X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureColourChooser.java;h=da3819c81298e6ae4c20d1a9c01f21acbd91d5d7;hb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;hp=5594e1adec0f2a0e39701e0ced810c3ebc4cb4e6;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java index 5594e1a..da3819c 100644 --- a/src/jalview/gui/FeatureColourChooser.java +++ b/src/jalview/gui/FeatureColourChooser.java @@ -22,24 +22,33 @@ package jalview.gui; import jalview.api.FeatureColourI; import jalview.datamodel.GraphLine; +import jalview.datamodel.features.FeatureAttributes; import jalview.schemes.FeatureColour; import jalview.util.MessageManager; -import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import java.util.ArrayList; +import java.util.List; import javax.swing.BorderFactory; +import javax.swing.BoxLayout; +import javax.swing.ButtonGroup; import javax.swing.JCheckBox; import javax.swing.JColorChooser; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JPanel; +import javax.swing.JRadioButton; import javax.swing.JSlider; import javax.swing.JTextField; import javax.swing.border.LineBorder; @@ -48,56 +57,117 @@ import javax.swing.event.ChangeListener; public class FeatureColourChooser extends JalviewDialog { - // FeatureSettings fs; - FeatureRenderer fr; + private static final String COLON = ":"; + + private static final int MAX_TOOLTIP_LENGTH = 50; + + private static int NO_COLOUR_OPTION = 0; + + private static int MIN_COLOUR_OPTION = 1; + + private static int MAX_COLOUR_OPTION = 2; + + private FeatureRenderer fr; private FeatureColourI cs; private FeatureColourI oldcs; - /** - * - * @return the last colour setting selected by user - either oldcs (which may - * be a java.awt.Color) or the new GraduatedColor + private AlignmentPanel ap; + + private boolean adjusting = false; + + private float min; + + private float max; + + private float scaleFactor; + + private String type = null; + + private JPanel minColour = new JPanel(); + + private JPanel maxColour = new JPanel(); + + private Color noColour; + + private JComboBox threshold = new JComboBox<>(); + + private JSlider slider = new JSlider(); + + private JTextField thresholdValue = new JTextField(20); + + private JCheckBox thresholdIsMin = new JCheckBox(); + + private GraphLine threshline; + + private Color oldmaxColour; + + private Color oldminColour; + + private Color oldNoColour; + + private ActionListener colourEditor = null; + + /* + * radio buttons to select what to colour by + * label, attribute text, score, attribute value */ - public FeatureColourI getLastColour() - { - if (cs == null) - { - return oldcs; - } - return cs; - } + private JRadioButton byDescription = new JRadioButton(); + + private JRadioButton byAttributeText = new JRadioButton(); - AlignmentPanel ap; + private JRadioButton byScore = new JRadioButton(); - boolean adjusting = false; + private JRadioButton byAttributeValue = new JRadioButton(); - final private float min; + private ActionListener changeColourAction; - final private float max; + private ActionListener changeMinMaxAction; - final private float scaleFactor; + /* + * choice of option for 'colour for no value' + */ + private JComboBox noValueCombo; - String type = null; + /* + * choice of attribute (if any) for 'colour by text' + */ + private JComboBox textAttributeCombo; - public FeatureColourChooser(FeatureRenderer frender, String type) + /* + * choice of attribute (if any) for 'colour by value' + */ + private JComboBox valueAttributeCombo; + + /** + * 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; - String title = MessageManager.formatMessage( - "label.graduated_color_for_params", new String[] { type }); - initDialogFrame(this, true, block, title, 480, 185); - // frame.setLayer(JLayeredPane.PALETTE_LAYER); - // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, - // 480, 145); + String title = MessageManager.formatMessage("label.variable_color_for", + new String[] { theType }); + initDialogFrame(this, true, blocking, title, 470, 300); slider.addChangeListener(new ChangeListener() { @@ -107,7 +177,7 @@ public class FeatureColourChooser extends JalviewDialog if (!adjusting) { thresholdValue.setText((slider.getValue() / scaleFactor) + ""); - valueChanged(); + sliderValueChanged(); } } }); @@ -116,15 +186,19 @@ public class FeatureColourChooser extends JalviewDialog @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); + ap.paintAlignment(true, true); } - ; } }); - float mm[] = fr.getMinMax().get(type)[0]; + // todo move all threshold setup inside a method + float mm[] = fr.getMinMax().get(theType)[0]; min = mm[0]; max = mm[1]; @@ -135,7 +209,7 @@ public class FeatureColourChooser extends JalviewDialog */ scaleFactor = (max == min) ? 1f : 100f / (max - min); - oldcs = fr.getFeatureColours().get(type); + oldcs = fr.getFeatureColours().get(theType); if (!oldcs.isSimpleColour()) { if (oldcs.isAutoScaled()) @@ -150,7 +224,10 @@ public class FeatureColourChooser extends JalviewDialog } else { - // promote original color to a graduated color + /* + * promote original simple color to a graduated color + * - by score if there is a score range, else by label + */ Color bl = oldcs.getColour(); if (bl == null) { @@ -158,10 +235,12 @@ public class FeatureColourChooser extends JalviewDialog } // original colour becomes the maximum colour cs = new FeatureColour(Color.white, bl, mm[0], mm[1]); - cs.setColourByLabel(false); + cs.setColourByLabel(mm[0] == mm[1]); } minColour.setBackground(oldminColour = cs.getMinColour()); maxColour.setBackground(oldmaxColour = cs.getMaxColour()); + noColour = cs.getNoColour(); + adjusting = true; try @@ -169,28 +248,211 @@ public class FeatureColourChooser extends JalviewDialog jbInit(); } catch (Exception ex) { + ex.printStackTrace(); + return; + } + + /* + * set the initial state of options on screen + */ + if (cs.isColourByLabel()) + { + if (cs.isColourByAttribute()) + { + byAttributeText.setSelected(true); + textAttributeCombo.setEnabled(true); + String[] attributeName = cs.getAttributeName(); + textAttributeCombo + .setSelectedItem(String.join(COLON, attributeName)); + } + else + { + byDescription.setSelected(true); + textAttributeCombo.setEnabled(false); + } + } + else + { + if (cs.isColourByAttribute()) + { + byAttributeValue.setSelected(true); + String[] attributeName = cs.getAttributeName(); + valueAttributeCombo + .setSelectedItem(String.join(COLON, attributeName)); + valueAttributeCombo.setEnabled(true); + updateMinMax(); + } + else + { + byScore.setSelected(true); + valueAttributeCombo.setEnabled(false); + } + } + + if (noColour == null) + { + noValueCombo.setSelectedIndex(NO_COLOUR_OPTION); + } + else if (noColour.equals(oldminColour)) + { + noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION); } - // update the gui from threshold state - thresholdIsMin.setSelected(!cs.isAutoScaled()); - colourByLabel.setSelected(cs.isColourByLabel()); + else if (noColour.equals(oldmaxColour)) + { + noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION); + } + + threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black); + threshline.value = cs.getThreshold(); + if (cs.hasThreshold()) { // initialise threshold slider and selector threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2); slider.setEnabled(true); + slider.setValue((int) (cs.getThreshold() * scaleFactor)); thresholdValue.setEnabled(true); - threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black); - } adjusting = false; - changeColour(); + changeColour(false); waitForInput(); } - private void jbInit() throws Exception + /** + * Configures the initial layout + */ + private void jbInit() + { + this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); + this.setBackground(Color.white); + + changeColourAction = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + changeColour(true); + } + }; + + changeMinMaxAction = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + updateMinMax(); + changeColour(true); + } + }; + + /* + * this panel + * detailsPanel + * colourByTextPanel + * colourByScorePanel + * okCancelPanel + */ + JPanel detailsPanel = new JPanel(); + detailsPanel.setLayout(new BoxLayout(detailsPanel, BoxLayout.Y_AXIS)); + + JPanel colourByTextPanel = initColourByTextPanel(); + detailsPanel.add(colourByTextPanel); + + JPanel colourByValuePanel = initColourByValuePanel(); + detailsPanel.add(colourByValuePanel); + + /* + * 4 radio buttons select between colour by description, by + * attribute text, by score, or by attribute value + */ + ButtonGroup bg = new ButtonGroup(); + bg.add(byDescription); + bg.add(byAttributeText); + bg.add(byScore); + bg.add(byAttributeValue); + + JPanel okCancelPanel = initOkCancelPanel(); + + this.add(detailsPanel); + this.add(okCancelPanel); + } + + /** + * Updates the min-max range for a change in choice of Colour by Score, or + * Colour by Attribute (value) + */ + protected void updateMinMax() + { + float[] minMax = null; + if (byScore.isSelected()) + { + minMax = fr.getMinMax().get(type)[0]; + } + else if (byAttributeValue.isSelected()) + { + String attName = (String) valueAttributeCombo.getSelectedItem(); + String[] attNames = attName.split(COLON); + minMax = FeatureAttributes.getInstance().getMinMax(type, attNames); + } + if (minMax != null) + { + min = minMax[0]; + max = minMax[1]; + scaleFactor = (max == min) ? 1f : 100f / (max - min); + slider.setValue((int) (min * scaleFactor)); + } + } + + /** + * Lay out fields for graduated colour by value + * + * @return + */ + protected JPanel initColourByValuePanel() { + JPanel byValuePanel = new JPanel(); + byValuePanel.setLayout(new BoxLayout(byValuePanel, BoxLayout.Y_AXIS)); + JvSwingUtils.createItalicTitledBorder(byValuePanel, + MessageManager.getString("label.colour_by_value"), true); + byValuePanel.setBackground(Color.white); + + /* + * first row - choose colour by score or by attribute, choose attribute + */ + JPanel byWhatPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + byWhatPanel.setBackground(Color.white); + byValuePanel.add(byWhatPanel); + + byScore.setText(MessageManager.getString("label.score")); + byWhatPanel.add(byScore); + byScore.addActionListener(changeMinMaxAction); + + byAttributeValue.setText(MessageManager.getString("label.attribute")); + byAttributeValue.addActionListener(changeMinMaxAction); + byWhatPanel.add(byAttributeValue); + + List attNames = FeatureAttributes.getInstance() + .getAttributes(type); + valueAttributeCombo = populateAttributesDropdown(type, attNames, true); + + /* + * if no numeric atttibutes found, disable colour by attribute value + */ + if (valueAttributeCombo.getItemCount() == 0) + { + byAttributeValue.setEnabled(false); + } + + byWhatPanel.add(valueAttributeCombo); + + /* + * second row - min/max/no colours + */ + JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + colourRangePanel.setBackground(Color.white); + byValuePanel.add(colourRangePanel); minColour.setFont(JvSwingUtils.getLabelFont()); minColour.setBorder(BorderFactory.createLineBorder(Color.black)); @@ -207,6 +469,7 @@ public class FeatureColourChooser extends JalviewDialog } } }); + maxColour.setFont(JvSwingUtils.getLabelFont()); maxColour.setBorder(BorderFactory.createLineBorder(Color.black)); maxColour.setPreferredSize(new Dimension(40, 20)); @@ -223,22 +486,42 @@ public class FeatureColourChooser extends JalviewDialog } }); maxColour.setBorder(new LineBorder(Color.black)); - minText.setText(MessageManager.getString("label.min")); - minText.setFont(JvSwingUtils.getLabelFont()); - maxText.setText(MessageManager.getString("label.max")); - maxText.setFont(JvSwingUtils.getLabelFont()); - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); - jPanel1.setBackground(Color.white); - jPanel2.setBackground(Color.white); - threshold.addActionListener(new ActionListener() + + noValueCombo = new JComboBox<>(); + noValueCombo.addItem(MessageManager.getString("label.no_colour")); + noValueCombo.addItem(MessageManager.getString("label.min_colour")); + noValueCombo.addItem(MessageManager.getString("label.max_colour")); + noValueCombo.addItemListener(new ItemListener() { @Override - public void actionPerformed(ActionEvent e) + public void itemStateChanged(ItemEvent e) { - threshold_actionPerformed(e); + setNoValueColour(); } }); + + JLabel minText = new JLabel(MessageManager.getString("label.min_value")); + minText.setFont(JvSwingUtils.getLabelFont()); + JLabel maxText = new JLabel(MessageManager.getString("label.max_value")); + maxText.setFont(JvSwingUtils.getLabelFont()); + JLabel noText = new JLabel(MessageManager.getString("label.no_value")); + noText.setFont(JvSwingUtils.getLabelFont()); + + colourRangePanel.add(minText); + colourRangePanel.add(minColour); + colourRangePanel.add(maxText); + colourRangePanel.add(maxColour); + colourRangePanel.add(noText); + colourRangePanel.add(noValueCombo); + + /* + * third row - threshold options and value + */ + JPanel thresholdPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + thresholdPanel.setBackground(Color.white); + byValuePanel.add(thresholdPanel); + + threshold.addActionListener(changeColourAction); threshold.setToolTipText(MessageManager .getString("label.threshold_feature_display_by_score")); threshold.addItem(MessageManager @@ -247,13 +530,21 @@ public class FeatureColourChooser extends JalviewDialog .getString("label.threshold_feature_above_threshold")); // index 1 threshold.addItem(MessageManager .getString("label.threshold_feature_below_threshold")); // index 2 - jPanel3.setLayout(flowLayout2); + thresholdValue.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - thresholdValue_actionPerformed(e); + thresholdValue_actionPerformed(); + } + }); + thresholdValue.addFocusListener(new FocusAdapter() + { + @Override + public void focusLost(FocusEvent e) + { + thresholdValue_actionPerformed(); } }); slider.setPaintLabels(false); @@ -266,94 +557,107 @@ public class FeatureColourChooser extends JalviewDialog .getString("label.adjust_threshold")); thresholdValue.setEnabled(false); thresholdValue.setColumns(7); - jPanel3.setBackground(Color.white); + + thresholdPanel.add(threshold); + thresholdPanel.add(slider); + thresholdPanel.add(thresholdValue); + + /* + * 4th row - threshold is min / max + */ + JPanel isMinMaxPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + isMinMaxPanel.setBackground(Color.white); + byValuePanel.add(isMinMaxPanel); thresholdIsMin.setBackground(Color.white); thresholdIsMin.setText(MessageManager .getString("label.threshold_minmax")); thresholdIsMin.setToolTipText(MessageManager .getString("label.toggle_absolute_relative_display_threshold")); - thresholdIsMin.addActionListener(new ActionListener() + thresholdIsMin.addActionListener(changeColourAction); + isMinMaxPanel.add(thresholdIsMin); + + return byValuePanel; + } + + /** + * Action on user choice of no / min / max colour to use when there is no + * value to colour by + */ + protected void setNoValueColour() + { + int i = noValueCombo.getSelectedIndex(); + if (i == NO_COLOUR_OPTION) { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - thresholdIsMin_actionPerformed(actionEvent); - } - }); - colourByLabel.setBackground(Color.white); - colourByLabel - .setText(MessageManager.getString("label.colour_by_label")); - colourByLabel - .setToolTipText(MessageManager - .getString("label.display_features_same_type_different_label_using_different_colour")); - colourByLabel.addActionListener(new ActionListener() + noColour = null; + } + else if (i == MIN_COLOUR_OPTION) { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - colourByLabel_actionPerformed(actionEvent); - } - }); - colourPanel.setBackground(Color.white); - jPanel1.add(ok); - jPanel1.add(cancel); - jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST); - jPanel2.add(colourPanel, java.awt.BorderLayout.EAST); - colourPanel.add(minText); - colourPanel.add(minColour); - colourPanel.add(maxText); - colourPanel.add(maxColour); - this.add(jPanel3, java.awt.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); + noColour = minColour.getBackground(); + } + else if (i == MAX_COLOUR_OPTION) + { + noColour = maxColour.getBackground(); + } + changeColour(true); } - 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(); + /** + * Lay out OK and Cancel buttons + * + * @return + */ + protected JPanel initOkCancelPanel() + { + JPanel okCancelPanel = new JPanel(); + okCancelPanel.setBackground(Color.white); + okCancelPanel.add(ok); + okCancelPanel.add(cancel); + return okCancelPanel; + } - private GraphLine threshline; + /** + * Lay out Colour by Label and attribute choice elements + * + * @return + */ + protected JPanel initColourByTextPanel() + { + JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); + byTextPanel.setBackground(Color.white); + JvSwingUtils.createItalicTitledBorder(byTextPanel, + MessageManager.getString("label.colour_by_text"), true); + + byDescription.setText(MessageManager.getString("label.label")); + byDescription.setToolTipText(MessageManager + .getString("label.colour_by_label_tip")); + byDescription.addActionListener(changeColourAction); + byTextPanel.add(byDescription); + + byAttributeText.setText(MessageManager.getString("label.attribute")); + byAttributeText.addActionListener(changeColourAction); + byTextPanel.add(byAttributeText); + + List attNames = FeatureAttributes.getInstance() + .getAttributes(type); + textAttributeCombo = populateAttributesDropdown(type, attNames, false); + byTextPanel.add(textAttributeCombo); - private Color oldmaxColour; + /* + * disable colour by attribute if no attributes + */ + if (attNames.isEmpty()) + { + byAttributeText.setEnabled(false); + } - private Color oldminColour; + return byTextPanel; + } - 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"), @@ -364,10 +668,14 @@ public class FeatureColourChooser extends JalviewDialog 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"), @@ -378,10 +686,17 @@ public class FeatureColourChooser extends JalviewDialog 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 updateStructsAndOverview + */ + void changeColour(boolean updateStructsAndOverview) { // Check if combobox is still adjusting if (adjusting) @@ -404,6 +719,9 @@ public class FeatureColourChooser extends JalviewDialog slider.setEnabled(true); thresholdValue.setEnabled(true); + /* + * make the feature colour + */ FeatureColourI acg; if (cs.isColourByLabel()) { @@ -412,8 +730,27 @@ public class FeatureColourChooser extends JalviewDialog else { acg = new FeatureColour(oldminColour = minColour.getBackground(), - oldmaxColour = maxColour.getBackground(), min, max); - + oldmaxColour = maxColour.getBackground(), + oldNoColour = noColour, min, max); + } + String attribute = null; + textAttributeCombo.setEnabled(false); + valueAttributeCombo.setEnabled(false); + if (byAttributeText.isSelected()) + { + attribute = (String) textAttributeCombo.getSelectedItem(); + textAttributeCombo.setEnabled(true); + acg.setAttributeName(attribute.split(COLON)); + } + else if (byAttributeValue.isSelected()) + { + attribute = (String) valueAttributeCombo.getSelectedItem(); + valueAttributeCombo.setEnabled(true); + acg.setAttributeName(attribute.split(COLON)); + } + else + { + acg.setAttributeName((String) null); } if (!hasThreshold) @@ -425,8 +762,11 @@ public class FeatureColourChooser extends JalviewDialog } else if (threshline == null) { - // todo visual indication of feature threshold - threshline = new 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 (hasThreshold) @@ -438,12 +778,13 @@ public class FeatureColourChooser extends JalviewDialog slider.setMinimum((int) (min * scaleFactor)); slider.setMaximum((int) (max * scaleFactor)); - slider.setValue((int) (threshline.value * 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); thresholdValue.setEnabled(true); - thresholdIsMin.setEnabled(!colourByLabel.isSelected()); + thresholdIsMin.setEnabled(!byDescription.isSelected()); adjusting = false; } @@ -465,29 +806,37 @@ public class FeatureColourChooser extends JalviewDialog { acg.setAutoScaled(true); } - acg.setColourByLabel(colourByLabel.isSelected()); + acg.setColourByLabel(byDescription.isSelected() + || byAttributeText.isSelected()); + if (acg.isColourByLabel()) { maxColour.setEnabled(false); minColour.setEnabled(false); + noValueCombo.setEnabled(false); maxColour.setBackground(this.getBackground()); maxColour.setForeground(this.getBackground()); minColour.setBackground(this.getBackground()); minColour.setForeground(this.getBackground()); - } else { maxColour.setEnabled(true); minColour.setEnabled(true); + noValueCombo.setEnabled(true); maxColour.setBackground(oldmaxColour); - minColour.setBackground(oldminColour); maxColour.setForeground(oldmaxColour); + minColour.setBackground(oldminColour); minColour.setForeground(oldminColour); + noColour = oldNoColour; } + + /* + * save the colour, and repaint stuff + */ fr.setColour(type, acg); cs = acg; - ap.paintAlignment(false); + ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview); } @Override @@ -502,7 +851,7 @@ public class FeatureColourChooser extends JalviewDialog @Override public void okPressed() { - changeColour(); + changeColour(false); } @Override @@ -511,68 +860,147 @@ public class FeatureColourChooser extends JalviewDialog 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, true); cs = null; } - public void thresholdCheck_actionPerformed(ActionEvent e) - { - changeColour(); - } - - public void annotations_actionPerformed(ActionEvent e) - { - changeColour(); - } - - public void threshold_actionPerformed(ActionEvent e) - { - changeColour(); - } - - 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 * scaleFactor)); threshline.value = f; + + /* + * force repaint of any Overview window or structure + */ + ap.paintAlignment(true, 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 = slider.getValue() / scaleFactor; + /* + * 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); - changeColour(); - ap.paintAlignment(false); + + /* + * repaint alignment, but not Overview or structure, + * to avoid overload while dragging the slider + */ + changeColour(false); } - public void thresholdIsMin_actionPerformed(ActionEvent actionEvent) + void addActionListener(ActionListener graduatedColorEditor) { - changeColour(); + if (colourEditor != null) + { + System.err.println( + "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser"); + } + colourEditor = graduatedColorEditor; } - public void colourByLabel_actionPerformed(ActionEvent actionEvent) + /** + * Answers the last colour setting selected by user - either oldcs (which may + * be a java.awt.Color) or the new GraduatedColor + * + * @return + */ + FeatureColourI getLastColour() { - changeColour(); + if (cs == null) + { + return oldcs; + } + return cs; } - ActionListener colourEditor = null; - - public void addActionListener(ActionListener graduatedColorEditor) + /** + * A helper method to build the drop-down choice of attributes for a feature. + * Where metadata is available with a description for an attribute, that is + * added as a tooltip. The list may optionally be restricted to attributes for + * which we hold a range of numerical values (so suitable candidates for a + * graduated colour scheme). + *

+ * Attribute names may be 'simple' e.g. "AC" or 'compound' e.g. {"CSQ", + * "Allele"}. Compound names are rendered for display as (e.g.) CSQ:Allele. + * + * @param featureType + * @param attNames + * @param withNumericRange + */ + protected JComboBox populateAttributesDropdown( + String featureType, List attNames, + boolean withNumericRange) { - if (colourEditor != null) + List validAtts = new ArrayList<>(); + List tooltips = new ArrayList<>(); + + FeatureAttributes fa = FeatureAttributes.getInstance(); + for (String[] attName : attNames) { - System.err - .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser"); + if (withNumericRange) + { + float[] minMax = fa.getMinMax(featureType, attName); + if (minMax == null) + { + continue; + } + } + validAtts.add(String.join(COLON, attName)); + String desc = fa.getDescription(featureType, attName); + if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH) + { + desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "..."; + } + tooltips.add(desc == null ? "" : desc); } - colourEditor = graduatedColorEditor; + + JComboBox attCombo = JvSwingUtils.buildComboWithTooltips( + validAtts, tooltips); + + attCombo.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent e) + { + changeMinMaxAction.actionPerformed(null); + } + }); + + if (validAtts.isEmpty()) + { + attCombo.setToolTipText(MessageManager + .getString(withNumericRange ? "label.no_numeric_attributes" + : "label.no_attributes")); + } + + return attCombo; } }