Package com.biomatters.geneious.publicapi.implementations

Class DefaultSequenceGraphFactories

java.lang.Object

com.biomatters.geneious.publicapi.implementations.DefaultSequenceGraphFactories

public final class DefaultSequenceGraphFactories
extends java.lang.Object

Provides convenience functionality to create a SequenceGraphFactory which draws a bar graph from some simpler interfaces. For example, used for creating the hydrophobicity, PI, and similarity graphs. These graphs automatically handle calculating scores in background threads where appropriate (on very large sequences and alignments) and averaging scores over multiple residues. It also efficiently handles sequences with long endgaps (e.g. for contig assemblies). More complex graphs (such as the sequence logo graph) should be created directly via the SequenceGraphFactory and SequenceGraph classes.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DefaultSequenceGraphFactories.SequenceAlignmentScorer	Provides methods to supply a score for a given set of sequence residues and provide a color for a given score.
static class	DefaultSequenceGraphFactories.SingleSequenceScorer	Provides methods to supply a score for a given sequence residue and provide a color for a given score.

Method Summary

Modifier and Type	Method	Description
static SequenceGraphFactory	createSequenceAlignmentGraphFactory(java.lang.String name, java.lang.String description, boolean defaultVisibility, int defaultHeight, SequenceDocument.Alphabet alphabet, DefaultSequenceGraphFactories.SequenceAlignmentScorer multipleSequenceScorer, boolean lineGraph)	Create a SequenceGraphFactory for sequence alignments.
static SequenceGraphFactory	createSequenceAlignmentGraphFactory(java.lang.String name, java.lang.String description, boolean defaultVisibility, int defaultHeight, SequenceDocument.Alphabet alphabet, DefaultSequenceGraphFactories.SingleSequenceScorer singleSequenceScorer, boolean lineGraph)	Create a SequenceGraphFactory that is averaged over multiple sequences from a single sequence scorer.
static SequenceGraphFactory	createSingleSequenceGraphFactory(java.lang.String name, java.lang.String description, boolean defaultVisibility, int defaultHeight, SequenceDocument.Alphabet alphabet, DefaultSequenceGraphFactories.SingleSequenceScorer singleSequenceScorer, boolean lineGraph)	Create a SequenceGraphFactory for a single sequence where graph points depend only on the residue at that point.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

createSingleSequenceGraphFactory

public static SequenceGraphFactory createSingleSequenceGraphFactory(java.lang.String name,
                                                                    java.lang.String description,
                                                                    boolean defaultVisibility,
                                                                    int defaultHeight,
                                                                    SequenceDocument.Alphabet alphabet,
                                                                    DefaultSequenceGraphFactories.SingleSequenceScorer singleSequenceScorer,
                                                                    boolean lineGraph)

Create a SequenceGraphFactory for a single sequence where graph points depend only on the residue at that point. For example, this is used to create the hydrophobicity and PI graphs in protein sequences.

Parameters:

name - name displayed next to graphs generated by this factory

description - a more verbose description displayed as a tool tip or null to provide no description

defaultVisibility - the default visibility for this graph.

defaultHeight - the default height for this graph, which the user can override.

alphabet - the alphabet of the graph (either protein or nucleotide)

singleSequenceScorer - a scorer to calculate the score and Color based on a residue.

lineGraph - true if this should be a line graph rather than a bar graph

Returns:

a SequenceGraphFactory

createSequenceAlignmentGraphFactory

public static SequenceGraphFactory createSequenceAlignmentGraphFactory(java.lang.String name,
                                                                       java.lang.String description,
                                                                       boolean defaultVisibility,
                                                                       int defaultHeight,
                                                                       SequenceDocument.Alphabet alphabet,
                                                                       DefaultSequenceGraphFactories.SingleSequenceScorer singleSequenceScorer,
                                                                       boolean lineGraph)

Create a SequenceGraphFactory that is averaged over multiple sequences from a single sequence scorer. For example, this is used to create the average hydrophobicity and average PI graphs in protein sequence alignments.

Parameters:

name - name displayed next to graphs generated by this factory

description - a more verbose description displayed as a tool tip or null to provide no description

defaultVisibility - the default visibility for this graph.

defaultHeight - the default height for this graph, which the user can override.

alphabet - the alphabet of the graph (either protein or nucleotide)

singleSequenceScorer - a scorer to calculate the score and Color based on a residue.

lineGraph - true if this should be a line graph rather than a bar graph

Returns:

a SequenceGraphFactory

createSequenceAlignmentGraphFactory

public static SequenceGraphFactory createSequenceAlignmentGraphFactory(java.lang.String name,
                                                                       java.lang.String description,
                                                                       boolean defaultVisibility,
                                                                       int defaultHeight,
                                                                       SequenceDocument.Alphabet alphabet,
                                                                       DefaultSequenceGraphFactories.SequenceAlignmentScorer multipleSequenceScorer,
                                                                       boolean lineGraph)

Create a SequenceGraphFactory for sequence alignments. For example, this is used to create the similarity graph for sequence alignments.

Parameters:

name - name displayed next to graphs generated by this factory

description - a more verbose description displayed as a tool tip or null to provide no description

defaultVisibility - the default visibility for this graph.

defaultHeight - the default height for this graph, which the user can override.

alphabet - the alphabet of the graph (either protein or nucleotide)

multipleSequenceScorer - a scorer to calculate the score and Color based on a set of residues.

lineGraph - true if this should be a line graph rather than a bar graph

Returns:

a SequenceGraphFactory