCES
```
    The value that the number of sequences returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_IDENTICAL_SITES
```
public static final double POSITION_IDENTICAL_SITES
```
    The value that the number of identical sites returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_PERCENTAGE_PAIRWISE_IDENTITY
```
public static final double POSITION_PERCENTAGE_PAIRWISE_IDENTITY
```
    The value that the percentage pairwise identity returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_COVERAGE
```
public static final double POSITION_COVERAGE
```
    The value that the read length distributions returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_READ_LENGTHS
```
public static final double POSITION_READ_LENGTHS
```
    The value that the read length distributions returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_PROTEIN_MOLECULAR_WEIGHT
```
public static final double POSITION_PROTEIN_MOLECULAR_WEIGHT
```
    The value that the protein molecular weight returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_PROTEIN_ISOELECTRIC_POINT
```
public static final double POSITION_PROTEIN_ISOELECTRIC_POINT
```
    The value that the protein molecular weight returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_PROTEIN_EXTINCTION_COEFFICIENT
```
public static final double POSITION_PROTEIN_EXTINCTION_COEFFICIENT
```
    The value that the protein molecular weight returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_MEAN_CONFIDENCE
```
public static final double POSITION_MEAN_CONFIDENCE
```
    The value that the mean confidence returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_EXPECTED_ERRORS
```
public static final double POSITION_EXPECTED_ERRORS
```
    The value that the expected errors returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_QUALITY_THRESHOLD_COUNTS
```
public static final double POSITION_QUALITY_THRESHOLD_COUNTS
```
    The value that the quality threshold counts (e.g. 'At least Q20...') returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_FREQUENCIES
```
public static final double POSITION_FREQUENCIES
```
    The value that the frequencies of nucleotides or amino acids in the sequence returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_AMINO_ACID_TRANSLATION_FREQUENCIES
```
public static final double POSITION_AMINO_ACID_TRANSLATION_FREQUENCIES
```
    The value that amino acid translation frequencies returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - POSITION_CODON_FREQUENCIES
```
public static final double POSITION_CODON_FREQUENCIES
```
    The value that codon frequencies returns from getVerticalPosition()
    
    See Also:
    
    Constant Field Values
  - RELATIVE_POSITION_DIRECTLY_BELOW
```
public static final double RELATIVE_POSITION_DIRECTLY_BELOW
```
    Added to the position of a statistic to position it directly below the other statistic. See StatisticsSection(String, Number, String, double) for more details.
    
    See Also:
    
    RELATIVE_POSITION_BELOW, StatisticsSection(String, Number, String, double), Constant Field Values
  - RELATIVE_POSITION_BELOW
```
public static final double RELATIVE_POSITION_BELOW
```
    Added to the position of a statistic to position it below the other statistic. See StatisticsSection(String, Number, String, double) for more details.
    
    See Also:
    
    RELATIVE_POSITION_DIRECTLY_BELOW, StatisticsSection(String, Number, String, double), Constant Field Values
- Constructor Detail
  - StatisticsSection
```
public StatisticsSection(java.lang.String name,
                         java.lang.Number numericValue,
                         java.lang.String nicelyFormattedNameAndValue,
                         double verticalPosition,
                         java.util.List<DocumentFieldAndValue> documentFieldsAndValues)
```
    Creates a new statistics section
    
    Parameters:
    
    name - the name of this statistic used for programmatic purposes only to distinguish it from other sections returned by this same plugin. May be an empty String if this plugin returns only a single section.
    
    numericValue - a numeric value for this statistic for use with other plugins that may wish to obtain the value. May be null for statistics that have no numeric value.
    
    nicelyFormattedNameAndValue - the text displayed in the sequence viewer statistics.
    
    verticalPosition - a vertical position for this text between 0 and 1. For example POSITION_SEQUENCE_LENGTH+RELATIVE_POSITION_BELOW could be used to position it below the sequence length section. Use 1.0 to position it below all other statistics. Generally you should add RELATIVE_POSITION_DIRECTLY_BELOW to some existing section position if it is closely associated with it. If you just want to position it below another statistic which it isn't closely associated with, add RELATIVE_POSITION_BELOW and prefix nicelyFormattedNameAndValue with a newline character (\n) to separate your statistic into its own section.
    
    documentFieldsAndValues - this statistics section as a list of fields and values. May be empty, in which case this statistic won't appear in the document table.
    
    Since:
    
    API 4.202100 (Geneious 2021.0.0)
    
    See Also:
    
    POSITION_SEQUENCE_LENGTH, POSITION_FREQUENCIES, POSITION_AMINO_ACID_TRANSLATION_FREQUENCIES, POSITION_CODON_FREQUENCIES
  - StatisticsSection
```
public StatisticsSection(java.lang.String name,
                         java.lang.Number numericValue,
                         java.lang.String nicelyFormattedNameAndValue,
                         double verticalPosition)
```
    Equivalent to (StatisticsSection(name, numericValue, nicelyFormattedNameAndValue, verticalPosition, Collections.emptyList()
- Method Detail
  - getNicelyFormattedNameAndValue
```
public java.lang.String getNicelyFormattedNameAndValue()
```
    Returns:
    
    the text to display in the sequence viewer, which may contain html fragments
  - getNumericValue
```
public java.lang.Number getNumericValue()
```
    Returns:
    
    a numeric value for this statistic for use with other plugins that may wish to obtain the value. May be null for statistics that have no numeric value.
  - getName
```
public java.lang.String getName()
```
    Returns:
    
    the name of this statistic used for programmatic purposes only to distinguish it from other sections returned by this same plugin. May be an empty String if this plugin returns only a single section.
  - getVerticalPosition
```
public double getVerticalPosition()
```
    Returns:
    
    the vertical position for this text between 0 and 1. See StatisticsSection(String, Number, String, double) for details
  - getDocumentFieldsAndValues
```
public java.util.List<DocumentFieldAndValue> getDocumentFieldsAndValues()
```
    Returns:
    
    this statistics section as a list of fields and values. May be empty, in which case this statistic won't appear in the document table.
    
    Since:
    
    API 4.202100 (Geneious 2021.0.0)

Class SequenceViewerExtension.StatisticsSection

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

POSITION_STATISTICS_HEADER

POSITION_SEQUENCE_LENGTH

POSITION_NUMBER_OF_SEQUENCES

POSITION_IDENTICAL_SITES

POSITION_PERCENTAGE_PAIRWISE_IDENTITY

POSITION_COVERAGE

POSITION_READ_LENGTHS

POSITION_PROTEIN_MOLECULAR_WEIGHT

POSITION_PROTEIN_ISOELECTRIC_POINT

POSITION_PROTEIN_EXTINCTION_COEFFICIENT

POSITION_MEAN_CONFIDENCE

POSITION_EXPECTED_ERRORS

POSITION_QUALITY_THRESHOLD_COUNTS

POSITION_FREQUENCIES

POSITION_AMINO_ACID_TRANSLATION_FREQUENCIES

POSITION_CODON_FREQUENCIES

RELATIVE_POSITION_DIRECTLY_BELOW

RELATIVE_POSITION_BELOW

Constructor Detail

StatisticsSection

StatisticsSection

Method Detail

getNicelyFormattedNameAndValue

getNumericValue

getName

getVerticalPosition

getDocumentFieldsAndValues