Fix NCBI taxonomy parsing

This commit fixes the parsing of the NCBI taxonomy web whose structure has been
slightly changed recently.

Author: hlfernandez

pom.xml

@@ -5,7 +5,7 @@
 
 	<groupId>org.sing_group</groupId>
 	<artifactId>seda-all</artifactId>
-	<version>0.4.0</version>
+	<version>0.4.1</version>
 	<packaging>pom</packaging>
 
 	<name>SEquence DAtaset builder</name>

seda-docs/source/conf.py

@@ -54,7 +54,7 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.4.0'
+version = u'0.4.1'
 # The full version, including alpha/beta/rc tags.
 release = u'0.4'
 

seda-plugin-blast/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>0.4.0</version>
+		<version>0.4.1</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda-plugin-clustalomega/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>0.4.0</version>
+		<version>0.4.1</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda/pom.xml

@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>org.sing_group</groupId>
 		<artifactId>seda-all</artifactId>
-		<version>0.4.0</version>
+		<version>0.4.1</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

seda/src/main/java/org/sing_group/seda/core/ncbi/NcbiTaxonomyResolver.java

@@ -65,10 +65,8 @@ private Optional<Element> findLineageDl(Document doc) {
         if (dtChild.childNodeSize() > 0) {
           if (dtChild.child(0).tagName().equals("a")) {
             Element link = dtChild.child(0);
-            if (link.childNodeSize() == 1 && link.child(0).tagName().equals("em")) {
-              if (link.child(0).text().equals("Lineage")) {
-                return Optional.of(dlElement);
-              }
+            if (link.childNodeSize() == 1 && link.childNode(0).outerHtml().equals("Lineage")) {
+              return Optional.of(dlElement);
             }
           }
         }
@@ -90,7 +88,6 @@ private Optional<NcbiTaxonomyInfo> extractNcbiTaxonomyInfo(Element lineageDl) {
           }
         }
       }
-
     }
     return Optional.of(new NcbiTaxonomyInfo(values));
   }

seda/src/main/java/org/sing_group/seda/gui/concatenate/ConcatenateSequencesConfigurationPanel.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.