Uses of Class
org.forester.archaeopteryx.Configuration

Packages that use Configuration

Package	Description
org.forester.archaeopteryx
org.forester.archaeopteryx.phylogeny.data
org.forester.archaeopteryx.tools

Uses of Configuration in org.forester.archaeopteryx

Methods in org.forester.archaeopteryx that return Configuration

Modifier and Type	Method	Description
Configuration	MainFrame.getConfiguration()

Methods in org.forester.archaeopteryx with parameters of type Configuration

Modifier and Type	Method	Description
void	MainPanel.addPhylogenyInNewTab(Phylogeny phy, Configuration config, java.lang.String default_name, java.lang.String full_path)
static MainFrame	Archaeopteryx.createApplication(Phylogeny phylogeny, Configuration config, java.lang.String title)
static MainFrameApplication	MainFrameApplication.createInstance(Phylogeny[] phys, Configuration config)
static MainFrame	MainFrameApplication.createInstance(Phylogeny[] phys, Configuration config, java.lang.String title, java.io.File current_dir)
static Options	Options.createInstance(Configuration configuration)
static java.lang.String	TreePanelUtil.createUriForSeqWeb(PhylogenyNode node, Configuration conf, TreePanel tp)
static java.util.List<java.lang.String>	TreePanelUtil.createUrisForPdbWeb(PhylogenyNode node, java.util.List<Accession> pdb_accs, Configuration configuration, TreePanel treePanel)
static void	AptxUtil.writePhylogenyToGraphicsFile(java.io.File intree, java.io.File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)
static void	AptxUtil.writePhylogenyToGraphicsFile(Phylogeny phy, java.io.File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)

Constructors in org.forester.archaeopteryx with parameters of type Configuration

Constructor	Description
MainPanel(Configuration configuration, MainFrame parent)

Uses of Configuration in org.forester.archaeopteryx.phylogeny.data

Methods in org.forester.archaeopteryx.phylogeny.data with parameters of type Configuration

Modifier and Type	Method	Description
static RenderableMsaSequence	RenderableMsaSequence.createInstance(java.lang.String seq, java.lang.String type, Configuration configuration)
static RenderableVector	RenderableVector.createInstance(java.util.List<java.lang.Double> values, DescriptiveStatistics stats, Configuration configuration)

Uses of Configuration in org.forester.archaeopteryx.tools

Methods in org.forester.archaeopteryx.tools with parameters of type Configuration

Modifier and Type	Method	Description
static InferenceManager	InferenceManager.createInstance(Configuration c)
static PhylogeneticInferenceOptions	PhylogeneticInferenceOptions.createInstance(Configuration configuration)