JAL-1551 formatting

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 2a4d582..3739b3c 100644 (file)
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -20,15 +20,30 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Iterator;
+
 public class SliderPanel extends Panel implements ActionListener,
         AdjustmentListener, MouseListener
 {
@@ -221,7 +236,9 @@ public class SliderPanel extends Panel implements ActionListener,
       {
         while ((toChange = allGroups.next().cs) == null
                 && allGroups.hasNext())
+        {
           ;
+        }
       }
       else
       {

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index da8f91e..e8d8363 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -20,15 +20,33 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.ScrollPane;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class TreeCanvas extends Panel implements MouseListener,
         MouseMotionListener

diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 6c9c400..a6e6c8d 100755 (executable)
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -20,9 +20,14 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+import javax.swing.JPanel;
 
 /**
  * DOCUMENT ME!

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index f536efc..970ca3f 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -20,16 +20,20 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
 
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Iterator;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.util.MessageManager;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 /**
  * DOCUMENT ME!

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index d921ba4..61d7d7e 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -20,17 +20,44 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JColorChooser;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
 
 /**
  * DOCUMENT ME!
@@ -208,7 +235,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
       if (node.element() instanceof SequenceI)
       {
-        SequenceI seq = (SequenceI) ((SequenceNode) node).element();
+        SequenceI seq = (SequenceI) node.element();
 
         if (av.getSequenceColour(seq) == Color.white)
         {
@@ -258,14 +285,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       Rectangle rect = new Rectangle(xend + 10, ypos - charHeight / 2,
               charWidth, charHeight);
 
-      nameHash.put((SequenceI) node.element(), rect);
+      nameHash.put(node.element(), rect);
 
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
 
       if ((selected != null)
               && selected.getSequences(null).contains(
-                      (SequenceI) node.element()))
+                      node.element()))
       {
         g.setColor(Color.gray);
 
@@ -290,7 +317,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       int xend = (int) (height * scale) + offx;
       int ypos = (int) (node.ycount * chunk) + offy;
 
-      g.setColor(((SequenceNode) node).color.darker());
+      g.setColor(node.color.darker());
 
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
@@ -682,7 +709,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
 
     labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar
 
-    float wscale = (float) (width - labelLength - (offx * 2))
+    float wscale = (width - labelLength - (offx * 2))
             / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
@@ -708,7 +735,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g2.setColor(Color.gray);
       }
 
-      int x = (int) ((threshold * (float) (getWidth() - labelLength - (2 * offx))) + offx);
+      int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx);
 
       g2.drawLine(x, 0, x, getHeight());
     }