JAL-2797 added constructor including embedded/standalone boolean

[jalview.git] / forester / java / src / org / forester / analysis / TaxonomyDataManager.java

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 4cc61cd..f99dc7f 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -130,6 +130,8 @@ public final class TaxonomyDataManager extends RunnableProcess {
         return _sn_up_cache_map;
     }
 
+    
+    @SuppressWarnings("unchecked")
     private final static UniProtTaxonomy obtainTaxonomy( final HashMap<String, UniProtTaxonomy> cache,
                                                          final Object query,
                                                          final QUERY_TYPE qt ) throws IOException,
@@ -154,6 +156,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                     break;
                 case LIN:
                     return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
+                    
                 default:
                     throw new RuntimeException();
             }
@@ -479,7 +482,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
             not_found = obtainDetailedTaxonomicInformation( _phy, _delete, _allow_simple_names );
         }
         catch ( final UnknownHostException e ) {
-            JOptionPane.showMessageDialog( _mf,
+            JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                            "Could not connect to \"" + getBaseUrl() + "\"",
                                            "Network error during taxonomic information gathering",
                                            JOptionPane.ERROR_MESSAGE );
@@ -487,7 +490,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         }
         catch ( final IOException e ) {
             e.printStackTrace();
-            JOptionPane.showMessageDialog( _mf,
+            JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                            e.toString(),
                                            "Failed to obtain taxonomic information",
                                            JOptionPane.ERROR_MESSAGE );
@@ -495,7 +498,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         }
         catch ( final AncestralTaxonomyInferenceException e ) {
             e.printStackTrace();
-            JOptionPane.showMessageDialog( _mf,
+            JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                            e.toString(),
                                            "Failed to obtain taxonomic information",
                                            JOptionPane.ERROR_MESSAGE );
@@ -506,7 +509,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         }
         if ( ( _phy == null ) || _phy.isEmpty() ) {
             try {
-                JOptionPane.showMessageDialog( _mf,
+                JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                                "None of the external node taxonomies could be resolved",
                                                "Taxonomy Tool Failed",
                                                JOptionPane.WARNING_MESSAGE );
@@ -558,7 +561,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                 sb.append( "..." );
             }
             try {
-                JOptionPane.showMessageDialog( _mf,
+                JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                                sb.toString(),
                                                "Taxonomy Tool Completed",
                                                JOptionPane.WARNING_MESSAGE );
@@ -569,7 +572,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         }
         else {
             try {
-                JOptionPane.showMessageDialog( _mf,
+                JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                                "Taxonomy tool successfully completed",
                                                "Taxonomy Tool Completed",
                                                JOptionPane.INFORMATION_MESSAGE );