removed some uncheck warnings

diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
index 4cc61cd..78c75f9 100644 (file)
--- a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
+++ b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java
@@ -130,6 +130,8 @@ public final class TaxonomyDataManager extends RunnableProcess {
         return _sn_up_cache_map;
     }
 
+    
+    @SuppressWarnings("unchecked")
     private final static UniProtTaxonomy obtainTaxonomy( final HashMap<String, UniProtTaxonomy> cache,
                                                          final Object query,
                                                          final QUERY_TYPE qt ) throws IOException,
@@ -154,6 +156,7 @@ public final class TaxonomyDataManager extends RunnableProcess {
                     break;
                 case LIN:
                     return obtainUniProtTaxonomyFromLineage( ( List<String> ) query );
+                    
                 default:
                     throw new RuntimeException();
             }

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index 2b5c7c4..eb994cb 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -270,7 +270,7 @@ public class surfacing {
     public static final String                                      INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX        = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
     public static final String                                      INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
     private static final boolean                                    CALC_SIMILARITY_SCORES                                                        = false;
-
+    @SuppressWarnings("unchecked")
     public static void main( final String args[] ) {
         final long start_time = new Date().getTime();
         // final StringBuffer log = new StringBuffer();

diff --git a/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java b/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java
index 59ec4b2..027b316 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java
+++ b/forester/java/src/org/forester/archaeopteryx/ColorSchemeChooser.java
@@ -51,7 +51,7 @@ final class ColorSchemeChooser extends JDialog implements ActionListener {
 
     private static final long  serialVersionUID = 6150960100859081126L;
     private final TreeColorSet _colorset;
-    private final JComboBox    _selector;
+    private final JComboBox<String>    _selector;
     private final JPanel       _color_panel;
     private final JPanel       _color_labels[];
     private final JButton      _ok_btn;
@@ -77,7 +77,7 @@ final class ColorSchemeChooser extends JDialog implements ActionListener {
         for( final String element : TreeColorSet.SCHEME_NAMES ) {
             list.add( element );
         }
-        _selector = new JComboBox( list );
+        _selector = new JComboBox<String>( list );
         _selector.setMaximumRowCount( list.size() );
         _selector.getModel().addListDataListener( new ListDataListener() {
 

diff --git a/forester/java/src/org/forester/archaeopteryx/FontChooser.java b/forester/java/src/org/forester/archaeopteryx/FontChooser.java
index 694a6ee..232737a 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/FontChooser.java
+++ b/forester/java/src/org/forester/archaeopteryx/FontChooser.java
@@ -49,9 +49,9 @@ public class FontChooser extends JDialog implements ActionListener, ListSelectio
     private String                _type;
     private int                   _style;
     private int                   _size;
-    private final JList           _font_list        = new JList( AptxUtil.getAvailableFontFamiliesSorted() );
-    private final JList           _style_list       = new JList( STYLE );
-    private final JList           _size_list        = new JList( SIZE );
+    private final JList<String>           _font_list        = new JList<String>( AptxUtil.getAvailableFontFamiliesSorted() );
+    private final JList<String>           _style_list       = new JList<String>( STYLE );
+    private final JList<String>           _size_list        = new JList<String>( SIZE );
     private final JTextField      _fonts_tf         = new JTextField();
     private final JTextField      _style_tf         = new JTextField();
     private final JTextField      _size_tf          = new JTextField();
@@ -224,7 +224,7 @@ public class FontChooser extends JDialog implements ActionListener, ListSelectio
         _font = font;
     }
 
-    private void setScrollPos( final JScrollPane sp, final JList list, final int index ) {
+    private void setScrollPos( final JScrollPane sp, final JList<String> list, final int index ) {
         final int unit_size = sp.getVerticalScrollBar().getMaximum() / list.getModel().getSize();
         sp.getVerticalScrollBar().setValue( ( index - 2 ) * unit_size );
     }

diff --git a/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java b/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java
index 7b1055f..974cc61 100644 (file)
--- a/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java
+++ b/forester/java/src/org/forester/evoinference/matrix/character/BasicCharacterStateMatrix.java
@@ -120,6 +120,7 @@ public class BasicCharacterStateMatrix<S> implements CharacterStateMatrix<S> {
     }
 
     @Override
+    @SuppressWarnings("unchecked")
     public boolean equals( final Object o ) {
         if ( this == o ) {
             return true;
@@ -216,6 +217,7 @@ public class BasicCharacterStateMatrix<S> implements CharacterStateMatrix<S> {
     }
 
     @Override
+    @SuppressWarnings("unchecked")
     public S getState( final int identifier_index, final int character_index ) {
         return ( S ) _states[ identifier_index ][ character_index ];
     }

diff --git a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
index 4b5f1bb..b20ee0f 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainParsimonyCalculator.java
@@ -543,7 +543,7 @@ public final class DomainParsimonyCalculator {
         }
         return new DomainParsimonyCalculator( phylogeny, gwcd_list, domain_id_to_secondary_features_map );
     }
-
+    @SuppressWarnings("unchecked")
     public static CharacterStateMatrix<BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list ) {
         if ( gwcd_list.isEmpty() ) {
             throw new IllegalArgumentException( "genome wide combinable domains list is empty" );
@@ -662,7 +662,7 @@ public final class DomainParsimonyCalculator {
         }
         return matrix;
     }
-
+    @SuppressWarnings("unchecked")
     public static CharacterStateMatrix<BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List<GenomeWideCombinableDomains> gwcd_list,
                                                                                                                              final Map<String, String> domain_id_to_second_features_map ) {
         if ( gwcd_list.isEmpty() ) {