--- /dev/null
+package jalview.gui;
+
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+
+import net.miginfocom.swing.MigLayout;
+
+@SuppressWarnings("serial")
+public class AnnotationColumnChooser extends AnnotationRowFilter
+{
+
+ private JComboBox<String> annotations;
+
+ JButton ok = new JButton();
+
+ JButton cancel = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JPanel jPanel2 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ private JComboBox<String> threshold = new JComboBox<String>();
+
+
+ public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
+ {
+ super(av, ap);
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
+
+ addSliderChangeListener();
+ addSliderMouseListeners();
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ adjusting = true;
+
+ setAnnotations(new JComboBox<String>(
+ getAnnotationItems(seqAssociated.isSelected())));
+ populateThresholdComboBox(threshold);
+
+ if (av.getCurrentAnnotationColumnSelectionState() != null)
+ {
+ annotations.setSelectedIndex(av
+ .getCurrentAnnotationColumnSelectionState().getAnnotations()
+ .getSelectedIndex());
+ threshold.setSelectedIndex(av
+ .getCurrentAnnotationColumnSelectionState().getThreshold()
+ .getSelectedIndex());
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ }
+ adjusting = false;
+
+ updateView();
+ frame.invalidate();
+ frame.pack();
+ }
+
+
+ public AnnotationColumnChooser()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ ok.setOpaque(false);
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ cancel.setOpaque(false);
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+
+ getAnnotations().addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ getThreshold().addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ threshold_actionPerformed(e);
+ }
+ });
+ thresholdValue.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ thresholdValue_actionPerformed(e);
+ }
+ });
+ slider.setPaintLabels(false);
+ slider.setPaintTicks(true);
+ slider.setBackground(Color.white);
+ slider.setEnabled(false);
+ slider.setOpaque(false);
+ slider.setPreferredSize(new Dimension(100, 32));
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+ thresholdIsMin.setBackground(Color.white);
+ thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+ thresholdIsMin.setText(MessageManager
+ .getString("label.threshold_minmax"));
+ thresholdIsMin.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ thresholdIsMin_actionPerformed(actionEvent);
+ }
+ });
+ seqAssociated.setBackground(Color.white);
+ seqAssociated.setFont(JvSwingUtils.getLabelFont());
+ seqAssociated.setText(MessageManager
+ .getString("label.per_sequence_only"));
+ seqAssociated.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+ }
+ });
+
+ this.setLayout(borderLayout1);
+ jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
+ jPanel1.setBackground(Color.white);
+ jPanel2.setBackground(Color.white);
+
+ jPanel1.add(ok);
+ jPanel1.add(cancel);
+ jPanel2.add(getAnnotations(), "grow, wrap");
+ jPanel2.add(seqAssociated, "wrap");
+ jPanel2.add(getThreshold(), "grow, wrap");
+ jPanel2.add(thresholdIsMin, "wrap");
+ jPanel2.add(slider, "grow");
+ jPanel2.add(thresholdValue, "grow");
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);
+ this.validate();
+ }
+
+
+ public void reset()
+ {
+ av.getColumnSelection().clear();
+ }
+
+ public void valueChanged(boolean updateAllAnnotation)
+ {
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ updateView();
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false);
+ }
+
+ public JComboBox<String> getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setThreshold(JComboBox<String> threshold)
+ {
+ this.threshold = threshold;
+ }
+
+ public JComboBox<String> getAnnotations()
+ {
+ return annotations;
+ }
+
+ public void setAnnotations(JComboBox<String> annotations)
+ {
+ this.annotations = annotations;
+ }
+
+ @Override
+ public void updateView()
+ {
+ changeColumnSelection();
+ }
+ void changeColumnSelection()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
+ {
+ return;
+ }
+
+ setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]]);
+
+
+ int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+ .getSelectedIndex());
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
+
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ thresholdIsMin.setEnabled(false);
+ }
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
+ && getCurrentAnnotation().threshold == null)
+ {
+ getCurrentAnnotation()
+ .setThreshold(new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
+ }
+
+ if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ adjusting = true;
+ float range = getCurrentAnnotation().graphMax * 1000
+ - getCurrentAnnotation().graphMin * 1000;
+
+ slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
+ slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
+ slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+ thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+ slider.setMajorTickSpacing((int) (range / 10f));
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+ }
+
+ markColumnsContaining(getCurrentAnnotation(), selectedThresholdItem);
+ av.setCurrentAnnotationColumnSelectionState(this);
+ ap.alignmentChanged();
+ ap.paintAlignment(true);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff