JAL-1483 organise imports

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index a8ca3f7..ec5b79b 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -20,13 +20,21 @@
  */
 package jalview.analysis;
 
-import java.util.*;
-
 import jalview.api.analysis.ScoreModelI;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.CigarArray;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
+
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!

diff --git a/src/jalview/analysis/scoremodels/FeatureScoreModel.java b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
index b946bba..0be1550 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureScoreModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
@@ -1,17 +1,17 @@
 package jalview.analysis.scoremodels;
 
-import java.awt.Color;
-import java.util.List;
-
-import jalview.analysis.AlignSeq;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+
 public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
 {
   jalview.api.FeatureRenderer fr;

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index b7c766a..2fb34b0 100644 (file)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -20,14 +20,26 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.analysis.NJTree;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.NewickFile;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.ScrollPane;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
 public class TreePanel extends EmbmenuFrame implements ActionListener,
         ItemListener
 {

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index ee0bfaf..5bedf36 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -20,27 +20,47 @@
  */
 package jalview.gui;
 
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-import java.util.List;
-
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import org.jibble.epsgraphics.*;
-import jalview.analysis.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.Cache;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.NewickFile;
+import jalview.jbgui.GTreePanel;
+import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+
+import org.jibble.epsgraphics.EpsGraphics2D;
+
 /**
  * DOCUMENT ME!
  * 

diff --git a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
index ebe070b..b04764c 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
+++ b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
@@ -4,10 +4,7 @@ import jalview.api.FeaturesDisplayedI;
 
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.Hashtable;
 import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
 
 public class FeaturesDisplayed implements FeaturesDisplayedI
 {