Dialog used in displaying options for calculating read counts and rpkm

uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java

+/* ReadCountDialog.java
+ *
+ * created: 2012
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2012  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
+
+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.Box;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.components.FeatureDisplay;
+import uk.ac.sanger.artemis.components.ListSelectionPanel;
+import uk.ac.sanger.artemis.io.InvalidRelationException;
+import uk.ac.sanger.artemis.io.Qualifier;
+import uk.ac.sanger.artemis.util.StringVector;
+
+
+  class ReadCountDialog extends JDialog 
+  {
+    private static final long serialVersionUID = 1L;
+    private static ListSelectionPanel systematicListSelectionPanel;
+    private static StringVector qNames;
+    private int status = 0;
+    
+    ReadCountDialog(final JFrame frame, final String title, 
+                    final FeatureDisplay feature_display, final Box yBox) 
+    {
+      super(frame, title, true);
+
+      qNames = null;
+      final Object systematic_names[] =
+          Options.getOptions().getSystematicQualifierNames().toArray();
+      final String[] description = 
+            { "Qualifiers to search when getting the feature(s) name." } ;
+      
+      if(systematicListSelectionPanel == null)
+        systematicListSelectionPanel =
+              new ListSelectionPanel(feature_display.getEntryGroup(), systematic_names,
+                     description, false);
+      systematicListSelectionPanel.setVisible(false);
+      final JButton advanced = new JButton("Name Options >>");
+      advanced.setToolTipText("Define the qualifier list to search for the feature name");
+      advanced.addActionListener(new ActionListener(){
+
+        public void actionPerformed(ActionEvent arg0)
+        {
+          systematicListSelectionPanel.setVisible(
+              !systematicListSelectionPanel.isVisible());
+          if(systematicListSelectionPanel.isVisible())
+            advanced.setText("Name Options <<");
+          else
+            advanced.setText("Name Options >>");
+          pack();
+        }
+      });
+      
+      final JPanel pane = new JPanel(new GridBagLayout());
+      final GridBagConstraints c = new GridBagConstraints();
+      c.gridx = 0;
+      c.gridy = 0;
+      c.ipady = 10;
+      c.anchor = GridBagConstraints.NORTHWEST;
+      pane.add(yBox, c);
+      
+      c.gridy = 1;
+      pane.add(advanced, c);
+      
+      c.gridy = 2;
+      c.fill = GridBagConstraints.HORIZONTAL;
+      pane.add(systematicListSelectionPanel, c);
+      
+      Box xBox = Box.createHorizontalBox();
+      final JButton okButton = new JButton("OK");
+      okButton.addActionListener(new ActionListener(){
+        public void actionPerformed(ActionEvent arg0)
+        {
+          setVisible(false); 
+          dispose();
+          status = 0;
+          
+          Options.getOptions().setSystematicQualifierNames(
+              systematicListSelectionPanel.getResultString());
+        }
+      });
+      xBox.add(okButton);
+
+      final JButton cancelButton = new JButton("Cancel");
+      cancelButton.addActionListener(new ActionListener(){
+        public void actionPerformed(ActionEvent arg0)
+        {
+          setVisible(false); 
+          dispose();
+          status = -1;
+        }
+      });
+      xBox.add(cancelButton);
+      c.fill = GridBagConstraints.NONE;
+      c.gridy = 3;
+      pane.add(xBox, c);
+      
+      getContentPane().add(pane);
+      pack();
+      setLocationRelativeTo(frame);
+      setVisible(true);
+    }
+    
+    protected static String getFeatureName(Feature f)
+    {
+      if(qNames == null)
+      {
+        qNames = new StringVector();
+        Object objs[] = systematicListSelectionPanel.getResultArray();
+        for(Object o: objs)
+          qNames.add(o);
+      }
+      
+      return pickName(f, qNames);
+    }
+    
+    protected int getStatus()
+    {
+      return status;
+    }
+    
+    /**
+     *  Look at the qualifier_names one-by-one and return the first value of the
+     *  first qualifier found.
+     **/
+    private static String pickName(final Feature f, final StringVector qualifier_names) 
+    {
+      int qn_size = qualifier_names.size();
+      for(int i = 0; i < qn_size; ++i)
+      {
+        try
+        {
+          final Qualifier qualifier =
+            f.getQualifierByName((String)qualifier_names.elementAt(i));
+
+          if(qualifier != null)
+          {
+            final StringVector values = qualifier.getValues();
+
+            if(values != null && values.size() > 0)
+            {
+              for(int j=0; j<values.size(); j++)
+              {
+                final String value = (String)values.elementAt(j);
+                if(value != null && !value.endsWith("current=false") && !value.equals(""))
+                  return value;
+              }
+            }
+          }
+        } 
+        catch(InvalidRelationException e){}
+      }
+
+      return f.getIDString();
+    }
+  }
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