label.about = About...
label.show_sequence_limits = Show Sequence Limits
action.feature_settings = Feature Settings...
-label.feature_settings = Feature Settings
label.all_columns = All Columns
label.all_sequences = All Sequences
label.selected_columns = Selected Columns
label.group_colour = Group Colour
label.sequence = Sequence
label.view_pdb_structure = View PDB Structure
-label.min_value = Min value:
-label.max_value = Max value:
-label.no_value = No value:
+label.min_value = Min value
+label.max_value = Max value
+label.no_value = No value
label.new_feature = New Feature
label.match_case = Match Case
label.view_alignment_editor = View in alignment editor
label.threshold_feature_below_threshold = Below Threshold
label.adjust_threshold = Adjust threshold
label.toggle_absolute_relative_display_threshold = Toggle between absolute and relative display threshold.
-label.colour_by_label_tip = Display features of the same type with a different label using a different colour. (e.g. domain features)
label.select_colour_minimum_value = Select Colour for Minimum Value
label.select_colour_maximum_value = Select Colour for Maximum Value
label.open_url_param = Open URL {0}
label.service_called_is_not_seq_search_service = The Service called \n{0}\nis not a \nSequence Search Service\!
label.seq_search_service_is_unknown = The Sequence Search Service named {0} is unknown
label.feature_type = Feature Type
-label.display = Display
+label.show = Show
label.service_url = Service URL
label.copied_sequences = Copied sequences
label.cut_sequences = Cut Sequences
label.matchCondition_gt = >
label.matchCondition_ge = >=
label.numeric_required = The value should be numeric
-label.no_attributes = No attributes known
-label.no_numeric_attributes = No numeric attributes known
+label.filter = Filter
label.filters = Filters
-label.match_condition = Match condition
label.join_conditions = Join conditions with
-label.feature_to_filter = Feature to filter
-label.colour_by_value = Colour by value
-label.colour_by_text = Colour by text
label.score = Score
-label.attribute = Attribute
label.colour_by_label = Colour by label
label.variable_colour = Variable colour
-label.select_new_colour = Select new colour
-label.no_feature_attributes = No feature attributes found
+label.select_colour = Select colour
option.enable_disable_autosearch = When ticked, search is performed automatically.
option.autosearch = Autosearch
label.retrieve_ids = Retrieve IDs
+label.display_settings_for = Display settings for {0} features
+label.simple = Simple
+label.simple_colour = Simple Colour
+label.colour_by_text = Colour by text
+label.graduated_colour = Graduated Colour
+label.by_text_of = By text of
+label.by_range_of = By range of
+label.filters_tooltip = Click to set or amend filters
+label.or = Or
+label.and = And
\ No newline at end of file
label.documentation = Documentación
label.about = Acerca de...
label.show_sequence_limits = Mostrar los límites de la secuencia
-label.feature_settings = Ajustar funciones...
label.all_columns = Todas las columnas
label.all_sequences = Todas las secuencias
label.selected_columns = Columnas seleccionadas
label.autocalculated_annotation = Anotación autocalculada
label.min_colour = Color mínimo
label.max_colour = Color máximo
+label.no_colour = Sin color
label.use_original_colours = Usar colores originales
label.threshold_minmax = El umbral es mín/máx
label.represent_group_with = Representar al grupo con
label.group_colour = Color del grupo
label.sequence = Secuencia
label.view_pdb_structure = Ver estructura PDB
-label.min = Mín:
-label.max = Máx:
+label.max_value = Valor máximo
+label.min_value = Valor mínimo
+label.no_value = Sin valor
label.colour_by_label = Color por etiquetas
label.new_feature = Nueva función
label.match_case = Hacer corresponder mayúsculas y minúsculas
label.view_full_application = Ver en la aplicación completa
label.load_associated_tree = Cargar árbol asociado ...
label.load_features_annotations = Cargar características/anotaciones ...
+label.load_vcf = Cargar variantes SNP desde fichero VCF texto o tab-indexado
+label.load_vcf_file = Cargar fichero VCF
+label.searching_vcf = Cargando variantes VCF...
+label.added_vcf= {0} variantes VCF añadidas a {1} secuencia(s)
label.export_features = Exportar características...
label.export_annotations = Exportar anotaciones ...
label.to_upper_case = Pasar a mayúsculas
label.threshold_feature_below_threshold = Por debajo del umbral
label.adjust_threshold = Ajustar umbral
label.toggle_absolute_relative_display_threshold = Cambiar entre mostrar el umbral absoluto y el relativo.
-label.display_features_same_type_different_label_using_different_colour = Mostrar las características del mismo tipo con una etiqueta diferente y empleando un color distinto (p.e. características del dominio)
label.select_colour_minimum_value = Seleccionar el color para el valor mínimo
label.select_colour_maximum_value = Seleccionar el color para el valor máximo
label.open_url_param = Abrir URL {0}
label.service_called_is_not_seq_search_service = El Servicio llamando \n{0}\nno es un \nServicio de B\u00FAsqueda de Secuencias\!
label.seq_search_service_is_unknown = El Servicio de Búsqueda de Sencuencias llamado {0} es desconocido
label.feature_type = Tipo de característisca
-label.display = Representación
+label.show = Mostrar
label.service_url = URL del servicio
label.copied_sequences = Secuencias copiadas
label.cut_sequences = Cortar secuencias
label.overview = Resumen
label.reset_to_defaults = Restablecen a los predeterminados
label.oview_calc = Recalculando resumen
+label.feature_details = Detalles de característica
+label.matchCondition_contains = Contiene
+label.matchCondition_notcontains = No contiene
+label.matchCondition_matches = Es igual a
+label.matchCondition_notmatches = No es igual a
+label.matchCondition_eq = =
+label.matchCondition_ne = not =
+label.matchCondition_lt = <
+label.matchCondition_le = <=
+label.matchCondition_gt = >
+label.matchCondition_ge = >=
+label.numeric_required = Valor numérico requerido
+label.filter = Filtro
+label.filters = Filtros
+label.join_conditions = Combinar condiciones con
+label.score = Puntuación
+label.colour_by_label = Colorear por texto
+label.variable_colour = Color variable
+label.select_colour = Seleccionar color
+option.enable_disable_autosearch = Marque para buscar automáticamente
+option.autosearch = Búsqueda automática
+label.retrieve_ids = Recuperar IDs
+label.display_settings_for = Visualización de características {0}
+label.simple = Simple
+label.simple_colour = Color simple
+label.colour_by_text = Colorear por texto
+label.graduated_colour = Color graduado
+label.by_text_of = Por texto de
+label.by_range_of = Por rango de
+label.filters_tooltip = Haga clic para configurar o modificar los filtros
+label.or = O
+label.and = Y
\ No newline at end of file
*/
private static final int SCALE_FACTOR_1K = 1000;
+ private static final String COLON = ":";
+
private JVDialog frame;
private Frame owner;
private void jbInit() throws Exception
{
- Label minLabel = new Label(MessageManager.getString("label.min_value"));
- Label maxLabel = new Label(MessageManager.getString("label.max_value"));
+ Label minLabel = new Label(
+ MessageManager.getString("label.min_value") + COLON);
+ Label maxLabel = new Label(
+ MessageManager.getString("label.max_value") + COLON);
minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
// minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
*/
package jalview.appletgui;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.TYPE_COLUMN;
+
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.datamodel.AlignmentI;
Component[] comps = featurePanel.getComponents();
int cSize = comps.length;
- Object[][] tmp = new Object[cSize][3];
+ /*
+ * temporary! leave column[2] empty - used for Filter in
+ * gui.FeatureSettings
+ */
+ int columnCount = 4;
+ Object[][] tmp = new Object[cSize][columnCount];
int tmpSize = 0;
for (int i = 0; i < cSize; i++)
{
MyCheckbox check = (MyCheckbox) comps[i];
- tmp[tmpSize][0] = check.type;
- tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
- tmp[tmpSize][2] = new Boolean(check.getState());
+ tmp[tmpSize][TYPE_COLUMN /* 0 */] = check.type;
+ tmp[tmpSize][COLOUR_COLUMN /* 1 */] = fr.getFeatureStyle(check.type);
+ tmp[tmpSize][SHOW_COLUMN /* 3 */] = new Boolean(check.getState());
tmpSize++;
}
- Object[][] data = new Object[tmpSize][3];
+ Object[][] data = new Object[tmpSize][columnCount];
System.arraycopy(tmp, 0, data, 0, tmpSize);
fr.setFeaturePriority(data);
+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-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.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;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-
-public class FeatureColourChooser extends JalviewDialog
-{
- 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;
-
- 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<String> 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
- */
- 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<String> noValueCombo;
-
- /*
- * choice of attribute (if any) for 'colour by text'
- */
- private JComboBox<String> textAttributeCombo;
-
- /*
- * choice of attribute (if any) for 'colour by value'
- */
- private JComboBox<String> valueAttributeCombo;
-
- /**
- * Constructor
- *
- * @param frender
- * @param theType
- */
- public FeatureColourChooser(FeatureRenderer frender, String theType)
- {
- this(frender, false, theType);
- }
-
- /**
- * 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 = theType;
- ap = fr.ap;
- String title = MessageManager.formatMessage("label.variable_color_for",
- new String[] { theType });
- initDialogFrame(this, true, blocking, title, 470, 300);
-
- slider.addChangeListener(new ChangeListener()
- {
- @Override
- public void stateChanged(ChangeEvent evt)
- {
- if (!adjusting)
- {
- 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, true);
- }
- }
- });
-
- // todo move all threshold setup inside a method
- float mm[] = fr.getMinMax().get(theType)[0];
- min = mm[0];
- max = mm[1];
-
- /*
- * 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 (oldcs.isAutoScaled())
- {
- // update the scale
- cs = new FeatureColour((FeatureColour) oldcs, min, max);
- }
- else
- {
- cs = new FeatureColour((FeatureColour) oldcs);
- }
- }
- else
- {
- /*
- * 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)
- {
- bl = Color.BLACK;
- }
- // original colour becomes the maximum colour
- cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
- cs.setColourByLabel(mm[0] == mm[1]);
- }
- minColour.setBackground(oldminColour = cs.getMinColour());
- maxColour.setBackground(oldmaxColour = cs.getMaxColour());
- noColour = cs.getNoColour();
-
- adjusting = true;
-
- try
- {
- 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(toAttributeDisplayName(attributeName));
- }
- else
- {
- byDescription.setSelected(true);
- textAttributeCombo.setEnabled(false);
- }
- }
- else
- {
- if (cs.isColourByAttribute())
- {
- byAttributeValue.setSelected(true);
- String[] attributeName = cs.getAttributeName();
- valueAttributeCombo
- .setSelectedItem(toAttributeDisplayName(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
- threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2);
- slider.setEnabled(true);
- slider.setValue((int) (cs.getThreshold() * scaleFactor));
- thresholdValue.setEnabled(true);
- }
-
- adjusting = false;
-
- changeColour(false);
- waitForInput();
- }
-
- /**
- * 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 = fromAttributeDisplayName(attName);
- 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<String[]> 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 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));
-
- 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
- .getString("label.threshold_feature_no_threshold")); // index 0
- threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_threshold")); // index 1
- threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_threshold")); // index 2
-
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- thresholdValue_actionPerformed();
- }
- });
- thresholdValue.addFocusListener(new FocusAdapter()
- {
- @Override
- public void focusLost(FocusEvent e)
- {
- thresholdValue_actionPerformed();
- }
- });
- slider.setPaintLabels(false);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setEnabled(false);
- slider.setOpaque(false);
- slider.setPreferredSize(new Dimension(100, 32));
- slider.setToolTipText(MessageManager
- .getString("label.adjust_threshold"));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
-
- 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(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)
- {
- noColour = null;
- }
- else if (i == MIN_COLOUR_OPTION)
- {
- noColour = minColour.getBackground();
- }
- else if (i == MAX_COLOUR_OPTION)
- {
- noColour = maxColour.getBackground();
- }
- changeColour(true);
- }
-
- /**
- * 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;
- }
-
- /**
- * 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<String[]> attNames = FeatureAttributes.getInstance()
- .getAttributes(type);
- textAttributeCombo = populateAttributesDropdown(type, attNames, false);
- byTextPanel.add(textAttributeCombo);
-
- /*
- * disable colour by attribute if no attributes
- */
- if (attNames.isEmpty())
- {
- byAttributeText.setEnabled(false);
- }
-
- return byTextPanel;
- }
-
- /**
- * 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.getBackground());
- if (col != null)
- {
- minColour.setBackground(col);
- minColour.setForeground(col);
- }
- minColour.repaint();
- changeColour(true);
- }
-
- /**
- * 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.getBackground());
- if (col != null)
- {
- maxColour.setBackground(col);
- maxColour.setForeground(col);
- }
- maxColour.repaint();
- changeColour(true);
- }
-
- /**
- * 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)
- {
- return;
- }
-
- boolean aboveThreshold = false;
- boolean belowThreshold = false;
- if (threshold.getSelectedIndex() == 1)
- {
- aboveThreshold = true;
- }
- else if (threshold.getSelectedIndex() == 2)
- {
- belowThreshold = true;
- }
- boolean hasThreshold = aboveThreshold || belowThreshold;
-
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
-
- /*
- * make the feature colour
- */
- FeatureColourI acg;
- if (cs.isColourByLabel())
- {
- acg = new FeatureColour(oldminColour, oldmaxColour, min, max);
- }
- else
- {
- acg = new FeatureColour(oldminColour = minColour.getBackground(),
- 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(fromAttributeDisplayName(attribute));
- }
- else if (byAttributeValue.isSelected())
- {
- attribute = (String) valueAttributeCombo.getSelectedItem();
- valueAttributeCombo.setEnabled(true);
- acg.setAttributeName(fromAttributeDisplayName(attribute));
- }
- else
- {
- acg.setAttributeName((String[]) null);
- }
-
- if (!hasThreshold)
- {
- slider.setEnabled(false);
- thresholdValue.setEnabled(false);
- thresholdValue.setText("");
- thresholdIsMin.setEnabled(false);
- }
- else if (threshline == null)
- {
- /*
- * todo not yet implemented: visual indication of feature threshold
- */
- threshline = new GraphLine((max - min) / 2f, "Threshold",
- Color.black);
- }
-
- if (hasThreshold)
- {
- adjusting = true;
- acg.setThreshold(threshline.value);
-
- float range = (max - min) * scaleFactor;
-
- 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);
- thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(!byDescription.isSelected());
- adjusting = false;
- }
-
- acg.setAboveThreshold(aboveThreshold);
- acg.setBelowThreshold(belowThreshold);
- if (thresholdIsMin.isSelected() && hasThreshold)
- {
- acg.setAutoScaled(false);
- if (aboveThreshold)
- {
- acg = new FeatureColour((FeatureColour) acg, threshline.value, max);
- }
- else
- {
- acg = new FeatureColour((FeatureColour) acg, min, threshline.value);
- }
- }
- else
- {
- acg.setAutoScaled(true);
- }
- 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);
- 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);
- }
-
- private String[] fromAttributeDisplayName(String attribute)
- {
- return attribute == null ? null : attribute.split(COLON);
- }
-
- @Override
- protected void raiseClosed()
- {
- if (this.colourEditor != null)
- {
- colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
- }
- }
-
- @Override
- public void okPressed()
- {
- 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(true, true);
- cs = null;
- }
-
- /**
- * 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)
- {
- }
- }
-
- /**
- * 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()
- {
- /*
- * 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);
- }
-
- void addActionListener(ActionListener graduatedColorEditor)
- {
- if (colourEditor != null)
- {
- System.err.println(
- "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
- }
- 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;
- }
-
- /**
- * 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).
- * <p>
- * 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<String> populateAttributesDropdown(
- String featureType, List<String[]> attNames,
- boolean withNumericRange)
- {
- List<String> validAtts = new ArrayList<>();
- List<String> 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(toAttributeDisplayName(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<String> 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;
- }
-
- private String toAttributeDisplayName(String[] attName)
- {
- return attName == null ? "" : String.join(COLON, attName);
- }
-
-}
final JSpinner end = new JSpinner();
start.setPreferredSize(new Dimension(80, 20));
end.setPreferredSize(new Dimension(80, 20));
- final FeatureRenderer me = this;
final JLabel colour = new JLabel();
colour.setOpaque(true);
// colour.setBorder(BorderFactory.createEtchedBorder());
colour.setMaximumSize(new Dimension(30, 16));
colour.addMouseListener(new MouseAdapter()
{
- FeatureColourChooser fcc = null;
-
+ /*
+ * open colour chooser on click in colour panel
+ */
@Override
public void mousePressed(MouseEvent evt)
{
}
else
{
- if (fcc == null)
+ /*
+ * variable colour dialog - on OK, refetch the updated
+ * feature colour and update this display
+ */
+ final String ft = features.get(featureIndex).getType();
+ final String type = ft == null ? lastFeatureAdded : ft;
+ FeatureTypeSettings fcc = new FeatureTypeSettings(
+ FeatureRenderer.this, type);
+ fcc.setRequestFocusEnabled(true);
+ fcc.requestFocus();
+ fcc.addActionListener(new ActionListener()
{
- final String ft = features.get(featureIndex).getType();
- final String type = ft == null ? lastFeatureAdded : ft;
- fcc = new FeatureColourChooser(me, type);
- fcc.setRequestFocusEnabled(true);
- fcc.requestFocus();
-
- fcc.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent e)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- fcol = fcc.getLastColour();
- fcc = null;
- setColour(type, fcol);
- updateColourButton(mainPanel, colour, fcol);
- }
- });
-
- }
+ fcol = FeatureRenderer.this.getFeatureStyle(ft);
+ setColour(type, fcol);
+ updateColourButton(mainPanel, colour, fcol);
+ }
+ });
}
}
});
*/
package jalview.gui;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.FILTER_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.TYPE_COLUMN;
+
import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsControllerI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureAttributes;
import jalview.gui.Help.HelpId;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.QuickSort;
-import jalview.util.ReverseListIterator;
-import jalview.util.matcher.Condition;
-import jalview.util.matcher.KeyedMatcher;
-import jalview.util.matcher.KeyedMatcherI;
import jalview.util.matcher.KeyedMatcherSet;
import jalview.util.matcher.KeyedMatcherSetI;
import jalview.viewmodel.AlignmentViewport;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
-import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.GridLayout;
-import java.awt.LayoutManager;
+import java.awt.Point;
import java.awt.Rectangle;
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.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Hashtable;
import javax.help.HelpSetException;
import javax.swing.AbstractCellEditor;
import javax.swing.BorderFactory;
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JColorChooser;
-import javax.swing.JComboBox;
import javax.swing.JDialog;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
-import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
-import javax.swing.JTabbedPane;
import javax.swing.JTable;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
import javax.swing.SwingConstants;
import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
-import javax.swing.plaf.basic.BasicArrowButton;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
public class FeatureSettings extends JPanel
implements FeatureSettingsControllerI
{
+ private static final int COLUMN_COUNT = 4;
+
private static final String COLON = ":";
private static final int MIN_WIDTH = 400;
JPanel groupPanel;
JSlider transparency = new JSlider();
-
+
/*
* when true, constructor is still executing - so ignore UI events
*/
*/
Map<String, float[]> typeWidth = null;
- /*
- * fields of the feature filters tab
- */
- private JPanel filtersPane;
-
- private JPanel chooseFiltersPanel;
-
- private JComboBox<String> filteredFeatureChoice;
-
- private JRadioButton andFilters;
-
- private JRadioButton orFilters;
-
- /*
- * filters for the currently selected feature type
- */
- private List<KeyedMatcherI> filters;
-
- private JTextArea filtersAsText;
-
- // set white normally, black to debug layout
- private Color debugBorderColour = Color.white;
-
/**
* Constructor
*
@Override
public String getToolTipText(MouseEvent e)
{
- if (table.columnAtPoint(e.getPoint()) == 0)
+ String tip = null;
+ int column = table.columnAtPoint(e.getPoint());
+ switch (column)
{
- /*
- * Tooltip for feature name only
- */
- return JvSwingUtils.wrapTooltip(true, MessageManager
+ case TYPE_COLUMN:
+ tip = JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.feature_settings_click_drag"));
+ break;
+ case FILTER_COLUMN:
+ int row = table.rowAtPoint(e.getPoint());
+ KeyedMatcherSet o = (KeyedMatcherSet) table.getValueAt(row,
+ column);
+ tip = o.isEmpty()
+ ? MessageManager.getString("label.filters_tooltip")
+ : o.toString();
+ break;
+ default:
+ break;
}
- return null;
+ return tip;
}
};
table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
table.setFont(new Font("Verdana", Font.PLAIN, 12));
- table.setDefaultRenderer(Color.class, new ColorRenderer());
-
- table.setDefaultEditor(Color.class, new ColorEditor(this));
+ // table.setDefaultRenderer(Color.class, new ColorRenderer());
+ // table.setDefaultEditor(Color.class, new ColorEditor(this));
+ //
table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
+
+ table.setDefaultEditor(KeyedMatcherSet.class, new FilterEditor(this));
+ table.setDefaultRenderer(KeyedMatcherSet.class, new FilterRenderer());
+
+ TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
+ new ColorRenderer(), new ColorEditor(this));
+ table.addColumn(colourColumn);
+
+ TableColumn filterColumn = new TableColumn(FILTER_COLUMN, 75,
+ new FilterRenderer(), new FilterEditor(this));
+ table.addColumn(filterColumn);
+
table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
table.addMouseListener(new MouseAdapter()
public void mousePressed(MouseEvent evt)
{
selectedRow = table.rowAtPoint(evt.getPoint());
+ String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
if (evt.isPopupTrigger())
{
- popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.getMinMax(),
- evt.getX(), evt.getY());
+ Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
+ popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
+ evt.getY());
}
else if (evt.getClickCount() == 2)
{
boolean toggleSelection = Platform.isControlDown(evt);
boolean extendSelection = evt.isShiftDown();
fr.ap.alignFrame.avc.markColumnsContainingFeatures(
- invertSelection, extendSelection, toggleSelection,
- (String) table.getValueAt(selectedRow, 0));
+ invertSelection, extendSelection, toggleSelection, type);
}
}
selectedRow = table.rowAtPoint(evt.getPoint());
if (evt.isPopupTrigger())
{
- popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
- table.getValueAt(selectedRow, 1), fr.getMinMax(),
- evt.getX(), evt.getY());
+ String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
+ Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
+ popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
+ evt.getY());
}
}
});
if (!fs.resettingTable && !fs.handlingUpdate)
{
fs.handlingUpdate = true;
- fs.resetTable(null); // new groups may be added with new seuqence
- // feature types only
+ fs.resetTable(null);
+ // new groups may be added with new sequence feature types only
fs.handlingUpdate = false;
}
}
inConstruction = false;
}
- protected void popupSort(final int selectedRow, final String type,
+ protected void popupSort(final int rowSelected, final String type,
final Object typeCol, final Map<String, float[][]> minmax, int x,
int y)
{
{
if (featureColour.isSimpleColour())
{
- FeatureColourChooser fc = new FeatureColourChooser(me.fr, type);
+ FeatureTypeSettings fc = new FeatureTypeSettings(me.fr, type);
fc.addActionListener(this);
}
else
{
// bring up simple color chooser
colorChooser = new JColorChooser();
+ String title = MessageManager
+ .getString("label.select_colour");
JDialog dialog = JColorChooser.createDialog(me,
- "Select new Colour", true, // modal
+ title, true, // modal
colorChooser, this, // OK button handler
null); // no CANCEL button handler
colorChooser.setColor(featureColour.getMaxColour());
}
else
{
- if (e.getSource() instanceof FeatureColourChooser)
+ if (e.getSource() instanceof FeatureTypeSettings)
{
- FeatureColourChooser fc = (FeatureColourChooser) e.getSource();
- table.setValueAt(fc.getLastColour(), selectedRow, 1);
+ /*
+ * update after OK in feature colour dialog; the updated
+ * colour will have already been set in the FeatureRenderer
+ */
+ FeatureColourI fci = fr.getFeatureColours().get(type);
+ table.setValueAt(fci, rowSelected, 1);
table.validate();
}
else
{
// probably the color chooser!
table.setValueAt(new FeatureColour(colorChooser.getColor()),
- selectedRow, 1);
+ rowSelected, 1);
table.validate();
me.updateFeatureRenderer(
- ((FeatureTableModel) table.getModel()).getData(), false);
+ ((FeatureTableModel) table.getModel()).getData(),
+ false);
}
}
}
}
}
- populateFilterableFeatures();
-
resetTable(null);
validate();
}
}
- Object[][] data = new Object[displayableTypes.size()][3];
+ int columnCount = COLUMN_COUNT;
+ Object[][] data = new Object[displayableTypes.size()][columnCount];
int dataIndex = 0;
if (fr.hasRenderOrder())
continue;
}
- data[dataIndex][0] = type;
- data[dataIndex][1] = fr.getFeatureStyle(type);
- data[dataIndex][2] = new Boolean(
+ data[dataIndex][TYPE_COLUMN] = type;
+ data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
+ KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type);
+ data[dataIndex][FILTER_COLUMN] = featureFilter == null
+ ? new KeyedMatcherSet()
+ : featureFilter;
+ data[dataIndex][SHOW_COLUMN] = new Boolean(
af.getViewport().getFeaturesDisplayed().isVisible(type));
dataIndex++;
displayableTypes.remove(type);
while (!displayableTypes.isEmpty())
{
String type = displayableTypes.iterator().next();
- data[dataIndex][0] = type;
+ data[dataIndex][TYPE_COLUMN] = type;
- data[dataIndex][1] = fr.getFeatureStyle(type);
- if (data[dataIndex][1] == null)
+ data[dataIndex][COLOUR_COLUMN] = fr.getFeatureStyle(type);
+ if (data[dataIndex][COLOUR_COLUMN] == null)
{
// "Colour has been updated in another view!!"
fr.clearRenderOrder();
return;
}
-
- data[dataIndex][2] = new Boolean(true);
+ KeyedMatcherSetI featureFilter = fr.getFeatureFilter(type);
+ data[dataIndex][FILTER_COLUMN] = featureFilter == null
+ ? new KeyedMatcherSet()
+ : featureFilter;
+ data[dataIndex][SHOW_COLUMN] = new Boolean(true);
dataIndex++;
displayableTypes.remove(type);
}
if (originalData == null)
{
- originalData = new Object[data.length][3];
+ int size = data[0].length;
+ originalData = new Object[data.length][size];
for (int i = 0; i < data.length; i++)
{
- System.arraycopy(data[i], 0, originalData[i], 0, 3);
+ System.arraycopy(data[i], 0, originalData[i], 0, size);
}
}
else
}
/**
- * Updates 'originalData' (used for restore on Cancel) if we detect that
- * changes have been made outwith this dialog
+ * Updates 'originalData' (used for restore on Cancel) if we detect that changes
+ * have been made outwith this dialog
* <ul>
* <li>a new feature type added (and made visible)</li>
* <li>a feature colour changed (in the Amend Features dialog)</li>
.getData();
for (Object[] row : foundData)
{
- String type = (String) row[0];
+ String type = (String) row[TYPE_COLUMN];
boolean found = false;
for (Object[] current : currentData)
{
- if (type.equals(current[0]))
+ if (type.equals(current[TYPE_COLUMN]))
{
found = true;
/*
* currently dependent on object equality here;
* really need an equals method on FeatureColour
*/
- if (!row[1].equals(current[1]))
+ if (!row[COLOUR_COLUMN].equals(current[COLOUR_COLUMN]))
{
/*
* feature colour has changed externally - update originalData
*/
for (Object[] original : originalData)
{
- if (type.equals(original[0]))
+ if (type.equals(original[TYPE_COLUMN]))
{
- original[1] = row[1];
+ original[COLOUR_COLUMN] = row[COLOUR_COLUMN];
break;
}
}
/*
* new feature detected - add to original data (on top)
*/
- Object[][] newData = new Object[originalData.length + 1][3];
+ int size = currentData[0].length;
+ Object[][] newData = new Object[originalData.length + 1][size];
for (int i = 0; i < originalData.length; i++)
{
- System.arraycopy(originalData[i], 0, newData[i + 1], 0, 3);
+ System.arraycopy(originalData[i], 0, newData[i + 1], 0, size);
}
newData[0] = row;
originalData = newData;
/**
* Remove from the groups panel any checkboxes for groups that are not in the
- * foundGroups set. This enables removing a group from the display when the
- * last feature in that group is deleted.
+ * foundGroups set. This enables removing a group from the display when the last
+ * feature in that group is deleted.
*
* @param foundGroups
*/
{
for (int i = 0; i < table.getRowCount(); i++)
{
- Boolean value = (Boolean) table.getValueAt(i, 2);
+ Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
- table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
+ table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
}
}
float[] width = new float[data.length];
float[] awidth;
float max = 0;
- int num = 0;
+
for (int i = 0; i < data.length; i++)
{
- awidth = typeWidth.get(data[i][0]);
+ awidth = typeWidth.get(data[i][TYPE_COLUMN]);
if (awidth[0] > 0)
{
width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
// weight - but have to make per
// sequence, too (awidth[2])
// if (width[i]==1) // hack to distinguish single width sequences.
- num++;
}
else
{
// awidth = (float[]) typeWidth.get(data[i][0]);
if (width[i] == 0)
{
- width[i] = fr.getOrder(data[i][0].toString());
+ width[i] = fr.getOrder(data[i][TYPE_COLUMN].toString());
if (width[i] < 0)
{
- width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
+ width[i] = fr.setOrder(data[i][TYPE_COLUMN].toString(),
+ i / data.length);
}
}
else
{
width[i] /= max; // normalize
- fr.setOrder(data[i][0].toString(), width[i]); // store for later
+ fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later
}
if (i > 0)
{
}
/**
- * Update the priority order of features; only repaint if this changed the
- * order of visible features
+ * Update the priority order of features; only repaint if this changed the order
+ * of visible features
*
* @param data
* @param visibleNew
JPanel settingsPane = new JPanel();
settingsPane.setLayout(new BorderLayout());
- filtersPane = new JPanel();
-
dasSettingsPane.setLayout(new BorderLayout());
JPanel bigPanel = new JPanel();
if (!inConstruction)
{
fr.setTransparency((100 - transparency.getValue()) / 100f);
- af.alignPanel.paintAlignment(true,true);
+ af.alignPanel.paintAlignment(true, true);
}
}
});
}
});
- JTabbedPane tabbedPane = new JTabbedPane();
- this.add(tabbedPane, BorderLayout.CENTER);
- tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
- settingsPane);
- tabbedPane.addTab(MessageManager.getString("label.filters"),
- filtersPane);
- // tabbedPane.addTab(MessageManager.getString("label.das_settings"),
- // dasSettingsPane);
-
JPanel transPanel = new JPanel(new GridLayout(1, 2));
bigPanel.add(transPanel, BorderLayout.SOUTH);
dasButtonPanel.add(saveDAS);
settingsPane.add(bigPanel, BorderLayout.CENTER);
settingsPane.add(buttonPanel, BorderLayout.SOUTH);
-
- initFiltersTab();
- }
-
- /**
- * Populates initial layout of the feature attribute filters panel
- */
- protected void initFiltersTab()
- {
- filters = new ArrayList<>();
-
- /*
- * choose feature type
- */
- JPanel chooseTypePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
- chooseTypePanel.setBackground(Color.white);
- JvSwingUtils.createItalicTitledBorder(chooseTypePanel,
- MessageManager.getString("label.feature_type"), true);
- filteredFeatureChoice = new JComboBox<>();
- filteredFeatureChoice.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- refreshFiltersDisplay();
- }
- });
- chooseTypePanel.add(new JLabel(MessageManager
- .getString("label.feature_to_filter")));
- chooseTypePanel.add(filteredFeatureChoice);
- populateFilterableFeatures();
-
- /*
- * the panel with the filters for the selected feature type
- */
- JPanel filtersPanel = new JPanel();
- filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
- filtersPanel.setBackground(Color.white);
- JvSwingUtils.createItalicTitledBorder(filtersPanel,
- MessageManager.getString("label.filters"), true);
-
- /*
- * add AND or OR radio buttons
- */
- JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
- andOrPanel.setBackground(Color.white);
- andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour));
- andFilters = new JRadioButton("And");
- orFilters = new JRadioButton("Or");
- ActionListener actionListener = new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- filtersChanged();
- }
- };
- andFilters.addActionListener(actionListener);
- orFilters.addActionListener(actionListener);
- ButtonGroup andOr = new ButtonGroup();
- andOr.add(andFilters);
- andOr.add(orFilters);
- andFilters.setSelected(true);
- andOrPanel.add(new JLabel(MessageManager
- .getString("label.join_conditions")));
- andOrPanel.add(andFilters);
- andOrPanel.add(orFilters);
- filtersPanel.add(andOrPanel);
-
- /*
- * panel with filters - populated by refreshFiltersDisplay
- */
- chooseFiltersPanel = new JPanel();
- LayoutManager box = new BoxLayout(chooseFiltersPanel,
- BoxLayout.Y_AXIS);
- chooseFiltersPanel.setLayout(box);
- filtersPanel.add(chooseFiltersPanel);
-
- /*
- * a read-only text view of the current filters
- */
- JPanel showFiltersPanel = new JPanel(new BorderLayout(5, 5));
- showFiltersPanel.setBackground(Color.white);
- JvSwingUtils.createItalicTitledBorder(showFiltersPanel,
- MessageManager.getString("label.match_condition"), true);
- filtersAsText = new JTextArea();
- filtersAsText.setLineWrap(true);
- filtersAsText.setWrapStyleWord(true);
- filtersAsText.setEnabled(false); // for display only
- showFiltersPanel.add(filtersAsText);
-
- filtersPane.setLayout(new BorderLayout());
- filtersPane.add(chooseTypePanel, BorderLayout.NORTH);
- filtersPane.add(filtersPanel, BorderLayout.CENTER);
- filtersPane.add(showFiltersPanel, BorderLayout.SOUTH);
-
- /*
- * update display for initial feature type selection
- */
- refreshFiltersDisplay();
- }
-
- /**
- * Adds entries to the 'choose feature to filter' drop-down choice. Only
- * feature types which have known attributes (so can be filtered) are
- * included, so recall this method to update the list (check for newly added
- * attributes).
- */
- protected void populateFilterableFeatures()
- {
- /*
- * suppress action handler while updating the list
- */
- ItemListener listener = filteredFeatureChoice.getItemListeners()[0];
- filteredFeatureChoice.removeItemListener(listener);
-
- filteredFeatureChoice.removeAllItems();
- ReverseListIterator<String> types = new ReverseListIterator<>(
- fr.getRenderOrder());
-
- boolean found = false;
- while (types.hasNext())
- {
- String type = types.next();
- if (FeatureAttributes.getInstance().hasAttributes(type))
- {
- filteredFeatureChoice.addItem(type);
- found = true;
- }
- }
- if (!found)
- {
- filteredFeatureChoice.addItem(MessageManager
- .getString("label.no_feature_attributes"));
- filteredFeatureChoice.setEnabled(false);
- }
-
- filteredFeatureChoice.addItemListener(listener);
- }
-
- /**
- * Refreshes the display to show any filters currently configured for the
- * selected feature type (editable, with 'remove' option), plus one extra row
- * for adding a condition. This should be called on change of selected feature
- * type, or after a filter has been removed, added or amended.
- */
- protected void refreshFiltersDisplay()
- {
- /*
- * clear the panel and list of filter conditions
- */
- chooseFiltersPanel.removeAll();
- filters.clear();
-
- /*
- * look up attributes known for feature type
- */
- String selectedType = (String) filteredFeatureChoice.getSelectedItem();
- List<String[]> attNames = FeatureAttributes.getInstance()
- .getAttributes(selectedType);
-
- /*
- * if this feature type has filters set, load them first
- */
- KeyedMatcherSetI featureFilters = fr.getFeatureFilter(selectedType);
- filtersAsText.setText("");
- if (featureFilters != null)
- {
- filtersAsText.setText(featureFilters.toString());
- if (!featureFilters.isAnded())
- {
- orFilters.setSelected(true);
- }
- featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
- }
-
- /*
- * and an empty filter for the user to populate (add)
- */
- KeyedMatcherI noFilter = new KeyedMatcher(Condition.values()[0], "",
- (String) null);
- filters.add(noFilter);
-
- /*
- * render the conditions in rows, each in its own JPanel
- */
- int filterIndex = 0;
- for (KeyedMatcherI filter : filters)
- {
- String[] attName = filter.getKey();
- Condition condition = filter.getMatcher()
- .getCondition();
- String pattern = filter.getMatcher().getPattern();
- JPanel row = addFilter(attName, attNames, condition, pattern, filterIndex);
- row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
- chooseFiltersPanel.add(row);
- filterIndex++;
- }
- // chooseFiltersPanel.add(Box.createVerticalGlue());
-
- filtersPane.validate();
- filtersPane.repaint();
- }
-
- /**
- * A helper method that constructs a panel with one filter condition:
- * <ul>
- * <li>a drop-down list of attribute names to choose from</li>
- * <li>a drop-down list of conditions to choose from</li>
- * <li>a text field for input of a match pattern</li>
- * <li>optionally, a 'remove' button</li>
- * </ul>
- * If attribute, condition or pattern are not null, they are set as defaults for
- * the input fields. The 'remove' button is added unless the pattern is null or
- * empty (incomplete filter condition).
- *
- * @param attName
- * @param attNames
- * @param cond
- * @param pattern
- * @param filterIndex
- * @return
- */
- protected JPanel addFilter(String[] attName, List<String[]> attNames,
- Condition cond, String pattern, int filterIndex)
- {
- JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
- filterRow.setBackground(Color.white);
-
- /*
- * drop-down choice of attribute, with description as a tooltip
- * if we can obtain it
- */
- String featureType = (String) filteredFeatureChoice.getSelectedItem();
- final JComboBox<String> attCombo = populateAttributesDropdown(
- featureType, attNames);
- JComboBox<Condition> condCombo = new JComboBox<>();
- JTextField patternField = new JTextField(8);
-
- /*
- * action handlers that validate and (if valid) apply changes
- */
- ActionListener actionListener = new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- if (attCombo.getSelectedItem() != null)
- {
- if (validateFilter(patternField, condCombo))
- {
- updateFilter(attCombo, condCombo, patternField, filterIndex);
- filtersChanged();
- }
- }
- }
- };
- ItemListener itemListener = new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- actionListener.actionPerformed(null);
- }
- };
-
- if (attName == null) // the 'add a condition' row
- {
- attCombo.setSelectedItem(null);
- }
- else
- {
- attCombo.setSelectedItem(String.join(COLON, attName));
- }
- attCombo.addItemListener(itemListener);
-
- filterRow.add(attCombo);
-
- /*
- * drop-down choice of test condition
- */
- for (Condition c : Condition.values())
- {
- condCombo.addItem(c);
- }
- if (cond != null)
- {
- condCombo.setSelectedItem(cond);
- }
- condCombo.addItemListener(itemListener);
- filterRow.add(condCombo);
-
- /*
- * pattern to match against
- */
- patternField.setText(pattern);
- patternField.addActionListener(actionListener);
- patternField.addFocusListener(new FocusAdapter()
- {
- @Override
- public void focusLost(FocusEvent e)
- {
- actionListener.actionPerformed(null);
- }
- });
- filterRow.add(patternField);
-
- /*
- * add remove button if filter is populated (non-empty pattern)
- */
- if (pattern != null && pattern.trim().length() > 0)
- {
- // todo: gif for button drawing '-' or 'x'
- JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
- removeCondition.setToolTipText(MessageManager
- .getString("label.delete_row"));
- removeCondition.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- filters.remove(filterIndex);
- filtersChanged();
- }
- });
- filterRow.add(removeCondition);
- }
-
- return filterRow;
- }
-
- /**
- * 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.
- *
- * @param featureType
- * @param attNames
- */
- protected JComboBox<String> populateAttributesDropdown(
- String featureType, List<String[]> attNames)
- {
- List<String> displayNames = new ArrayList<>();
- List<String> tooltips = new ArrayList<>();
- FeatureAttributes fa = FeatureAttributes.getInstance();
- for (String[] attName : attNames)
- {
- String desc = fa.getDescription(featureType, attName);
- if (desc != null && desc.length() > MAX_TOOLTIP_LENGTH)
- {
- desc = desc.substring(0, MAX_TOOLTIP_LENGTH) + "...";
- }
- displayNames.add(String.join(COLON, attName));
- tooltips.add(desc == null ? "" : desc);
- }
-
- JComboBox<String> attCombo = JvSwingUtils.buildComboWithTooltips(
- displayNames, tooltips);
- if (attNames.isEmpty())
- {
- attCombo.setToolTipText(MessageManager
- .getString("label.no_attributes"));
- }
- return attCombo;
- }
-
- /**
- * Action on any change to feature filtering, namely
- * <ul>
- * <li>change of selected attribute</li>
- * <li>change of selected condition</li>
- * <li>change of match pattern</li>
- * <li>removal of a condition</li>
- * </ul>
- * The action should be to
- * <ul>
- * <li>parse and validate the filters</li>
- * <li>if valid, update the filter text box</li>
- * <li>and apply the filters to the viewport</li>
- * </ul>
- */
- protected void filtersChanged()
- {
- /*
- * update the filter conditions for the feature type
- */
- String featureType = (String) filteredFeatureChoice.getSelectedItem();
- boolean anded = andFilters.isSelected();
- KeyedMatcherSetI combined = new KeyedMatcherSet();
-
- for (KeyedMatcherI filter : filters)
- {
- String pattern = filter.getMatcher().getPattern();
- if (pattern.trim().length() > 0)
- {
- if (anded)
- {
- combined.and(filter);
- }
- else
- {
- combined.or(filter);
- }
- }
- }
-
- /*
- * save the filter conditions in the FeatureRenderer
- * (note this might now be an empty filter with no conditions)
- */
- fr.setFeatureFilter(featureType, combined);
-
- filtersAsText.setText(combined.toString());
-
- refreshFiltersDisplay();
-
- af.alignPanel.paintAlignment(true, true);
- }
-
- /**
- * Constructs a filter condition from the given input fields, and replaces the
- * condition at filterIndex with the new one
- *
- * @param attCombo
- * @param condCombo
- * @param valueField
- * @param filterIndex
- */
- protected void updateFilter(JComboBox<String> attCombo,
- JComboBox<Condition> condCombo, JTextField valueField,
- int filterIndex)
- {
- String attName = (String) attCombo.getSelectedItem();
- Condition cond = (Condition) condCombo.getSelectedItem();
- String pattern = valueField.getText();
- KeyedMatcherI km = new KeyedMatcher(cond, pattern,
- attName.split(COLON));
-
- filters.set(filterIndex, km);
+ this.add(settingsPane);
}
public void fetchDAS_actionPerformed(ActionEvent e)
JvOptionPane.DEFAULT_OPTION, JvOptionPane.INFORMATION_MESSAGE);
}
- /**
- * Answers true unless a numeric condition has been selected with a
- * non-numeric value. Sets the value field to RED with a tooltip if in error.
- * <p>
- * If the pattern entered is empty, this method returns false, but does not
- * mark the field as invalid. This supports selecting an attribute for a new
- * condition before a match pattern has been entered.
- *
- * @param value
- * @param condCombo
- */
- protected boolean validateFilter(JTextField value,
- JComboBox<Condition> condCombo)
- {
- if (value == null || condCombo == null)
- {
- return true; // fields not populated
- }
-
- Condition cond = (Condition) condCombo.getSelectedItem();
- value.setBackground(Color.white);
- value.setToolTipText("");
- String v1 = value.getText().trim();
- if (v1.length() == 0)
- {
- return false;
- }
-
- if (cond.isNumeric())
- {
- try
- {
- Float.valueOf(v1);
- } catch (NumberFormatException e)
- {
- value.setBackground(Color.red);
- value.setToolTipText(MessageManager
- .getString("label.numeric_required"));
- return false;
- }
- }
-
- return true;
- }
-
// ///////////////////////////////////////////////////////////////////////
// http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
// ///////////////////////////////////////////////////////////////////////
class FeatureTableModel extends AbstractTableModel
{
- FeatureTableModel(Object[][] data)
- {
- this.data = data;
- }
private String[] columnNames = {
MessageManager.getString("label.feature_type"),
MessageManager.getString("action.colour"),
- MessageManager.getString("label.display") };
+ MessageManager.getString("label.filter"),
+ MessageManager.getString("label.show") };
private Object[][] data;
+ FeatureTableModel(Object[][] data)
+ {
+ this.data = data;
+ }
+
public Object[][] getData()
{
return data;
return data[row][col];
}
+ /**
+ * Answers the class of the object in column c of the first row of the table
+ */
@Override
- public Class getColumnClass(int c)
+ public Class<?> getColumnClass(int c)
{
- return getValueAt(0, c).getClass();
+ Object v = getValueAt(0, c);
+ return v == null ? null : v.getClass();
}
@Override
}
}
+ class FilterRenderer extends JLabel implements TableCellRenderer
+ {
+ javax.swing.border.Border unselectedBorder = null;
+
+ javax.swing.border.Border selectedBorder = null;
+
+ public FilterRenderer()
+ {
+ setOpaque(true); // MUST do this for background to show up.
+ setHorizontalTextPosition(SwingConstants.CENTER);
+ setVerticalTextPosition(SwingConstants.CENTER);
+ }
+
+ @Override
+ public Component getTableCellRendererComponent(JTable tbl,
+ Object filter, boolean isSelected, boolean hasFocus, int row,
+ int column)
+ {
+ KeyedMatcherSetI theFilter = (KeyedMatcherSetI) filter;
+ setOpaque(true);
+ String asText = theFilter.toString();
+ setBackground(tbl.getBackground());
+ this.setText(asText);
+ this.setIcon(null);
+
+ if (isSelected)
+ {
+ if (selectedBorder == null)
+ {
+ selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+ tbl.getSelectionBackground());
+ }
+ setBorder(selectedBorder);
+ }
+ else
+ {
+ if (unselectedBorder == null)
+ {
+ unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
+ tbl.getBackground());
+ }
+ setBorder(unselectedBorder);
+ }
+
+ return this;
+ }
+ }
+
/**
* update comp using rendering settings from gcol
*
}
else
{
- comp.setToolTipText(tt.append(" ").append(comp.getToolTipText())
- .toString());
+ comp.setToolTipText(
+ tt.append(" ").append(comp.getToolTipText()).toString());
}
}
}
+
+ class ColorEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
+ {
+ FeatureSettings me;
+
+ FeatureColourI currentColor;
+
+ FeatureTypeSettings chooser;
+
+ String type;
+
+ JButton button;
+
+ JColorChooser colorChooser;
+
+ JDialog dialog;
+
+ protected static final String EDIT = "edit";
+
+ int rowSelected = 0;
+
+ public ColorEditor(FeatureSettings me)
+ {
+ this.me = me;
+ // Set up the editor (from the table's point of view),
+ // which is a button.
+ // This button brings up the color chooser dialog,
+ // which is the editor from the user's point of view.
+ button = new JButton();
+ button.setActionCommand(EDIT);
+ button.addActionListener(this);
+ button.setBorderPainted(false);
+ // Set up the dialog that the button brings up.
+ colorChooser = new JColorChooser();
+ dialog = JColorChooser.createDialog(button,
+ MessageManager.getString("label.select_colour"), true, // modal
+ colorChooser, this, // OK button handler
+ null); // no CANCEL button handler
+ }
+
+ /**
+ * Handles events from the editor button and from the dialog's OK button.
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ // todo test e.getSource() instead here
+ if (EDIT.equals(e.getActionCommand()))
+ {
+ // The user has clicked the cell, so
+ // bring up the dialog.
+ if (currentColor.isSimpleColour())
+ {
+ // bring up simple color chooser
+ button.setBackground(currentColor.getColour());
+ colorChooser.setColor(currentColor.getColour());
+ dialog.setVisible(true);
+ }
+ else
+ {
+ // bring up graduated chooser.
+ chooser = new FeatureTypeSettings(me.fr, type);
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ chooser.addActionListener(this);
+ chooser.showTab(true);
+ }
+ // Make the renderer reappear.
+ fireEditingStopped();
+
+ }
+ else
+ {
+ if (currentColor.isSimpleColour())
+ {
+ /*
+ * read off colour picked in colour chooser after OK pressed
+ */
+ currentColor = new FeatureColour(colorChooser.getColor());
+ me.table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
+ }
+ else
+ {
+ /*
+ * after OK in variable colour dialog, any changes to colour
+ * (or filters!) are already set in FeatureRenderer, so just
+ * update table data without triggering updateFeatureRenderer
+ */
+ currentColor = fr.getFeatureColours().get(type);
+ KeyedMatcherSetI currentFilter = me.fr.getFeatureFilter(type);
+ if (currentFilter == null)
+ {
+ currentFilter = new KeyedMatcherSet();
+ }
+ Object[] data = ((FeatureTableModel) table.getModel())
+ .getData()[rowSelected];
+ data[COLOUR_COLUMN] = currentColor;
+ data[FILTER_COLUMN] = currentFilter;
+ }
+ fireEditingStopped();
+ me.table.validate();
+ }
+ }
+
+ // Implement the one CellEditor method that AbstractCellEditor doesn't.
+ @Override
+ public Object getCellEditorValue()
+ {
+ return currentColor;
+ }
+
+ // Implement the one method defined by TableCellEditor.
+ @Override
+ public Component getTableCellEditorComponent(JTable theTable, Object value,
+ boolean isSelected, int row, int column)
+ {
+ currentColor = (FeatureColourI) value;
+ this.rowSelected = row;
+ type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ button.setOpaque(true);
+ button.setBackground(me.getBackground());
+ if (!currentColor.isSimpleColour())
+ {
+ JLabel btn = new JLabel();
+ btn.setSize(button.getSize());
+ FeatureSettings.renderGraduatedColor(btn, currentColor);
+ button.setBackground(btn.getBackground());
+ button.setIcon(btn.getIcon());
+ button.setText(btn.getText());
+ }
+ else
+ {
+ button.setText("");
+ button.setIcon(null);
+ button.setBackground(currentColor.getColour());
+ }
+ return button;
+ }
+ }
+
+ /**
+ * The cell editor for the Filter column. It displays the text of any filters
+ * for the feature type in that row (in full as a tooltip, possible abbreviated
+ * as display text). On click in the cell, opens the Feature Display Settings
+ * dialog at the Filters tab.
+ */
+ class FilterEditor extends AbstractCellEditor
+ implements TableCellEditor, ActionListener
+ {
+ FeatureSettings me;
+
+ KeyedMatcherSetI currentFilter;
+
+ Point lastLocation;
+
+ String type;
+
+ JButton button;
+
+ protected static final String EDIT = "edit";
+
+ int rowSelected = 0;
+
+ public FilterEditor(FeatureSettings me)
+ {
+ this.me = me;
+ button = new JButton();
+ button.setActionCommand(EDIT);
+ button.addActionListener(this);
+ button.setBorderPainted(false);
+ }
+
+ /**
+ * Handles events from the editor button
+ */
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (button == e.getSource())
+ {
+ FeatureTypeSettings chooser = new FeatureTypeSettings(me.fr, type);
+ chooser.addActionListener(this);
+ chooser.setRequestFocusEnabled(true);
+ chooser.requestFocus();
+ if (lastLocation != null)
+ {
+ // todo open at its last position on screen
+ chooser.setBounds(lastLocation.x, lastLocation.y,
+ chooser.getWidth(), chooser.getHeight());
+ chooser.validate();
+ }
+ chooser.showTab(false);
+ fireEditingStopped();
+ }
+ else if (e.getSource() instanceof Component)
+ {
+
+ /*
+ * after OK in variable colour dialog, any changes to filter
+ * (or colours!) are already set in FeatureRenderer, so just
+ * update table data without triggering updateFeatureRenderer
+ */
+ FeatureColourI currentColor = fr.getFeatureColours().get(type);
+ currentFilter = me.fr.getFeatureFilter(type);
+ if (currentFilter == null)
+ {
+ currentFilter = new KeyedMatcherSet();
+ }
+ Object[] data = ((FeatureTableModel) table.getModel())
+ .getData()[rowSelected];
+ data[COLOUR_COLUMN] = currentColor;
+ data[FILTER_COLUMN] = currentFilter;
+ fireEditingStopped();
+ me.table.validate();
+ }
+ }
+
+ @Override
+ public Object getCellEditorValue()
+ {
+ return currentFilter;
+ }
+
+ @Override
+ public Component getTableCellEditorComponent(JTable theTable, Object value,
+ boolean isSelected, int row, int column)
+ {
+ currentFilter = (KeyedMatcherSetI) value;
+ this.rowSelected = row;
+ type = me.table.getValueAt(row, TYPE_COLUMN).toString();
+ button.setOpaque(true);
+ button.setBackground(me.getBackground());
+ button.setText(currentFilter.toString());
+ button.setToolTipText(currentFilter.toString());
+ button.setIcon(null);
+ return button;
+ }
+ }
}
class FeatureIcon implements Icon
}
}
}
-
-class ColorEditor extends AbstractCellEditor
- implements TableCellEditor, ActionListener
-{
- FeatureSettings me;
-
- FeatureColourI currentColor;
-
- FeatureColourChooser chooser;
-
- String type;
-
- JButton button;
-
- JColorChooser colorChooser;
-
- JDialog dialog;
-
- protected static final String EDIT = "edit";
-
- int selectedRow = 0;
-
- public ColorEditor(FeatureSettings me)
- {
- this.me = me;
- // Set up the editor (from the table's point of view),
- // which is a button.
- // This button brings up the color chooser dialog,
- // which is the editor from the user's point of view.
- button = new JButton();
- button.setActionCommand(EDIT);
- button.addActionListener(this);
- button.setBorderPainted(false);
- // Set up the dialog that the button brings up.
- colorChooser = new JColorChooser();
- dialog = JColorChooser.createDialog(button,
- MessageManager.getString("label.select_new_colour"), true, // modal
- colorChooser, this, // OK button handler
- null); // no CANCEL button handler
- }
-
- /**
- * Handles events from the editor button and from the dialog's OK button.
- */
- @Override
- public void actionPerformed(ActionEvent e)
- {
-
- if (EDIT.equals(e.getActionCommand()))
- {
- // The user has clicked the cell, so
- // bring up the dialog.
- if (currentColor.isSimpleColour())
- {
- // bring up simple color chooser
- button.setBackground(currentColor.getColour());
- colorChooser.setColor(currentColor.getColour());
- dialog.setVisible(true);
- }
- else
- {
- // bring up graduated chooser.
- chooser = new FeatureColourChooser(me.fr, type);
- chooser.setRequestFocusEnabled(true);
- chooser.requestFocus();
- chooser.addActionListener(this);
- }
- // Make the renderer reappear.
- fireEditingStopped();
-
- }
- else
- { // User pressed dialog's "OK" button.
- if (currentColor.isSimpleColour())
- {
- currentColor = new FeatureColour(colorChooser.getColor());
- }
- else
- {
- currentColor = chooser.getLastColour();
- }
- me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
- fireEditingStopped();
- me.table.validate();
- }
- }
-
- // Implement the one CellEditor method that AbstractCellEditor doesn't.
- @Override
- public Object getCellEditorValue()
- {
- return currentColor;
- }
-
- // Implement the one method defined by TableCellEditor.
- @Override
- public Component getTableCellEditorComponent(JTable table, Object value,
- boolean isSelected, int row, int column)
- {
- currentColor = (FeatureColourI) value;
- this.selectedRow = row;
- type = me.table.getValueAt(row, 0).toString();
- button.setOpaque(true);
- button.setBackground(me.getBackground());
- if (!currentColor.isSimpleColour())
- {
- JLabel btn = new JLabel();
- btn.setSize(button.getSize());
- FeatureSettings.renderGraduatedColor(btn, currentColor);
- button.setBackground(btn.getBackground());
- button.setIcon(btn.getIcon());
- button.setText(btn.getText());
- }
- else
- {
- button.setText("");
- button.setIcon(null);
- button.setBackground(currentColor.getColour());
- }
- return button;
- }
-}
--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.features.FeatureAttributes;
+import jalview.datamodel.features.FeatureAttributes.Datatype;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.util.matcher.Condition;
+import jalview.util.matcher.KeyedMatcher;
+import jalview.util.matcher.KeyedMatcherI;
+import jalview.util.matcher.KeyedMatcherSet;
+import jalview.util.matcher.KeyedMatcherSetI;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.LayoutManager;
+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.JButton;
+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.JTabbedPane;
+import javax.swing.JTextField;
+import javax.swing.SwingConstants;
+import javax.swing.border.LineBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.plaf.basic.BasicArrowButton;
+
+/**
+ * A dialog where the user can configure colour scheme, and any filters, for one
+ * feature type
+ * <p>
+ * (Was FeatureColourChooser prior to Jalview 1.11, renamed with the addition of
+ * filter options)
+ */
+public class FeatureTypeSettings extends JalviewDialog
+{
+ private static final int RADIO_WIDTH = 130;
+
+ private static final String COLON = ":";
+
+ private static final int MAX_TOOLTIP_LENGTH = 50;
+
+ private static final int NO_COLOUR_OPTION = 0;
+
+ private static final int MIN_COLOUR_OPTION = 1;
+
+ private static final int MAX_COLOUR_OPTION = 2;
+
+ private static final int ABOVE_THRESHOLD_OPTION = 1;
+
+ private static final int BELOW_THRESHOLD_OPTION = 2;
+
+ /*
+ * FeatureRenderer holds colour scheme and filters for feature types
+ */
+ private final FeatureRenderer fr; // todo refactor to allow interface type here
+
+ /*
+ * the view panel to update when settings change
+ */
+ private final AlignmentViewPanel ap;
+
+ private final String featureType;
+
+ /*
+ * the colour and filters to reset to on Cancel
+ */
+ private final FeatureColourI originalColour;
+
+ private final KeyedMatcherSetI originalFilter;
+
+ /*
+ * set flag to true when setting values programmatically,
+ * to avoid invocation of action handlers
+ */
+ private boolean adjusting = false;
+
+ private float min;
+
+ private float max;
+
+ private float scaleFactor;
+
+ /*
+ * radio button group, to select what to colour by:
+ * simple colour, by category (text), or graduated
+ */
+ private JRadioButton simpleColour = new JRadioButton();
+
+ private JRadioButton byCategory = new JRadioButton();
+
+ private JRadioButton graduatedColour = new JRadioButton();
+
+ private JPanel singleColour = new JPanel();
+
+ private JPanel minColour = new JPanel();
+
+ private JPanel maxColour = new JPanel();
+
+ private JComboBox<String> threshold = new JComboBox<>();
+
+ private JSlider slider = new JSlider();
+
+ private JTextField thresholdValue = new JTextField(20);
+
+ private JCheckBox thresholdIsMin = new JCheckBox();
+
+ private GraphLine threshline;
+
+ private ActionListener featureSettings = null;
+
+ private ActionListener changeColourAction;
+
+ /*
+ * choice of option for 'colour for no value'
+ */
+ private JComboBox<String> noValueCombo;
+
+ /*
+ * choice of what to colour by text (Label or attribute)
+ */
+ private JComboBox<String> colourByTextCombo;
+
+ /*
+ * choice of what to colour by range (Score or attribute)
+ */
+ private JComboBox<String> colourByRangeCombo;
+
+ private JRadioButton andFilters;
+
+ private JRadioButton orFilters;
+
+ /*
+ * filters for the currently selected feature type
+ */
+ private List<KeyedMatcherI> filters;
+
+ // set white normally, black to debug layout
+ private Color debugBorderColour = Color.white;
+
+ private JPanel chooseFiltersPanel;
+
+ private JTabbedPane tabbedPane;
+
+ /**
+ * Constructor
+ *
+ * @param frender
+ * @param theType
+ */
+ public FeatureTypeSettings(FeatureRenderer frender, String theType)
+ {
+ this(frender, false, theType);
+ }
+
+ /**
+ * 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
+ */
+ FeatureTypeSettings(FeatureRenderer frender, boolean blocking,
+ String theType)
+ {
+ this.fr = frender;
+ this.featureType = theType;
+ ap = fr.ap;
+ originalFilter = fr.getFeatureFilter(theType);
+ originalColour = fr.getFeatureColours().get(theType);
+
+ adjusting = true;
+
+ try
+ {
+ initialise();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return;
+ }
+
+ updateColoursTab();
+
+ updateFiltersTab();
+
+ adjusting = false;
+
+ colourChanged(false);
+
+ String title = MessageManager
+ .formatMessage("label.display_settings_for", new String[]
+ { theType });
+ initDialogFrame(this, true, blocking, title, 600, 360);
+
+ waitForInput();
+ }
+
+ /**
+ * Configures the widgets on the Colours tab according to the current feature
+ * colour scheme
+ */
+ private void updateColoursTab()
+ {
+ FeatureColourI fc = fr.getFeatureColours().get(featureType);
+
+ /*
+ * suppress action handling while updating values programmatically
+ */
+ adjusting = true;
+ try
+ {
+ /*
+ * single colour
+ */
+ if (fc.isSimpleColour())
+ {
+ simpleColour.setSelected(true);
+ singleColour.setBackground(fc.getColour());
+ singleColour.setForeground(fc.getColour());
+ }
+
+ /*
+ * colour by text (Label or attribute text)
+ */
+ if (fc.isColourByLabel())
+ {
+ byCategory.setSelected(true);
+ colourByTextCombo.setEnabled(colourByTextCombo.getItemCount() > 1);
+ if (fc.isColourByAttribute())
+ {
+ String[] attributeName = fc.getAttributeName();
+ colourByTextCombo
+ .setSelectedItem(toAttributeDisplayName(attributeName));
+ }
+ else
+ {
+ colourByTextCombo
+ .setSelectedItem(MessageManager.getString("label.label"));
+ }
+ }
+ else
+ {
+ colourByTextCombo.setEnabled(false);
+ }
+
+ if (!fc.isGraduatedColour())
+ {
+ colourByRangeCombo.setEnabled(false);
+ minColour.setEnabled(false);
+ maxColour.setEnabled(false);
+ noValueCombo.setEnabled(false);
+ threshold.setEnabled(false);
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdIsMin.setEnabled(false);
+ return;
+ }
+
+ /*
+ * Graduated colour, by score or attribute value range
+ */
+ graduatedColour.setSelected(true);
+ colourByRangeCombo.setEnabled(colourByRangeCombo.getItemCount() > 1);
+ minColour.setEnabled(true);
+ maxColour.setEnabled(true);
+ noValueCombo.setEnabled(true);
+ threshold.setEnabled(true);
+ minColour.setBackground(fc.getMinColour());
+ maxColour.setBackground(fc.getMaxColour());
+
+ if (fc.isColourByAttribute())
+ {
+ String[] attributeName = fc.getAttributeName();
+ colourByRangeCombo
+ .setSelectedItem(toAttributeDisplayName(attributeName));
+ }
+ else
+ {
+ colourByRangeCombo
+ .setSelectedItem(MessageManager.getString("label.score"));
+ }
+ Color noColour = fc.getNoColour();
+ if (noColour == null)
+ {
+ noValueCombo.setSelectedIndex(NO_COLOUR_OPTION);
+ }
+ else if (noColour.equals(fc.getMinColour()))
+ {
+ noValueCombo.setSelectedIndex(MIN_COLOUR_OPTION);
+ }
+ else if (noColour.equals(fc.getMaxColour()))
+ {
+ noValueCombo.setSelectedIndex(MAX_COLOUR_OPTION);
+ }
+
+ /*
+ * update min-max scaling if there is a range to work with,
+ * else disable the widgets (this shouldn't happen if only
+ * valid options are offered in the combo box)
+ */
+ scaleFactor = (max == min) ? 1f : 100f / (max - min);
+ float range = (max - min) * scaleFactor;
+ slider.setMinimum((int) (min * scaleFactor));
+ slider.setMaximum((int) (max * scaleFactor));
+ slider.setMajorTickSpacing((int) (range / 10f));
+
+ threshline = new GraphLine((max - min) / 2f, "Threshold",
+ Color.black);
+ threshline.value = fc.getThreshold();
+
+ if (fc.hasThreshold())
+ {
+ threshold.setSelectedIndex(
+ fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
+ : BELOW_THRESHOLD_OPTION);
+ slider.setEnabled(true);
+ slider.setValue((int) (fc.getThreshold() * scaleFactor));
+ thresholdValue.setText(String.valueOf(getRoundedSliderValue()));
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
+ }
+ else
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdIsMin.setEnabled(false);
+ }
+ thresholdIsMin.setSelected(!fc.isAutoScaled());
+ } finally
+ {
+ adjusting = false;
+ }
+ }
+
+ /**
+ * Configures the initial layout
+ */
+ private void initialise()
+ {
+ this.setLayout(new BorderLayout());
+ tabbedPane = new JTabbedPane();
+ this.add(tabbedPane, BorderLayout.CENTER);
+
+ /*
+ * an ActionListener that applies colour changes
+ */
+ changeColourAction = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ colourChanged(true);
+ }
+ };
+
+ /*
+ * first tab: colour options
+ */
+ JPanel coloursPanel = initialiseColoursPanel();
+ tabbedPane.addTab(MessageManager.getString("action.colour"),
+ coloursPanel);
+
+ /*
+ * second tab: filter options
+ */
+ JPanel filtersPanel = initialiseFiltersPanel();
+ tabbedPane.addTab(MessageManager.getString("label.filters"),
+ filtersPanel);
+
+ JPanel okCancelPanel = initialiseOkCancelPanel();
+
+ this.add(okCancelPanel, BorderLayout.SOUTH);
+ }
+
+ /**
+ * Updates the min-max range if Colour By selected item is Score, or an
+ * attribute, with a min-max range
+ */
+ protected void updateMinMax()
+ {
+ if (!graduatedColour.isSelected())
+ {
+ return;
+ }
+
+ float[] minMax = null;
+ String colourBy = (String) colourByRangeCombo.getSelectedItem();
+ if (MessageManager.getString("label.score").equals(colourBy))
+ {
+ minMax = fr.getMinMax().get(featureType)[0];
+ }
+ else
+ {
+ // colour by attribute range
+ String[] attNames = fromAttributeDisplayName(colourBy);
+ minMax = FeatureAttributes.getInstance().getMinMax(featureType,
+ attNames);
+ }
+
+ if (minMax != null)
+ {
+ min = minMax[0];
+ max = minMax[1];
+ }
+ }
+
+ /**
+ * Lay out fields for graduated colour (by score or attribute value)
+ *
+ * @return
+ */
+ private JPanel initialiseGraduatedColourPanel()
+ {
+ JPanel graduatedColourPanel = new JPanel();
+ graduatedColourPanel.setLayout(
+ new BoxLayout(graduatedColourPanel, BoxLayout.Y_AXIS));
+ JvSwingUtils.createTitledBorder(graduatedColourPanel,
+ MessageManager.getString("label.graduated_colour"), true);
+ graduatedColourPanel.setBackground(Color.white);
+
+ /*
+ * first row: graduated colour radio button, score/attribute drop-down
+ */
+ JPanel graduatedChoicePanel = new JPanel(
+ new FlowLayout(FlowLayout.LEFT));
+ graduatedChoicePanel.setBackground(Color.white);
+ graduatedColour = new JRadioButton(
+ MessageManager.getString("label.by_range_of") + COLON);
+ graduatedColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
+ graduatedColour.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (graduatedColour.isSelected())
+ {
+ colourChanged(true);
+ }
+ }
+ });
+ graduatedChoicePanel.add(graduatedColour);
+
+ List<String[]> attNames = FeatureAttributes.getInstance()
+ .getAttributes(featureType);
+ colourByRangeCombo = populateAttributesDropdown(attNames, true, false);
+ colourByRangeCombo.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ colourChanged(true);
+ }
+ });
+
+ /*
+ * disable graduated colour option if no range found
+ */
+ graduatedColour.setEnabled(colourByRangeCombo.getItemCount() > 0);
+
+ graduatedChoicePanel.add(colourByRangeCombo);
+ graduatedColourPanel.add(graduatedChoicePanel);
+
+ /*
+ * second row - min/max/no colours
+ */
+ JPanel colourRangePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ colourRangePanel.setBackground(Color.white);
+ graduatedColourPanel.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 mousePressed(MouseEvent e)
+ {
+ if (minColour.isEnabled())
+ {
+ showColourChooser(minColour, "label.select_colour_minimum_value");
+ }
+ }
+ });
+
+ 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())
+ {
+ showColourChooser(maxColour, "label.select_colour_maximum_value");
+ }
+ }
+ });
+ maxColour.setBorder(new LineBorder(Color.black));
+
+ /*
+ * default max colour to current colour (if a plain colour),
+ * or to Black if colour by label; make min colour a pale
+ * version of max colour
+ */
+ FeatureColourI fc = fr.getFeatureColours().get(featureType);
+ Color bg = fc.isSimpleColour() ? fc.getColour() : Color.BLACK;
+ maxColour.setBackground(bg);
+ minColour.setBackground(ColorUtils.bleachColour(bg, 0.9f));
+
+ 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)
+ {
+ colourChanged(true);
+ }
+ });
+
+ JLabel minText = new JLabel(
+ MessageManager.getString("label.min_value") + COLON);
+ minText.setFont(JvSwingUtils.getLabelFont());
+ JLabel maxText = new JLabel(
+ MessageManager.getString("label.max_value") + COLON);
+ maxText.setFont(JvSwingUtils.getLabelFont());
+ JLabel noText = new JLabel(
+ MessageManager.getString("label.no_value") + COLON);
+ 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);
+ graduatedColourPanel.add(thresholdPanel);
+
+ threshold.addActionListener(changeColourAction);
+ threshold.setToolTipText(MessageManager
+ .getString("label.threshold_feature_display_by_score"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_threshold")); // index 0
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_threshold")); // index 1
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_threshold")); // index 2
+
+ thresholdValue.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ thresholdValue_actionPerformed();
+ }
+ });
+ thresholdValue.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ thresholdValue_actionPerformed();
+ }
+ });
+ slider.setPaintLabels(false);
+ slider.setPaintTicks(true);
+ slider.setBackground(Color.white);
+ slider.setEnabled(false);
+ slider.setOpaque(false);
+ slider.setPreferredSize(new Dimension(100, 32));
+ slider.setToolTipText(
+ MessageManager.getString("label.adjust_threshold"));
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (!adjusting)
+ {
+ thresholdValue
+ .setText(String.valueOf(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, true);
+ }
+ }
+ });
+
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+
+ thresholdPanel.add(threshold);
+ thresholdPanel.add(slider);
+ thresholdPanel.add(thresholdValue);
+
+ thresholdIsMin.setBackground(Color.white);
+ thresholdIsMin
+ .setText(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setToolTipText(MessageManager
+ .getString("label.toggle_absolute_relative_display_threshold"));
+ thresholdIsMin.addActionListener(changeColourAction);
+ thresholdPanel.add(thresholdIsMin);
+
+ return graduatedColourPanel;
+ }
+
+ /**
+ * Lay out OK and Cancel buttons
+ *
+ * @return
+ */
+ private JPanel initialiseOkCancelPanel()
+ {
+ JPanel okCancelPanel = new JPanel();
+ // okCancelPanel.setBackground(Color.white);
+ okCancelPanel.add(ok);
+ okCancelPanel.add(cancel);
+ return okCancelPanel;
+ }
+
+ /**
+ * Lay out Colour options panel, containing
+ * <ul>
+ * <li>plain colour, with colour picker</li>
+ * <li>colour by text, with choice of Label or other attribute</li>
+ * <li>colour by range, of score or other attribute, when available</li>
+ * </ul>
+ *
+ * @return
+ */
+ private JPanel initialiseColoursPanel()
+ {
+ JPanel colourByPanel = new JPanel();
+ colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
+
+ /*
+ * simple colour radio button and colour picker
+ */
+ JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ simpleColourPanel.setBackground(Color.white);
+ JvSwingUtils.createTitledBorder(simpleColourPanel,
+ MessageManager.getString("label.simple"), true);
+ colourByPanel.add(simpleColourPanel);
+
+ simpleColour = new JRadioButton(
+ MessageManager.getString("label.simple_colour"));
+ simpleColour.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
+ simpleColour.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (simpleColour.isSelected() && !adjusting)
+ {
+ showColourChooser(singleColour, "label.select_colour");
+ }
+ }
+
+ });
+
+ singleColour.setFont(JvSwingUtils.getLabelFont());
+ singleColour.setBorder(BorderFactory.createLineBorder(Color.black));
+ singleColour.setPreferredSize(new Dimension(40, 20));
+ singleColour.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (simpleColour.isSelected())
+ {
+ showColourChooser(singleColour, "label.select_colour");
+ }
+ }
+ });
+ simpleColourPanel.add(simpleColour); // radio button
+ simpleColourPanel.add(singleColour); // colour picker button
+
+ /*
+ * colour by text (category) radio button and drop-down choice list
+ */
+ JPanel byTextPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ byTextPanel.setBackground(Color.white);
+ JvSwingUtils.createTitledBorder(byTextPanel,
+ MessageManager.getString("label.colour_by_text"), true);
+ colourByPanel.add(byTextPanel);
+ byCategory = new JRadioButton(
+ MessageManager.getString("label.by_text_of") + COLON);
+ byCategory.setPreferredSize(new Dimension(RADIO_WIDTH, 20));
+ byCategory.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (byCategory.isSelected())
+ {
+ colourChanged(true);
+ }
+ }
+ });
+ byTextPanel.add(byCategory);
+
+ List<String[]> attNames = FeatureAttributes.getInstance()
+ .getAttributes(featureType);
+ colourByTextCombo = populateAttributesDropdown(attNames, false, true);
+ colourByTextCombo.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ colourChanged(true);
+ }
+ });
+ byTextPanel.add(colourByTextCombo);
+
+ /*
+ * graduated colour panel
+ */
+ JPanel graduatedColourPanel = initialiseGraduatedColourPanel();
+ colourByPanel.add(graduatedColourPanel);
+
+ /*
+ * 3 radio buttons select between simple colour,
+ * by category (text), or graduated
+ */
+ ButtonGroup bg = new ButtonGroup();
+ bg.add(simpleColour);
+ bg.add(byCategory);
+ bg.add(graduatedColour);
+
+ return colourByPanel;
+ }
+
+ private void showColourChooser(JPanel colourPanel, String key)
+ {
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString(key), colourPanel.getBackground());
+ if (col != null)
+ {
+ colourPanel.setBackground(col);
+ colourPanel.setForeground(col);
+ }
+ colourPanel.repaint();
+ colourChanged(true);
+ }
+
+ /**
+ * 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 colourChanged(boolean updateStructsAndOverview)
+ {
+ if (adjusting)
+ {
+ /*
+ * ignore action handlers while setting values programmatically
+ */
+ return;
+ }
+
+ /*
+ * ensure min-max range is for the latest choice of
+ * 'graduated colour by'
+ */
+ updateMinMax();
+
+ FeatureColourI acg = makeColourFromInputs();
+
+ /*
+ * save the colour, and repaint stuff
+ */
+ fr.setColour(featureType, acg);
+ ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
+
+ updateColoursTab();
+ }
+
+ /**
+ * Converts the input values into an instance of FeatureColour
+ *
+ * @return
+ */
+ private FeatureColourI makeColourFromInputs()
+ {
+ /*
+ * easiest case - a single colour
+ */
+ if (simpleColour.isSelected())
+ {
+ return new FeatureColour(singleColour.getBackground());
+ }
+
+ /*
+ * next easiest case - colour by Label, or attribute text
+ */
+ if (byCategory.isSelected())
+ {
+ Color c = this.getBackground();
+ FeatureColourI fc = new FeatureColour(c, c, null, 0f, 0f);
+ fc.setColourByLabel(true);
+ String byWhat = (String) colourByTextCombo.getSelectedItem();
+ if (!MessageManager.getString("label.label").equals(byWhat))
+ {
+ fc.setAttributeName(fromAttributeDisplayName(byWhat));
+ }
+ return fc;
+ }
+
+ /*
+ * remaining case - graduated colour by score, or attribute value
+ */
+ Color noColour = null;
+ if (noValueCombo.getSelectedIndex() == MIN_COLOUR_OPTION)
+ {
+ noColour = minColour.getBackground();
+ }
+ else if (noValueCombo.getSelectedIndex() == MAX_COLOUR_OPTION)
+ {
+ noColour = maxColour.getBackground();
+ }
+
+ float thresh = 0f;
+ try
+ {
+ thresh = Float.valueOf(thresholdValue.getText());
+ } catch (NumberFormatException e)
+ {
+ // invalid inputs are already handled on entry
+ }
+
+ /*
+ * min-max range is to (or from) threshold value if
+ * 'threshold is min/max' is selected
+ */
+ float minValue = min;
+ float maxValue = max;
+ final int thresholdOption = threshold.getSelectedIndex();
+ if (thresholdIsMin.isSelected()
+ && thresholdOption == ABOVE_THRESHOLD_OPTION)
+ {
+ minValue = thresh;
+ }
+ if (thresholdIsMin.isSelected()
+ && thresholdOption == BELOW_THRESHOLD_OPTION)
+ {
+ maxValue = thresh;
+ }
+
+ /*
+ * make the graduated colour
+ */
+ FeatureColourI fc = new FeatureColour(minColour.getBackground(),
+ maxColour.getBackground(), noColour, minValue, maxValue);
+
+ /*
+ * set attribute to colour by if selected
+ */
+ String byWhat = (String) colourByRangeCombo.getSelectedItem();
+ if (!MessageManager.getString("label.score").equals(byWhat))
+ {
+ fc.setAttributeName(fromAttributeDisplayName(byWhat));
+ }
+
+ /*
+ * set threshold options and 'autoscaled' which is
+ * false if 'threshold is min/max' is selected
+ * else true (colour range is on actual range of values)
+ */
+ fc.setThreshold(thresh);
+ fc.setAutoScaled(!thresholdIsMin.isSelected());
+ fc.setAboveThreshold(thresholdOption == ABOVE_THRESHOLD_OPTION);
+ fc.setBelowThreshold(thresholdOption == BELOW_THRESHOLD_OPTION);
+
+ if (threshline == null)
+ {
+ /*
+ * todo not yet implemented: visual indication of feature threshold
+ */
+ threshline = new GraphLine((max - min) / 2f, "Threshold",
+ Color.black);
+ }
+
+ return fc;
+ }
+
+ /**
+ * A helper method that converts a 'compound' attribute name from its display
+ * form, e.g. CSQ:PolyPhen to array form, e.g. { "CSQ", "PolyPhen" }
+ *
+ * @param attribute
+ * @return
+ */
+ private String[] fromAttributeDisplayName(String attribute)
+ {
+ return attribute == null ? null : attribute.split(COLON);
+ }
+
+ /**
+ * A helper method that converts a 'compound' attribute name to its display
+ * form, e.g. CSQ:PolyPhen from its array form, e.g. { "CSQ", "PolyPhen" }
+ *
+ * @param attName
+ * @return
+ */
+ private String toAttributeDisplayName(String[] attName)
+ {
+ return attName == null ? "" : String.join(COLON, attName);
+ }
+
+ @Override
+ protected void raiseClosed()
+ {
+ if (this.featureSettings != null)
+ {
+ featureSettings.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
+ }
+ }
+
+ /**
+ * Action on OK is just to dismiss the dialog - any changes have already been
+ * applied
+ */
+ @Override
+ public void okPressed()
+ {
+ }
+
+ /**
+ * Action on Cancel is to restore colour scheme and filters as they were when
+ * the dialog was opened
+ */
+ @Override
+ public void cancelPressed()
+ {
+ fr.setColour(featureType, originalColour);
+ fr.setFeatureFilter(featureType, originalFilter);
+ ap.paintAlignment(true, true);
+ }
+
+ /**
+ * Action on text entry of a threshold value
+ */
+ protected void thresholdValue_actionPerformed()
+ {
+ try
+ {
+ adjusting = true;
+ float f = Float.parseFloat(thresholdValue.getText());
+ slider.setValue((int) (f * scaleFactor));
+ threshline.value = f;
+ thresholdValue.setBackground(Color.white); // ok
+
+ /*
+ * force repaint of any Overview window or structure
+ */
+ ap.paintAlignment(true, true);
+ } catch (NumberFormatException ex)
+ {
+ thresholdValue.setBackground(Color.red); // not ok
+ } finally
+ {
+ adjusting = false;
+ }
+ }
+
+ /**
+ * 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 = getRoundedSliderValue();
+
+ /*
+ * repaint alignment, but not Overview or structure,
+ * to avoid overload while dragging the slider
+ */
+ colourChanged(false);
+ }
+
+ /**
+ * Converts the slider value to its absolute value by dividing by the
+ * scaleFactor. Rounding errors are squashed by forcing min/max of slider range
+ * to the actual min/max of feature score range
+ *
+ * @return
+ */
+ private float getRoundedSliderValue()
+ {
+ int value = slider.getValue();
+ float f = value == slider.getMaximum() ? max
+ : (value == slider.getMinimum() ? min : value / scaleFactor);
+ return f;
+ }
+
+ void addActionListener(ActionListener listener)
+ {
+ if (featureSettings != null)
+ {
+ System.err.println(
+ "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
+ }
+ featureSettings = listener;
+ }
+
+ /**
+ * A helper method to build the drop-down choice of attributes for a feature. If
+ * 'withRange' is true, then Score, and any attributes with a min-max range, are
+ * added. If 'withText' is true, Label and any known attributes are added. This
+ * allows 'categorical numerical' attributes e.g. codon position to be coloured
+ * by text.
+ * <p>
+ * Where metadata is available with a description for an attribute, that is
+ * added as a tooltip.
+ * <p>
+ * 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.
+ * <p>
+ * This method does not add any ActionListener to the JComboBox.
+ *
+ * @param attNames
+ * @param withRange
+ * @param withText
+ */
+ protected JComboBox<String> populateAttributesDropdown(
+ List<String[]> attNames, boolean withRange, boolean withText)
+ {
+ List<String> displayAtts = new ArrayList<>();
+ List<String> tooltips = new ArrayList<>();
+
+ if (withText)
+ {
+ displayAtts.add(MessageManager.getString("label.label"));
+ tooltips.add(MessageManager.getString("label.description"));
+ }
+ if (withRange)
+ {
+ float[][] minMax = fr.getMinMax().get(featureType);
+ if (minMax != null && minMax[0][0] != minMax[0][1])
+ {
+ displayAtts.add(MessageManager.getString("label.score"));
+ tooltips.add(MessageManager.getString("label.score"));
+ }
+ }
+
+ FeatureAttributes fa = FeatureAttributes.getInstance();
+ for (String[] attName : attNames)
+ {
+ float[] minMax = fa.getMinMax(featureType, attName);
+ boolean hasRange = minMax != null && minMax[0] != minMax[1];
+ if (!withText && !hasRange)
+ {
+ continue;
+ }
+ displayAtts.add(toAttributeDisplayName(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<String> attCombo = JvSwingUtils
+ .buildComboWithTooltips(displayAtts, tooltips);
+
+ return attCombo;
+ }
+
+ /**
+ * Populates initial layout of the feature attribute filters panel
+ */
+ private JPanel initialiseFiltersPanel()
+ {
+ filters = new ArrayList<>();
+
+ JPanel filtersPanel = new JPanel();
+ filtersPanel.setLayout(new BoxLayout(filtersPanel, BoxLayout.Y_AXIS));
+ filtersPanel.setBackground(Color.white);
+ JvSwingUtils.createTitledBorder(filtersPanel,
+ MessageManager.getString("label.filters"), true);
+
+ JPanel andOrPanel = initialiseAndOrPanel();
+ filtersPanel.add(andOrPanel);
+
+ /*
+ * panel with filters - populated by refreshFiltersDisplay
+ */
+ chooseFiltersPanel = new JPanel();
+ LayoutManager box = new BoxLayout(chooseFiltersPanel, BoxLayout.Y_AXIS);
+ chooseFiltersPanel.setLayout(box);
+ filtersPanel.add(chooseFiltersPanel);
+
+ return filtersPanel;
+ }
+
+ /**
+ * Lays out the panel with radio buttons to AND or OR filter conditions
+ *
+ * @return
+ */
+ private JPanel initialiseAndOrPanel()
+ {
+ JPanel andOrPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ andOrPanel.setBackground(Color.white);
+ andOrPanel.setBorder(BorderFactory.createLineBorder(debugBorderColour));
+ andFilters = new JRadioButton(MessageManager.getString("label.and"));
+ orFilters = new JRadioButton(MessageManager.getString("label.or"));
+ ActionListener actionListener = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filtersChanged();
+ }
+ };
+ andFilters.addActionListener(actionListener);
+ orFilters.addActionListener(actionListener);
+ ButtonGroup andOr = new ButtonGroup();
+ andOr.add(andFilters);
+ andOr.add(orFilters);
+ andFilters.setSelected(true);
+ andOrPanel.add(
+ new JLabel(MessageManager.getString("label.join_conditions")));
+ andOrPanel.add(andFilters);
+ andOrPanel.add(orFilters);
+ return andOrPanel;
+ }
+
+ /**
+ * Refreshes the display to show any filters currently configured for the
+ * selected feature type (editable, with 'remove' option), plus one extra row
+ * for adding a condition. This should be called after a filter has been
+ * removed, added or amended.
+ */
+ private void updateFiltersTab()
+ {
+ /*
+ * clear the panel and list of filter conditions
+ */
+ chooseFiltersPanel.removeAll();
+ filters.clear();
+
+ /*
+ * look up attributes known for feature type
+ */
+ List<String[]> attNames = FeatureAttributes.getInstance()
+ .getAttributes(featureType);
+
+ /*
+ * if this feature type has filters set, load them first
+ */
+ KeyedMatcherSetI featureFilters = fr.getFeatureFilter(featureType);
+ if (featureFilters != null)
+ {
+ if (!featureFilters.isAnded())
+ {
+ orFilters.setSelected(true);
+ }
+ featureFilters.getMatchers().forEach(matcher -> filters.add(matcher));
+ }
+
+ /*
+ * and an empty filter for the user to populate (add)
+ */
+ KeyedMatcherI noFilter = new KeyedMatcher(Condition.values()[0], "",
+ (String) null);
+ filters.add(noFilter);
+
+ /*
+ * render the conditions in rows, each in its own JPanel
+ */
+ int filterIndex = 0;
+ for (KeyedMatcherI filter : filters)
+ {
+ String[] attName = filter.getKey();
+ Condition condition = filter.getMatcher().getCondition();
+ String pattern = filter.getMatcher().getPattern();
+ JPanel row = addFilter(attName, attNames, condition, pattern,
+ filterIndex);
+ row.setBorder(BorderFactory.createLineBorder(debugBorderColour));
+ chooseFiltersPanel.add(row);
+ filterIndex++;
+ }
+
+ this.validate();
+ this.repaint();
+ }
+
+ /**
+ * A helper method that constructs a row (panel) with one filter condition:
+ * <ul>
+ * <li>a drop-down list of attribute names to choose from</li>
+ * <li>a drop-down list of conditions to choose from</li>
+ * <li>a text field for input of a match pattern</li>
+ * <li>optionally, a 'remove' button</li>
+ * </ul>
+ * If attribute, condition or pattern are not null, they are set as defaults for
+ * the input fields. The 'remove' button is added unless the pattern is null or
+ * empty (incomplete filter condition).
+ *
+ * @param attName
+ * @param attNames
+ * @param cond
+ * @param pattern
+ * @param filterIndex
+ * @return
+ */
+ protected JPanel addFilter(String[] attName, List<String[]> attNames,
+ Condition cond, String pattern, int filterIndex)
+ {
+ JPanel filterRow = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ filterRow.setBackground(Color.white);
+
+ /*
+ * drop-down choice of attribute, with description as a tooltip
+ * if we can obtain it
+ */
+ final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
+ true, true);
+ JComboBox<Condition> condCombo = new JComboBox<>();
+ JTextField patternField = new JTextField(8);
+
+ /*
+ * action handlers that validate and (if valid) apply changes
+ */
+ ActionListener actionListener = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ if (attCombo.getSelectedItem() != null)
+ {
+ if (validateFilter(patternField, condCombo))
+ {
+ updateFilter(attCombo, condCombo, patternField, filterIndex);
+ filtersChanged();
+ }
+ }
+ }
+ };
+ ItemListener itemListener = new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ actionListener.actionPerformed(null);
+ }
+ };
+
+ if (attName == null) // the 'add a condition' row
+ {
+ attCombo.setSelectedIndex(0);
+ }
+ else
+ {
+ attCombo.setSelectedItem(toAttributeDisplayName(attName));
+ }
+ attCombo.addItemListener(itemListener);
+
+ filterRow.add(attCombo);
+
+ /*
+ * drop-down choice of test condition
+ */
+ populateConditions((String) attCombo.getSelectedItem(), cond,
+ condCombo);
+ condCombo.addItemListener(itemListener);
+ filterRow.add(condCombo);
+
+ /*
+ * pattern to match against
+ */
+ patternField.setText(pattern);
+ patternField.addActionListener(actionListener);
+ patternField.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ actionListener.actionPerformed(null);
+ }
+ });
+ filterRow.add(patternField);
+
+ /*
+ * add remove button if filter is populated (non-empty pattern)
+ */
+ if (pattern != null && pattern.trim().length() > 0)
+ {
+ // todo: gif for button drawing '-' or 'x'
+ JButton removeCondition = new BasicArrowButton(SwingConstants.WEST);
+ removeCondition
+ .setToolTipText(MessageManager.getString("label.delete_row"));
+ removeCondition.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filters.remove(filterIndex);
+ filtersChanged();
+ }
+ });
+ filterRow.add(removeCondition);
+ }
+
+ return filterRow;
+ }
+
+ /**
+ * Populates the drop-down list of comparison conditions for the given attribute
+ * name. The conditions added depend on the datatype of the attribute values.
+ * The supplied condition is set as the selected item in the list, provided it
+ * is in the list.
+ *
+ * @param attName
+ * @param cond
+ * @param condCombo
+ */
+ private void populateConditions(String attName, Condition cond,
+ JComboBox<Condition> condCombo)
+ {
+ Datatype type = FeatureAttributes.getInstance().getDatatype(featureType,
+ attName);
+ if (MessageManager.getString("label.label").equals(attName))
+ {
+ type = Datatype.Character;
+ }
+ else if (MessageManager.getString("label.score").equals(attName))
+ {
+ type = Datatype.Number;
+ }
+
+ for (Condition c : Condition.values())
+ {
+ if ((c.isNumeric() && type != Datatype.Character)
+ || (!c.isNumeric() && type != Datatype.Number))
+ {
+ condCombo.addItem(c);
+ }
+ }
+
+ /*
+ * set the selected condition (does nothing if not in the list)
+ */
+ if (cond != null)
+ {
+ condCombo.setSelectedItem(cond);
+ }
+ }
+
+ /**
+ * Answers true unless a numeric condition has been selected with a non-numeric
+ * value. Sets the value field to RED with a tooltip if in error.
+ * <p>
+ * If the pattern entered is empty, this method returns false, but does not mark
+ * the field as invalid. This supports selecting an attribute for a new
+ * condition before a match pattern has been entered.
+ *
+ * @param value
+ * @param condCombo
+ */
+ protected boolean validateFilter(JTextField value,
+ JComboBox<Condition> condCombo)
+ {
+ if (value == null || condCombo == null)
+ {
+ return true; // fields not populated
+ }
+
+ Condition cond = (Condition) condCombo.getSelectedItem();
+ value.setBackground(Color.white);
+ value.setToolTipText("");
+ String v1 = value.getText().trim();
+ if (v1.length() == 0)
+ {
+ return false;
+ }
+
+ if (cond.isNumeric())
+ {
+ try
+ {
+ Float.valueOf(v1);
+ } catch (NumberFormatException e)
+ {
+ value.setBackground(Color.red);
+ value.setToolTipText(
+ MessageManager.getString("label.numeric_required"));
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ /**
+ * Constructs a filter condition from the given input fields, and replaces the
+ * condition at filterIndex with the new one
+ *
+ * @param attCombo
+ * @param condCombo
+ * @param valueField
+ * @param filterIndex
+ */
+ protected void updateFilter(JComboBox<String> attCombo,
+ JComboBox<Condition> condCombo, JTextField valueField,
+ int filterIndex)
+ {
+ String attName = (String) attCombo.getSelectedItem();
+ Condition cond = (Condition) condCombo.getSelectedItem();
+ String pattern = valueField.getText();
+ KeyedMatcherI km = new KeyedMatcher(cond, pattern,
+ fromAttributeDisplayName(attName));
+
+ filters.set(filterIndex, km);
+ }
+
+ /**
+ * Makes the dialog visible, at the Feature Colour tab or at the Filters tab
+ *
+ * @param coloursTab
+ */
+ public void showTab(boolean coloursTab)
+ {
+ setVisible(true);
+ tabbedPane.setSelectedIndex(coloursTab ? 0 : 1);
+ }
+
+ /**
+ * Action on any change to feature filtering, namely
+ * <ul>
+ * <li>change of selected attribute</li>
+ * <li>change of selected condition</li>
+ * <li>change of match pattern</li>
+ * <li>removal of a condition</li>
+ * </ul>
+ * The inputs are parsed into a combined filter and this is set for the feature
+ * type, and the alignment redrawn.
+ */
+ protected void filtersChanged()
+ {
+ /*
+ * update the filter conditions for the feature type
+ */
+ boolean anded = andFilters.isSelected();
+ KeyedMatcherSetI combined = new KeyedMatcherSet();
+
+ for (KeyedMatcherI filter : filters)
+ {
+ String pattern = filter.getMatcher().getPattern();
+ if (pattern.trim().length() > 0)
+ {
+ if (anded)
+ {
+ combined.and(filter);
+ }
+ else
+ {
+ combined.or(filter);
+ }
+ }
+ }
+
+ /*
+ * save the filter conditions in the FeatureRenderer
+ * (note this might now be an empty filter with no conditions)
+ */
+ fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
+ ap.paintAlignment(true, true);
+
+ updateFiltersTab();
+ }
+}
public abstract class FeatureRendererModel
implements jalview.api.FeatureRenderer
{
+ /*
+ * column indices of fields in Feature Settings table
+ * todo: transfer valuers as data beans instead of Object[][]
+ */
+ public static final int TYPE_COLUMN = 0;
+
+ public static final int COLOUR_COLUMN = 1;
+
+ public static final int FILTER_COLUMN = 2;
+
+ public static final int SHOW_COLUMN = 3;
/*
* global transparency for feature
{
for (int i = 0; i < data.length; i++)
{
- String type = data[i][0].toString();
- setColour(type, (FeatureColourI) data[i][1]);
- if (((Boolean) data[i][2]).booleanValue())
+ String type = data[i][TYPE_COLUMN].toString();
+ setColour(type, (FeatureColourI) data[i][COLOUR_COLUMN]);
+ if (((Boolean) data[i][SHOW_COLUMN]).booleanValue())
{
av_featuresdisplayed.setVisible(type);
}
protected boolean featureMatchesFilters(SequenceFeature sf)
{
KeyedMatcherSetI filter = featureFilters.get(sf.getType());
- return filter == null ? true : filter.matches(key -> sf
- .getValueAsString(key));
+ // TODO temporary fudge for Score and Label
+ return filter == null ? true
+ : filter.matches(
+ key -> "Label".equals(key[0]) ? sf.getDescription()
+ : ("Score".equals(key[0])
+ ? String.valueOf(sf.getScore())
+ : sf.getValueAsString(key)));
}
}
git://source.jalview.org / jalview.git / commitdiff