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
moved to: https://sites.google.com/site/cmzmasek/home/software/forester
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
webservices
/
WebserviceUtil.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
index
71c047a
..
d619022
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
+++ b/
forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
@@
-20,7
+20,7
@@
// 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.archaeopteryx.webservices;
package org.forester.archaeopteryx.webservices;
@@
-28,6
+28,7
@@
import java.util.ArrayList;
import java.util.List;
import org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat;
import java.util.List;
import org.forester.archaeopteryx.webservices.WebservicesManager.WsPhylogenyFormat;
+import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
@@
-135,7
+136,8
@@
public final class WebserviceUtil {
}
}
}
}
- public static void processInstructions( final PhylogeniesWebserviceClient client, final Phylogeny phylogeny ) {
+ public static void processInstructions( final PhylogeniesWebserviceClient client, final Phylogeny phylogeny )
+ throws PhyloXmlDataFormatException {
if ( client.getProcessingInstructions().equals( WebserviceUtil.TAX_CODE_TO_SCI_NAME ) ) {
WebserviceUtil.transferTaxonomyCodeToScientificName( phylogeny );
}
if ( client.getProcessingInstructions().equals( WebserviceUtil.TAX_CODE_TO_SCI_NAME ) ) {
WebserviceUtil.transferTaxonomyCodeToScientificName( phylogeny );
}
@@
-162,7
+164,7
@@
public final class WebserviceUtil {
}
}
}
}
- static void transferExternalScientificNameToTaxonomyCode( final Phylogeny phy ) {
+ static void transferExternalScientificNameToTaxonomyCode( final Phylogeny phy ) throws PhyloXmlDataFormatException {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
@@
-176,7
+178,7
@@
public final class WebserviceUtil {
}
}
}
}
- static void transferInternalTaxonomyCodeToScientificName( final Phylogeny phy ) {
+ static void transferInternalTaxonomyCodeToScientificName( final Phylogeny phy ) throws PhyloXmlDataFormatException {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
@@
-204,7
+206,7
@@
public final class WebserviceUtil {
}
}
}
}
- static void transferTaxonomyCodeToScientificName( final Phylogeny phy ) {
+ static void transferTaxonomyCodeToScientificName( final Phylogeny phy ) throws PhyloXmlDataFormatException {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
final PhylogenyNode n = it.next();