in progress...

[jalview.git] / forester / java / src / org / forester / ws / uniprot / UniProtEntry.java

diff --git a/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java b/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java
index f74b1c7..2b74883 100644 (file)
--- a/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java
+++ b/forester/java/src/org/forester/ws/uniprot/UniProtEntry.java
@@ -42,44 +42,36 @@ public final class UniProtEntry implements SequenceDatabaseEntry {
         final UniProtEntry e = new UniProtEntry();
         for( final String line : lines ) {
             if ( line.startsWith( "AC" ) ) {
-                e.setAc( extract( line, "AC", ";" ) );
+                e.setAc( DatabaseTools.extract( line, "AC", ";" ) );
             }
             else if ( line.startsWith( "DE" ) ) {
                 if ( ( line.indexOf( "RecName:" ) > 0 ) && ( line.indexOf( "Full=" ) > 0 ) ) {
-                    e.setRecName( extract( line, "Full=", ";" ) );
+                    e.setRecName( DatabaseTools.extract( line, "Full=", ";" ) );
                 }
             }
             else if ( line.startsWith( "GN" ) ) {
                 if ( ( line.indexOf( "Name=" ) > 0 ) ) {
-                    e.setSymbol( extract( line, "Name=", ";" ) );
+                    e.setSymbol( DatabaseTools.extract( line, "Name=", ";" ) );
                 }
             }
             else if ( line.startsWith( "OS" ) ) {
                 if ( line.indexOf( "(" ) > 0 ) {
-                    e.setOsScientificName( extract( line, "OS", "(" ) );
+                    e.setOsScientificName( DatabaseTools.extract( line, "OS", "(" ) );
                 }
                 else {
-                    e.setOsScientificName( extract( line, "OS", "." ) );
+                    e.setOsScientificName( DatabaseTools.extract( line, "OS", "." ) );
                 }
             }
             else if ( line.startsWith( "OX" ) ) {
                 if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
-                    e.setTaxId( extract( line, "NCBI_TaxID=", ";" ) );
+                    e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
                 }
             }
         }
         return e;
     }
 
-    private static String extract( final String target, final String a, final String b ) {
-        final int i_a = target.indexOf( a );
-        final int i_b = target.indexOf( b );
-        if ( ( i_a < 0 ) || ( i_b < i_a ) ) {
-            throw new IllegalArgumentException( "attempt to extract from [" + target + "] between [" + a + "] and ["
-                    + b + "]" );
-        }
-        return target.substring( i_a + a.length(), i_b ).trim();
-    }
+   
 
     @Override
     public String getAccession() {