/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
+import jalview.api.FeatureColourI;
import jalview.datamodel.GraphLine;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
import jalview.util.MessageManager;
import java.awt.BorderLayout;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.util.Hashtable;
import javax.swing.BorderFactory;
import javax.swing.JCheckBox;
public class FeatureColourChooser extends JalviewDialog
{
// FeatureSettings fs;
- FeatureRenderer fr;
+ private FeatureRenderer fr;
- private GraduatedColor cs;
+ private FeatureColourI cs;
- private Object oldcs;
+ private FeatureColourI oldcs;
- /**
- *
- * @return the last colour setting selected by user - either oldcs (which may
- * be a java.awt.Color) or the new GraduatedColor
- */
- public Object getLastColour()
- {
- if (cs == null)
- {
- return oldcs;
- }
- return cs;
- }
+ private AlignmentPanel ap;
+
+ private boolean adjusting = false;
+
+ final private float min;
+
+ final private float max;
+
+ final private float scaleFactor;
- Hashtable oldgroupColours;
+ private String type = null;
- AlignmentPanel ap;
+ private JPanel minColour = new JPanel();
- boolean adjusting = false;
+ private JPanel maxColour = new JPanel();
- private float min;
+ private JComboBox<String> threshold = new JComboBox<>();
- private float max;
+ private JSlider slider = new JSlider();
- String type = null;
+ private JTextField thresholdValue = new JTextField(20);
- public FeatureColourChooser(FeatureRenderer frender, String type)
+ // TODO implement GUI for tolower flag
+ // JCheckBox toLower = new JCheckBox();
+
+ private JCheckBox thresholdIsMin = new JCheckBox();
+
+ private JCheckBox colourByLabel = new JCheckBox();
+
+ private GraphLine threshline;
+
+ private Color oldmaxColour;
+
+ private Color oldminColour;
+
+ private ActionListener colourEditor = null;
+
+ /**
+ * Constructor
+ *
+ * @param frender
+ * @param theType
+ */
+ public FeatureColourChooser(FeatureRenderer frender, String theType)
{
- this(frender, false, type);
+ this(frender, false, theType);
}
- public FeatureColourChooser(FeatureRenderer frender, boolean block,
- String type)
+ /**
+ * Constructor, with option to make a blocking dialog (has to complete in the
+ * AWT event queue thread). Currently this option is always set to false.
+ *
+ * @param frender
+ * @param blocking
+ * @param theType
+ */
+ FeatureColourChooser(FeatureRenderer frender, boolean blocking,
+ String theType)
{
this.fr = frender;
- this.type = type;
+ this.type = theType;
ap = fr.ap;
- initDialogFrame(this, true, block, "Graduated Feature Colour for "
- + type, 480, 185);
- // frame.setLayer(JLayeredPane.PALETTE_LAYER);
- // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
- // 480, 145);
+ String title = MessageManager.formatMessage(
+ "label.graduated_color_for_params", new String[] { theType });
+ initDialogFrame(this, true, blocking, title, 480, 185);
slider.addChangeListener(new ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
- valueChanged();
+ thresholdValue.setText((slider.getValue() / scaleFactor) + "");
+ sliderValueChanged();
}
}
});
slider.addMouseListener(new MouseAdapter()
{
+ @Override
public void mouseReleased(MouseEvent evt)
{
+ /*
+ * only update Overview and/or structure colouring
+ * when threshold slider drag ends (mouse up)
+ */
if (ap != null)
{
ap.paintAlignment(true);
}
- ;
}
});
- float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
+ float mm[] = fr.getMinMax().get(theType)[0];
min = mm[0];
max = mm[1];
- oldcs = fr.getFeatureColours().get(type);
- if (oldcs instanceof GraduatedColor)
+
+ /*
+ * ensure scale factor allows a scaled range with
+ * 10 integer divisions ('ticks'); if we have got here,
+ * we should expect that max != min
+ */
+ scaleFactor = (max == min) ? 1f : 100f / (max - min);
+
+ oldcs = fr.getFeatureColours().get(theType);
+ if (!oldcs.isSimpleColour())
{
- if (((GraduatedColor) oldcs).isAutoScale())
+ if (oldcs.isAutoScaled())
{
// update the scale
- cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
+ cs = new FeatureColour((FeatureColour) oldcs, min, max);
}
else
{
- cs = new GraduatedColor((GraduatedColor) oldcs);
+ cs = new FeatureColour((FeatureColour) oldcs);
}
}
else
{
// promote original color to a graduated color
- Color bl = Color.black;
- if (oldcs instanceof Color)
+ Color bl = oldcs.getColour();
+ if (bl == null)
{
- bl = (Color) oldcs;
+ bl = Color.BLACK;
}
// original colour becomes the maximum colour
- cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
+ cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
cs.setColourByLabel(false);
}
- minColour.setBackground(oldminColour = cs.getMinColor());
- maxColour.setBackground(oldmaxColour = cs.getMaxColor());
+ minColour.setBackground(oldminColour = cs.getMinColour());
+ maxColour.setBackground(oldmaxColour = cs.getMaxColour());
adjusting = true;
try
{
}
// update the gui from threshold state
- thresholdIsMin.setSelected(!cs.isAutoScale());
+ thresholdIsMin.setSelected(!cs.isAutoScaled());
colourByLabel.setSelected(cs.isColourByLabel());
- if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ if (cs.hasThreshold())
{
// initialise threshold slider and selector
- threshold
- .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
- : 2);
+ threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2);
slider.setEnabled(true);
+ slider.setValue((int) (cs.getThreshold() * scaleFactor));
thresholdValue.setEnabled(true);
- threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
- "Threshold", Color.black);
-
+ threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
+ threshline.value = cs.getThreshold();
}
adjusting = false;
- changeColour();
+ changeColour(false);
waitForInput();
}
- public FeatureColourChooser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
private void jbInit() throws Exception
{
minColour.setToolTipText(MessageManager.getString("label.min_colour"));
minColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (minColour.isEnabled())
maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
maxColour.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
if (maxColour.isEnabled())
}
});
maxColour.setBorder(new LineBorder(Color.black));
- minText.setText(MessageManager.getString("label.min"));
+ JLabel minText = new JLabel(MessageManager.getString("label.min"));
minText.setFont(JvSwingUtils.getLabelFont());
- maxText.setText(MessageManager.getString("label.max"));
+ JLabel maxText = new JLabel(MessageManager.getString("label.max"));
maxText.setFont(JvSwingUtils.getLabelFont());
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
+ this.setLayout(new BorderLayout());
+ JPanel jPanel1 = new JPanel();
jPanel1.setBackground(Color.white);
+ JPanel jPanel2 = new JPanel();
+ jPanel2.setLayout(new FlowLayout());
jPanel2.setBackground(Color.white);
threshold.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- threshold_actionPerformed(e);
+ threshold_actionPerformed();
}
});
threshold.setToolTipText(MessageManager
.getString("label.threshold_feature_display_by_score"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold")); // index 0
+ .getString("label.threshold_feature_no_threshold")); // index 0
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold")); // index 1
+ .getString("label.threshold_feature_above_threshold")); // index 1
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold")); // index 2
- jPanel3.setLayout(flowLayout2);
+ .getString("label.threshold_feature_below_threshold")); // index 2
+
+ JPanel jPanel3 = new JPanel();
+ jPanel3.setLayout(new FlowLayout());
thresholdValue.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- thresholdValue_actionPerformed(e);
+ thresholdValue_actionPerformed();
}
});
slider.setPaintLabels(false);
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
slider.setToolTipText(MessageManager
- .getString("label.adjust_thereshold"));
+ .getString("label.adjust_threshold"));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
jPanel3.setBackground(Color.white);
.getString("label.toggle_absolute_relative_display_threshold"));
thresholdIsMin.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
- thresholdIsMin_actionPerformed(actionEvent);
+ thresholdIsMin_actionPerformed();
}
});
colourByLabel.setBackground(Color.white);
.getString("label.display_features_same_type_different_label_using_different_colour"));
colourByLabel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent actionEvent)
{
- colourByLabel_actionPerformed(actionEvent);
+ colourByLabel_actionPerformed();
}
});
+
+ JPanel colourPanel = new JPanel();
colourPanel.setBackground(Color.white);
jPanel1.add(ok);
jPanel1.add(cancel);
- jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
- jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
+ jPanel2.add(colourByLabel, BorderLayout.WEST);
+ jPanel2.add(colourPanel, BorderLayout.EAST);
colourPanel.add(minText);
colourPanel.add(minColour);
colourPanel.add(maxText);
colourPanel.add(maxColour);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ this.add(jPanel3, BorderLayout.CENTER);
jPanel3.add(threshold);
jPanel3.add(slider);
jPanel3.add(thresholdValue);
jPanel3.add(thresholdIsMin);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
+ this.add(jPanel1, BorderLayout.SOUTH);
+ this.add(jPanel2, BorderLayout.NORTH);
}
- JLabel minText = new JLabel();
-
- JLabel maxText = new JLabel();
-
- JPanel minColour = new JPanel();
-
- JPanel maxColour = new JPanel();
-
- JPanel colourPanel = new JPanel();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- JComboBox threshold = new JComboBox();
-
- FlowLayout flowLayout1 = new FlowLayout();
-
- JPanel jPanel3 = new JPanel();
-
- FlowLayout flowLayout2 = new FlowLayout();
-
- JSlider slider = new JSlider();
-
- JTextField thresholdValue = new JTextField(20);
-
- // TODO implement GUI for tolower flag
- // JCheckBox toLower = new JCheckBox();
-
- JCheckBox thresholdIsMin = new JCheckBox();
-
- JCheckBox colourByLabel = new JCheckBox();
-
- private GraphLine threshline;
-
- private Color oldmaxColour;
-
- private Color oldminColour;
-
- public void minColour_actionPerformed()
+ /**
+ * Action on clicking the 'minimum colour' - open a colour chooser dialog, and
+ * set the selected colour (if the user does not cancel out of the dialog)
+ */
+ protected void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_minimum_value"),
minColour.setForeground(col);
}
minColour.repaint();
- changeColour();
+ changeColour(true);
}
- public void maxColour_actionPerformed()
+ /**
+ * Action on clicking the 'maximum colour' - open a colour chooser dialog, and
+ * set the selected colour (if the user does not cancel out of the dialog)
+ */
+ protected void maxColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_colour_maximum_value"),
maxColour.setForeground(col);
}
maxColour.repaint();
- changeColour();
+ changeColour(true);
}
- void changeColour()
+ /**
+ * Constructs and sets the selected colour options as the colour for the
+ * feature type, and repaints the alignment, and optionally the Overview
+ * and/or structure viewer if open
+ *
+ * @param updateOverview
+ */
+ void changeColour(boolean updateOverview)
{
// Check if combobox is still adjusting
if (adjusting)
return;
}
- int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
+ boolean aboveThreshold = false;
+ boolean belowThreshold = false;
if (threshold.getSelectedIndex() == 1)
{
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ aboveThreshold = true;
}
else if (threshold.getSelectedIndex() == 2)
{
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+ belowThreshold = true;
}
+ boolean hasThreshold = aboveThreshold || belowThreshold;
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- GraduatedColor acg;
+ FeatureColourI acg;
if (cs.isColourByLabel())
{
- acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
+ acg = new FeatureColour(oldminColour, oldmaxColour, min, max);
}
else
{
- acg = new GraduatedColor(oldminColour = minColour.getBackground(),
+ acg = new FeatureColour(oldminColour = minColour.getBackground(),
oldmaxColour = maxColour.getBackground(), min, max);
-
}
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+ if (!hasThreshold)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
thresholdIsMin.setEnabled(false);
}
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
- && threshline == null)
+ else if (threshline == null)
{
- // todo visual indication of feature threshold
- threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
- "Threshold", Color.black);
+ /*
+ * todo not yet implemented: visual indication of feature threshold
+ */
+ threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
}
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ if (hasThreshold)
{
adjusting = true;
- acg.setThresh(threshline.value);
+ acg.setThreshold(threshline.value);
- float range = max * 1000f - min * 1000f;
+ float range = (max - min) * scaleFactor;
- slider.setMinimum((int) (min * 1000));
- slider.setMaximum((int) (max * 1000));
- slider.setValue((int) (threshline.value * 1000));
+ slider.setMinimum((int) (min * scaleFactor));
+ slider.setMaximum((int) (max * scaleFactor));
+ // slider.setValue((int) (threshline.value * scaleFactor));
+ slider.setValue(Math.round(threshline.value * scaleFactor));
thresholdValue.setText(threshline.value + "");
slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
adjusting = false;
}
- acg.setThreshType(aboveThreshold);
- if (thresholdIsMin.isSelected()
- && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ acg.setAboveThreshold(aboveThreshold);
+ acg.setBelowThreshold(belowThreshold);
+ if (thresholdIsMin.isSelected() && hasThreshold)
{
acg.setAutoScaled(false);
- if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
+ if (aboveThreshold)
{
- acg = new GraduatedColor(acg, threshline.value, max);
+ acg = new FeatureColour((FeatureColour) acg, threshline.value, max);
}
else
{
- acg = new GraduatedColor(acg, min, threshline.value);
+ acg = new FeatureColour((FeatureColour) acg, min, threshline.value);
}
}
else
}
fr.setColour(type, acg);
cs = acg;
- ap.paintAlignment(false);
+ ap.paintAlignment(updateOverview);
}
+ @Override
protected void raiseClosed()
{
if (this.colourEditor != null)
}
}
+ @Override
public void okPressed()
{
- changeColour();
+ changeColour(false);
}
+ @Override
public void cancelPressed()
{
reset();
}
+ /**
+ * Action when the user cancels the dialog. All previous settings should be
+ * restored and rendered on the alignment, and any linked Overview window or
+ * structure.
+ */
void reset()
{
fr.setColour(type, oldcs);
- ap.paintAlignment(false);
+ ap.paintAlignment(true);
cs = null;
}
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void threshold_actionPerformed(ActionEvent e)
+ /**
+ * Action on change of choice of No / Above / Below Threshold
+ */
+ protected void threshold_actionPerformed()
{
- changeColour();
+ changeColour(true);
}
- public void thresholdValue_actionPerformed(ActionEvent e)
+ /**
+ * Action on text entry of a threshold value
+ */
+ protected void thresholdValue_actionPerformed()
{
try
{
float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue((int) (f * 1000));
+ slider.setValue((int) (f * scaleFactor));
threshline.value = f;
+
+ /*
+ * force repaint of any Overview window or structure
+ */
+ ap.paintAlignment(true);
} catch (NumberFormatException ex)
{
}
}
- public void valueChanged()
+ /**
+ * Action on change of threshold slider value. This may be done interactively
+ * (by moving the slider), or programmatically (to update the slider after
+ * manual input of a threshold value).
+ */
+ protected void sliderValueChanged()
{
- threshline.value = (float) slider.getValue() / 1000f;
- cs.setThresh(threshline.value);
- changeColour();
- ap.paintAlignment(false);
+ /*
+ * squash rounding errors by forcing min/max of slider to
+ * actual min/max of feature score range
+ */
+ int value = slider.getValue();
+ threshline.value = value == slider.getMaximum() ? max
+ : (value == slider.getMinimum() ? min : value / scaleFactor);
+ cs.setThreshold(threshline.value);
+
+ /*
+ * repaint alignment, but not Overview or structure,
+ * to avoid overload while dragging the slider
+ */
+ changeColour(false);
}
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ protected void thresholdIsMin_actionPerformed()
{
- changeColour();
+ changeColour(true);
}
- public void colourByLabel_actionPerformed(ActionEvent actionEvent)
+ protected void colourByLabel_actionPerformed()
{
- changeColour();
+ changeColour(true);
}
- ActionListener colourEditor = null;
-
- public void addActionListener(ActionListener graduatedColorEditor)
+ void addActionListener(ActionListener graduatedColorEditor)
{
if (colourEditor != null)
{
colourEditor = graduatedColorEditor;
}
+ /**
+ * Answers the last colour setting selected by user - either oldcs (which may
+ * be a java.awt.Color) or the new GraduatedColor
+ *
+ * @return
+ */
+ FeatureColourI getLastColour()
+ {
+ if (cs == null)
+ {
+ return oldcs;
+ }
+ return cs;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff