tidy imports

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 3c4698f..2ba8c56 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -28,8 +28,6 @@ import jalview.io.*;
 import jalview.schemes.*;
 import jalview.ws.ebi.EBIFetchClient;
 
-import java.awt.BorderLayout;
-
 public class PDBViewer extends JInternalFrame implements Runnable
 {
 

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 82a11a8..a3a0fe1 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -17,7 +17,6 @@
  */
 package jalview.analysis;
 
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
 
@@ -26,7 +25,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.FeatureProperties;
 import jalview.datamodel.Mapping;

diff --git a/src/jalview/analysis/Grouping.java b/src/jalview/analysis/Grouping.java
index 4eee9c0..32ea204 100644 (file)
--- a/src/jalview/analysis/Grouping.java
+++ b/src/jalview/analysis/Grouping.java
@@ -17,12 +17,9 @@
  */
 package jalview.analysis;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 9dd241b..e386e5c 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -21,7 +21,6 @@
 
 package jalview.analysis;
 
-import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Stack;
 import java.util.Vector;

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index f3b0274..f42293d 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -22,12 +22,10 @@ import java.util.Map;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.RNAHelicesColour;
 
 /**
  * @author jimp

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6d8faaf..0f0ba4e 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -17,7 +17,6 @@
  */
 package jalview.appletgui;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.Conservation;
 import jalview.api.SequenceStructureBinding;
@@ -35,7 +34,6 @@ import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
@@ -83,7 +81,6 @@ import java.awt.event.KeyListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.IOException;
-import java.io.InputStreamReader;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Enumeration;

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 5264019..cc04b58 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -22,7 +22,6 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.bin.*;
 import jalview.datamodel.*;
@@ -30,8 +29,6 @@ import jalview.schemes.*;
 import jalview.structure.SelectionSource;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.ConservationThread;
-import jalview.workers.ConsensusThread;
 
 public class AlignViewport extends AlignmentViewport implements
         AlignViewportI, SelectionSource, VamsasSource

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 6c866ee..4941b11 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -19,8 +19,6 @@ package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Hashtable;
-import java.util.Vector;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.*;

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 8b891e5..d26680d 100755 (executable)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -24,9 +24,6 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.awt.Rectangle;
-
-import javax.swing.BoxLayout;
 
 public class AnnotationColourChooser extends Panel implements
         ActionListener, AdjustmentListener, ItemListener, MouseListener

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index d20881b..c85de33 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -21,7 +21,6 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.image.BufferedImage;
 
 import jalview.datamodel.*;
 import jalview.util.ParseHtmlBodyAndLinks;

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 4800a13..540a0e0 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -21,7 +21,6 @@ import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.image.BufferedImage;
 
 import jalview.datamodel.*;
 import jalview.renderer.AnnotationRenderer;

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 299b70c..a3dbe22 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -26,11 +26,6 @@ import jalview.datamodel.*;
 import jalview.structure.*;
 import jalview.io.*;
 
-import org.jmol.api.*;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
 import jalview.schemes.*;
 
 public class AppletJmol extends EmbmenuFrame implements

diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java
index 858a5a3..c6ffba1 100644 (file)
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@ -19,19 +19,15 @@ package jalview.appletgui;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
-import java.awt.Container;
 import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.Frame;
-import java.awt.GraphicsConfiguration;
 import java.awt.HeadlessException;
 import java.awt.Label;
 import java.awt.Menu;
 import java.awt.MenuBar;
 import java.awt.Panel;
 import java.awt.PopupMenu;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.util.Enumeration;

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index f73fb41..aaab8bd 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -28,7 +28,6 @@ import org.jmol.api.JmolViewer;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 20ecc8e..235e82c 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -24,7 +24,6 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.awt.Rectangle;
 
 public class FeatureColourChooser extends Panel implements ActionListener,
         AdjustmentListener, ItemListener, MouseListener

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index f5bc39b..dd236bd 100755 (executable)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -23,7 +23,6 @@ import java.awt.*;
 
 import java.awt.event.*;
 
-import jalview.appletgui.FeatureSettings.MyCheckbox;
 import jalview.datamodel.*;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index b6d3a9c..9ddb132 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -17,12 +17,9 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.viewmodel.PCAModel;
 

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 90d5227..d25caa4 100755 (executable)
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -18,7 +18,6 @@
 package jalview.appletgui;
 
 import java.util.*;
-import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 8c18b5b..65f3d91 100644 (file)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -19,7 +19,6 @@ package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.util.Hashtable;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 717fa83..5e4569a 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -24,7 +24,6 @@ import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.lang.reflect.Constructor;
-import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URL;
 import java.net.URLDecoder;

diff --git a/src/jalview/bin/JalviewLiteURLRetrieve.java b/src/jalview/bin/JalviewLiteURLRetrieve.java
index b8968d3..bd7e8de 100644 (file)
--- a/src/jalview/bin/JalviewLiteURLRetrieve.java
+++ b/src/jalview/bin/JalviewLiteURLRetrieve.java
@@ -22,10 +22,7 @@ import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
 
 import java.applet.Applet;
-import java.io.BufferedInputStream;
-import java.io.BufferedReader;
 import java.io.InputStream;
-import java.io.InputStreamReader;
 
 public class JalviewLiteURLRetrieve extends Applet
 {

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index b18c047..b21e388 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -19,7 +19,6 @@ package jalview.datamodel;
 
 import java.util.Enumeration;
 import java.util.Hashtable;
-import java.util.Vector;
 
 import jalview.analysis.*;
 import jalview.util.*;

diff --git a/src/jalview/datamodel/xdb/embl/EmblFeature.java b/src/jalview/datamodel/xdb/embl/EmblFeature.java
index aaae520..58b4c39 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblFeature.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeature.java
@@ -17,7 +17,6 @@
  */
 package jalview.datamodel.xdb.embl;
 
-import java.util.Hashtable;
 import java.util.Vector;
 
 public class EmblFeature

diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index 6a69970..559b055 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -18,7 +18,6 @@
 package jalview.datamodel.xdb.embl;
 
 import java.util.Enumeration;
-import java.util.Iterator;
 import java.util.Vector;
 
 public class EmblFeatureLocations

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index aa8cf0c..e25dab4 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -24,7 +24,6 @@ import jalview.datamodel.SequenceI;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.ArrayList;

diff --git a/src/jalview/ext/varna/JalviewVarnaBinding.java b/src/jalview/ext/varna/JalviewVarnaBinding.java
index 003e6d7..a21cd37 100644 (file)
--- a/src/jalview/ext/varna/JalviewVarnaBinding.java
+++ b/src/jalview/ext/varna/JalviewVarnaBinding.java
@@ -16,36 +16,11 @@
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.ext.varna;
-
-import java.io.File;
-
-import java.net.URL;
-import java.util.*;
-import java.applet.Applet;
-import java.awt.*;
 import java.awt.event.*;
 
-import javax.swing.JPanel;
-
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
 import jalview.api.SequenceStructureBinding;
 import jalview.api.StructureSelectionManagerProvider;
-import jalview.datamodel.*;
 import jalview.structure.*;
-import jalview.io.*;
-
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-import org.jmol.viewer.Viewer;
-
-import jalview.schemes.*;
-
-import fr.orsay.lri.varna.applications.*;
 
 public abstract class JalviewVarnaBinding implements StructureListener,
         SequenceStructureBinding, ComponentListener,

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index 95f2fc1..527a847 100644 (file)
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -23,7 +23,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.ArrayList;

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index a283c01..f8a2543 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -19,7 +19,6 @@ package jalview.gui;
 
 import java.beans.*;
 import java.io.*;
-import java.util.Hashtable;
 
 import java.awt.*;
 import java.awt.event.*;

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 80bfcf3..b1f7e4c 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -26,12 +26,10 @@ import java.awt.event.*;
 import java.io.*;
 
 import jalview.jbgui.GStructureViewer;
-import jalview.api.AlignmentViewPanel;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.structure.*;
 import jalview.datamodel.PDBEntry;
 import jalview.io.*;
 import jalview.schemes.*;

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index b8b60bc..6734200 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -18,17 +18,10 @@
 package jalview.gui;
 
 import java.awt.Container;
-import java.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
 import java.util.BitSet;
 
-import javax.swing.JPanel;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index b37b374..1a4c7ac 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -23,24 +23,13 @@ import java.util.regex.Pattern;
 import java.awt.*;
 
 import javax.swing.*;
-import javax.swing.event.*;
 
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceStructureBinding;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.structure.*;
-import jalview.io.*;
-import jalview.schemes.*;
 import jalview.util.ShiftList;
 import fr.orsay.lri.varna.VARNAPanel;
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
 import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
@@ -48,7 +37,6 @@ import fr.orsay.lri.varna.models.BaseList;
 import fr.orsay.lri.varna.models.VARNAConfig;
 import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
 import fr.orsay.lri.varna.models.rna.ModeleBase;
-import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
 import fr.orsay.lri.varna.models.rna.RNA;
 
 public class AppVarna extends JInternalFrame implements

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index b114c59..81452af 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -37,10 +37,8 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.io.File;
-import java.text.DateFormat;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Date;
 import java.util.List;
 
 import javax.swing.DefaultListModel;

diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index cb00e39..6896863 100644 (file)
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -20,7 +20,6 @@ package jalview.gui;
 import javax.swing.JOptionPane;
 
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 /**

diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index 8a7d6f8..ccb6c59 100644 (file)
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -27,7 +27,6 @@ import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkListener;
 import javax.swing.event.HyperlinkEvent.EventType;
 
-import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index c9b8de2..877aebb 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -59,7 +59,6 @@ import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -83,7 +82,6 @@ import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
-import javax.swing.JTextArea;
 import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.MenuEvent;

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 909b55d..069c1f9 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -19,7 +19,6 @@ package jalview.gui;
 
 import java.util.*;
 
-import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 41dd71d..3459fc8 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -38,7 +38,6 @@ import jalview.schemabinding.version2.*;
 import jalview.schemes.*;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
-import jalview.ws.jws2.AAConClient;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.jabaws2.Jws2Instance;

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index e50c149..639b9b2 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -18,7 +18,6 @@
 package jalview.gui;
 
 import java.io.*;
-import java.net.*;
 import java.util.*;
 import java.util.jar.*;
 

diff --git a/src/jalview/gui/JvSwingUtils.java b/src/jalview/gui/JvSwingUtils.java
index ac455bb..6518af8 100644 (file)
--- a/src/jalview/gui/JvSwingUtils.java
+++ b/src/jalview/gui/JvSwingUtils.java
@@ -28,7 +28,6 @@ import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
-import javax.swing.JTextArea;
 import javax.swing.SwingConstants;
 
 /**

diff --git a/src/jalview/gui/OptsParametersContainerI.java b/src/jalview/gui/OptsParametersContainerI.java
index 11d14c7..98f4d16 100644 (file)
--- a/src/jalview/gui/OptsParametersContainerI.java
+++ b/src/jalview/gui/OptsParametersContainerI.java
@@ -17,9 +17,6 @@
  */
 package jalview.gui;
 
-import jalview.gui.OptsAndParamsPage.ParamBox;
-import jalview.gui.OptsAndParamsPage.OptionBox;
-
 public interface OptsParametersContainerI
 {
 

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index f423a43..d2a6426 100755 (executable)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -24,7 +24,6 @@ import java.awt.event.*;
 import java.awt.print.*;
 import javax.swing.*;
 
-import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
 import jalview.viewmodel.PCAModel;

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4d23429..1a367c5 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -24,7 +24,6 @@ import java.awt.event.*;
 
 import javax.swing.*;
 
-import MCview.*;
 import jalview.analysis.*;
 import jalview.commands.*;
 import jalview.datamodel.*;

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 69d3eb7..a0fa216 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -28,7 +28,6 @@ import jalview.bin.*;
 import jalview.io.*;
 import jalview.jbgui.*;
 import jalview.schemes.*;
-import jalview.ws.EnfinEnvision2OneWay;
 
 /**
  * DOCUMENT ME!

diff --git a/src/jalview/gui/PromptUserConfig.java b/src/jalview/gui/PromptUserConfig.java
index cfe9da4..507d1f2 100644 (file)
--- a/src/jalview/gui/PromptUserConfig.java
+++ b/src/jalview/gui/PromptUserConfig.java
@@ -20,8 +20,6 @@ package jalview.gui;
 import jalview.bin.Cache;
 
 import java.awt.Component;
-import java.io.*;
-import java.net.*;
 
 import javax.swing.*;
 

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index f994f4e..08481d0 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -27,7 +27,6 @@ import jalview.analysis.AlignSeq;
 import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.jbgui.*;
-import jalview.util.*;
 
 /**
  * DOCUMENT ME!

diff --git a/src/jalview/gui/RestInputParamEditDialog.java b/src/jalview/gui/RestInputParamEditDialog.java
index fc27d76..18abbcd 100644 (file)
--- a/src/jalview/gui/RestInputParamEditDialog.java
+++ b/src/jalview/gui/RestInputParamEditDialog.java
@@ -20,8 +20,6 @@ package jalview.gui;
 import java.util.ArrayList;
 import java.util.Hashtable;
 
-import javax.swing.JDialog;
-import javax.swing.JInternalFrame;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.event.ListSelectionEvent;
@@ -29,7 +27,6 @@ import javax.swing.event.ListSelectionEvent;
 import net.miginfocom.swing.MigLayout;
 
 import jalview.jbgui.GRestInputParamEditDialog;
-import jalview.ws.params.ArgumentI;
 import jalview.ws.params.InvalidArgumentException;
 import jalview.ws.params.OptionI;
 import jalview.ws.params.ParameterI;

diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index 8bc01b8..9a0e1b7 100644 (file)
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -17,8 +17,6 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 4ec2ad4..13f6692 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -45,7 +45,6 @@ import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IClient;
 import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.InvalidSessionDocumentException;
-import uk.ac.vamsas.client.NoDefaultSessionException;
 import uk.ac.vamsas.client.UserHandle;
 import uk.ac.vamsas.client.VorbaId;
 import uk.ac.vamsas.client.picking.IMessageHandler;

diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 16670b9..c44e041 100755 (executable)
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -25,11 +25,9 @@ import java.awt.image.*;
 import javax.swing.*;
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkListener;
-import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.text.html.HTMLEditorKit;
 import javax.swing.text.html.StyleSheet;
 
-import jalview.bin.Cache;
 import jalview.jbgui.*;
 import jalview.ws.WSClientI;
 

diff --git a/src/jalview/io/AlignmentProperties.java b/src/jalview/io/AlignmentProperties.java
index 9eb6d25..38f61cf 100644 (file)
--- a/src/jalview/io/AlignmentProperties.java
+++ b/src/jalview/io/AlignmentProperties.java
@@ -17,7 +17,6 @@
  */
 package jalview.io;
 
-import java.io.IOException;
 import java.io.StringWriter;
 import java.io.PrintWriter;
 import java.util.Enumeration;

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 2569f7d..b06edc5 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -18,7 +18,6 @@
 package jalview.io;
 
 import java.io.*;
-import java.net.*;
 
 /**
  * DOCUMENT ME!

diff --git a/src/jalview/io/MatrixFile.java b/src/jalview/io/MatrixFile.java
index a8f13c3..30535bd 100644 (file)
--- a/src/jalview/io/MatrixFile.java
+++ b/src/jalview/io/MatrixFile.java
@@ -17,8 +17,6 @@
  */
 package jalview.io;
 
-import java.io.IOException;
-
 /**
  * IO for asymmetric matrix with arbitrary dimension with labels, as displayed
  * by PCA viewer. Form is: tab separated entity defs header line TITLE\ttitle

diff --git a/src/jalview/io/SimpleBlastFile.java b/src/jalview/io/SimpleBlastFile.java
index 4deb3f1..5cbf78d 100644 (file)
--- a/src/jalview/io/SimpleBlastFile.java
+++ b/src/jalview/io/SimpleBlastFile.java
@@ -21,7 +21,6 @@ import java.io.*;
 import java.util.*;
 
 import jalview.datamodel.*;
-import jalview.util.*;
 
 /**
  * parse a simple blast report. Attempt to cope with query anchored and pairwise

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 5ff3551..669181a 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -25,7 +25,6 @@ import java.util.*;
 
 import com.stevesoft.pat.*;
 import jalview.datamodel.*;
-import jalview.analysis.Rna;
 
 // import org.apache.log4j.*;
 

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index 1455c63..42a2caa 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -24,12 +24,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.io.Reader;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashMap;

diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index 1e54ef8..cceefb3 100644 (file)
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -17,7 +17,6 @@
  */
 package jalview.io.vamsas;
 
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;

diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 65463f0..0da8ea9 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -18,8 +18,6 @@
 package jalview.io.vamsas;
 
 import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.gui.TreePanel;
 import jalview.io.VamsasAppDatastore;
 
 import java.util.Enumeration;
@@ -27,12 +25,9 @@ import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Vector;
 
-import org.apache.commons.logging.Log;
-
 import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.client.VorbaId;
-import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Entry;
 import uk.ac.vamsas.objects.core.Provenance;
 import uk.ac.vamsas.objects.core.Seg;

diff --git a/src/jalview/io/vamsas/DatastoreRegistry.java b/src/jalview/io/vamsas/DatastoreRegistry.java
index eddb5bf..f7876e2 100644 (file)
--- a/src/jalview/io/vamsas/DatastoreRegistry.java
+++ b/src/jalview/io/vamsas/DatastoreRegistry.java
@@ -17,13 +17,10 @@
  */
 package jalview.io.vamsas;
 
-import java.util.Enumeration;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 import java.util.Map;
 
-import uk.ac.vamsas.client.Vobject;
-
 public class DatastoreRegistry
 {
   protected static org.apache.log4j.Logger log = org.apache.log4j.Logger

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index 265fed3..d4aafe8 100644 (file)
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -23,7 +23,6 @@ import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Map;
 import uk.ac.vamsas.objects.core.Sequence;
-import uk.ac.vamsas.objects.core.SequenceType;
 import jalview.io.VamsasAppDatastore;
 
 public class Dbref extends Rangetype

diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index 94e277a..a542b5d 100644 (file)
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -21,13 +21,10 @@ import java.util.Vector;
 
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.Local;
-import uk.ac.vamsas.objects.core.Map;
 import uk.ac.vamsas.objects.core.MapType;
 import uk.ac.vamsas.objects.core.Mapped;
 import uk.ac.vamsas.objects.core.RangeType;
 import uk.ac.vamsas.objects.core.Seg;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Mapping;
 import jalview.io.VamsasAppDatastore;
 
 /**

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index f02fe3e..6c4c285 100644 (file)
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -20,7 +20,6 @@ package jalview.io.vamsas;
 import java.util.Enumeration;
 import java.util.Vector;
 
-import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DataSetAnnotations;
 import uk.ac.vamsas.objects.core.Link;
 import uk.ac.vamsas.objects.core.Property;
@@ -28,7 +27,6 @@ import uk.ac.vamsas.objects.core.Provenance;
 import uk.ac.vamsas.objects.core.RangeAnnotation;
 import uk.ac.vamsas.objects.core.Score;
 import uk.ac.vamsas.objects.core.Seg;
-import uk.ac.vamsas.objects.core.Sequence;
 import uk.ac.vamsas.objects.utils.Properties;
 import jalview.bin.Cache;
 import jalview.datamodel.SequenceFeature;

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 9ac0ae5..6c31e45 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -27,9 +27,6 @@ import jalview.io.VamsasAppDatastore;
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.DataSet;
-import uk.ac.vamsas.objects.core.Local;
-import uk.ac.vamsas.objects.core.RangeType;
-import uk.ac.vamsas.objects.core.Seg;
 import uk.ac.vamsas.objects.core.Sequence;
 import uk.ac.vamsas.objects.core.SequenceMapping;
 import uk.ac.vamsas.objects.core.SequenceType;

diff --git a/src/jalview/javascript/JSFunctionExec.java b/src/jalview/javascript/JSFunctionExec.java
index 3e10294..09036e6 100644 (file)
--- a/src/jalview/javascript/JSFunctionExec.java
+++ b/src/jalview/javascript/JSFunctionExec.java
@@ -20,7 +20,6 @@ package jalview.javascript;
 import java.net.URL;
 import java.util.Vector;
 
-import netscape.javascript.JSException;
 import netscape.javascript.JSObject;
 import jalview.bin.JalviewLite;
 

diff --git a/src/jalview/javascript/JsSelectionSender.java b/src/jalview/javascript/JsSelectionSender.java
index 8e11699..f803759 100644 (file)
--- a/src/jalview/javascript/JsSelectionSender.java
+++ b/src/jalview/javascript/JsSelectionSender.java
@@ -17,14 +17,11 @@
  */
 package jalview.javascript;
 
-import java.net.URL;
 import jalview.appletgui.AlignFrame;
-import jalview.appletgui.AlignViewport;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceGroup;
 import jalview.structure.SelectionSource;
-import netscape.javascript.JSObject;
 
 public class JsSelectionSender extends JSFunctionExec implements
         jalview.structure.SelectionListener, JsCallBack

diff --git a/src/jalview/javascript/MouseOverListener.java b/src/jalview/javascript/MouseOverListener.java
index 4d03c39..e7b14ad 100644 (file)
--- a/src/jalview/javascript/MouseOverListener.java
+++ b/src/jalview/javascript/MouseOverListener.java
@@ -17,14 +17,11 @@
  */
 package jalview.javascript;
 
-import java.util.Vector;
-
 import jalview.appletgui.AlignFrame;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceI;
 import jalview.structure.VamsasListener;
 import jalview.structure.VamsasSource;
-import netscape.javascript.JSObject;
 
 public class MouseOverListener extends JSFunctionExec implements
         VamsasListener, JsCallBack

diff --git a/src/jalview/jbgui/GRestServiceEditorPane.java b/src/jalview/jbgui/GRestServiceEditorPane.java
index 6779488..a403088 100644 (file)
--- a/src/jalview/jbgui/GRestServiceEditorPane.java
+++ b/src/jalview/jbgui/GRestServiceEditorPane.java
@@ -20,15 +20,11 @@ package jalview.jbgui;
 import jalview.gui.JvSwingUtils;
 
 import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.FlowLayout;
-import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 
-import javax.swing.BoxLayout;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
@@ -38,15 +34,8 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
 import javax.swing.JTextArea;
-import javax.swing.JViewport;
 import javax.swing.ListSelectionModel;
-import javax.swing.UIManager;
 import javax.swing.border.TitledBorder;
-import javax.swing.event.CaretEvent;
-import javax.swing.event.CaretListener;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-import javax.swing.event.ListSelectionListener;
 
 import net.miginfocom.swing.MigLayout;
 

diff --git a/src/jalview/jbgui/GRnaStructureViewer.java b/src/jalview/jbgui/GRnaStructureViewer.java
index 0ce05f1..2297136 100644 (file)
--- a/src/jalview/jbgui/GRnaStructureViewer.java
+++ b/src/jalview/jbgui/GRnaStructureViewer.java
@@ -18,8 +18,6 @@
 package jalview.jbgui;
 
 import javax.swing.*;
-import java.awt.event.ActionListener;
-import java.awt.event.ActionEvent;
 
 public class GRnaStructureViewer extends JInternalFrame
 {

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 6fe1466..a55658b 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -33,7 +33,6 @@ import jalview.gui.OOMWarning;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.lang.reflect.Array;
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Hashtable;

diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 70ef609..ec979df 100644 (file)
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -30,20 +30,9 @@ import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import java.awt.Component;
 import java.awt.Cursor;
 import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedOutputStream;
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
 import java.net.URL;
 import java.net.URLEncoder;
-import java.nio.charset.Charset;
-import java.nio.charset.CharsetEncoder;
 import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
@@ -57,9 +46,6 @@ import javax.swing.event.MenuListener;
 import javax.xml.parsers.SAXParser;
 import javax.xml.parsers.SAXParserFactory;
 
-import org.apache.axis.utils.StringUtils;
-import org.apache.http.client.utils.URLEncodedUtils;
-import org.apache.http.entity.StringEntity;
 import org.xml.sax.Attributes;
 import org.xml.sax.SAXException;
 import org.xml.sax.helpers.DefaultHandler;

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 0520221..14b6997 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -22,7 +22,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;\r
 import jalview.datamodel.SequenceI;\r
 import jalview.ws.dbsources.das.api.jalviewSourceI;\r
-import jalview.ws.dbsources.das.datamodel.DasSequenceSource;\r
 import jalview.ws.seqfetcher.ASequenceFetcher;\r
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 \r

diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
index 21c8865..09232ec 100644 (file)
--- a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
+++ b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java
@@ -20,10 +20,6 @@ package jalview.ws.dbsources;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.AlignmentI;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 1329077..78f2477 100644 (file)
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -17,8 +17,6 @@
  */
 package jalview.ws.dbsources;
 
-import java.util.Hashtable;
-
 import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.AlignmentI;

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index f249fbc..4495be1 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -17,21 +17,11 @@
  */
 package jalview.ws.dbsources;
 
-import java.io.File;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.StringTokenizer;
-
 import com.stevesoft.pat.Regex;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * @author JimP

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 47179e2..a851896 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -25,7 +25,6 @@ import jalview.ws.ebi.EBIFetchClient;
 
 import java.io.File;
 import java.util.Iterator;
-import java.util.Vector;
 
 public abstract class EmblXmlSource extends EbiFileRetrievedProxy
 {

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 2a3d7bb..125a295 100644 (file)
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -17,21 +17,12 @@
  */
 package jalview.ws.dbsources;
 
-import java.io.File;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.StringTokenizer;
 
 import com.stevesoft.pat.Regex;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * Test class for accessing GeneDB - not yet finished.

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 0c2c52c..b432dff 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -22,10 +22,6 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
 
-import java.io.BufferedInputStream;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.Hashtable;
 import java.util.Vector;
 
 import MCview.PDBChain;
@@ -34,10 +30,8 @@ import MCview.PDBfile;
 import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.AlignmentI;
-import jalview.io.FileParse;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * @author JimP

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 8b09f16..b2443e8 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -17,17 +17,12 @@
  */
 package jalview.ws.dbsources;
 
-import java.util.Hashtable;
 
 import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FastaFile;
-import jalview.io.StockholmFile;
 import jalview.ws.seqfetcher.DbSourceProxy;
-import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
  * TODO: later PFAM is a complex datasource - it could return a tree in addition

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index fc3eb01..48f8649 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -19,9 +19,7 @@ package jalview.ws.dbsources;
 
 import java.io.File;
 import java.io.FileReader;
-import java.io.IOException;
 import java.util.Enumeration;
-import java.util.Hashtable;
 import java.util.Vector;
 
 import org.exolab.castor.xml.Unmarshaller;
@@ -37,9 +35,6 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.UniprotEntry;
 import jalview.datamodel.UniprotFile;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.ws.DBRefFetcher;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;

diff --git a/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java b/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
index 12bb742..c83ee62 100644 (file)
--- a/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
+++ b/src/jalview/ws/dbsources/das/api/DasSourceRegistryI.java
@@ -17,13 +17,9 @@
  */
 package jalview.ws.dbsources.das.api;
 
-import java.util.Hashtable;
 import java.util.List;
-import java.util.Map;
 
-import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
-import org.biodas.jdas.schema.sources.SOURCE;
 
 /**
  * API for a registry that provides datasources that jalview can access

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index f9b4c48..95ff7d0 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -25,7 +25,6 @@ import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.SequenceClient;
 import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index e7f51f2..9d044bc 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -21,20 +21,12 @@ import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
-import javax.swing.JOptionPane;
-
-import org.apache.http.auth.InvalidCredentialsException;
 import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.SourcesClient;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;

diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index 93d83a6..eb9d807 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -27,7 +27,6 @@ import java.util.Map;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
 import org.biodas.jdas.dassources.Capabilities;
 import org.biodas.jdas.dassources.utils.DasTimeFormat;
-import org.biodas.jdas.dassources.utils.RegistrySourceAdapter;
 import org.biodas.jdas.schema.sources.CAPABILITY;
 import org.biodas.jdas.schema.sources.COORDINATES;
 import org.biodas.jdas.schema.sources.MAINTAINER;

diff --git a/src/jalview/ws/jws1/JWS1Thread.java b/src/jalview/ws/jws1/JWS1Thread.java
index ec153c4..fb40ae0 100644 (file)
--- a/src/jalview/ws/jws1/JWS1Thread.java
+++ b/src/jalview/ws/jws1/JWS1Thread.java
@@ -17,9 +17,6 @@
  */
 package jalview.ws.jws1;
 
-import javax.swing.*;
-
-import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
 import jalview.ws.AWSThread;

diff --git a/src/jalview/ws/jws2/AAConClient.java b/src/jalview/ws/jws2/AAConClient.java
index b6f67d9..7f3847b 100644 (file)
--- a/src/jalview/ws/jws2/AAConClient.java
+++ b/src/jalview/ws/jws2/AAConClient.java
@@ -18,7 +18,6 @@
 package jalview.ws.jws2;
 
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
 import jalview.ws.jws2.dm.AAConSettings;

diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java
index 3faa390..d64a956 100644 (file)
--- a/src/jalview/ws/jws2/AADisorderClient.java
+++ b/src/jalview/ws/jws2/AADisorderClient.java
@@ -18,7 +18,6 @@
 package jalview.ws.jws2;
 
 import jalview.api.AlignCalcWorkerI;
-import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 
 import jalview.datamodel.GraphLine;
@@ -41,7 +40,6 @@ import compbio.data.sequence.Range;
 import compbio.data.sequence.Score;
 import compbio.data.sequence.ScoreManager.ScoreHolder;
 import compbio.metadata.Argument;
-import compbio.ws.client.Services;
 
 public class AADisorderClient extends JabawsAlignCalcWorker implements
         AlignCalcWorkerI

diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java
index 195d3c0..204e0df 100644 (file)
--- a/src/jalview/ws/jws2/JabaParamStore.java
+++ b/src/jalview/ws/jws2/JabaParamStore.java
@@ -17,10 +17,7 @@
  */
 package jalview.ws.jws2;
 
-import java.io.BufferedReader;
 import java.io.IOException;
-import java.io.Reader;
-import java.io.Writer;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index bb7ad3a..896292a 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -19,7 +19,6 @@ package jalview.ws.jws2;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.*;
@@ -28,10 +27,6 @@ import jalview.datamodel.*;
 import jalview.gui.*;
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
 

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 4df8108..f0602c4 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -20,8 +20,6 @@ package jalview.ws.jws2;
 import java.util.*;
 
 import compbio.data.msa.MsaWS;
-import compbio.data.sequence.AlignmentMetadata;
-import compbio.data.sequence.Program;
 import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;

diff --git a/src/jalview/ws/jws2/ParameterUtils.java b/src/jalview/ws/jws2/ParameterUtils.java
index 80d71b5..16959ff 100644 (file)
--- a/src/jalview/ws/jws2/ParameterUtils.java
+++ b/src/jalview/ws/jws2/ParameterUtils.java
@@ -17,9 +17,6 @@
  */
 package jalview.ws.jws2;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.Reader;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;

diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java
index 9efe4c3..d3ba1a7 100644 (file)
--- a/src/jalview/ws/jws2/dm/AAConSettings.java
+++ b/src/jalview/ws/jws2/dm/AAConSettings.java
@@ -22,14 +22,12 @@ import java.util.List;
 
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
-import compbio.metadata.Preset;
 
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.JabaPreset;
 import jalview.ws.jws2.ParameterUtils;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
 
 /**

diff --git a/src/jalview/ws/jws2/dm/JabaParameter.java b/src/jalview/ws/jws2/dm/JabaParameter.java
index 4c2754b..b98c170 100644 (file)
--- a/src/jalview/ws/jws2/dm/JabaParameter.java
+++ b/src/jalview/ws/jws2/dm/JabaParameter.java
@@ -20,7 +20,6 @@ package jalview.ws.jws2.dm;
 import jalview.ws.jws2.ParameterUtils;
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
-import compbio.metadata.Argument;
 import compbio.metadata.Parameter;
 import compbio.metadata.ValueConstrain;
 

diff --git a/src/jalview/ws/jws2/dm/JabaValueConstrain.java b/src/jalview/ws/jws2/dm/JabaValueConstrain.java
index c4ab157..bbcff21 100644 (file)
--- a/src/jalview/ws/jws2/dm/JabaValueConstrain.java
+++ b/src/jalview/ws/jws2/dm/JabaValueConstrain.java
@@ -18,7 +18,6 @@
 package jalview.ws.jws2.dm;
 
 import compbio.metadata.ValueConstrain;
-import compbio.metadata.ValueConstrain.Type;
 
 import jalview.ws.params.ValueConstrainI;
 

diff --git a/src/jalview/ws/jws2/dm/JabaWsParamSet.java b/src/jalview/ws/jws2/dm/JabaWsParamSet.java
index afe92dc..f78f5fa 100644 (file)
--- a/src/jalview/ws/jws2/dm/JabaWsParamSet.java
+++ b/src/jalview/ws/jws2/dm/JabaWsParamSet.java
@@ -17,20 +17,13 @@
  */
 package jalview.ws.jws2.dm;
 
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Writer;
 import java.util.ArrayList;
 import java.util.List;
 
-import compbio.metadata.Argument;
 import compbio.metadata.Option;
 
 import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.ParameterUtils;
 import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.WsParamSetI;
 
 public class JabaWsParamSet implements WsParamSetI

diff --git a/src/jalview/ws/params/ParamManager.java b/src/jalview/ws/params/ParamManager.java
index e6b27f9..112a32e 100644 (file)
--- a/src/jalview/ws/params/ParamManager.java
+++ b/src/jalview/ws/params/ParamManager.java
@@ -17,7 +17,6 @@
  */
 package jalview.ws.params;
 
-import jalview.ws.jws2.dm.JabaWsParamSet;
 
 /**
  * Interface implemented by classes for maintaining user's parameters in a

diff --git a/src/jalview/ws/params/ParameterI.java b/src/jalview/ws/params/ParameterI.java
index a977b86..e2c63dc 100644 (file)
--- a/src/jalview/ws/params/ParameterI.java
+++ b/src/jalview/ws/params/ParameterI.java
@@ -17,10 +17,6 @@
  */
 package jalview.ws.params;
 
-import java.net.URL;
-
-import compbio.metadata.ValueConstrain;
-
 public interface ParameterI extends OptionI
 {
 

diff --git a/src/jalview/ws/params/ValueConstrainI.java b/src/jalview/ws/params/ValueConstrainI.java
index 9c2f539..088f2d4 100644 (file)
--- a/src/jalview/ws/params/ValueConstrainI.java
+++ b/src/jalview/ws/params/ValueConstrainI.java
@@ -17,8 +17,6 @@
  */
 package jalview.ws.params;
 
-import compbio.metadata.ValueConstrain.Type;
-
 /**
  * @author JimP
  * 

diff --git a/src/jalview/ws/params/simple/IntegerParameter.java b/src/jalview/ws/params/simple/IntegerParameter.java
index 41695ac..f9360e7 100644 (file)
--- a/src/jalview/ws/params/simple/IntegerParameter.java
+++ b/src/jalview/ws/params/simple/IntegerParameter.java
@@ -21,8 +21,6 @@ package jalview.ws.params.simple;
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
 
-import compbio.metadata.ValueConstrain.Type;
-
 /**
  * @author jimp
  * 

diff --git a/src/jalview/ws/rest/HttpResultSet.java b/src/jalview/ws/rest/HttpResultSet.java
index f323c33..7ecbd27 100644 (file)
--- a/src/jalview/ws/rest/HttpResultSet.java
+++ b/src/jalview/ws/rest/HttpResultSet.java
@@ -37,7 +37,6 @@ import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpRequestBase;
 import org.apache.http.entity.mime.MultipartEntity;
 import org.apache.james.mime4j.MimeException;
-import org.apache.james.mime4j.parser.ContentHandler;
 import org.apache.james.mime4j.parser.MimeStreamParser;
 
 /**

diff --git a/src/jalview/ws/rest/InputType.java b/src/jalview/ws/rest/InputType.java
index d5cf6d4..4c51d57 100644 (file)
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -23,28 +23,18 @@ import jalview.ws.params.OptionI;
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.Option;
-import jalview.ws.rest.params.SeqGroupIndexVector;
 
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
-import java.util.Map;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
 
-import sun.io.CharacterEncoding;
-import sun.misc.CharacterEncoder;
-
 /***
  * InputType is the abstract model of each input parameter that a rest service
  * might take. It enables the engine to validate input by providing { formatter

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 70f2507..ba6dbeb 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -19,7 +19,6 @@ package jalview.ws.rest;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.Collection;
 import java.util.Hashtable;
 import java.util.Vector;
 

diff --git a/src/jalview/ws/rest/RestJob.java b/src/jalview/ws/rest/RestJob.java
index 695c4cb..d2a0a05 100644 (file)
--- a/src/jalview/ws/rest/RestJob.java
+++ b/src/jalview/ws/rest/RestJob.java
@@ -17,28 +17,19 @@
  */
 package jalview.ws.rest;
 
-import java.io.IOException;
-import java.sql.ResultSet;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Hashtable;
-import java.util.List;
 import java.util.Map;
-import java.util.Map.Entry;
 import java.util.Set;
 import java.util.Vector;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.io.packed.DataProvider;
 import jalview.io.packed.JalviewDataset;
-import jalview.io.packed.ParsePackedSet;
-import jalview.io.packed.SimpleDataProvider;
-import jalview.io.packed.DataProvider.JvDataType;
 import jalview.ws.AWsJob;
 import jalview.ws.rest.params.Alignment;
 import jalview.ws.rest.params.SeqGroupIndexVector;

diff --git a/src/jalview/ws/rest/RestJobThread.java b/src/jalview/ws/rest/RestJobThread.java
index 84c1b96..5ac1959 100644 (file)
--- a/src/jalview/ws/rest/RestJobThread.java
+++ b/src/jalview/ws/rest/RestJobThread.java
@@ -40,11 +40,9 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map.Entry;
-import java.util.Vector;
 
 import org.apache.axis.transport.http.HTTPConstants;
 import org.apache.http.Header;

diff --git a/src/jalview/ws/rest/RestServiceDescription.java b/src/jalview/ws/rest/RestServiceDescription.java
index 74bfe47..6828f2d 100644 (file)
--- a/src/jalview/ws/rest/RestServiceDescription.java
+++ b/src/jalview/ws/rest/RestServiceDescription.java
@@ -18,14 +18,9 @@
 package jalview.ws.rest;
 
 import jalview.datamodel.SequenceI;
-import jalview.io.packed.DataProvider;
-import jalview.io.packed.SimpleDataProvider;
 import jalview.io.packed.DataProvider.JvDataType;
-import jalview.util.GroupUrlLink.UrlStringTooLongException;
-import jalview.util.Platform;
 import jalview.ws.rest.params.Alignment;
 import jalview.ws.rest.params.AnnotationFile;
-import jalview.ws.rest.params.JobConstant;
 import jalview.ws.rest.params.SeqGroupIndexVector;
 
 import java.net.URL;
@@ -36,15 +31,9 @@ import java.util.List;
 import java.util.Map;
 import java.util.NoSuchElementException;
 import java.util.StringTokenizer;
-import java.util.Vector;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.swing.JViewport;
-
-import com.stevesoft.pat.Regex;
-import com.sun.org.apache.xml.internal.serialize.OutputFormat.DTD;
-
 public class RestServiceDescription
 {
   /**

diff --git a/src/jalview/ws/rest/params/Alignment.java b/src/jalview/ws/rest/params/Alignment.java
index 1e66a5a..2cea06e 100644 (file)
--- a/src/jalview/ws/rest/params/Alignment.java
+++ b/src/jalview/ws/rest/params/Alignment.java
@@ -24,19 +24,13 @@ import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.InputType.molType;
-import jalview.ws.rest.RestServiceDescription;
 
 import java.io.BufferedOutputStream;
-import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
-import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
-import java.net.URLEncoder;
-import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;

diff --git a/src/jalview/ws/rest/params/AnnotationFile.java b/src/jalview/ws/rest/params/AnnotationFile.java
index f00f46e..37e051f 100644 (file)
--- a/src/jalview/ws/rest/params/AnnotationFile.java
+++ b/src/jalview/ws/rest/params/AnnotationFile.java
@@ -23,8 +23,6 @@ import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;

diff --git a/src/jalview/ws/rest/params/SeqGroupIndexVector.java b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
index 4b21229..766720b 100644 (file)
--- a/src/jalview/ws/rest/params/SeqGroupIndexVector.java
+++ b/src/jalview/ws/rest/params/SeqGroupIndexVector.java
@@ -27,14 +27,11 @@ import jalview.ws.rest.AlignmentProcessor;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Vector;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;

diff --git a/src/jalview/ws/rest/params/SeqIdVector.java b/src/jalview/ws/rest/params/SeqIdVector.java
index 55c19f2..cdfcf87 100644 (file)
--- a/src/jalview/ws/rest/params/SeqIdVector.java
+++ b/src/jalview/ws/rest/params/SeqIdVector.java
@@ -24,15 +24,11 @@ import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;

diff --git a/src/jalview/ws/rest/params/SeqVector.java b/src/jalview/ws/rest/params/SeqVector.java
index b6d316b..a633e0f 100644 (file)
--- a/src/jalview/ws/rest/params/SeqVector.java
+++ b/src/jalview/ws/rest/params/SeqVector.java
@@ -24,8 +24,6 @@ import jalview.ws.params.simple.Option;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.NoValidInputDataException;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
@@ -34,7 +32,6 @@ import java.util.List;
 
 import org.apache.http.entity.mime.content.ContentBody;
 import org.apache.http.entity.mime.content.StringBody;
-import org.jmol.util.ArrayUtil;
 
 /**
  * input a list of sequences separated by some separator

diff --git a/src/jalview/ws/rest/params/Tree.java b/src/jalview/ws/rest/params/Tree.java
index 3d0e726..69bc93c 100644 (file)
--- a/src/jalview/ws/rest/params/Tree.java
+++ b/src/jalview/ws/rest/params/Tree.java
@@ -17,13 +17,9 @@
  */
 package jalview.ws.rest.params;
 
-import jalview.datamodel.AlignmentI;
-import jalview.ws.params.ArgumentI;
 import jalview.ws.params.OptionI;
 import jalview.ws.rest.InputType;
 import jalview.ws.rest.RestJob;
-import jalview.ws.rest.RestServiceDescription;
-import jalview.ws.rest.InputType.molType;
 
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index f449570..45b866e 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -23,7 +23,6 @@ import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index 0e91a38..b8f7eab 100644 (file)
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -18,7 +18,6 @@
 package jalview.ws.seqfetcher;
 
 import jalview.datamodel.Alignment;
-import jalview.datamodel.DBRefSource;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;