org.forester.archaeopteryx

Class AptxUtil

java.lang.Object

org.forester.archaeopteryx.AptxUtil

public final class AptxUtil
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AptxUtil.GraphicsExportType

Constructor Summary

Constructors

Constructor and Description
AptxUtil()

Method Summary

Modifier and Type	Method and Description
static Color	calculateColorFromString(String str, boolean is_taxonomy)
static MaskFormatter	createMaskFormatter(String s)
static boolean	isHasAtLeastNodeWithEvent(Phylogeny phy)
static boolean	isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy) Returns true if at least one branch has a length larger than zero.
static boolean	isHasAtLeastOneBranchWithSupportSD(Phylogeny phy)
static boolean	isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)
static boolean	isHasAtLeastOneNodeWithScientificName(Phylogeny phy)
static boolean	isHasAtLeastOneNodeWithSequenceAnnotation(Phylogeny phy)
static void	launchWebBrowser(URI uri, boolean is_applet, JApplet applet, String frame_name)
static Set<Taxonomy>	obtainAllDistinctTaxonomies(PhylogenyNode node)
static void	printWarningMessage(String name, String message)
static Phylogeny[]	readPhylogeniesFromUrl(URL url, boolean phyloxml_validate_against_xsd, boolean replace_underscores, boolean internal_numbers_are_confidences, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean midpoint_reroot)
static void	showErrorMessage(Component parent, String error_msg)
static void	writePhylogenyToGraphicsFile(File intree, File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)
static void	writePhylogenyToGraphicsFile(Phylogeny phy, File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)
static void	writePhylogenyToGraphicsFileNonInteractive(File outfile, int width, int height, TreePanel tree_panel, org.forester.archaeopteryx.ControlPanel ac, AptxUtil.GraphicsExportType type, Options options)

Methods inherited from class java.lang.Object

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

Constructor Detail

AptxUtil

public AptxUtil()

Method Detail

calculateColorFromString

public static final Color calculateColorFromString(String str,
                                                   boolean is_taxonomy)

createMaskFormatter

public static MaskFormatter createMaskFormatter(String s)

isHasAtLeastNodeWithEvent

public static final boolean isHasAtLeastNodeWithEvent(Phylogeny phy)

isHasAtLeastOneBranchLengthLargerThanZero

public static final boolean isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy)

Returns true if at least one branch has a length larger than zero.

Parameters:

phy -

isHasAtLeastOneBranchWithSupportSD

public static final boolean isHasAtLeastOneBranchWithSupportSD(Phylogeny phy)

isHasAtLeastOneBranchWithSupportValues

public static final boolean isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)

isHasAtLeastOneNodeWithScientificName

public static final boolean isHasAtLeastOneNodeWithScientificName(Phylogeny phy)

isHasAtLeastOneNodeWithSequenceAnnotation

public static final boolean isHasAtLeastOneNodeWithSequenceAnnotation(Phylogeny phy)

launchWebBrowser

public static final void launchWebBrowser(URI uri,
                                          boolean is_applet,
                                          JApplet applet,
                                          String frame_name)
                                   throws IOException

Throws:

IOException

obtainAllDistinctTaxonomies

public static Set<Taxonomy> obtainAllDistinctTaxonomies(PhylogenyNode node)

printWarningMessage

public static final void printWarningMessage(String name,
                                             String message)

readPhylogeniesFromUrl

public static final Phylogeny[] readPhylogeniesFromUrl(URL url,
                                                       boolean phyloxml_validate_against_xsd,
                                                       boolean replace_underscores,
                                                       boolean internal_numbers_are_confidences,
                                                       NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction,
                                                       boolean midpoint_reroot)
                                                throws FileNotFoundException,
                                                       IOException

Throws:

FileNotFoundException

IOException

showErrorMessage

public static final void showErrorMessage(Component parent,
                                          String error_msg)

writePhylogenyToGraphicsFile

public static void writePhylogenyToGraphicsFile(File intree,
                                                File outfile,
                                                int width,
                                                int height,
                                                AptxUtil.GraphicsExportType type,
                                                Configuration config)
                                         throws IOException

Throws:

IOException

writePhylogenyToGraphicsFile

public static void writePhylogenyToGraphicsFile(Phylogeny phy,
                                                File outfile,
                                                int width,
                                                int height,
                                                AptxUtil.GraphicsExportType type,
                                                Configuration config)
                                         throws IOException

Throws:

IOException

writePhylogenyToGraphicsFileNonInteractive

public static final void writePhylogenyToGraphicsFileNonInteractive(File outfile,
                                                                    int width,
                                                                    int height,
                                                                    TreePanel tree_panel,
                                                                    org.forester.archaeopteryx.ControlPanel ac,
                                                                    AptxUtil.GraphicsExportType type,
                                                                    Options options)
                                                             throws IOException

Throws:

IOException