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 6301504..f99dc7f 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -130,10 +130,12 @@ 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,
-            AncestralTaxonomyInferenceException {
+                                                         AncestralTaxonomyInferenceException {
         if ( cache.containsKey( query ) ) {
             return cache.get( query ).copy();
         }
@@ -154,6 +156,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                     break;
                 case LIN:
                     return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
+                    
                 default:
                     throw new RuntimeException();
             }
@@ -199,7 +202,10 @@ public final class TaxonomyDataManager extends RunnableProcess {
     }
 
     private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
-        if ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) ) {
+        //FIXME fix "SPHAR" issue
+        if ( ( ( query.indexOf( "XX" ) == 3 ) && TaxonomyUtil.isHasTaxIdFromFakeTaxCode( query ) )
+                || query.equals( "SPHAR" ) /* TODO remove me, is same as Sphingomonas aromaticivorans */
+                ) {
             final int id = TaxonomyUtil.getTaxIdFromFakeTaxCode( query );
             return SequenceDbWsTools.getTaxonomiesFromId( String.valueOf( id ), MAX_TAXONOMIES_TO_RETURN );
         }
@@ -216,7 +222,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
     synchronized final private static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
                                                                                             final boolean delete,
                                                                                             final boolean allow_to_use_basic_node_names )
-            throws IOException, AncestralTaxonomyInferenceException {
+                                                                                                    throws IOException, AncestralTaxonomyInferenceException {
         clearCachesIfTooLarge();
         final SortedSet<String> not_found = new TreeSet<String>();
         List<PhylogenyNode> not_found_external_nodes = null;
@@ -373,7 +379,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         else {
             final List<UniProtTaxonomy> matching_taxonomies = new ArrayList<UniProtTaxonomy>();
             final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
-                    .get( lineage.size() - 1 ) );
+                                                                                         .get( lineage.size() - 1 ) );
             if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
                 for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
                     boolean match = true;
@@ -422,7 +428,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
             }
             else {
                 throw new AncestralTaxonomyInferenceException( "taxonomy \"" + ( lineage.get( lineage.size() - 1 ) )
-                        + "\" not found" );
+                                                               + "\" not found" );
             }
         }
     }
@@ -431,7 +437,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                                                            final PhylogenyNode node,
                                                            final Taxonomy tax,
                                                            final UniProtTaxonomy up_tax )
-            throws PhyloXmlDataFormatException {
+                                                                   throws PhyloXmlDataFormatException {
         if ( ( qt != QUERY_TYPE.SN ) && !ForesterUtil.isEmpty( up_tax.getScientificName() )
                 && ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             tax.setScientificName( up_tax.getScientificName() );
@@ -476,7 +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 );
@@ -484,7 +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 );
@@ -492,7 +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 );
@@ -503,13 +509,13 @@ 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 );
             }
             catch ( final Exception e ) {
-                // Not important if this fails, do nothing. 
+                // Not important if this fails, do nothing.
             }
             return;
         }
@@ -555,18 +561,18 @@ public final class TaxonomyDataManager extends RunnableProcess {
                 sb.append( "..." );
             }
             try {
-                JOptionPane.showMessageDialog( _mf,
+                JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                                sb.toString(),
                                                "Taxonomy Tool Completed",
                                                JOptionPane.WARNING_MESSAGE );
             }
             catch ( final Exception e ) {
-                // Not important if this fails, do nothing. 
+                // Not important if this fails, do nothing.
             }
         }
         else {
             try {
-                JOptionPane.showMessageDialog( _mf,
+                JOptionPane.showMessageDialog( _mf.getThisFrame(),
                                                "Taxonomy tool successfully completed",
                                                "Taxonomy Tool Completed",
                                                JOptionPane.INFORMATION_MESSAGE );