Package org.forester.archaeopteryx

Class AptxUtil

  • public final class AptxUtil
extends java.lang.Object

    • Constructor Detail

      • AptxUtil

        public AptxUtil()

    • Method Detail

      • calculateColorFromString

        public static final java.awt.Color calculateColorFromString​(java.lang.String str,
                                                            boolean is_taxonomy)

      • createMaskFormatter

        public static javax.swing.text.MaskFormatter createMaskFormatter​(java.lang.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​(java.net.URI uri,
                                          boolean is_applet,
                                          javax.swing.JApplet applet,
                                          java.lang.String frame_name)
                                   throws java.io.IOException
        Throws:
        java.io.IOException

      • obtainAllDistinctTaxonomies

        public static java.util.Set<Taxonomy> obtainAllDistinctTaxonomies​(PhylogenyNode node)

      • printWarningMessage

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

      • 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

      • showErrorMessage

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

      • 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

      • 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