rio, lca, refactoring

[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 1918587..86ff0d6 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/webservices/WebserviceUtil.java
@@ -28,8 +28,10 @@ import java.util.ArrayList;
 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.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Accession;
 import org.forester.phylogeny.data.Identifier;
@@ -37,7 +39,6 @@ import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.ForesterUtil;
-import org.forester.util.ForesterUtil.PhylogenyNodeField;
 
 public final class WebserviceUtil {
 
@@ -60,7 +61,7 @@ public final class WebserviceUtil {
                                                            "Please enter a Tree of Life node identifier\n(Examples: "
                                                                    + "19386 for Cephalopoda, 2461 for Cnidaria, 2466 for Deuterostomia)",
                                                            WsPhylogenyFormat.TOL_XML_RESPONSE,
-                                                           PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
                                                            WebserviceUtil.TOL_WEBSERVER,
                                                            true,
                                                            "http://tolweb.org",
@@ -70,7 +71,7 @@ public final class WebserviceUtil {
                                                            "Use TreeBASE to obtain a phylogeny",
                                                            "Please enter a TreeBASE tree identifier\n(Examples: 2654, 825, 4931, 2518, 2406, 4934)",
                                                            WsPhylogenyFormat.NEXUS,
-                                                           PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
+                                                           PhylogenyMethods.PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME,
                                                            "http://purl.org/phylo/treebase/phylows/tree/TB2:Tr"
                                                                    + PhylogeniesWebserviceClient.QUERY_PLACEHOLDER
                                                                    + "?format=nexus",
@@ -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 );
         }
@@ -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();
@@ -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();
@@ -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();