public final class AptxUtil
extends java.lang.Object
Modifier and Type | Class | Description |
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static class |
AptxUtil.GraphicsExportType |
Constructor | Description |
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AptxUtil() |
Modifier and Type | Method | Description |
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static java.awt.Color |
calculateColorFromString(java.lang.String str,
boolean is_taxonomy) |
|
static javax.swing.text.MaskFormatter |
createMaskFormatter(java.lang.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(java.net.URI uri,
boolean is_applet,
javax.swing.JApplet applet,
java.lang.String frame_name) |
|
static java.util.Set<Taxonomy> |
obtainAllDistinctTaxonomies(PhylogenyNode node) |
|
static void |
printWarningMessage(java.lang.String name,
java.lang.String message) |
|
static Phylogeny[] |
readPhylogeniesFromUrl(java.net.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(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 java.awt.Color calculateColorFromString(java.lang.String str, boolean is_taxonomy)
public static javax.swing.text.MaskFormatter createMaskFormatter(java.lang.String s)
public static final boolean isHasAtLeastNodeWithEvent(Phylogeny phy)
public static final boolean isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy)
phy
- public static final boolean isHasAtLeastOneBranchWithSupportSD(Phylogeny phy)
public static final boolean isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)
public static final boolean isHasAtLeastOneNodeWithScientificName(Phylogeny phy)
public static final boolean isHasAtLeastOneNodeWithSequenceAnnotation(Phylogeny phy)
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 java.util.Set<Taxonomy> obtainAllDistinctTaxonomies(PhylogenyNode node)
public static final void printWarningMessage(java.lang.String name, java.lang.String message)
public static final Phylogeny[] readPhylogeniesFromUrl(java.net.URL url, boolean phyloxml_validate_against_xsd, boolean replace_underscores, boolean internal_numbers_are_confidences, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean midpoint_reroot) throws java.io.FileNotFoundException, java.io.IOException
java.io.FileNotFoundException
java.io.IOException
public static final void showErrorMessage(java.awt.Component parent, java.lang.String error_msg)
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 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