From ad20cd92225f2ee8c251d39b00b90555d382a616 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 8 Nov 2012 15:41:34 +0000 Subject: [PATCH] tidy imports --- src/MCview/PDBViewer.java | 2 -- src/jalview/analysis/Dna.java | 2 -- src/jalview/analysis/Grouping.java | 3 --- src/jalview/analysis/Rna.java | 1 - src/jalview/api/AlignViewportI.java | 2 -- src/jalview/appletgui/AlignFrame.java | 3 --- src/jalview/appletgui/AlignViewport.java | 3 --- src/jalview/appletgui/AlignmentPanel.java | 2 -- src/jalview/appletgui/AnnotationColourChooser.java | 3 --- src/jalview/appletgui/AnnotationLabels.java | 1 - src/jalview/appletgui/AnnotationPanel.java | 1 - src/jalview/appletgui/AppletJmol.java | 5 ---- src/jalview/appletgui/EmbmenuFrame.java | 4 ---- src/jalview/appletgui/ExtJmol.java | 1 - src/jalview/appletgui/FeatureColourChooser.java | 1 - src/jalview/appletgui/FeatureRenderer.java | 1 - src/jalview/appletgui/PCAPanel.java | 3 --- src/jalview/appletgui/SliderPanel.java | 1 - src/jalview/appletgui/TreePanel.java | 1 - src/jalview/bin/Jalview.java | 1 - src/jalview/bin/JalviewLiteURLRetrieve.java | 3 --- src/jalview/datamodel/SeqCigar.java | 1 - src/jalview/datamodel/xdb/embl/EmblFeature.java | 1 - .../datamodel/xdb/embl/EmblFeatureLocations.java | 1 - src/jalview/ext/jmol/JmolCommands.java | 1 - src/jalview/ext/varna/JalviewVarnaBinding.java | 25 -------------------- src/jalview/ext/varna/VarnaCommands.java | 1 - src/jalview/gui/AlignmentPanel.java | 1 - src/jalview/gui/AppJmol.java | 2 -- src/jalview/gui/AppJmolBinding.java | 7 ------ src/jalview/gui/AppVarna.java | 12 ---------- src/jalview/gui/AppVarnaBinding.java | 2 -- src/jalview/gui/AssociatePdbFileWithSeq.java | 1 - src/jalview/gui/CutAndPasteHtmlTransfer.java | 1 - src/jalview/gui/Desktop.java | 2 -- src/jalview/gui/Finder.java | 1 - src/jalview/gui/Jalview2XML.java | 1 - src/jalview/gui/Jalview2XML_V1.java | 1 - src/jalview/gui/JvSwingUtils.java | 1 - src/jalview/gui/OptsParametersContainerI.java | 3 --- src/jalview/gui/PCAPanel.java | 1 - src/jalview/gui/PopupMenu.java | 1 - src/jalview/gui/Preferences.java | 1 - src/jalview/gui/PromptUserConfig.java | 2 -- src/jalview/gui/RedundancyPanel.java | 1 - src/jalview/gui/RestInputParamEditDialog.java | 3 --- src/jalview/gui/TextColourChooser.java | 2 -- src/jalview/gui/VamsasApplication.java | 1 - src/jalview/gui/WebserviceInfo.java | 2 -- src/jalview/io/AlignmentProperties.java | 1 - src/jalview/io/IdentifyFile.java | 1 - src/jalview/io/MatrixFile.java | 2 -- src/jalview/io/SimpleBlastFile.java | 1 - src/jalview/io/StockholmFile.java | 1 - src/jalview/io/TCoffeeScoreFile.java | 5 ---- src/jalview/io/vamsas/Datasetsequence.java | 1 - src/jalview/io/vamsas/DatastoreItem.java | 5 ---- src/jalview/io/vamsas/DatastoreRegistry.java | 3 --- src/jalview/io/vamsas/Dbref.java | 1 - src/jalview/io/vamsas/Rangetype.java | 3 --- src/jalview/io/vamsas/Sequencefeature.java | 2 -- src/jalview/io/vamsas/Sequencemapping.java | 3 --- src/jalview/javascript/JSFunctionExec.java | 1 - src/jalview/javascript/JsSelectionSender.java | 3 --- src/jalview/javascript/MouseOverListener.java | 3 --- src/jalview/jbgui/GRestServiceEditorPane.java | 11 --------- src/jalview/jbgui/GRnaStructureViewer.java | 2 -- src/jalview/ws/DBRefFetcher.java | 1 - src/jalview/ws/EnfinEnvision2OneWay.java | 14 ----------- src/jalview/ws/SequenceFetcher.java | 1 - .../ws/dbsources/EbiFileRetrievedProxy.java | 4 ---- src/jalview/ws/dbsources/EmblCdsSouce.java | 2 -- src/jalview/ws/dbsources/EmblSource.java | 10 -------- src/jalview/ws/dbsources/EmblXmlSource.java | 1 - src/jalview/ws/dbsources/GeneDbSource.java | 9 ------- src/jalview/ws/dbsources/Pdb.java | 6 ----- src/jalview/ws/dbsources/Pfam.java | 5 ---- src/jalview/ws/dbsources/Uniprot.java | 5 ---- .../ws/dbsources/das/api/DasSourceRegistryI.java | 4 ---- .../dbsources/das/datamodel/DasSequenceSource.java | 1 - .../dbsources/das/datamodel/DasSourceRegistry.java | 8 ------- .../ws/dbsources/das/datamodel/JalviewSource.java | 1 - src/jalview/ws/jws1/JWS1Thread.java | 3 --- src/jalview/ws/jws2/AAConClient.java | 1 - src/jalview/ws/jws2/AADisorderClient.java | 2 -- src/jalview/ws/jws2/JabaParamStore.java | 3 --- src/jalview/ws/jws2/MsaWSClient.java | 5 ---- src/jalview/ws/jws2/MsaWSThread.java | 2 -- src/jalview/ws/jws2/ParameterUtils.java | 3 --- src/jalview/ws/jws2/dm/AAConSettings.java | 2 -- src/jalview/ws/jws2/dm/JabaParameter.java | 1 - src/jalview/ws/jws2/dm/JabaValueConstrain.java | 1 - src/jalview/ws/jws2/dm/JabaWsParamSet.java | 7 ------ src/jalview/ws/params/ParamManager.java | 1 - src/jalview/ws/params/ParameterI.java | 4 ---- src/jalview/ws/params/ValueConstrainI.java | 2 -- src/jalview/ws/params/simple/IntegerParameter.java | 2 -- src/jalview/ws/rest/HttpResultSet.java | 1 - src/jalview/ws/rest/InputType.java | 10 -------- src/jalview/ws/rest/RestClient.java | 1 - src/jalview/ws/rest/RestJob.java | 9 ------- src/jalview/ws/rest/RestJobThread.java | 2 -- src/jalview/ws/rest/RestServiceDescription.java | 11 --------- src/jalview/ws/rest/params/Alignment.java | 6 ----- src/jalview/ws/rest/params/AnnotationFile.java | 2 -- .../ws/rest/params/SeqGroupIndexVector.java | 3 --- src/jalview/ws/rest/params/SeqIdVector.java | 4 ---- src/jalview/ws/rest/params/SeqVector.java | 3 --- src/jalview/ws/rest/params/Tree.java | 4 ---- src/jalview/ws/seqfetcher/ASequenceFetcher.java | 1 - src/jalview/ws/seqfetcher/DbSourceProxyImpl.java | 1 - 111 files changed, 341 deletions(-) diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index 3c4698f..2ba8c56 100755 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 . */ 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- a/src/jalview/ws/SequenceFetcher.java +++ b/src/jalview/ws/SequenceFetcher.java @@ -22,7 +22,6 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; import jalview.ws.dbsources.das.api.jalviewSourceI; -import jalview.ws.dbsources.das.datamodel.DasSequenceSource; import jalview.ws.seqfetcher.ASequenceFetcher; import jalview.ws.seqfetcher.DbSourceProxy; diff --git a/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java b/src/jalview/ws/dbsources/EbiFileRetrievedProxy.java index 21c8865..09232ec 100644 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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; -- 1.7.10.2