src/jalview/gui/AnnotationColumnChooser.java

   1 package jalview.gui;
   2
   3 import jalview.datamodel.ColumnSelection;
   4 import jalview.schemes.AnnotationColourGradient;
   5 import jalview.util.MessageManager;
   6
   7 import java.awt.BorderLayout;
   8 import java.awt.Color;
   9 import java.awt.Dimension;
  10 import java.awt.event.ActionEvent;
  11 import java.awt.event.ActionListener;
  12
  13 import javax.swing.JButton;
  14 import javax.swing.JComboBox;
  15 import javax.swing.JInternalFrame;
  16 import javax.swing.JLayeredPane;
  17 import javax.swing.JPanel;
  18
  19 import net.miginfocom.swing.MigLayout;
  20
  21 @SuppressWarnings("serial")
  22 public class AnnotationColumnChooser extends AnnotationRowFilter
  23 {
  24
  25   private ColumnSelection oldColumnSelection;
  26
  27   private JComboBox<String> annotations;
  28
  29   JButton ok = new JButton();
  30
  31   JButton cancel = new JButton();
  32
  33   JPanel jPanel1 = new JPanel();
  34
  35   JPanel jPanel2 = new JPanel();
  36
  37   BorderLayout borderLayout1 = new BorderLayout();
  38
  39   private JComboBox<String> threshold = new JComboBox<String>();
  40
  41
  42   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  43   {
  44     super(av, ap);
  45     frame = new JInternalFrame();
  46     frame.setContentPane(this);
  47     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  48     Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
  49
  50     addSliderChangeListener();
  51     addSliderMouseListeners();
  52
  53     if (av.getAlignment().getAlignmentAnnotation() == null)
  54     {
  55       return;
  56     }
  57     setOldColumnSelection(av.getColumnSelection());
  58     adjusting = true;
  59
  60     setAnnotations(new JComboBox<String>(
  61             getAnnotationItems(seqAssociated.isSelected())));
  62     populateThresholdComboBox(threshold);
  63
  64     if (av.getCurrentAnnotationColumnSelectionState() != null)
  65     {
  66       annotations.setSelectedIndex(av
  67               .getCurrentAnnotationColumnSelectionState().getAnnotations()
  68               .getSelectedIndex());
  69       threshold.setSelectedIndex(av
  70               .getCurrentAnnotationColumnSelectionState().getThreshold()
  71               .getSelectedIndex());
  72     }
  73
  74     try
  75     {
  76       jbInit();
  77     } catch (Exception ex)
  78     {
  79     }
  80     adjusting = false;
  81
  82     updateView();
  83     frame.invalidate();
  84     frame.pack();
  85   }
  86
  87
  88   public AnnotationColumnChooser()
  89   {
  90     try
  91     {
  92       jbInit();
  93     } catch (Exception ex)
  94     {
  95       ex.printStackTrace();
  96     }
  97   }
  98
  99   private void jbInit() throws Exception
 100   {
 101     ok.setOpaque(false);
 102     ok.setText(MessageManager.getString("action.ok"));
 103     ok.addActionListener(new ActionListener()
 104     {
 105       @Override
 106       public void actionPerformed(ActionEvent e)
 107       {
 108         ok_actionPerformed(e);
 109       }
 110     });
 111     cancel.setOpaque(false);
 112     cancel.setText(MessageManager.getString("action.cancel"));
 113     cancel.addActionListener(new ActionListener()
 114     {
 115       @Override
 116       public void actionPerformed(ActionEvent e)
 117       {
 118         cancel_actionPerformed(e);
 119       }
 120     });
 121
 122     getAnnotations().addActionListener(new ActionListener()
 123     {
 124       @Override
 125       public void actionPerformed(ActionEvent e)
 126       {
 127         annotations_actionPerformed(e);
 128       }
 129     });
 130     getThreshold().addActionListener(new ActionListener()
 131     {
 132       @Override
 133       public void actionPerformed(ActionEvent e)
 134       {
 135         threshold_actionPerformed(e);
 136       }
 137     });
 138     thresholdValue.addActionListener(new ActionListener()
 139     {
 140       @Override
 141       public void actionPerformed(ActionEvent e)
 142       {
 143         thresholdValue_actionPerformed(e);
 144       }
 145     });
 146     slider.setPaintLabels(false);
 147     slider.setPaintTicks(true);
 148     slider.setBackground(Color.white);
 149     slider.setEnabled(false);
 150     slider.setOpaque(false);
 151     slider.setPreferredSize(new Dimension(100, 32));
 152     thresholdValue.setEnabled(false);
 153     thresholdValue.setColumns(7);
 154     thresholdIsMin.setBackground(Color.white);
 155     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 156     thresholdIsMin.setText(MessageManager
 157             .getString("label.threshold_minmax"));
 158     thresholdIsMin.addActionListener(new ActionListener()
 159     {
 160       @Override
 161       public void actionPerformed(ActionEvent actionEvent)
 162       {
 163         thresholdIsMin_actionPerformed(actionEvent);
 164       }
 165     });
 166     seqAssociated.setBackground(Color.white);
 167     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 168     seqAssociated.setText(MessageManager
 169             .getString("label.per_sequence_only"));
 170     seqAssociated.addActionListener(new ActionListener()
 171     {
 172
 173       @Override
 174       public void actionPerformed(ActionEvent arg0)
 175       {
 176         seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
 177       }
 178     });
 179
 180     this.setLayout(borderLayout1);
 181     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 182     jPanel1.setBackground(Color.white);
 183     jPanel2.setBackground(Color.white);
 184
 185     jPanel1.add(ok);
 186     jPanel1.add(cancel);
 187     jPanel2.add(getAnnotations(), "grow, wrap");
 188     jPanel2.add(seqAssociated, "wrap");
 189     jPanel2.add(getThreshold(), "grow, wrap");
 190     jPanel2.add(thresholdIsMin, "wrap");
 191     jPanel2.add(slider, "grow");
 192     jPanel2.add(thresholdValue, "grow");
 193     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 194     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 195     this.validate();
 196   }
 197
 198
 199   public void reset()
 200   {
 201     av.getColumnSelection().clear();
 202     av.setColumnSelection(this.getOldColumnSelection());
 203   }
 204
 205   public void valueChanged(boolean updateAllAnnotation)
 206   {
 207     getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 208     updateView();
 209     propagateSeqAssociatedThreshold(updateAllAnnotation,
 210             getCurrentAnnotation());
 211     ap.paintAlignment(false);
 212   }
 213
 214   public JComboBox<String> getThreshold()
 215   {
 216     return threshold;
 217   }
 218
 219   public void setThreshold(JComboBox<String> threshold)
 220   {
 221     this.threshold = threshold;
 222   }
 223
 224   public JComboBox<String> getAnnotations()
 225   {
 226     return annotations;
 227   }
 228
 229   public void setAnnotations(JComboBox<String> annotations)
 230   {
 231     this.annotations = annotations;
 232   }
 233
 234   @Override
 235   public void updateView()
 236   {
 237     changeColumnSelection();
 238   }
 239   void changeColumnSelection()
 240   {
 241     // Check if combobox is still adjusting
 242     if (adjusting)
 243     {
 244       return;
 245     }
 246
 247     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 248             .getSelectedIndex()]]);
 249
 250
 251     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 252             .getSelectedIndex());
 253
 254     slider.setEnabled(true);
 255     thresholdValue.setEnabled(true);
 256     thresholdIsMin.setEnabled(true);
 257
 258     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 259     {
 260       slider.setEnabled(false);
 261       thresholdValue.setEnabled(false);
 262       thresholdValue.setText("");
 263       thresholdIsMin.setEnabled(false);
 264     }
 265     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 266             && getCurrentAnnotation().threshold == null)
 267     {
 268       getCurrentAnnotation()
 269               .setThreshold(new jalview.datamodel.GraphLine(
 270                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 271                       "Threshold", Color.black));
 272     }
 273
 274     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 275     {
 276       adjusting = true;
 277       float range = getCurrentAnnotation().graphMax * 1000
 278               - getCurrentAnnotation().graphMin * 1000;
 279
 280       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 281       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 282       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 283       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 284       slider.setMajorTickSpacing((int) (range / 10f));
 285       slider.setEnabled(true);
 286       thresholdValue.setEnabled(true);
 287       adjusting = false;
 288     }
 289
 290     markColumnsContaining(getCurrentAnnotation(), selectedThresholdItem);
 291     av.setCurrentAnnotationColumnSelectionState(this);
 292     ap.alignmentChanged();
 293     ap.paintAlignment(true);
 294   }
 295
 296   public ColumnSelection getOldColumnSelection()
 297   {
 298     return oldColumnSelection;
 299   }
 300
 301   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 302   {
 303     if (currentColumnSelection != null)
 304     {
 305       this.oldColumnSelection = new ColumnSelection();
 306       this.oldColumnSelection.setElementsFrom(currentColumnSelection);
 307     }
 308   }
 309 }