JAL-3446 unused imports removed

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index b70e9f7..1044802 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -20,6 +20,10 @@
  */
 package jalview.analysis;
 
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -32,12 +36,6 @@ import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.ws.SequenceFetcher;
-import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
 
 /**
  * Functions for cross-referencing sequence databases.

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 8bf0c24..3fbcee2 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -20,6 +20,12 @@
  */
 package jalview.analysis;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.Iterator;
+import java.util.List;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
@@ -28,7 +34,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.Mapping;
@@ -41,12 +46,6 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.ShiftList;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.Iterator;
-import java.util.List;
-
 public class Dna
 {
   private static final String STOP_ASTERIX = "*";

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 3dae998..f89b67c 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -20,18 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-import jalview.renderer.AwtRenderPanelI;
-import jalview.schemes.ResidueProperties;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
@@ -51,6 +39,17 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.beans.PropertyChangeEvent;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 public class AnnotationPanel extends Panel
         implements AwtRenderPanelI, AdjustmentListener, ActionListener,
         MouseListener, MouseMotionListener, ViewportListenerI

diff --git a/src/jalview/appletgui/TitledPanel.java b/src/jalview/appletgui/TitledPanel.java
index feeaf83..dec6573 100644 (file)
--- a/src/jalview/appletgui/TitledPanel.java
+++ b/src/jalview/appletgui/TitledPanel.java
@@ -20,13 +20,9 @@
  */
 package jalview.appletgui;
 
-import java.awt.Frame;
 import java.awt.Graphics;
 import java.awt.Insets;
-import java.awt.Label;
 import java.awt.Panel;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
 
 public class TitledPanel extends Panel
 {

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 69f5f63..09004f4 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,21 +20,8 @@
  */
 package jalview.bin;
 
-import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ColorUtils;
-import jalview.util.Platform;
-import jalview.ws.sifts.SiftsSettings;
-
 import java.awt.Color;
 import java.io.BufferedReader;
-import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.InputStream;
@@ -55,6 +42,18 @@ import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
 
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
+
 /**
  * Stores and retrieves Jalview Application Properties Lists and fields within
  * list entries are separated by '|' symbols unless otherwise stated (|) clauses

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index d39e9f1..a7e5afe 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -20,13 +20,12 @@
  */
 package jalview.datamodel;
 
-import jalview.util.CaseInsensitiveString;
-import jalview.ws.params.InvalidArgumentException;
-
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import jalview.util.CaseInsensitiveString;
+
 public class PDBEntry
 {
 

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index e28cc7f..ab35829 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -20,16 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.gff.SequenceOntologyI;
-import jalview.util.JSONUtils;
-import jalview.util.Platform;
-
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -40,6 +30,14 @@ import java.util.Map;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.JSONUtils;
+
 /**
  * A client for fetching and processing Ensembl feature data in GFF format by
  * calling the overlap REST service

diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index 97ad242..85f421d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -20,11 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.util.JSONUtils;
-
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -36,6 +31,9 @@ import java.util.Set;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+
 public class EnsemblInfo extends EnsemblRestClient
 {
 

diff --git a/src/jalview/ext/ensembl/EnsemblXref.java b/src/jalview/ext/ensembl/EnsemblXref.java
index eedfe97..9b58e58 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblXref.java
+++ b/src/jalview/ext/ensembl/EnsemblXref.java
@@ -20,12 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.util.DBRefUtils;
-import jalview.util.JSONUtils;
-
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -36,6 +30,10 @@ import java.util.Map;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.util.DBRefUtils;
+
 /**
  * A class to fetch cross-references from Ensembl by calling the /xrefs REST
  * service

diff --git a/src/jalview/gui/RestInputParamEditDialog.java b/src/jalview/gui/RestInputParamEditDialog.java
index 8ae5408..34d456f 100644 (file)
--- a/src/jalview/gui/RestInputParamEditDialog.java
+++ b/src/jalview/gui/RestInputParamEditDialog.java
@@ -20,20 +20,18 @@
  */
 package jalview.gui;
 
-import jalview.jbgui.GRestInputParamEditDialog;
-import jalview.ws.params.InvalidArgumentException;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.rest.InputType;
-import jalview.ws.rest.RestServiceDescription;
-
 import java.util.ArrayList;
 import java.util.Hashtable;
 
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.event.ListSelectionEvent;
 
+import jalview.jbgui.GRestInputParamEditDialog;
+import jalview.ws.params.InvalidArgumentException;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.RestServiceDescription;
 import net.miginfocom.swing.MigLayout;
 
 public class RestInputParamEditDialog extends GRestInputParamEditDialog

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 7effb0f..a577b69 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -20,13 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.Conservation;
-import jalview.datamodel.SequenceGroup;
-import jalview.jbgui.GSliderPanel;
-import jalview.renderer.ResidueShaderI;
-import jalview.util.MessageManager;
-
-import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.beans.PropertyVetoException;
@@ -39,6 +32,12 @@ import javax.swing.event.ChangeListener;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
+import jalview.analysis.Conservation;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.MessageManager;
+
 /**
  * DOCUMENT ME!
  * 

diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index bfa714a..83346fc 100755 (executable)
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -30,7 +30,6 @@ import java.awt.MediaTracker;
 import java.awt.Toolkit;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.net.URL;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index c30d8c7..47c9a00 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -21,24 +21,6 @@
 
 package jalview.gui;
 
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.fts.api.FTSData;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.io.DataSourceType;
-import jalview.jbgui.GStructureChooser;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -56,6 +38,23 @@ import javax.swing.JTable;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
 
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
+import jalview.jbgui.GStructureChooser;
+import jalview.util.MessageManager;
+
 /**
  * Provides the behaviors for the Structure chooser Panel
  * 

diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java
index e12586a..2f6a5c2 100644 (file)
--- a/src/jalview/gui/UserQuestionnaireCheck.java
+++ b/src/jalview/gui/UserQuestionnaireCheck.java
@@ -20,13 +20,11 @@
  */
 package jalview.gui;
 
-import jalview.util.MessageManager;
-
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
 import java.net.URL;
 
-import javax.swing.JOptionPane;
+import jalview.util.MessageManager;
 
 public class UserQuestionnaireCheck implements Runnable
 {

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index b97a25e..8b5e664 100644 (file)
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -20,12 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.jbgui.GWsPreferences;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.rest.RestServiceDescription;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -37,13 +31,18 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JLabel;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JTable;
 import javax.swing.JTextField;
 import javax.swing.table.AbstractTableModel;
 import javax.swing.table.TableCellRenderer;
 
+import jalview.bin.Cache;
+import jalview.jbgui.GWsPreferences;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.rest.RestServiceDescription;
+
 public class WsPreferences extends GWsPreferences
 {
 

diff --git a/src/jalview/io/AlignmentFileReaderI.java b/src/jalview/io/AlignmentFileReaderI.java
index c3e148d..1c42896 100644 (file)
--- a/src/jalview/io/AlignmentFileReaderI.java
+++ b/src/jalview/io/AlignmentFileReaderI.java
@@ -20,8 +20,6 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingsI;
-import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;

diff --git a/src/jalview/io/AlignmentFileWriterI.java b/src/jalview/io/AlignmentFileWriterI.java
index 2049032..7497005 100644 (file)
--- a/src/jalview/io/AlignmentFileWriterI.java
+++ b/src/jalview/io/AlignmentFileWriterI.java
@@ -22,8 +22,6 @@ package jalview.io;
 
 import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureSettingsModelI;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
 public interface AlignmentFileWriterI

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index d40446d..2b95081 100644 (file)
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -20,7 +20,12 @@
  */
 package jalview.io.packed;
 
-import jalview.api.FeatureColourI;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
 import jalview.datamodel.AlignmentI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileFormatI;
@@ -29,12 +34,6 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.packed.DataProvider.JvDataType;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
 public class ParsePackedSet
 {
 

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 38ad437..6c6d123 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,23 +20,8 @@
  */
 package jalview.jbgui;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.GeneticCodeI;
-import jalview.analysis.GeneticCodes;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.PaintRefresher;
-import jalview.gui.Preferences;
-import jalview.gui.TreePanel;
-import jalview.io.FileFormats;
-import jalview.schemes.ResidueColourScheme;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
-import java.awt.Component;
 import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -46,9 +31,7 @@ import java.awt.event.InputEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 
 import javax.swing.BorderFactory;
@@ -67,6 +50,18 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 @SuppressWarnings("serial")
 public class GAlignFrame extends JInternalFrame
 {

diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index bd3e8dc..83394cf 100755 (executable)
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -20,13 +20,8 @@
  */
 package jalview.jbgui;
 
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.awt.BorderLayout;
 import java.awt.Font;
-import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
@@ -40,6 +35,10 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
 
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * DOCUMENT ME!
  * 

diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 359f787..4b10546 100755 (executable)
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -20,10 +20,6 @@
  */
 package jalview.jbgui;
 
-import jalview.bin.Jalview;
-import jalview.gui.JvSwingUtils;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -45,6 +41,9 @@ import javax.swing.JTextField;
 import javax.swing.SwingConstants;
 import javax.swing.colorchooser.AbstractColorChooserPanel;
 
+import jalview.gui.JvSwingUtils;
+import jalview.util.MessageManager;
+
 /**
  * DOCUMENT ME!
  * 

diff --git a/src/jalview/util/ShortcutKeyMaskExWrapper.java b/src/jalview/util/ShortcutKeyMaskExWrapper.java
index 5b26f3d..4c33cf8 100644 (file)
--- a/src/jalview/util/ShortcutKeyMaskExWrapper.java
+++ b/src/jalview/util/ShortcutKeyMaskExWrapper.java
@@ -20,11 +20,6 @@
  */
 package jalview.util;
 
-import java.awt.GraphicsEnvironment;
-import java.awt.Toolkit;
-import java.awt.event.KeyEvent;
-import java.lang.reflect.Method;
-
 public class ShortcutKeyMaskExWrapper
 {
 //

diff --git a/src/jalview/ws/SequenceFetcherFactory.java b/src/jalview/ws/SequenceFetcherFactory.java
deleted file mode 100644 (file)
index 25144fc..0000000
--- a/src/jalview/ws/SequenceFetcherFactory.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws;
-
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
-public class SequenceFetcherFactory
-{
-  // BH the two methods in this class merged into SequenceFetcher
-}
-//public class SequenceFetcherFactory
-//{
-//
-//  private static SequenceFetcher instance;
-//
-//  /**
-//   * Returns a new SequenceFetcher object, or a mock object if one has been set
-//   * 
-//   * @return
-//   */
-//  public static ASequenceFetcher getSequenceFetcher()
-//  {
-//    return instance == null ? new SequenceFetcher() : instance;
-//  }
-//
-//  /**
-//   * Set the instance object to use (intended for unit testing with mock
-//   * objects).
-//   * 
-//   * Be sure to reset to null in the tearDown method of any tests!
-//   * 
-//   * @param sf
-//   */
-//  public static void setSequenceFetcher(SequenceFetcher sf)
-//  {
-//    instance = sf;
-//  }
-//}

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 19366e0..5198026 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -20,6 +20,25 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStream;
+import java.text.ParseException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
 import jalview.analysis.SequenceIdMatcher;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -40,29 +59,9 @@ import jalview.ws.ebi.EBIFetchClient;
 import jalview.xml.binding.embl.EntryType;
 import jalview.xml.binding.embl.EntryType.Feature;
 import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
-import jalview.xml.binding.jalview.JalviewModel;
 import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.embl.XrefType;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStream;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 {
   /*

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 6fc913b..fa6c3c7 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -20,6 +20,23 @@
  */
 package jalview.ws.dbsources;
 
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.FactoryConfigurationError;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -29,12 +46,10 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.gui.Preferences;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.uniprot.DbReferenceType;
 import jalview.xml.binding.uniprot.Entry;
 import jalview.xml.binding.uniprot.FeatureType;
@@ -42,23 +57,6 @@ import jalview.xml.binding.uniprot.LocationType;
 import jalview.xml.binding.uniprot.PositionType;
 import jalview.xml.binding.uniprot.PropertyType;
 
-import java.io.InputStream;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Vector;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.stream.FactoryConfigurationError;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import com.stevesoft.pat.Regex;
-
 /**
  * This class queries the Uniprot database for sequence data, unmarshals the
  * returned XML, and converts it to Jalview Sequence records (including attached

diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java
index 6aa3f48..59843f2 100644 (file)
--- a/src/jalview/ws/jws1/Discoverer.java
+++ b/src/jalview/ws/jws1/Discoverer.java
@@ -20,15 +20,8 @@
  */
 package jalview.ws.jws1;
 
-import jalview.bin.ApplicationSingletonProvider;
-import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.JvOptionPane;
-import jalview.util.MessageManager;
-
 import java.net.URL;
 import java.util.Hashtable;
-import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -37,6 +30,10 @@ import ext.vamsas.IRegistryServiceLocator;
 import ext.vamsas.RegistryServiceSoapBindingStub;
 import ext.vamsas.ServiceHandle;
 import ext.vamsas.ServiceHandles;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
 
 public class Discoverer implements Runnable, ApplicationSingletonI
 {

diff --git a/src/jalview/ws/utils/UrlDownloadClient.java b/src/jalview/ws/utils/UrlDownloadClient.java
index 227fe23..7d45313 100644 (file)
--- a/src/jalview/ws/utils/UrlDownloadClient.java
+++ b/src/jalview/ws/utils/UrlDownloadClient.java
@@ -21,18 +21,10 @@
 
 package jalview.ws.utils;
 
-import jalview.util.Platform;
-
 import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
-import java.net.URL;
-import java.nio.channels.Channels;
-import java.nio.channels.ReadableByteChannel;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.nio.file.StandardCopyOption;
+
+import jalview.util.Platform;
 
 public class UrlDownloadClient
 {

diff --git a/src/javajs/async/Assets.java b/src/javajs/async/Assets.java
index 3650544..05614ce 100644 (file)
--- a/src/javajs/async/Assets.java
+++ b/src/javajs/async/Assets.java
@@ -1,6 +1,5 @@
 package javajs.async;
 
-import java.awt.Toolkit;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;

diff --git a/src/org/json/JSONObject.java b/src/org/json/JSONObject.java
index 42d34de..f0b5512 100644 (file)
--- a/src/org/json/JSONObject.java
+++ b/src/org/json/JSONObject.java
@@ -32,7 +32,6 @@ import java.io.Closeable;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.io.Writer;
-import java.lang.annotation.Annotation;
 import java.lang.reflect.Field;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;

diff --git a/src/swingjs/api/js/HTML5Video.java b/src/swingjs/api/js/HTML5Video.java
index a47732a..073f1ed 100644 (file)
--- a/src/swingjs/api/js/HTML5Video.java
+++ b/src/swingjs/api/js/HTML5Video.java
@@ -3,7 +3,6 @@ package swingjs.api.js;
 import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.Frame;
-import java.awt.Graphics;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.image.BufferedImage;

diff --git a/test/jalview/analysis/AlignmentGenerator.java b/test/jalview/analysis/AlignmentGenerator.java
index 9d3877c..1ddcfb4 100644 (file)
--- a/test/jalview/analysis/AlignmentGenerator.java
+++ b/test/jalview/analysis/AlignmentGenerator.java
@@ -20,20 +20,17 @@
  */
 package jalview.analysis;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.io.FastaFile;
-
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.util.Arrays;
 import java.util.Random;
 
-import org.testng.annotations.BeforeClass;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
 
 /**
  * Generates, and outputs in Fasta format, a random peptide or nucleotide alignment for given

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 9eec241..b45547e 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -27,7 +27,16 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentUtils.DnaVariant;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -41,7 +50,6 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
@@ -51,18 +59,6 @@ import jalview.io.FormatAdapter;
 import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
 
 public class AlignmentUtilsTests
 {

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 0123551..9a0d610 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -28,6 +28,14 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.Alignment;
@@ -41,16 +49,6 @@ import jalview.gui.JvOptionPane;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.ws.SequenceFetcher;
-import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
 
 public class CrossRefTest
 {

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 129d7b3..7238d27 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -28,14 +28,6 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.AlignmentGenerator;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.PDBEntry.Type;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -49,6 +41,12 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
 import junit.extensions.PA;
 
 public class SequenceTest

diff --git a/test/jalview/fts/service/pdb/PDBFTSPanelTest.java b/test/jalview/fts/service/pdb/PDBFTSPanelTest.java
index 224a712..a5b26f1 100644 (file)
--- a/test/jalview/fts/service/pdb/PDBFTSPanelTest.java
+++ b/test/jalview/fts/service/pdb/PDBFTSPanelTest.java
@@ -23,9 +23,6 @@ package jalview.fts.service.pdb;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.gui.JvOptionPane;
-
-import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
 
 import org.testng.annotations.AfterMethod;
@@ -33,6 +30,7 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.gui.JvOptionPane;
 import junit.extensions.PA;
 
 public class PDBFTSPanelTest

diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java
index 34e88ad..cd37b61 100644 (file)
--- a/test/jalview/gui/SeqCanvasTest.java
+++ b/test/jalview/gui/SeqCanvasTest.java
@@ -20,27 +20,26 @@
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentI;
-import jalview.io.DataSourceType;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SearchResultsI;
-import jalview.io.FileLoader;
-import jalview.util.Platform;
-import jalview.viewmodel.ViewportRanges;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
 
 import java.awt.Font;
 import java.awt.FontMetrics;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertNotNull;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertTrue;
 
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportRanges;
 import junit.extensions.PA;
 
 public class SeqCanvasTest

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 073bde8..42c8826 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -24,15 +24,6 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.fts.api.FTSData;
-import jalview.jbgui.GStructureChooser.FilterOption;
-import jalview.ws.params.InvalidArgumentException;
-
 import java.util.Collection;
 import java.util.Vector;
 
@@ -41,6 +32,13 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.jbgui.GStructureChooser.FilterOption;
 import junit.extensions.PA;
 
 public class StructureChooserTest