+/*
+ * 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.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AnnotationFilterParameter;
import jalview.datamodel.ColumnSelection;
-import jalview.jbgui.FurtherActionPanel;
-import jalview.jbgui.SearchPanel;
-import jalview.jbgui.StructureFilterPanel;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import java.awt.BorderLayout;
import java.awt.CardLayout;
import java.awt.event.ItemListener;
import java.util.Iterator;
-import javax.swing.JButton;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
+import javax.swing.JTextField;
import javax.swing.border.TitledBorder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
import net.miginfocom.swing.MigLayout;
ItemListener
{
- private ColumnSelection oldColumnSelection;
-
private JComboBox<String> annotations;
- JButton ok = new JButton();
-
- JButton cancel = new JButton();
-
- JPanel actionPanel = new JPanel();
+ private JPanel actionPanel = new JPanel();
- JPanel thresholdPanel = new JPanel();
+ private JPanel thresholdPanel = new JPanel();
- JPanel switchableViewsPanel = new JPanel(new CardLayout());
+ private JPanel switchableViewsPanel = new JPanel(new CardLayout());
- CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
+ private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
.getLayout());
- JPanel noGraphFilterView = new JPanel();
+ private JPanel noGraphFilterView = new JPanel();
- JPanel graphFilterView = new JPanel();
+ private JPanel graphFilterView = new JPanel();
- JPanel annotationComboBoxPanel = new JPanel();
+ private JPanel annotationComboBoxPanel = new JPanel();
- StructureFilterPanel gStructureFilterPanel;
+ private BorderLayout borderLayout1 = new BorderLayout();
- StructureFilterPanel ngStructureFilterPanel;
-
- private StructureFilterPanel currentStructureFilterPanel;
+ private JComboBox<String> threshold = new JComboBox<String>();
- JLabel annotationLabel = new JLabel();
+ private StructureFilterPanel gStructureFilterPanel;
- BorderLayout borderLayout1 = new BorderLayout();
+ private StructureFilterPanel ngStructureFilterPanel;
- private JComboBox<String> threshold = new JComboBox<String>();
+ private StructureFilterPanel currentStructureFilterPanel;
private SearchPanel currentSearchPanel;
private int actionOption = ACTION_OPTION_SELECT;
+ private ColumnSelection oldColumnSelection;
+
+ public AnnotationColumnChooser()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
super(av, ap);
setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
- // restore the Object state from the previous session if one exists
+ // restore Object state from the previous session if one exists
if (av.getAnnotationColumnSelectionState() != null)
{
currentSearchPanel = av.getAnnotationColumnSelectionState()
.getThreshold().getSelectedIndex());
actionOption = av.getAnnotationColumnSelectionState()
.getActionOption();
-
}
try
frame.pack();
}
- public AnnotationColumnChooser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
private void jbInit() throws Exception
{
ok.setOpaque(false);
ok_actionPerformed(e);
}
});
+
cancel.setOpaque(false);
cancel.setText(MessageManager.getString("action.cancel"));
cancel.addActionListener(new ActionListener()
}
});
- getAnnotations().addItemListener(this);
- getThreshold().addActionListener(new ActionListener()
+ annotations.addItemListener(this);
+ annotations.setToolTipText(MessageManager
+ .getString("info.select_annotation_row"));
+ threshold.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
thresholdValue.addActionListener(new ActionListener()
{
@Override
thresholdValue_actionPerformed(e);
}
});
+
slider.setPaintLabels(false);
slider.setPaintTicks(true);
slider.setBackground(Color.white);
slider.setEnabled(false);
slider.setOpaque(false);
slider.setPreferredSize(new Dimension(100, 32));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- annotationLabel.setBackground(Color.white);
- annotationLabel.setFont(JvSwingUtils.getLabelFont());
- annotationLabel.setText("Select Annotation : ");
-
- thresholdPanel.setBorder(new TitledBorder("Threshold Filter"));
+ thresholdPanel.setBorder(new TitledBorder(MessageManager
+ .getString("label.threshold_filter")));
thresholdPanel.setBackground(Color.white);
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
actionPanel.setBackground(Color.white);
actionPanel.setFont(JvSwingUtils.getLabelFont());
- this.setLayout(borderLayout1);
graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
graphFilterView.setBackground(Color.white);
noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
noGraphFilterView.setBackground(Color.white);
+
annotationComboBoxPanel.setBackground(Color.white);
annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
gStructureFilterPanel = new StructureFilterPanel(this);
ngStructureFilterPanel = new StructureFilterPanel(this);
-
thresholdPanel.add(getThreshold());
thresholdPanel.add(thresholdValue, "wrap");
thresholdPanel.add(slider, "grow, span, wrap");
switchableViewsPanel.add(graphFilterView,
AnnotationColumnChooser.GRAPH_VIEW);
+ this.setLayout(borderLayout1);
this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
this.add(actionPanel, java.awt.BorderLayout.SOUTH);
selectedAnnotationChanged();
+ updateThresholdPanelToolTip();
this.validate();
}
- @SuppressWarnings("unchecked")
+ public void updateThresholdPanelToolTip()
+ {
+ thresholdValue.setToolTipText("");
+ slider.setToolTipText("");
+
+ String defaultTtip = MessageManager
+ .getString("info.change_threshold_mode_to_enable");
+
+ String threshold = getThreshold().getSelectedItem().toString();
+ if (threshold.equalsIgnoreCase("No Threshold"))
+ {
+ thresholdValue.setToolTipText(defaultTtip);
+ slider.setToolTipText(defaultTtip);
+ }
+ }
+
public void reset()
{
if (this.getOldColumnSelection() != null)
}
av.setColumnSelection(oldSelection);
}
- // ap.alignmentChanged();
ap.paintAlignment(true);
}
.setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
{
+ filterParams
+ .setThresholdValue(getCurrentAnnotation().threshold.value);
if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
{
}
}
+ updateThresholdPanelToolTip();
if (currentStructureFilterPanel != null)
{
- if (currentStructureFilterPanel.getAlphaHelix().isSelected())
+ if (currentStructureFilterPanel.alphaHelix.isSelected())
{
filterParams.setFilterAlphaHelix(true);
}
- if (currentStructureFilterPanel.getBetaStrand().isSelected())
+ if (currentStructureFilterPanel.betaStrand.isSelected())
{
filterParams.setFilterBetaSheet(true);
}
- if (currentStructureFilterPanel.getTurn().isSelected())
+ if (currentStructureFilterPanel.turn.isSelected())
{
filterParams.setFilterTurn(true);
}
if (currentSearchPanel != null)
{
- if (!currentSearchPanel.getSearchString().isEmpty())
+
+ if (!currentSearchPanel.searchBox.getText().isEmpty())
{
- currentSearchPanel.getDescription().setEnabled(true);
- currentSearchPanel.getDisplayName().setEnabled(true);
- filterParams.setRegexString(currentSearchPanel.getSearchString());
- if (currentSearchPanel.isDisplayNameChecked())
+ currentSearchPanel.description.setEnabled(true);
+ currentSearchPanel.displayName.setEnabled(true);
+ filterParams.setRegexString(currentSearchPanel.searchBox.getText());
+ if (currentSearchPanel.displayName.isSelected())
{
filterParams
.addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
}
- if (currentSearchPanel.isDescriptionChecked())
+ if (currentSearchPanel.description.isSelected())
{
filterParams
.addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
}
else
{
- currentSearchPanel.getDescription().setEnabled(false);
- currentSearchPanel.getDisplayName().setEnabled(false);
+ currentSearchPanel.description.setEnabled(false);
+ currentSearchPanel.displayName.setEnabled(false);
}
}
- filterAnnotations(getCurrentAnnotation().annotations, filterParams,
- av.getColumnSelection());
+ av.getColumnSelection().filterAnnotations(
+ getCurrentAnnotation().annotations, filterParams);
av.showAllHiddenColumns();
if (getActionOption() == ACTION_OPTION_HIDE)
}
}
+ public FurtherActionPanel getCurrentFutherActionPanel()
+ {
+ return currentFurtherActionPanel;
+ }
+
+ public void setCurrentFutherActionPanel(
+ FurtherActionPanel currentFutherActionPanel)
+ {
+ this.currentFurtherActionPanel = currentFutherActionPanel;
+ }
+
+ public SearchPanel getCurrentSearchPanel()
+ {
+ return currentSearchPanel;
+ }
+
+ public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
+ {
+ this.currentSearchPanel = currentSearchPanel;
+ }
+
+ public int getActionOption()
+ {
+ return actionOption;
+ }
+
+ public void setActionOption(int actionOption)
+ {
+ this.actionOption = actionOption;
+ }
+
+ public StructureFilterPanel getCurrentStructureFilterPanel()
+ {
+ return currentStructureFilterPanel;
+ }
+
+ public void setCurrentStructureFilterPanel(
+ StructureFilterPanel currentStructureFilterPanel)
+ {
+ this.currentStructureFilterPanel = currentStructureFilterPanel;
+ }
public void select_action(ActionEvent actionEvent)
{
}
}
-
@Override
public void itemStateChanged(ItemEvent e)
{
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}
- // else{
- // threshold.setSelectedIndex(AlignmentAnnotation.NO_GRAPH);
- // }
-
+
gSearchPanel.syncState();
gFurtherActionPanel.syncState();
- gFurtherActionPanel.syncState();
- gFurtherActionPanel.syncState();
+ gStructureFilterPanel.syncState();
ngSearchPanel.syncState();
ngFurtherActionPanel.syncState();
ngStructureFilterPanel.syncState();
- ngFurtherActionPanel.syncState();
switchableViewsLayout.show(switchableViewsPanel, currentView);
updateView();
}
-
- public FurtherActionPanel getCurrentFutherActionPanel()
+ public class FurtherActionPanel extends JPanel
{
- return currentFurtherActionPanel;
- }
+ private AnnotationColumnChooser aColChooser;
- public void setCurrentFutherActionPanel(
- FurtherActionPanel currentFutherActionPanel)
- {
- this.currentFurtherActionPanel = currentFutherActionPanel;
- }
+ private JRadioButton hideOption = new JRadioButton();
- public SearchPanel getCurrentSearchPanel()
- {
- return currentSearchPanel;
- }
+ private JRadioButton selectOption = new JRadioButton();
- public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
- {
- this.currentSearchPanel = currentSearchPanel;
- }
+ private ButtonGroup optionsGroup = new ButtonGroup();
- public int getActionOption()
- {
- return actionOption;
- }
+ public FurtherActionPanel(AnnotationColumnChooser aColChooser)
+ {
+ this.aColChooser = aColChooser;
+ JvSwingUtils.jvInitComponent(selectOption, "action.select");
+ selectOption.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectRadioAction(actionEvent);
+ }
+ });
- public void setActionOption(int actionOption)
- {
- this.actionOption = actionOption;
+ JvSwingUtils.jvInitComponent(hideOption, "action.hide");
+ hideOption.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ hideRadioAction(actionEvent);
+ }
+ });
+
+ optionsGroup.add(selectOption);
+ optionsGroup.add(hideOption);
+ optionsGroup.setSelected(selectOption.getModel(), true);
+
+ JvSwingUtils.jvInitComponent(this);
+ syncState();
+
+ this.add(selectOption);
+ this.add(hideOption);
+ }
+
+ public void selectRadioAction(ActionEvent actionEvent)
+ {
+ aColChooser.setCurrentFutherActionPanel(this);
+ aColChooser.select_action(actionEvent);
+ }
+
+ public void hideRadioAction(ActionEvent actionEvent)
+ {
+ aColChooser.setCurrentFutherActionPanel(this);
+ aColChooser.hide_action(actionEvent);
+ }
+
+ public void syncState()
+ {
+ if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+ {
+ this.optionsGroup.setSelected(this.hideOption.getModel(), true);
+ }
+ else
+ {
+ this.optionsGroup.setSelected(this.selectOption.getModel(), true);
+ }
+ }
}
- public StructureFilterPanel getCurrentStructureFilterPanel()
+ public class StructureFilterPanel extends JPanel
{
- return currentStructureFilterPanel;
+ private AnnotationColumnChooser aColChooser;
+
+ private JCheckBox alphaHelix = new JCheckBox();
+
+ private JCheckBox betaStrand = new JCheckBox();
+
+ private JCheckBox turn = new JCheckBox();
+
+ private JCheckBox all = new JCheckBox();
+
+ public StructureFilterPanel(AnnotationColumnChooser aColChooser)
+ {
+ this.aColChooser = aColChooser;
+
+ JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
+ alphaHelix.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ alphaHelix_actionPerformed();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
+ betaStrand.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ betaStrand_actionPerformed();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(turn, "label.turn");
+ turn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ turn_actionPerformed();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(all, "label.select_all");
+ all.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ all_actionPerformed();
+ }
+ });
+
+ this.setBorder(new TitledBorder(MessageManager
+ .getString("label.structures_filter")));
+ JvSwingUtils.jvInitComponent(this);
+
+ this.add(all);
+ this.add(alphaHelix);
+ this.add(betaStrand);
+ this.add(turn);
+ }
+
+ public void alphaHelix_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void betaStrand_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void turn_actionPerformed()
+ {
+ updateSelectAllState();
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void all_actionPerformed()
+ {
+ if (all.isSelected())
+ {
+ alphaHelix.setSelected(true);
+ betaStrand.setSelected(true);
+ turn.setSelected(true);
+ }
+ else
+ {
+ alphaHelix.setSelected(false);
+ betaStrand.setSelected(false);
+ turn.setSelected(false);
+ }
+ aColChooser.setCurrentStructureFilterPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void updateSelectAllState()
+ {
+ if (alphaHelix.isSelected() && betaStrand.isSelected()
+ && turn.isSelected())
+ {
+ all.setSelected(true);
+ }
+ else
+ {
+ all.setSelected(false);
+ }
+ }
+
+ public void syncState()
+ {
+ StructureFilterPanel sfp = aColChooser
+ .getCurrentStructureFilterPanel();
+ if (sfp != null)
+ {
+ alphaHelix.setSelected(sfp.alphaHelix.isSelected());
+ betaStrand.setSelected(sfp.betaStrand.isSelected());
+ turn.setSelected(sfp.turn.isSelected());
+ if (sfp.all.isSelected())
+ {
+ all.setSelected(true);
+ alphaHelix.setSelected(true);
+ betaStrand.setSelected(true);
+ turn.setSelected(true);
+ }
+ }
+
+ }
}
- public void setCurrentStructureFilterPanel(
- StructureFilterPanel currentStructureFilterPanel)
+ public class SearchPanel extends JPanel
{
- this.currentStructureFilterPanel = currentStructureFilterPanel;
+ private AnnotationColumnChooser aColChooser;
+
+ private JCheckBox displayName = new JCheckBox();
+
+ private JCheckBox description = new JCheckBox();
+
+ private JTextField searchBox = new JTextField(10);
+
+ public SearchPanel(AnnotationColumnChooser aColChooser)
+ {
+
+ this.aColChooser = aColChooser;
+ JvSwingUtils.jvInitComponent(this);
+ this.setBorder(new TitledBorder(MessageManager
+ .getString("label.search_filter")));
+
+ JvSwingUtils.jvInitComponent(searchBox);
+ searchBox.setToolTipText(MessageManager
+ .getString("info.enter_search_text_here"));
+ searchBox.getDocument().addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ searchStringAction();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(displayName, "label.label");
+ displayName.setEnabled(false);
+ displayName.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ displayNameCheckboxAction();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(description, "label.description");
+ description.setEnabled(false);
+ description.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ discriptionCheckboxAction();
+ }
+ });
+
+ syncState();
+ this.add(searchBox);
+ this.add(displayName);
+ this.add(description);
+ }
+
+ public void displayNameCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void discriptionCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void searchStringAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ updateSearchPanelToolTips();
+ }
+
+ public void syncState()
+ {
+ SearchPanel sp = aColChooser.getCurrentSearchPanel();
+ if (sp != null)
+ {
+ description.setEnabled(sp.description.isEnabled());
+ description.setSelected(sp.description.isSelected());
+
+ displayName.setEnabled(sp.displayName.isEnabled());
+ displayName.setSelected(sp.displayName.isSelected());
+
+ searchBox.setText(sp.searchBox.getText());
+ }
+ updateSearchPanelToolTips();
+ }
+
+ public void updateSearchPanelToolTips()
+ {
+ String defaultTtip = MessageManager
+ .getString("info.enter_search_text_to_enable");
+ String labelTtip = MessageManager.formatMessage(
+ "info.search_in_annotation_label", annotations
+ .getSelectedItem().toString());
+ String descTtip = MessageManager.formatMessage(
+ "info.search_in_annotation_description", annotations
+ .getSelectedItem().toString());
+ displayName.setToolTipText(displayName.isEnabled() ? labelTtip
+ : defaultTtip);
+ description.setToolTipText(description.isEnabled() ? descTtip
+ : defaultTtip);
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff