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[jalview.git] / forester / java / src / org / forester / archaeopteryx / AptxUtil.java

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index e71eeef..e355967 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -62,7 +62,7 @@ import javax.swing.JApplet;
 import javax.swing.JOptionPane;
 import javax.swing.text.MaskFormatter;
 
-import org.forester.analysis.AncestralTaxonomyInference;
+import org.forester.analysis.TaxonomyDataManager;
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.io.parsers.tol.TolParser;
@@ -82,7 +82,7 @@ import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.AsciiHistogram;
 import org.forester.util.DescriptiveStatistics;
 import org.forester.util.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
+import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public final class AptxUtil {
 
@@ -464,7 +464,7 @@ public final class AptxUtil {
                         else {
                             UniProtTaxonomy up = null;
                             try {
-                                up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null );
+                                up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
                             }
                             catch ( final Exception e ) {
                                 e.printStackTrace();
@@ -537,7 +537,7 @@ public final class AptxUtil {
         }
     }
 
-    final static String crateBasicInformation( final Phylogeny phy ) {
+    final static String createBasicInformation( final Phylogeny phy ) {
         final StringBuilder desc = new StringBuilder();
         if ( ( phy != null ) && !phy.isEmpty() ) {
             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
@@ -617,8 +617,14 @@ public final class AptxUtil {
                 desc.append( "    Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
                 desc.append( "\n" );
             }
-            final List<DescriptiveStatistics> css = PhylogenyMethods.calculatConfidenceStatistics( phy );
-            if ( css.size() > 0 ) {
+            List<DescriptiveStatistics> css = null;
+            try {
+                css = PhylogenyMethods.calculatConfidenceStatistics( phy );
+            }
+            catch ( final IllegalArgumentException e ) {
+                ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
+            }
+            if ( ( css != null ) && ( css.size() > 0 ) ) {
                 desc.append( "\n" );
                 for( int i = 0; i < css.size(); ++i ) {
                     final DescriptiveStatistics cs = css.get( i );