org.forester.archaeopteryx
Class AptxUtil

java.lang.Object
  org.forester.archaeopteryx.AptxUtil

public final class AptxUtil
extends java.lang.Object

Nested Class Summary

static class

AptxUtil.GraphicsExportType

Constructor Summary

AptxUtil()

Method Summary

static void	collapseSpeciesSpecificSubtrees(Phylogeny phy)
static javax.swing.text.MaskFormatter	createMaskFormatter(java.lang.String s)
static void	ensurePresenceOfDate(PhylogenyNode node)
static void	ensurePresenceOfDistribution(PhylogenyNode node)
static void	ensurePresenceOfSequence(PhylogenyNode node)
static void	ensurePresenceOfTaxonomy(PhylogenyNode node)
static java.lang.String[]	getAllPossibleRanks()
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	isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)
static void	launchWebBrowser(java.net.URI uri, boolean is_applet, javax.swing.JApplet applet, java.lang.String frame_name)
static Accession	obtainSequenceAccessionFromName(java.lang.String sequence_name)
static void	printWarningMessage(java.lang.String name, java.lang.String message)
static void	showErrorMessage(java.awt.Component parent, java.lang.String error_msg)
static void	writePhylogenyToGraphicsFile(java.io.File intree, java.io.File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)
static void	writePhylogenyToGraphicsFile(Phylogeny phy, java.io.File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config)
static void	writePhylogenyToGraphicsFileNonInteractive(java.io.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

obtainSequenceAccessionFromName

public static final Accession obtainSequenceAccessionFromName(java.lang.String sequence_name)

ensurePresenceOfTaxonomy

public static void ensurePresenceOfTaxonomy(PhylogenyNode node)

ensurePresenceOfSequence

public static void ensurePresenceOfSequence(PhylogenyNode node)

ensurePresenceOfDistribution

public static final void ensurePresenceOfDistribution(PhylogenyNode node)

ensurePresenceOfDate

public static final void ensurePresenceOfDate(PhylogenyNode node)

isHasAtLeastOneBranchWithSupportValues

public static final boolean isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)

writePhylogenyToGraphicsFile

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

Throws:

java.io.IOException

writePhylogenyToGraphicsFile

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

Throws:

java.io.IOException

isHasAtLeastOneBranchLengthLargerThanZero

public static final boolean isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy)

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

Parameters:

phy -

isHasAtLeastNodeWithEvent

public static final boolean isHasAtLeastNodeWithEvent(Phylogeny phy)

createMaskFormatter

public static javax.swing.text.MaskFormatter createMaskFormatter(java.lang.String s)

collapseSpeciesSpecificSubtrees

public static final void collapseSpeciesSpecificSubtrees(Phylogeny phy)

getAllPossibleRanks

public static java.lang.String[] getAllPossibleRanks()

launchWebBrowser

public static final void launchWebBrowser(java.net.URI uri,
                                          boolean is_applet,
                                          javax.swing.JApplet applet,
                                          java.lang.String frame_name)
                                   throws java.io.IOException

Throws:

java.io.IOException

printWarningMessage

public static final void printWarningMessage(java.lang.String name,
                                             java.lang.String message)

showErrorMessage

public static final void showErrorMessage(java.awt.Component parent,
                                          java.lang.String error_msg)

writePhylogenyToGraphicsFileNonInteractive

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

Throws:

java.io.IOException