From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Mon, 21 Oct 2013 22:35:21 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=df1d96a02980b8f3f1c5a73ace65ec50b2e98e9b;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/application/decorator.java b/forester/java/src/org/forester/application/decorator.java
index 8d04470..c318c76 100644
--- a/forester/java/src/org/forester/application/decorator.java
+++ b/forester/java/src/org/forester/application/decorator.java
@@ -305,17 +305,17 @@ public final class decorator {
             if ( ( value_column < 0 ) || ( value_column >= mapping_table.getNumberOfColumns() ) ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for value column" );
             }
-            if ( mapping_table.isEmpty() || mapping_table.getNumberOfColumns() < 1 ) {
+            if ( mapping_table.isEmpty() || ( mapping_table.getNumberOfColumns() < 1 ) ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table is empty" );
             }
             if ( mapping_table.getNumberOfColumns() == 1 ) {
                 ForesterUtil.fatalError( decorator.PRG_NAME, "mapping table has only one column" );
             }
             map = mapping_table.getColumnsAsMap( key_column, value_column );
-            Iterator<Entry<String, String>> iter = map.entrySet().iterator();
+            final Iterator<Entry<String, String>> iter = map.entrySet().iterator();
             System.out.println();
             while ( iter.hasNext() ) {
-                Entry<String, String> e = iter.next();
+                final Entry<String, String> e = iter.next();
                 System.out.println( e.getKey() + " => " + e.getValue() );
             }
             System.out.println();
diff --git a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
index 418d099..8446c19 100644
--- a/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
+++ b/forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java
@@ -75,8 +75,6 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         final Pattern hgnc_PATTERN = Pattern.compile( "\\s+/db_xref=\"[A-Z:]*HGNC:(\\d+)\"" );
         final Pattern geneid_PATTERN = Pattern.compile( "\\s+/db_xref=\"GeneID:(\\d+)\"" );
         final Pattern pdb_PATTERN = Pattern.compile( "\\s+/db_xref=\"PDB:([A-Z0-9]+)\"" );
-        
-        
         final Pattern ec_PATTERN = Pattern.compile( "\\s+/EC_number=\"([\\.\\-\\d]+)\"" );
         final Pattern product_PATTERN = Pattern.compile( "\\s+/product=\"(\\w{1,10})\"" );
         final EbiDbEntry e = new EbiDbEntry();
@@ -582,7 +580,7 @@ public final class EbiDbEntry implements SequenceDatabaseEntry {
         return _symbol;
     }
 
-    private void setSequenceSymbol( String symbol ) {
+    private void setSequenceSymbol( final String symbol ) {
         _symbol = symbol;
     }