git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
needed for https for treebase
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
test
/
examples
/
Example4.java
diff --git
a/forester/java/src/org/forester/test/examples/Example4.java
b/forester/java/src/org/forester/test/examples/Example4.java
index
b363ab3
..
7f35850
100644
(file)
--- a/
forester/java/src/org/forester/test/examples/Example4.java
+++ b/
forester/java/src/org/forester/test/examples/Example4.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.test.examples;
package org.forester.test.examples;
@@
-30,8
+30,10
@@
import java.io.File;
import java.io.IOException;
import org.forester.io.parsers.PhylogenyParser;
import java.io.IOException;
import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
import org.forester.util.ForesterUtil;
public class Example4 {
import org.forester.util.ForesterUtil;
public class Example4 {
@@
-41,14
+43,14
@@
public class Example4 {
final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
PhylogenyParser parser = null;
try {
final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
PhylogenyParser parser = null;
try {
- parser = ForesterUtil.createParserDependingOnFileType( treefile, true );
+ parser = ParserUtils.createParserDependingOnFileType( treefile, true );
}
catch ( final IOException e ) {
e.printStackTrace();
}
Phylogeny[] phys = null;
try {
}
catch ( final IOException e ) {
e.printStackTrace();
}
Phylogeny[] phys = null;
try {
- phys = ForesterUtil.readPhylogenies( parser, treefile );
+ phys = PhylogenyMethods.readPhylogenies( parser, treefile );
}
catch ( final IOException e ) {
e.printStackTrace();
}
catch ( final IOException e ) {
e.printStackTrace();