Package org.forester.archaeopteryx
Class AptxUtil
- java.lang.Object
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- org.forester.archaeopteryx.AptxUtil
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public final class AptxUtil extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AptxUtil.GraphicsExportType
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Constructor Summary
Constructors Constructor Description AptxUtil()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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)
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Method Detail
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calculateColorFromString
public static final java.awt.Color calculateColorFromString(java.lang.String str, boolean is_taxonomy)
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createMaskFormatter
public static javax.swing.text.MaskFormatter createMaskFormatter(java.lang.String s)
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isHasAtLeastNodeWithEvent
public static final boolean isHasAtLeastNodeWithEvent(Phylogeny phy)
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isHasAtLeastOneBranchLengthLargerThanZero
public static final boolean isHasAtLeastOneBranchLengthLargerThanZero(Phylogeny phy)
Returns true if at least one branch has a length larger than zero.- Parameters:
phy
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isHasAtLeastOneBranchWithSupportSD
public static final boolean isHasAtLeastOneBranchWithSupportSD(Phylogeny phy)
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isHasAtLeastOneBranchWithSupportValues
public static final boolean isHasAtLeastOneBranchWithSupportValues(Phylogeny phy)
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isHasAtLeastOneNodeWithScientificName
public static final boolean isHasAtLeastOneNodeWithScientificName(Phylogeny phy)
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isHasAtLeastOneNodeWithSequenceAnnotation
public static final boolean isHasAtLeastOneNodeWithSequenceAnnotation(Phylogeny phy)
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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
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obtainAllDistinctTaxonomies
public static java.util.Set<Taxonomy> obtainAllDistinctTaxonomies(PhylogenyNode node)
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printWarningMessage
public static final void printWarningMessage(java.lang.String name, java.lang.String message)
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readPhylogeniesFromUrl
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
- Throws:
java.io.FileNotFoundException
java.io.IOException
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showErrorMessage
public static final void showErrorMessage(java.awt.Component parent, java.lang.String error_msg)
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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
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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
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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
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