phylotastic hackathon at NESCENT 120607

[jalview.git] / forester / java / src / org / forester / test / Test.java

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 90430aa..814bf7c 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -104,10 +104,10 @@ import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
 import org.forester.util.GeneralTable;
 import org.forester.util.SequenceIdParser;
-import org.forester.ws.uniprot.DatabaseTools;
-import org.forester.ws.uniprot.SequenceDatabaseEntry;
-import org.forester.ws.uniprot.UniProtTaxonomy;
-import org.forester.ws.uniprot.UniProtWsTools;
+import org.forester.ws.seqdb.DatabaseTools;
+import org.forester.ws.seqdb.SequenceDatabaseEntry;
+import org.forester.ws.seqdb.SequenceDbWsTools;
+import org.forester.ws.seqdb.UniProtTaxonomy;
 import org.forester.ws.wabi.TxSearch;
 import org.forester.ws.wabi.TxSearch.RANKS;
 import org.forester.ws.wabi.TxSearch.TAX_NAME_CLASS;
@@ -7850,7 +7850,7 @@ public final class Test {
 
     private static boolean testUniprotTaxonomySearch() {
         try {
-            List<UniProtTaxonomy> results = UniProtWsTools
+            List<UniProtTaxonomy> results = SequenceDbWsTools
                     .getTaxonomiesFromCommonNameStrict( "starlet sea anemone", 10 );
             if ( results.size() != 1 ) {
                 return false;
@@ -7871,7 +7871,7 @@ public final class Test {
                 return false;
             }
             results = null;
-            results = UniProtWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
+            results = SequenceDbWsTools.getTaxonomiesFromScientificNameStrict( "Nematostella vectensis", 10 );
             if ( results.size() != 1 ) {
                 return false;
             }
@@ -7891,7 +7891,7 @@ public final class Test {
                 return false;
             }
             results = null;
-            results = UniProtWsTools.getTaxonomiesFromId( "45351", 10 );
+            results = SequenceDbWsTools.getTaxonomiesFromId( "45351", 10 );
             if ( results.size() != 1 ) {
                 return false;
             }
@@ -7911,7 +7911,7 @@ public final class Test {
                 return false;
             }
             results = null;
-            results = UniProtWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
+            results = SequenceDbWsTools.getTaxonomiesFromTaxonomyCode( "NEMVE", 10 );
             if ( results.size() != 1 ) {
                 return false;
             }
@@ -8002,47 +8002,47 @@ public final class Test {
     }
 
     private static boolean testUniprotEntryRetrieval() {
-        if ( !UniProtWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "3 4P12345" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "P12345E" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "P123455" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "P123455" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "EP12345E" ) != null ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "AY423861" ) != null ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1DDD5" ).equals( "P1DDD5" ) ) {
             return false;
         }
-        if ( UniProtWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
+        if ( SequenceDbWsTools.parseUniProtAccessor( "P1DDDD" ) != null ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345/12-42" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X P12345 12-42" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P12345/12-42" ).equals( "P12345" ) ) {
             return false;
         }
-        if ( !UniProtWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
+        if ( !SequenceDbWsTools.parseUniProtAccessor( "P1234X/P12345" ).equals( "P12345" ) ) {
             return false;
         }
         try {
-            final SequenceDatabaseEntry entry = UniProtWsTools.obtainUniProtEntry( "P12345", 200 );
+            final SequenceDatabaseEntry entry = SequenceDbWsTools.obtainUniProtEntry( "P12345", 200 );
             if ( !entry.getAccession().equals( "P12345" ) ) {
                 return false;
             }
@@ -9016,18 +9016,36 @@ public final class Test {
                 return false;
             }
             // 
-//            id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
-//            if ( id == null
-//                 || ForesterUtil.isEmpty( id.getValue() )
-//                 || ForesterUtil.isEmpty( id.getProvider() )
-//                 || !id.getValue().equals( "002434188" )
-//                 || !id.getProvider().equals( "genbank" ) ) {
-//                if ( id != null ) {
-//                    System.out.println( "value   =" + id.getValue() );
-//                    System.out.println( "provider=" + id.getProvider() );
-//                }
-//                return false;
-//            }
+            id = SequenceIdParser.parse( "mites|ref_XP_002434188_1" );
+            if ( id == null
+                 || ForesterUtil.isEmpty( id.getValue() )
+                 || ForesterUtil.isEmpty( id.getProvider() )
+                 || !id.getValue().equals( "XP_002434188" )
+                 || !id.getProvider().equals( "refseq" ) ) {
+                if ( id != null ) {
+                    System.out.println( "value   =" + id.getValue() );
+                    System.out.println( "provider=" + id.getProvider() );
+                }
+                return false;
+            }
+            // 
+            id = SequenceIdParser.parse( "mites_ref_XP_002434188_1_bla_XP_12345" );
+            if ( id == null
+                 || ForesterUtil.isEmpty( id.getValue() )
+                 || ForesterUtil.isEmpty( id.getProvider() )
+                 || !id.getValue().equals( "XP_002434188" )
+                 || !id.getProvider().equals( "refseq" ) ) {
+                if ( id != null ) {
+                    System.out.println( "value   =" + id.getValue() );
+                    System.out.println( "provider=" + id.getProvider() );
+                }
+                return false;
+            }
+            // 
+            id = SequenceIdParser.parse( "XP_12345" );
+            if ( id != null ) {
+                return false;
+            }
             
             // lcl_91970_unknown_
         }