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