diff --git a/build.xml b/build.xml index 66cd280..e5d26c9 100644 --- a/build.xml +++ b/build.xml @@ -34,7 +34,9 @@ + classpathref="lib.path" debug="${compile.debug}"> + + diff --git a/manual/manual.tex b/manual/manual.tex index b19faf8..283d9be 100644 --- a/manual/manual.tex +++ b/manual/manual.tex @@ -87,6 +87,12 @@ \subsection{Updates} \begin{itemize} + \item 20 Feb 2015 - Version 2.1.7 + + \begin{itemize} + \item Fixed bug in ML tree search operation. Console version was using NNI moves instead of "BEST" by default. + \end{itemize} + \item 20 Nov 2014 - Version 2.1.7 \begin{itemize} diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java b/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java index 3307de4..44b04d6 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/ApplicationOptions.java @@ -112,7 +112,7 @@ public static enum TreeSearch { // whether to optimize the BIONJ-model tree by ML public boolean optimizeMLTopology = true; - public TreeSearch treeSearchOperations = TreeSearch.NNI; + public TreeSearch treeSearchOperations = TreeSearch.BEST; // Threshold for the guided search mode. A QST == 0.0 means no model // but the GTR one is optimized. A high QST means the whole set of diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java b/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java index 85ecbfa..c1c50d0 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/ModelTest.java @@ -71,7 +71,7 @@ * * Description: Main class for selecting models of nucleotide substitition * - * @author Diego Darriba, University of Vigo / University of A Coru�a, Spain + * @author Diego Darriba, University of Vigo / University of A Coruna, Spain * ddarriba@udc.es * @author David Posada, University of Vigo, Spain dposada@uvigo.es | * darwin.uvigo.es @@ -95,7 +95,7 @@ public class ModelTest { public static final double INFINITY = 9999; public static final int MAX_NUM_MODELS = 88; public static final int MAX_NAME = 60; - public static final String CURRENT_VERSION = "2.1.7 v20141120"; + public static final String CURRENT_VERSION = "2.1.7 v20150220"; public static final String programName = ("jModeltest"); public static final String URL = "http://code.google.com/p/jmodeltest2"; public static final String WIKI = "http://code.google.com/p/jmodeltest2/wiki/GettingStarted"; diff --git a/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java b/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java index 0fd18cf..3f42b6a 100644 --- a/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java +++ b/src/main/java/es/uvigo/darwin/jmodeltest/utilities/Utilities.java @@ -123,7 +123,7 @@ public static String getBinaryVersion() { } public static String calculateRuntimeMinutes(long startTime, long endTime) { - long seconds = (long) Math.round((endTime - startTime) / 1000.0); + long seconds = Math.round((endTime - startTime) / 1000.0); int hours = (int) (seconds / 3600.0); int rest1 = (int) (seconds % (3600.0)); int minutes = (int) (rest1 / 60.0); @@ -145,7 +145,7 @@ public static String getCurrentTime(String format) { } public static String displayRuntime(long time) { - long decimes = (long) Math.round(time / 100.0); + long decimes = Math.round(time / 100.0); int hours = (int) (decimes / 36000.0); int rest1 = (int) (decimes % 36000.0); int minutes = (int) (rest1 / 600.0); @@ -330,7 +330,7 @@ public static String putSlashBeforeSpaces(String originalPath) { if (originalPath == null) return ""; - StringBuffer s = new StringBuffer((String) originalPath); + StringBuffer s = new StringBuffer(originalPath); for (int i = 0; i < s.length(); i++) { if (s.charAt(i) == ' ') @@ -349,7 +349,7 @@ public static String substituteSpaces(String originalPath) { if (originalPath == null) return ""; - StringBuffer s = new StringBuffer((String) originalPath); + StringBuffer s = new StringBuffer(originalPath); for (int i = 0; i < s.length(); i++) { if (s.charAt(i) == ' ') { @@ -508,4 +508,4 @@ public static double calculateShannonSampleSize (File alignmentFile, boolean doJ return (calculateShannonSampleSize(alignment, doJustShannonEntropy)); } -} // end of class \ No newline at end of file +} // end of class diff --git a/src/main/resources/CHANGELOG b/src/main/resources/CHANGELOG index 2c06087..10f0525 100644 --- a/src/main/resources/CHANGELOG +++ b/src/main/resources/CHANGELOG @@ -1,3 +1,8 @@ +20 Feb 2015 Version 2.1.7 Revision 20150220 + + * Fixed bug in ML tree search operation. Console version + was using NNI moves instead of "BEST" by default. + 20 Nov 2014 Version 2.1.7 Revision 20141120 * Fixed bug with special characters in paths