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more tests for isDuplication() and isSpecation() added
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
confadd.java
diff --git
a/forester/java/src/org/forester/application/confadd.java
b/forester/java/src/org/forester/application/confadd.java
index
fc4dd41
..
7684899
100644
(file)
--- a/
forester/java/src/org/forester/application/confadd.java
+++ b/
forester/java/src/org/forester/application/confadd.java
@@
-22,7
+22,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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.application;
package org.forester.application;
@@
-142,8
+142,8
@@
public class confadd {
}
if ( ( first < 0 ) || ( last < 0 ) ) {
ForesterUtil
}
if ( ( first < 0 ) || ( last < 0 ) ) {
ForesterUtil
- .fatalError( PRG_NAME,
- "attempt to set first or last evaluator topology to use to a number less than zero" );
+ .fatalError( PRG_NAME,
+ "attempt to set first or last evaluator topology to use to a number less than zero" );
}
if ( norm < 0 ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for normalizer [" + norm + "]" );
}
if ( norm < 0 ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for normalizer [" + norm + "]" );
@@
-200,11
+200,11
@@
public class confadd {
}
if ( ( last >= evaluators.length ) || ( last <= first ) ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first
}
if ( ( last >= evaluators.length ) || ( last <= first ) ) {
ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first
- + ", " + last + "]" );
+ + ", " + last + "]" );
}
double value = 1;
if ( norm > 0 ) {
}
double value = 1;
if ( norm > 0 ) {
- value = norm / ( 1 + last - first );
+ value = norm / ( ( 1 + last ) - first );
}
ForesterUtil.programMessage( PRG_NAME, "first topology to use: " + first );
String is_last = "";
}
ForesterUtil.programMessage( PRG_NAME, "first topology to use: " + first );
String is_last = "";
@@
-212,7
+212,7
@@
public class confadd {
is_last = " (corresponds to last topology in file)";
}
ForesterUtil.programMessage( PRG_NAME, "last topology to use : " + last + is_last );
is_last = " (corresponds to last topology in file)";
}
ForesterUtil.programMessage( PRG_NAME, "last topology to use : " + last + is_last );
- ForesterUtil.programMessage( PRG_NAME, "sum of topologies used as evaluators: " + ( last - first + 1 ) );
+ ForesterUtil.programMessage( PRG_NAME, "sum of topologies used as evaluators: " + ( ( last - first ) + 1 ) );
if ( norm > 0 ) {
ForesterUtil.programMessage( PRG_NAME, "normalizer: " + norm + " (" + ForesterUtil.round( value, 6 ) + ")" );
}
if ( norm > 0 ) {
ForesterUtil.programMessage( PRG_NAME, "normalizer: " + norm + " (" + ForesterUtil.round( value, 6 ) + ")" );
}
@@
-244,17
+244,17
@@
public class confadd {
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME
System.out.println( "Usage:" );
System.out.println();
System.out.println( PRG_NAME
- + " [options] <confidence type> <target tree file> <evaluators tree file> <outfile>" );
+ + " [options] <confidence type> <target tree file> <evaluators tree file> <outfile>" );
System.out.println();
System.out.println( "options:" );
System.out.println();
System.out.println( " -" + STRICT_OPTION
System.out.println();
System.out.println( "options:" );
System.out.println();
System.out.println( " -" + STRICT_OPTION
- + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
+ + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
System.out.println( " -" + NORMALIZE_OPTION
System.out.println( " -" + NORMALIZE_OPTION
- + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
+ + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
System.out.println( " -" + LAST_OPTION
System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
System.out.println( " -" + LAST_OPTION
- + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
+ + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
System.out.println();
}
System.out.println();
}
@@
-265,7
+265,7
@@
public class confadd {
final PhylogenyNode node = it.next();
if ( ext_nodes.contains( node ) ) {
throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg
final PhylogenyNode node = it.next();
if ( ext_nodes.contains( node ) ) {
throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg
- + " is not unique" );
+ + " is not unique" );
}
ext_nodes.add( node );
}
}
ext_nodes.add( node );
}