Uses of Class
org.forester.archaeopteryx.Configuration
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Packages that use Configuration Package Description org.forester.archaeopteryx org.forester.archaeopteryx.phylogeny.data org.forester.archaeopteryx.tools -
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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)
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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)
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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)
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