public final class AptxUtil
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
AptxUtil.GraphicsExportType |
Constructor and Description |
---|
AptxUtil() |
Modifier and Type | Method and Description |
---|---|
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) |
public static final Accession obtainSequenceAccessionFromName(java.lang.String sequence_name)
public static void ensurePresenceOfTaxonomy(PhylogenyNode node)
public static void ensurePresenceOfSequence(PhylogenyNode node)
public static final void ensurePresenceOfDistribution(PhylogenyNode node)
public static final void ensurePresenceOfDate(PhylogenyNode node)
public static final boolean isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)
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
java.io.IOException
public static void writePhylogenyToGraphicsFile(Phylogeny phy, java.io.File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config) throws java.io.IOException
java.io.IOException
public static final boolean isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy)
phy
- public static final boolean isHasAtLeastNodeWithEvent(Phylogeny phy)
public static javax.swing.text.MaskFormatter createMaskFormatter(java.lang.String s)
public static final void collapseSpeciesSpecificSubtrees(Phylogeny phy)
public static java.lang.String[] getAllPossibleRanks()
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
java.io.IOException
public static final void printWarningMessage(java.lang.String name, java.lang.String message)
public static final void showErrorMessage(java.awt.Component parent, java.lang.String error_msg)
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
java.io.IOException