in progress

[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 d0df4c7..d78720c 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -33,6 +33,7 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.SortedSet;
 import java.util.TreeSet;
+import java.util.regex.Matcher;
 
 import javax.swing.JOptionPane;
 
@@ -40,7 +41,9 @@ import org.forester.archaeopteryx.MainFrameApplication;
 import org.forester.archaeopteryx.TreePanel;
 import org.forester.archaeopteryx.tools.AncestralTaxonomyInferrer;
 import org.forester.archaeopteryx.tools.RunnableProcess;
+import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Identifier;
@@ -50,7 +53,6 @@ import org.forester.util.ForesterUtil;
 import org.forester.util.TaxonomyUtil;
 import org.forester.ws.seqdb.SequenceDbWsTools;
 import org.forester.ws.seqdb.UniProtTaxonomy;
-import org.forester.archaeopteryx.*;
 
 public final class TaxonomyDataManager extends RunnableProcess {
 
@@ -58,7 +60,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
         CODE, SN, CN, ID, LIN;
     }
     private static final int                              MAX_CACHE_SIZE           = 100000;
-    private static final int                              MAX_TAXONOMIES_TO_RETURN = 10;
+    private static final int                              MAX_TAXONOMIES_TO_RETURN = 2000;
     private static final HashMap<String, UniProtTaxonomy> _sn_up_cache_map         = new HashMap<String, UniProtTaxonomy>();
     private static final HashMap<String, UniProtTaxonomy> _lineage_up_cache_map    = new HashMap<String, UniProtTaxonomy>();
     private static final HashMap<String, UniProtTaxonomy> _code_up_cache_map       = new HashMap<String, UniProtTaxonomy>();
@@ -197,12 +199,13 @@ 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 );
- 
         }
-        
         return SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
@@ -248,7 +251,10 @@ public final class TaxonomyDataManager extends RunnableProcess {
             if ( ( ( tax != null ) && ( isHasAppropriateId( tax ) || !ForesterUtil.isEmpty( tax.getScientificName() )
                     || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil.isEmpty( tax.getCommonName() ) ) )
                     || ( allow_to_use_basic_node_names && !ForesterUtil.isEmpty( node.getName() ) ) ) {
-                if ( tax != null ) {
+                if ( ( ( tax != null ) && ( isHasAppropriateId( tax )
+                        || !ForesterUtil.isEmpty( tax.getScientificName() )
+                        || !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) || !ForesterUtil
+                            .isEmpty( tax.getCommonName() ) ) ) ) {
                     uniprot_tax = obtainUniProtTaxonomy( tax, null, qt );
                 }
                 else {
@@ -258,7 +264,6 @@ public final class TaxonomyDataManager extends RunnableProcess {
                     if ( tax == null ) {
                         tax = new Taxonomy();
                         node.getNodeData().addTaxonomy( tax );
-                        node.setName( "" );
                     }
                     updateTaxonomy( qt, node, tax, uniprot_tax );
                 }
@@ -325,15 +330,39 @@ public final class TaxonomyDataManager extends RunnableProcess {
         if ( ForesterUtil.isEmpty( simple_name ) ) {
             throw new IllegalArgumentException( "illegal attempt to use empty simple name" );
         }
-        qt = QUERY_TYPE.SN;
-        UniProtTaxonomy ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), simple_name, qt );
-        if ( ut == null ) {
+        UniProtTaxonomy ut = null;
+        final String code = ParserUtils.extractTaxonomyCodeFromNodeName( simple_name,
+                                                                         NHXParser.TAXONOMY_EXTRACTION.AGGRESSIVE );
+        if ( !ForesterUtil.isEmpty( code ) ) {
             qt = QUERY_TYPE.CODE;
-            ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), simple_name, qt );
+            ut = obtainTaxonomy( TaxonomyDataManager.getCodeTaxCacheMap(), code, qt );
         }
         if ( ut == null ) {
-            qt = QUERY_TYPE.CN;
-            ut = obtainTaxonomy( TaxonomyDataManager.getCnTaxCacheMap(), simple_name, qt );
+            final String sn = ParserUtils.extractScientificNameFromNodeName( simple_name );
+            if ( !ForesterUtil.isEmpty( sn ) ) {
+                qt = QUERY_TYPE.SN;
+                ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), sn, qt );
+            }
+        }
+        if ( ut == null ) {
+            final String id = ParserUtils
+                    .extractUniprotTaxonomyIdFromNodeName( simple_name,
+                                                           NHXParser.TAXONOMY_EXTRACTION.PFAM_STYLE_RELAXED );
+            if ( !ForesterUtil.isEmpty( id ) ) {
+                qt = QUERY_TYPE.ID;
+                ut = obtainTaxonomy( TaxonomyDataManager.getIdTaxCacheMap(), id, qt );
+            }
+        }
+        if ( ut == null ) {
+            String sn = "";
+            final Matcher m = ParserUtils.TAXOMONY_SN_PATTERN_GENUS.matcher( simple_name );
+            if ( m.matches() ) {
+                sn = m.group( 1 );
+            }
+            if ( !ForesterUtil.isEmpty( sn ) ) {
+                qt = QUERY_TYPE.SN;
+                ut = obtainTaxonomy( TaxonomyDataManager.getSnTaxCacheMap(), sn, qt );
+            }
         }
         return ut;
     }