in progress

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index 6999f8b..0b84522 100644 (file)
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -41,7 +41,7 @@ public final class AncestralTaxonomyInference {
 
     public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
             AncestralTaxonomyInferenceException {
-        TaxonomyDataObtainer.clearCachesIfTooLarge();
+        TaxonomyDataManager.clearCachesIfTooLarge();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             if ( !node.isExternal() ) {
@@ -61,12 +61,12 @@ public final class AncestralTaxonomyInference {
         int shortest_lin_length = Integer.MAX_VALUE;
         for( final PhylogenyNode desc : descs ) {
             if ( desc.getNodeData().isHasTaxonomy()
-                    && ( TaxonomyDataObtainer.isHasAppropriateId( desc.getNodeData().getTaxonomy() )
+                    && ( TaxonomyDataManager.isHasAppropriateId( desc.getNodeData().getTaxonomy() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
                             .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
-                final UniProtTaxonomy up_tax = TaxonomyDataObtainer.obtainUniProtTaxonomy( desc.getNodeData()
+                final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomy( desc.getNodeData()
                         .getTaxonomy(), null, null );
                 if ( ( up_tax == null ) && ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getLineage() ) ) {
                     String desc_str = "";
@@ -169,7 +169,7 @@ public final class AncestralTaxonomyInference {
         final Taxonomy tax = new Taxonomy();
         n.getNodeData().setTaxonomy( tax );
         tax.setScientificName( last_common );
-        final UniProtTaxonomy up_tax = TaxonomyDataObtainer.obtainUniProtTaxonomyFromLineage( last_common_lineage );
+        final UniProtTaxonomy up_tax = TaxonomyDataManager.obtainUniProtTaxonomyFromLineage( last_common_lineage );
         if ( up_tax != null ) {
             if ( !ForesterUtil.isEmpty( up_tax.getRank() ) ) {
                 try {

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataObtainer.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
similarity index 80%
rename from forester/java/src/org/forester/analysis/TaxonomyDataObtainer.java
rename to forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 9222c44..0e48458 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataObtainer.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -49,7 +49,7 @@ import org.forester.util.ForesterUtil;
 import org.forester.ws.uniprot.UniProtTaxonomy;
 import org.forester.ws.uniprot.UniProtWsTools;
 
-public class TaxonomyDataObtainer extends RunnableProcess {
+public final class TaxonomyDataManager extends RunnableProcess {
 
     enum QUERY_TYPE {
         CODE, SN, CN, ID, LIN;
@@ -62,6 +62,33 @@ public class TaxonomyDataObtainer extends RunnableProcess {
     private static final HashMap<String, UniProtTaxonomy> _cn_up_cache_map         = new HashMap<String, UniProtTaxonomy>();
     private static final HashMap<String, UniProtTaxonomy> _id_up_cache_map         = new HashMap<String, UniProtTaxonomy>();
 
+    private final Phylogeny            _phy;
+    private final MainFrameApplication _mf;
+    private final TreePanel            _treepanel;
+    private final boolean              _delete;
+    private final boolean _allow_simple_names;
+
+    public TaxonomyDataManager( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
+        _phy = phy;
+        _mf = mf;
+        _treepanel = treepanel;
+        _delete = false;
+        _allow_simple_names = false;
+    }
+
+    public TaxonomyDataManager( final MainFrameApplication mf,
+                                 final TreePanel treepanel,
+                                 final Phylogeny phy,
+                                 final boolean delete,
+                                 final boolean allow_simple_name ) {
+        _phy = phy;
+        _mf = mf;
+        _treepanel = treepanel;
+        _delete = delete;
+        _allow_simple_names = allow_simple_name;
+    }
+
+    
     synchronized static void clearCachesIfTooLarge() {
         if ( getSnTaxCacheMap().size() > MAX_CACHE_SIZE ) {
             getSnTaxCacheMap().clear();
@@ -80,27 +107,27 @@ public class TaxonomyDataObtainer extends RunnableProcess {
         }
     }
 
-    synchronized static HashMap<String, UniProtTaxonomy> getCnTaxCacheMap() {
+    synchronized final static HashMap<String, UniProtTaxonomy> getCnTaxCacheMap() {
         return _cn_up_cache_map;
     }
 
-    synchronized static HashMap<String, UniProtTaxonomy> getCodeTaxCacheMap() {
+    synchronized final static HashMap<String, UniProtTaxonomy> getCodeTaxCacheMap() {
         return _code_up_cache_map;
     }
 
-    synchronized static HashMap<String, UniProtTaxonomy> getIdTaxCacheMap() {
+    synchronized final static HashMap<String, UniProtTaxonomy> getIdTaxCacheMap() {
         return _id_up_cache_map;
     }
 
-    synchronized static HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
+    synchronized final static HashMap<String, UniProtTaxonomy> getLineageTaxCacheMap() {
         return _lineage_up_cache_map;
     }
 
-    synchronized static HashMap<String, UniProtTaxonomy> getSnTaxCacheMap() {
+    synchronized final static HashMap<String, UniProtTaxonomy> getSnTaxCacheMap() {
         return _sn_up_cache_map;
     }
 
-    private static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
+    private final static UniProtTaxonomy getTaxonomies( final HashMap<String, UniProtTaxonomy> cache,
                                                   final Object query,
                                                   final QUERY_TYPE qt ) throws IOException,
             AncestralTaxonomyInferenceException {
@@ -130,16 +157,16 @@ public class TaxonomyDataObtainer extends RunnableProcess {
             if ( ( up_taxonomies != null ) && ( up_taxonomies.size() == 1 ) ) {
                 final UniProtTaxonomy up_tax = up_taxonomies.get( 0 );
                 if ( !ForesterUtil.isEmpty( up_tax.getScientificName() ) ) {
-                    TaxonomyDataObtainer.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
+                    TaxonomyDataManager.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
                 }
                 if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
-                    TaxonomyDataObtainer.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
+                    TaxonomyDataManager.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
                 }
                 if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
-                    TaxonomyDataObtainer.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
+                    TaxonomyDataManager.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
                 }
                 if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
-                    TaxonomyDataObtainer.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
+                    TaxonomyDataManager.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
                 }
                 return up_tax;
             }
@@ -149,33 +176,34 @@ public class TaxonomyDataObtainer extends RunnableProcess {
         }
     }
 
-    private static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query ) throws IOException {
+    private final static List<UniProtTaxonomy> getTaxonomiesFromCommonName( final String query ) throws IOException {
         return UniProtWsTools.getTaxonomiesFromCommonNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
-    private static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
+    private final static List<UniProtTaxonomy> getTaxonomiesFromId( final String query ) throws IOException {
         return UniProtWsTools.getTaxonomiesFromId( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
-    //
-    private static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query ) throws IOException {
+   
+    private final static List<UniProtTaxonomy> getTaxonomiesFromScientificName( final String query ) throws IOException {
         return UniProtWsTools.getTaxonomiesFromScientificNameStrict( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
-    //
-    private static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
+    
+    private final static List<UniProtTaxonomy> getTaxonomiesFromTaxonomyCode( final String query ) throws IOException {
         return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
-    static boolean isHasAppropriateId( final Taxonomy tax ) {
+    static final boolean isHasAppropriateId( final Taxonomy tax ) {
         return ( ( tax.getIdentifier() != null ) && ( !ForesterUtil.isEmpty( tax.getIdentifier().getValue() ) && ( tax
                 .getIdentifier().getProvider().equalsIgnoreCase( "ncbi" )
                 || tax.getIdentifier().getProvider().equalsIgnoreCase( "uniprot" ) || tax.getIdentifier().getProvider()
                 .equalsIgnoreCase( "uniprotkb" ) ) ) );
     }
 
-    synchronized private static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
-                                                                                      final boolean delete )
+    synchronized final private static SortedSet<String> obtainDetailedTaxonomicInformation( final Phylogeny phy,
+                                                                                      final boolean delete,
+                                                                                      final boolean allow_to_use_basic_node_names )
             throws IOException, AncestralTaxonomyInferenceException {
         clearCachesIfTooLarge();
         final SortedSet<String> not_found = new TreeSet<String>();
@@ -190,6 +218,9 @@ public class TaxonomyDataObtainer extends RunnableProcess {
             if ( node.getNodeData().isHasTaxonomy() ) {
                 tax = node.getNodeData().getTaxonomy();
             }
+            else if ( allow_to_use_basic_node_names && !ForesterUtil.isEmpty( node.getName() ) ) {
+                // Nothing to be done.
+            }
             else if ( node.isExternal() ) {
                 if ( !ForesterUtil.isEmpty( node.getName() ) ) {
                     not_found.add( node.getName() );
@@ -202,10 +233,11 @@ public class TaxonomyDataObtainer extends RunnableProcess {
                 }
             }
             UniProtTaxonomy uniprot_tax = null;
-            if ( ( tax != null )
+            if ( ( ( tax != null )
                     && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() )
                             || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil.isEmpty( tax
-                            .getCommonName() ) ) ) {
+                            .getCommonName() ) ) ) ||
+                            ( allow_to_use_basic_node_names && !ForesterUtil.isEmpty( node.getName() ) ) ) {
                 uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
                 if ( uniprot_tax != null ) {
                     updateTaxonomy( qt, node, tax, uniprot_tax );
@@ -229,43 +261,48 @@ public class TaxonomyDataObtainer extends RunnableProcess {
         return not_found;
     }
 
-    public static UniProtTaxonomy obtainUniProtTaxonomy( final Taxonomy tax, Object query, QUERY_TYPE qt )
+    public final static UniProtTaxonomy obtainUniProtTaxonomy( final Taxonomy tax, Object query, QUERY_TYPE qt )
             throws IOException, AncestralTaxonomyInferenceException {
-        if ( TaxonomyDataObtainer.isHasAppropriateId( tax ) ) {
+        if ( tax == null ) {
+            throw new IllegalArgumentException( "illegal attempt to use empty taxonomy object");
+        }
+        
+        
+        if ( TaxonomyDataManager.isHasAppropriateId( tax ) ) {
             query = tax.getIdentifier().getValue();
             qt = QUERY_TYPE.ID;
-            return getTaxonomies( TaxonomyDataObtainer.getIdTaxCacheMap(), query, qt );
+            return getTaxonomies( TaxonomyDataManager.getIdTaxCacheMap(), query, qt );
         }
         else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             if ( !ForesterUtil.isEmpty( tax.getLineage() ) ) {
                 query = tax.getLineage();
                 qt = QUERY_TYPE.LIN;
-                return getTaxonomies( TaxonomyDataObtainer.getLineageTaxCacheMap(), query, qt );
+                return getTaxonomies( TaxonomyDataManager.getLineageTaxCacheMap(), query, qt );
             }
             else {
                 query = tax.getScientificName();
                 qt = QUERY_TYPE.SN;
-                return getTaxonomies( TaxonomyDataObtainer.getSnTaxCacheMap(), query, qt );
+                return getTaxonomies( TaxonomyDataManager.getSnTaxCacheMap(), query, qt );
             }
         }
         else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
             query = tax.getTaxonomyCode();
             qt = QUERY_TYPE.CODE;
-            return getTaxonomies( TaxonomyDataObtainer.getCodeTaxCacheMap(), query, qt );
+            return getTaxonomies( TaxonomyDataManager.getCodeTaxCacheMap(), query, qt );
         }
         else {
             query = tax.getCommonName();
             qt = QUERY_TYPE.CN;
-            return getTaxonomies( TaxonomyDataObtainer.getCnTaxCacheMap(), query, qt );
+            return getTaxonomies( TaxonomyDataManager.getCnTaxCacheMap(), query, qt );
         }
     }
 
-    static UniProtTaxonomy obtainUniProtTaxonomyFromLineage( final List<String> lineage )
+    static final UniProtTaxonomy obtainUniProtTaxonomyFromLineage( final List<String> lineage )
             throws AncestralTaxonomyInferenceException, IOException {
         final String lineage_str = ForesterUtil.stringListToString( lineage, ">" );
         UniProtTaxonomy up_tax = null;
-        if ( TaxonomyDataObtainer.getLineageTaxCacheMap().containsKey( lineage_str ) ) {
-            up_tax = TaxonomyDataObtainer.getLineageTaxCacheMap().get( lineage_str ).copy();
+        if ( TaxonomyDataManager.getLineageTaxCacheMap().containsKey( lineage_str ) ) {
+            up_tax = TaxonomyDataManager.getLineageTaxCacheMap().get( lineage_str ).copy();
         }
         else {
             final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage
@@ -291,25 +328,25 @@ public class TaxonomyDataObtainer extends RunnableProcess {
                     throw new AncestralTaxonomyInferenceException( "lineage \""
                             + ForesterUtil.stringListToString( lineage, " > " ) + "\" not found" );
                 }
-                TaxonomyDataObtainer.getLineageTaxCacheMap().put( lineage_str, up_tax );
+                TaxonomyDataManager.getLineageTaxCacheMap().put( lineage_str, up_tax );
                 if ( !ForesterUtil.isEmpty( up_tax.getScientificName() ) ) {
-                    TaxonomyDataObtainer.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
+                    TaxonomyDataManager.getSnTaxCacheMap().put( up_tax.getScientificName(), up_tax );
                 }
                 if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
-                    TaxonomyDataObtainer.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
+                    TaxonomyDataManager.getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
                 }
                 if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
-                    TaxonomyDataObtainer.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
+                    TaxonomyDataManager.getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
                 }
                 if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
-                    TaxonomyDataObtainer.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
+                    TaxonomyDataManager.getIdTaxCacheMap().put( up_tax.getId(), up_tax );
                 }
             }
         }
         return up_tax;
     }
 
-    synchronized private static void updateTaxonomy( final QUERY_TYPE qt,
+    synchronized final private static void updateTaxonomy( final QUERY_TYPE qt,
                                                      final PhylogenyNode node,
                                                      final Taxonomy tax,
                                                      final UniProtTaxonomy up_tax ) {
@@ -349,33 +386,12 @@ public class TaxonomyDataObtainer extends RunnableProcess {
             }
         }
     }
-    private final Phylogeny            _phy;
-    private final MainFrameApplication _mf;
-    private final TreePanel            _treepanel;
-    private final boolean              _delete;
-
-    public TaxonomyDataObtainer( final MainFrameApplication mf, final TreePanel treepanel, final Phylogeny phy ) {
-        _phy = phy;
-        _mf = mf;
-        _treepanel = treepanel;
-        _delete = false;
-    }
-
-    public TaxonomyDataObtainer( final MainFrameApplication mf,
-                                 final TreePanel treepanel,
-                                 final Phylogeny phy,
-                                 final boolean delete ) {
-        _phy = phy;
-        _mf = mf;
-        _treepanel = treepanel;
-        _delete = delete;
-    }
-
-    private void execute() {
+   
+    private final void execute() {
         start( _mf, "taxonomy data" );
         SortedSet<String> not_found = null;
         try {
-            not_found = obtainDetailedTaxonomicInformation( _phy, _delete );
+            not_found = obtainDetailedTaxonomicInformation( _phy, _delete, _allow_simple_names );
         }
         catch ( final UnknownHostException e ) {
             JOptionPane.showMessageDialog( _mf,
@@ -479,7 +495,7 @@ public class TaxonomyDataObtainer extends RunnableProcess {
         }
     }
 
-    private String getBaseUrl() {
+    private final String getBaseUrl() {
         return UniProtWsTools.BASE_URL;
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 5f8aa34..f49792c 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -63,7 +63,7 @@ import javax.swing.JOptionPane;
 import javax.swing.text.MaskFormatter;
 
 import org.forester.analysis.AncestralTaxonomyInference;
-import org.forester.analysis.TaxonomyDataObtainer;
+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;
@@ -465,7 +465,7 @@ public final class AptxUtil {
                         else {
                             UniProtTaxonomy up = null;
                             try {
-                                up = TaxonomyDataObtainer.obtainUniProtTaxonomy( temp_tax, null, null );
+                                up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
                             }
                             catch ( final Exception e ) {
                                 e.printStackTrace();

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index 51d1129..bdfd369 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -59,7 +59,7 @@ import javax.swing.event.ChangeListener;
 import javax.swing.filechooser.FileFilter;
 import javax.swing.plaf.synth.SynthLookAndFeel;
 
-import org.forester.analysis.TaxonomyDataObtainer;
+import org.forester.analysis.TaxonomyDataManager;
 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
 import org.forester.archaeopteryx.Options.NODE_LABEL_DIRECTION;
@@ -1516,7 +1516,7 @@ public final class MainFrameApplication extends MainFrame {
         if ( getCurrentTreePanel() != null ) {
             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
             if ( ( phy != null ) && !phy.isEmpty() ) {
-                final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+                final TaxonomyDataManager t = new TaxonomyDataManager( this,
                                                                          _mainpanel.getCurrentTreePanel(),
                                                                          phy.copy() );
                 new Thread( t ).start();
@@ -1528,10 +1528,10 @@ public final class MainFrameApplication extends MainFrame {
         if ( getCurrentTreePanel() != null ) {
             final Phylogeny phy = getCurrentTreePanel().getPhylogeny();
             if ( ( phy != null ) && !phy.isEmpty() ) {
-                final TaxonomyDataObtainer t = new TaxonomyDataObtainer( this,
+                final TaxonomyDataManager t = new TaxonomyDataManager( this,
                                                                          _mainpanel.getCurrentTreePanel(),
                                                                          phy.copy(),
-                                                                         true );
+                                                                         true,true );
                 new Thread( t ).start();
             }
         }