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
inprogress
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
UrlTreeReader.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
b/forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
index
f96864f
..
184e35e
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
+++ b/
forester/java/src/org/forester/archaeopteryx/UrlTreeReader.java
@@
-21,7
+21,7
@@
// 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;
package org.forester.archaeopteryx;
@@
-59,6
+59,11
@@
public class UrlTreeReader implements Runnable {
_webservice_client_index = webservice_client_index;
}
_webservice_client_index = webservice_client_index;
}
+ @Override
+ public void run() {
+ readPhylogeniesFromWebservice();
+ }
+
synchronized void readPhylogeniesFromWebservice() {
final long start_time = new Date().getTime();
URL url = null;
synchronized void readPhylogeniesFromWebservice() {
final long start_time = new Date().getTime();
URL url = null;
@@
-103,32
+108,31
@@
public class UrlTreeReader implements Runnable {
break;
case NH:
parser = new NHXParser();
break;
case NH:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( true );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
( ( NHXParser ) parser ).setReplaceUnderscores( true );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NH_EXTRACT_TAXONOMY:
parser = new NHXParser();
- ( ( NHXParser ) parser )
- .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser )
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PFAM:
parser = new NHXParser();
( ( NHXParser ) parser )
- .setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ .setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_STRICT );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NHX:
parser = new NHXParser();
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case NHX:
parser = new NHXParser();
- ( ( NHXParser ) parser ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.NO );
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PHYLOXML:
( ( NHXParser ) parser ).setReplaceUnderscores( false );
( ( NHXParser ) parser ).setGuessRootedness( true );
break;
case PHYLOXML:
- parser = new PhyloXmlParser();
+ parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
break;
default:
throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
break;
default:
throw new IllegalArgumentException( "unknown format: " + client.getReturnFormat() );
@@
-254,9
+258,4
@@
public class UrlTreeReader implements Runnable {
_main_frame.activateSaveAllIfNeeded();
System.gc();
}
_main_frame.activateSaveAllIfNeeded();
System.gc();
}
-
- @Override
- public void run() {
- readPhylogeniesFromWebservice();
- }
}
}