X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureColourChooser.java;h=da3819c81298e6ae4c20d1a9c01f21acbd91d5d7;hb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;hp=89b64a7e9db55b93d5428df56c2c472562a0b365;hpb=baa077bd19420018433d78927aad3ad139e47351;p=jalview.git diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java index 89b64a7..da3819c 100644 --- a/src/jalview/gui/FeatureColourChooser.java +++ b/src/jalview/gui/FeatureColourChooser.java @@ -22,27 +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.GridLayout; 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; @@ -51,7 +57,16 @@ import javax.swing.event.ChangeListener; public class FeatureColourChooser extends JalviewDialog { - // FeatureSettings fs; + 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; @@ -62,11 +77,11 @@ public class FeatureColourChooser extends JalviewDialog private boolean adjusting = false; - final private float min; + private float min; - final private float max; + private float max; - final private float scaleFactor; + private float scaleFactor; private String type = null; @@ -74,27 +89,57 @@ public class FeatureColourChooser extends JalviewDialog private JPanel maxColour = new JPanel(); + private Color noColour; + private JComboBox threshold = new JComboBox<>(); private JSlider slider = new JSlider(); private JTextField thresholdValue = new JTextField(20); - // 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 Color oldNoColour; + private ActionListener colourEditor = null; + /* + * radio buttons to select what to colour by + * label, attribute text, score, attribute value + */ + private JRadioButton byDescription = new JRadioButton(); + + private JRadioButton byAttributeText = new JRadioButton(); + + private JRadioButton byScore = new JRadioButton(); + + private JRadioButton byAttributeValue = new JRadioButton(); + + private ActionListener changeColourAction; + + private ActionListener changeMinMaxAction; + + /* + * choice of option for 'colour for no value' + */ + private JComboBox noValueCombo; + + /* + * choice of attribute (if any) for 'colour by text' + */ + private JComboBox textAttributeCombo; + + /* + * choice of attribute (if any) for 'colour by value' + */ + private JComboBox valueAttributeCombo; + /** * Constructor * @@ -120,10 +165,9 @@ public class FeatureColourChooser extends JalviewDialog this.fr = frender; this.type = theType; ap = fr.ap; - String title = MessageManager - .formatMessage("label.graduated_color_for_params", new String[] - { theType }); - initDialogFrame(this, true, blocking, title, 480, 185); + String title = MessageManager.formatMessage("label.variable_color_for", + new String[] { theType }); + initDialogFrame(this, true, blocking, title, 470, 300); slider.addChangeListener(new ChangeListener() { @@ -153,6 +197,7 @@ public class FeatureColourChooser extends JalviewDialog } }); + // todo move all threshold setup inside a method float mm[] = fr.getMinMax().get(theType)[0]; min = mm[0]; max = mm[1]; @@ -179,7 +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) { @@ -187,10 +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 @@ -198,10 +248,63 @@ public class FeatureColourChooser extends JalviewDialog jbInit(); } catch (Exception ex) { + ex.printStackTrace(); + return; } - // update the gui from threshold state - thresholdIsMin.setSelected(!cs.isAutoScaled()); - colourByLabel.setSelected(cs.isColourByLabel()); + + /* + * 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); + } + 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 @@ -209,9 +312,6 @@ public class FeatureColourChooser extends JalviewDialog slider.setEnabled(true); slider.setValue((int) (cs.getThreshold() * scaleFactor)); thresholdValue.setEnabled(true); - threshline = new GraphLine((max - min) / 2f, "Threshold", - Color.black); - threshline.value = cs.getThreshold(); } adjusting = false; @@ -220,39 +320,208 @@ public class FeatureColourChooser extends JalviewDialog waitForInput(); } - private void jbInit() throws Exception + /** + * Configures the initial layout + */ + private void jbInit() { - this.setLayout(new GridLayout(4, 1)); + this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS)); + this.setBackground(Color.white); + + changeColourAction = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + changeColour(true); + } + }; - JPanel colourByPanel = initColoursPanel(); + changeMinMaxAction = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + updateMinMax(); + changeColour(true); + } + }; - JPanel thresholdPanel = initThresholdPanel(); + /* + * this panel + * detailsPanel + * colourByTextPanel + * colourByScorePanel + * okCancelPanel + */ + JPanel detailsPanel = new JPanel(); + detailsPanel.setLayout(new BoxLayout(detailsPanel, BoxLayout.Y_AXIS)); - JPanel okCancelPanel = initOkCancelPanel(); + JPanel colourByTextPanel = initColourByTextPanel(); + detailsPanel.add(colourByTextPanel); - this.add(colourByPanel); - this.add(thresholdPanel); + 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); } /** - * Lay out fields for threshold options + * 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 initThresholdPanel() + protected JPanel initColourByValuePanel() { - JPanel thresholdPanel = new JPanel(); - thresholdPanel.setLayout(new FlowLayout()); - threshold.addActionListener(new ActionListener() + 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)); + minColour.setPreferredSize(new Dimension(40, 20)); + minColour.setToolTipText(MessageManager.getString("label.min_colour")); + minColour.addMouseListener(new MouseAdapter() { @Override - public void actionPerformed(ActionEvent e) + public void mousePressed(MouseEvent e) { - changeColour(true); + if (minColour.isEnabled()) + { + minColour_actionPerformed(); + } } }); + + maxColour.setFont(JvSwingUtils.getLabelFont()); + maxColour.setBorder(BorderFactory.createLineBorder(Color.black)); + maxColour.setPreferredSize(new Dimension(40, 20)); + maxColour.setToolTipText(MessageManager.getString("label.max_colour")); + maxColour.addMouseListener(new MouseAdapter() + { + @Override + public void mousePressed(MouseEvent e) + { + if (maxColour.isEnabled()) + { + maxColour_actionPerformed(); + } + } + }); + maxColour.setBorder(new LineBorder(Color.black)); + + 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 itemStateChanged(ItemEvent 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 @@ -284,29 +553,52 @@ public class FeatureColourChooser extends JalviewDialog slider.setEnabled(false); slider.setOpaque(false); slider.setPreferredSize(new Dimension(100, 32)); - slider.setToolTipText( - MessageManager.getString("label.adjust_threshold")); + slider.setToolTipText(MessageManager + .getString("label.adjust_threshold")); thresholdValue.setEnabled(false); thresholdValue.setColumns(7); - thresholdPanel.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.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) - { - changeColour(true); - } - }); - thresholdPanel.add(threshold); - thresholdPanel.add(slider); - thresholdPanel.add(thresholdValue); - thresholdPanel.add(thresholdIsMin); - return thresholdPanel; + noColour = null; + } + else if (i == MIN_COLOUR_OPTION) + { + noColour = minColour.getBackground(); + } + else if (i == MAX_COLOUR_OPTION) + { + noColour = maxColour.getBackground(); + } + changeColour(true); } /** @@ -324,76 +616,41 @@ public class FeatureColourChooser extends JalviewDialog } /** - * Lay out Colour by Label and min/max colour widgets + * Lay out Colour by Label and attribute choice elements * * @return */ - protected JPanel initColoursPanel() + protected JPanel initColourByTextPanel() { - JPanel colourByPanel = new JPanel(); - colourByPanel.setLayout(new FlowLayout()); - colourByPanel.setBackground(Color.white); - minColour.setFont(JvSwingUtils.getLabelFont()); - minColour.setBorder(BorderFactory.createLineBorder(Color.black)); - minColour.setPreferredSize(new Dimension(40, 20)); - minColour.setToolTipText(MessageManager.getString("label.min_colour")); - minColour.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent e) - { - if (minColour.isEnabled()) - { - minColour_actionPerformed(); - } - } - }); - maxColour.setFont(JvSwingUtils.getLabelFont()); - maxColour.setBorder(BorderFactory.createLineBorder(Color.black)); - maxColour.setPreferredSize(new Dimension(40, 20)); - maxColour.setToolTipText(MessageManager.getString("label.max_colour")); - maxColour.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent e) - { - if (maxColour.isEnabled()) - { - maxColour_actionPerformed(); - } - } - }); - maxColour.setBorder(new LineBorder(Color.black)); - JLabel minText = new JLabel(MessageManager.getString("label.min")); - minText.setFont(JvSwingUtils.getLabelFont()); - JLabel maxText = new JLabel(MessageManager.getString("label.max")); - maxText.setFont(JvSwingUtils.getLabelFont()); + 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); - JPanel colourPanel = new JPanel(); - colourPanel.setBackground(Color.white); - colourPanel.add(minText); - colourPanel.add(minColour); - colourPanel.add(maxText); - colourPanel.add(maxColour); - colourByPanel.add(colourByLabel, BorderLayout.WEST); - colourByPanel.add(colourPanel, BorderLayout.EAST); - - 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() + /* + * disable colour by attribute if no attributes + */ + if (attNames.isEmpty()) { - @Override - public void actionPerformed(ActionEvent actionEvent) - { - changeColour(true); - } - }); + byAttributeText.setEnabled(false); + } - return colourByPanel; + return byTextPanel; } /** @@ -462,6 +719,9 @@ public class FeatureColourChooser extends JalviewDialog slider.setEnabled(true); thresholdValue.setEnabled(true); + /* + * make the feature colour + */ FeatureColourI acg; if (cs.isColourByLabel()) { @@ -470,7 +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) @@ -504,7 +784,7 @@ public class FeatureColourChooser extends JalviewDialog slider.setMajorTickSpacing((int) (range / 10f)); slider.setEnabled(true); thresholdValue.setEnabled(true); - thresholdIsMin.setEnabled(!colourByLabel.isSelected()); + thresholdIsMin.setEnabled(!byDescription.isSelected()); adjusting = false; } @@ -526,27 +806,34 @@ 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(updateStructsAndOverview, updateStructsAndOverview); @@ -653,4 +940,67 @@ public class FeatureColourChooser extends JalviewDialog return cs; } + /** + * 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) + { + List validAtts = new ArrayList<>(); + List tooltips = new ArrayList<>(); + + FeatureAttributes fa = FeatureAttributes.getInstance(); + for (String[] attName : attNames) + { + 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); + } + + 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; + } + }