X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fdevelopment%2FDevelopmentTools.java;h=9c26d2cf8c4ba9ec0c68ab15eaf43b7c15121063;hb=c3a4da0b4a3bd5bfb06acec6717f6b2e138eb480;hp=8cc0cc56eb33a839554d601bc4e35ad3908e5f71;hpb=e174d62534f7fc6f3de133d523a402a87735b27f;p=jalview.git diff --git a/forester/java/src/org/forester/development/DevelopmentTools.java b/forester/java/src/org/forester/development/DevelopmentTools.java index 8cc0cc5..9c26d2c 100644 --- a/forester/java/src/org/forester/development/DevelopmentTools.java +++ b/forester/java/src/org/forester/development/DevelopmentTools.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.development; @@ -36,7 +36,7 @@ public final class DevelopmentTools { /** * Creates a completely unbalanced Phylogeny with i external nodes. - * + * * @return a newly created unbalanced Phylogeny */ // public static Phylogeny createUnbalancedTree( int i ) { @@ -46,7 +46,7 @@ public final class DevelopmentTools { // try { // PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); // t1 = factory.create( ":S=", new SimpleNHXParser() ); - // + // // t1.setRooted( true ); // // for ( int j = 1; j < i; ++j ) { @@ -71,7 +71,7 @@ public final class DevelopmentTools { /** * Creates a completely balanced rooted phylogeny with a given number of levels and * children per node. - * + * * @param levels * @param children_per_node * @return a completely balanced rooted phylogeny @@ -165,7 +165,7 @@ public final class DevelopmentTools { /** * Sets the species names of the external Nodes of Phylogeny t to a random * positive integer number between (and including) min and max. - * + * * @param t * whose external species names are to be randomized * @param min @@ -182,7 +182,7 @@ public final class DevelopmentTools { final Random r = new Random(); PhylogenyNode n = t.getFirstExternalNode(); while ( n != null ) { - final String code = ( ( Math.abs( r.nextInt() ) % ( ma - mi + 1 ) ) + mi ) + ""; + final String code = ( ( Math.abs( r.nextInt() ) % ( ( ma - mi ) + 1 ) ) + mi ) + ""; try { PhylogenyMethods.setTaxonomyCode( n, code ); }