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