From df1d96a02980b8f3f1c5a73ace65ec50b2e98e9b Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Mon, 21 Oct 2013 22:35:21 +0000 Subject: [PATCH] inprogress --- forester/java/src/org/forester/application/decorator.java | 6 +++--- forester/java/src/org/forester/ws/seqdb/EbiDbEntry.java | 4 +--- 2 files changed, 4 insertions(+), 6 deletions(-) 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> iter = map.entrySet().iterator(); + final Iterator> iter = map.entrySet().iterator(); System.out.println(); while ( iter.hasNext() ) { - Entry e = iter.next(); + final Entry 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; } -- 1.7.10.2