From b6366fd2ac865514d2ceacb63432dac532147a85 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 13 Feb 2015 01:05:45 +0000 Subject: [PATCH] removed some uncheck warnings --- .../java/src/org/forester/analysis/TaxonomyDataManager.java | 3 +++ forester/java/src/org/forester/application/surfacing.java | 2 +- .../src/org/forester/archaeopteryx/ColorSchemeChooser.java | 4 ++-- forester/java/src/org/forester/archaeopteryx/FontChooser.java | 8 ++++---- .../matrix/character/BasicCharacterStateMatrix.java | 2 ++ .../src/org/forester/surfacing/DomainParsimonyCalculator.java | 4 ++-- 6 files changed, 14 insertions(+), 9 deletions(-) diff --git a/forester/java/src/org/forester/analysis/TaxonomyDataManager.java b/forester/java/src/org/forester/analysis/TaxonomyDataManager.java index 4cc61cd..78c75f9 100644 --- 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 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 ) 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 --- 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 --- 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 _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( 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 --- 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 _font_list = new JList( AptxUtil.getAvailableFontFamiliesSorted() ); + private final JList _style_list = new JList( STYLE ); + private final JList _size_list = new JList( 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 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 --- 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 implements CharacterStateMatrix { } @Override + @SuppressWarnings("unchecked") public boolean equals( final Object o ) { if ( this == o ) { return true; @@ -216,6 +217,7 @@ public class BasicCharacterStateMatrix implements CharacterStateMatrix { } @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 --- 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 createMatrixOfBinaryDomainCombinationPresenceOrAbsence( final List 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 createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence( final List gwcd_list, final Map domain_id_to_second_features_map ) { if ( gwcd_list.isEmpty() ) { -- 1.7.10.2