Package org.forester.archaeopteryx

Class AptxUtil

java.lang.Object
org.forester.archaeopteryx.AptxUtil
public final class AptxUtil extends Object

  • Constructor Details

    • AptxUtil

      public AptxUtil()

  • Method Details

    • calculateColorFromString

      public static final Color calculateColorFromString(String str, boolean is_taxonomy)

    • createMaskFormatter

      public static MaskFormatter createMaskFormatter(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(URI uri, boolean is_applet, JApplet applet, String frame_name) throws IOException
      Throws:
      IOException

    • obtainAllDistinctTaxonomies

      public static Set<Taxonomy> obtainAllDistinctTaxonomies(PhylogenyNode node)

    • printWarningMessage

      public static final void printWarningMessage(String name, String message)

    • readPhylogeniesFromUrl

      public static final Phylogeny[] readPhylogeniesFromUrl(URL url, boolean phyloxml_validate_against_xsd, boolean replace_underscores, boolean internal_numbers_are_confidences, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean midpoint_reroot) throws FileNotFoundException, IOException
      Throws:
      FileNotFoundException
      IOException

    • showErrorMessage

      public static final void showErrorMessage(Component parent, String error_msg)

    • writePhylogenyToGraphicsFile

      public static void writePhylogenyToGraphicsFile(File intree, File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config) throws IOException
      Throws:
      IOException

    • writePhylogenyToGraphicsFile

      public static void writePhylogenyToGraphicsFile(Phylogeny phy, File outfile, int width, int height, AptxUtil.GraphicsExportType type, Configuration config) throws IOException
      Throws:
      IOException

    • writePhylogenyToGraphicsFileNonInteractive

      public static final void writePhylogenyToGraphicsFileNonInteractive(File outfile, int width, int height, TreePanel tree_panel, org.forester.archaeopteryx.ControlPanel ac, AptxUtil.GraphicsExportType type, Options options) throws IOException
      Throws:
      IOException