X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FOptions.java;h=a228d299268bf0a931b3281ec59b91bb26e65542;hb=c0439ed8b088887ffea2faf11bc7897333287cb3;hp=184e79505187526d43f07987698b73bd50f4cc4e;hpb=f6b29c53c14e1ef16e4cd614c7f9465e0073309e;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Options.java b/forester/java/src/org/forester/archaeopteryx/Options.java index 184e795..a228d29 100644 --- a/forester/java/src/org/forester/archaeopteryx/Options.java +++ b/forester/java/src/org/forester/archaeopteryx/Options.java @@ -51,6 +51,12 @@ final public class Options { public static enum PHYLOGENY_GRAPHICS_TYPE { CIRCULAR, CONVEX, CURVED, EURO_STYLE, RECTANGULAR, ROUNDED, TRIANGULAR, UNROOTED; } + + static enum PHYLOGENY_DISPLAY_TYPE { + CLADOGRAM, + ALIGNED_PHYLOGRAM, + UNALIGNED_PHYLOGRAM + } static enum OVERVIEW_PLACEMENT_TYPE { LOWER_LEFT( "lower left" ), @@ -73,6 +79,7 @@ final public class Options { return toString().replaceAll( " ", "_" ); } } + static final double MIN_CONFIDENCE_DEFAULT = 0.0; private boolean _abbreviate_scientific_names; private boolean _allow_errors_in_distance_to_parent;