src/jalview/gui/AnnotationColumnChooser.java

   1 package jalview.gui;
   2
   3 import jalview.schemes.AnnotationColourGradient;
   4 import jalview.util.MessageManager;
   5
   6 import java.awt.BorderLayout;
   7 import java.awt.Color;
   8 import java.awt.Dimension;
   9 import java.awt.event.ActionEvent;
  10 import java.awt.event.ActionListener;
  11
  12 import javax.swing.JButton;
  13 import javax.swing.JComboBox;
  14 import javax.swing.JInternalFrame;
  15 import javax.swing.JLayeredPane;
  16 import javax.swing.JPanel;
  17
  18 import net.miginfocom.swing.MigLayout;
  19
  20 @SuppressWarnings("serial")
  21 public class AnnotationColumnChooser extends AnnotationRowFilter
  22 {
  23
  24   private JComboBox<String> annotations;
  25
  26   JButton ok = new JButton();
  27
  28   JButton cancel = new JButton();
  29
  30   JPanel jPanel1 = new JPanel();
  31
  32   JPanel jPanel2 = new JPanel();
  33
  34   BorderLayout borderLayout1 = new BorderLayout();
  35
  36   private JComboBox<String> threshold = new JComboBox<String>();
  37
  38
  39   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  40   {
  41     super(av, ap);
  42     frame = new JInternalFrame();
  43     frame.setContentPane(this);
  44     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  45     Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
  46
  47     addSliderChangeListener();
  48     addSliderMouseListeners();
  49
  50     if (av.getAlignment().getAlignmentAnnotation() == null)
  51     {
  52       return;
  53     }
  54
  55     adjusting = true;
  56
  57     setAnnotations(new JComboBox<String>(
  58             getAnnotationItems(seqAssociated.isSelected())));
  59     populateThresholdComboBox(threshold);
  60
  61     if (av.getCurrentAnnotationColumnSelectionState() != null)
  62     {
  63       annotations.setSelectedIndex(av
  64               .getCurrentAnnotationColumnSelectionState().getAnnotations()
  65               .getSelectedIndex());
  66       threshold.setSelectedIndex(av
  67               .getCurrentAnnotationColumnSelectionState().getThreshold()
  68               .getSelectedIndex());
  69     }
  70
  71     try
  72     {
  73       jbInit();
  74     } catch (Exception ex)
  75     {
  76     }
  77     adjusting = false;
  78
  79     updateView();
  80     frame.invalidate();
  81     frame.pack();
  82   }
  83
  84
  85   public AnnotationColumnChooser()
  86   {
  87     try
  88     {
  89       jbInit();
  90     } catch (Exception ex)
  91     {
  92       ex.printStackTrace();
  93     }
  94   }
  95
  96   private void jbInit() throws Exception
  97   {
  98     ok.setOpaque(false);
  99     ok.setText(MessageManager.getString("action.ok"));
 100     ok.addActionListener(new ActionListener()
 101     {
 102       @Override
 103       public void actionPerformed(ActionEvent e)
 104       {
 105         ok_actionPerformed(e);
 106       }
 107     });
 108     cancel.setOpaque(false);
 109     cancel.setText(MessageManager.getString("action.cancel"));
 110     cancel.addActionListener(new ActionListener()
 111     {
 112       @Override
 113       public void actionPerformed(ActionEvent e)
 114       {
 115         cancel_actionPerformed(e);
 116       }
 117     });
 118
 119     getAnnotations().addActionListener(new ActionListener()
 120     {
 121       @Override
 122       public void actionPerformed(ActionEvent e)
 123       {
 124         annotations_actionPerformed(e);
 125       }
 126     });
 127     getThreshold().addActionListener(new ActionListener()
 128     {
 129       @Override
 130       public void actionPerformed(ActionEvent e)
 131       {
 132         threshold_actionPerformed(e);
 133       }
 134     });
 135     thresholdValue.addActionListener(new ActionListener()
 136     {
 137       @Override
 138       public void actionPerformed(ActionEvent e)
 139       {
 140         thresholdValue_actionPerformed(e);
 141       }
 142     });
 143     slider.setPaintLabels(false);
 144     slider.setPaintTicks(true);
 145     slider.setBackground(Color.white);
 146     slider.setEnabled(false);
 147     slider.setOpaque(false);
 148     slider.setPreferredSize(new Dimension(100, 32));
 149     thresholdValue.setEnabled(false);
 150     thresholdValue.setColumns(7);
 151     thresholdIsMin.setBackground(Color.white);
 152     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 153     thresholdIsMin.setText(MessageManager
 154             .getString("label.threshold_minmax"));
 155     thresholdIsMin.addActionListener(new ActionListener()
 156     {
 157       @Override
 158       public void actionPerformed(ActionEvent actionEvent)
 159       {
 160         thresholdIsMin_actionPerformed(actionEvent);
 161       }
 162     });
 163     seqAssociated.setBackground(Color.white);
 164     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 165     seqAssociated.setText(MessageManager
 166             .getString("label.per_sequence_only"));
 167     seqAssociated.addActionListener(new ActionListener()
 168     {
 169
 170       @Override
 171       public void actionPerformed(ActionEvent arg0)
 172       {
 173         seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
 174       }
 175     });
 176
 177     this.setLayout(borderLayout1);
 178     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 179     jPanel1.setBackground(Color.white);
 180     jPanel2.setBackground(Color.white);
 181
 182     jPanel1.add(ok);
 183     jPanel1.add(cancel);
 184     jPanel2.add(getAnnotations(), "grow, wrap");
 185     jPanel2.add(seqAssociated, "wrap");
 186     jPanel2.add(getThreshold(), "grow, wrap");
 187     jPanel2.add(thresholdIsMin, "wrap");
 188     jPanel2.add(slider, "grow");
 189     jPanel2.add(thresholdValue, "grow");
 190     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 191     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 192     this.validate();
 193   }
 194
 195
 196   public void reset()
 197   {
 198     av.getColumnSelection().clear();
 199   }
 200
 201   public void valueChanged(boolean updateAllAnnotation)
 202   {
 203     getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 204     updateView();
 205     propagateSeqAssociatedThreshold(updateAllAnnotation,
 206             getCurrentAnnotation());
 207     ap.paintAlignment(false);
 208   }
 209
 210   public JComboBox<String> getThreshold()
 211   {
 212     return threshold;
 213   }
 214
 215   public void setThreshold(JComboBox<String> threshold)
 216   {
 217     this.threshold = threshold;
 218   }
 219
 220   public JComboBox<String> getAnnotations()
 221   {
 222     return annotations;
 223   }
 224
 225   public void setAnnotations(JComboBox<String> annotations)
 226   {
 227     this.annotations = annotations;
 228   }
 229
 230   @Override
 231   public void updateView()
 232   {
 233     changeColumnSelection();
 234   }
 235   void changeColumnSelection()
 236   {
 237     // Check if combobox is still adjusting
 238     if (adjusting)
 239     {
 240       return;
 241     }
 242
 243     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 244             .getSelectedIndex()]]);
 245
 246
 247     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 248             .getSelectedIndex());
 249
 250     slider.setEnabled(true);
 251     thresholdValue.setEnabled(true);
 252     thresholdIsMin.setEnabled(true);
 253
 254     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 255     {
 256       slider.setEnabled(false);
 257       thresholdValue.setEnabled(false);
 258       thresholdValue.setText("");
 259       thresholdIsMin.setEnabled(false);
 260     }
 261     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 262             && getCurrentAnnotation().threshold == null)
 263     {
 264       getCurrentAnnotation()
 265               .setThreshold(new jalview.datamodel.GraphLine(
 266                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 267                       "Threshold", Color.black));
 268     }
 269
 270     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 271     {
 272       adjusting = true;
 273       float range = getCurrentAnnotation().graphMax * 1000
 274               - getCurrentAnnotation().graphMin * 1000;
 275
 276       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 277       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 278       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 279       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 280       slider.setMajorTickSpacing((int) (range / 10f));
 281       slider.setEnabled(true);
 282       thresholdValue.setEnabled(true);
 283       adjusting = false;
 284     }
 285
 286     markColumnsContaining(getCurrentAnnotation(), selectedThresholdItem);
 287     av.setCurrentAnnotationColumnSelectionState(this);
 288     ap.alignmentChanged();
 289     ap.paintAlignment(true);
 290   }
 291 }