JAL-1753 declare field with interface type; check for null dereference

[jalview.git] / src / jalview / gui / PCAPanel.java

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 2674617..f4fd70b 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -20,40 +20,34 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.PCAModel;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Graphics;
-import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.print.PageFormat;
 import java.awt.print.Printable;
 import java.awt.print.PrinterException;
 import java.awt.print.PrinterJob;
-import java.util.Hashtable;
 
 import javax.swing.ButtonGroup;
-import javax.swing.JButton;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
-import javax.swing.JLabel;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
 import javax.swing.JRadioButtonMenuItem;
 
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
 /**
  * DOCUMENT ME!
  * 
@@ -64,6 +58,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
         IProgressIndicator
 {
 
+  private IProgressIndicator progressBar;
+
   RotatableCanvas rc;
 
   AlignmentPanel ap;
@@ -87,6 +83,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     this.av = ap.av;
     this.ap = ap;
 
+    progressBar = new ProgressBar(statusPanel, statusBar);
+
     boolean sameLength = true;
     boolean selected = av.getSelectionGroup() != null
             && av.getSelectionGroup().getSize() > 0;
@@ -632,11 +630,6 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       cap.dispose();
     }
   }
-
-  // methods for implementing IProgressIndicator
-  // need to refactor to a reusable stub class
-  Hashtable progressBars, progressBarHandlers;
-
   /*
    * (non-Javadoc)
    * 
@@ -645,78 +638,82 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   @Override
   public void setProgressBar(String message, long id)
   {
-    if (progressBars == null)
-    {
-      progressBars = new Hashtable();
-      progressBarHandlers = new Hashtable();
-    }
-
-    JPanel progressPanel;
-    Long lId = new Long(id);
-    GridLayout layout = (GridLayout) statusPanel.getLayout();
-    if (progressBars.get(lId) != null)
-    {
-      progressPanel = (JPanel) progressBars.get(new Long(id));
-      statusPanel.remove(progressPanel);
-      progressBars.remove(lId);
-      progressPanel = null;
-      if (message != null)
-      {
-        statusBar.setText(message);
-      }
-      if (progressBarHandlers.contains(lId))
-      {
-        progressBarHandlers.remove(lId);
-      }
-      layout.setRows(layout.getRows() - 1);
-    }
-    else
-    {
-      progressPanel = new JPanel(new BorderLayout(10, 5));
-
-      JProgressBar progressBar = new JProgressBar();
-      progressBar.setIndeterminate(true);
-
-      progressPanel.add(new JLabel(message), BorderLayout.WEST);
-      progressPanel.add(progressBar, BorderLayout.CENTER);
-
-      layout.setRows(layout.getRows() + 1);
-      statusPanel.add(progressPanel);
-
-      progressBars.put(lId, progressPanel);
-    }
-    // update GUI
-    // setMenusForViewport();
-    validate();
+    progressBar.setProgressBar(message, id);
+    // if (progressBars == null)
+    // {
+    // progressBars = new Hashtable();
+    // progressBarHandlers = new Hashtable();
+    // }
+    //
+    // JPanel progressPanel;
+    // Long lId = new Long(id);
+    // GridLayout layout = (GridLayout) statusPanel.getLayout();
+    // if (progressBars.get(lId) != null)
+    // {
+    // progressPanel = (JPanel) progressBars.get(new Long(id));
+    // statusPanel.remove(progressPanel);
+    // progressBars.remove(lId);
+    // progressPanel = null;
+    // if (message != null)
+    // {
+    // statusBar.setText(message);
+    // }
+    // if (progressBarHandlers.contains(lId))
+    // {
+    // progressBarHandlers.remove(lId);
+    // }
+    // layout.setRows(layout.getRows() - 1);
+    // }
+    // else
+    // {
+    // progressPanel = new JPanel(new BorderLayout(10, 5));
+    //
+    // JProgressBar progressBar = new JProgressBar();
+    // progressBar.setIndeterminate(true);
+    //
+    // progressPanel.add(new JLabel(message), BorderLayout.WEST);
+    // progressPanel.add(progressBar, BorderLayout.CENTER);
+    //
+    // layout.setRows(layout.getRows() + 1);
+    // statusPanel.add(progressPanel);
+    //
+    // progressBars.put(lId, progressPanel);
+    // }
+    // // update GUI
+    // // setMenusForViewport();
+    // validate();
   }
 
   @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
-    if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
-    {
-      throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
-    }
-    progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
-    if (handler.canCancel())
-    {
-      JButton cancel = new JButton(
-              MessageManager.getString("action.cancel"));
-      final IProgressIndicator us = this;
-      cancel.addActionListener(new ActionListener()
-      {
-
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          handler.cancelActivity(id);
-          us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
-        }
-      });
-      progressPanel.add(cancel, BorderLayout.EAST);
-    }
+    progressBar.registerHandler(id, handler);
+    // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+    // {
+    // throw new
+    // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+    // }
+    // progressBarHandlers.put(new Long(id), handler);
+    // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+    // if (handler.canCancel())
+    // {
+    // JButton cancel = new JButton(
+    // MessageManager.getString("action.cancel"));
+    // final IProgressIndicator us = this;
+    // cancel.addActionListener(new ActionListener()
+    // {
+    //
+    // @Override
+    // public void actionPerformed(ActionEvent e)
+    // {
+    // handler.cancelActivity(id);
+    // us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
+    // new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id);
+    // }
+    // });
+    // progressPanel.add(cancel, BorderLayout.EAST);
+    // }
   }
 
   /**
@@ -726,11 +723,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   @Override
   public boolean operationInProgress()
   {
-    if (progressBars != null && progressBars.size() > 0)
-    {
-      return true;
-    }
-    return false;
+    return progressBar.operationInProgress();
   }
 
   @Override