+/*
+ * 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.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.io.cache.JvCacheableInputBox;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import java.awt.Dimension;
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.util.Iterator;
+import java.awt.event.KeyEvent;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
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;
@SuppressWarnings("serial")
-public class AnnotationColumnChooser extends AnnotationRowFilter implements
- ItemListener
+public class AnnotationColumnChooser extends AnnotationRowFilter
+ implements ItemListener
{
-
- private JComboBox<String> annotations;
-
- // private JButton ok = new JButton();
- //
- // private JButton cancel = new JButton();
-
- private JPanel actionPanel = new JPanel();
-
- private JPanel thresholdPanel = new JPanel();
-
private JPanel switchableViewsPanel = new JPanel(new CardLayout());
- private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
- .getLayout());
- private JPanel noGraphFilterView = new JPanel();
-
- private JPanel graphFilterView = new JPanel();
-
private JPanel annotationComboBoxPanel = new JPanel();
- private BorderLayout borderLayout1 = new BorderLayout();
-
- private JComboBox<String> threshold = new JComboBox<String>();
-
private StructureFilterPanel gStructureFilterPanel;
private StructureFilterPanel ngStructureFilterPanel;
private int actionOption = ACTION_OPTION_SELECT;
- private ColumnSelection oldColumnSelection;
+ private HiddenColumns oldHiddenColumns;
- public AnnotationColumnChooser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ protected int MIN_WIDTH = 420;
+
+ protected int MIN_HEIGHT = 430;
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
Desktop.addInternalFrame(frame,
MessageManager.getString("label.select_by_annotation"), 520,
215);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
{
return;
}
- setOldColumnSelection(av.getColumnSelection());
+ setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
- setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
+ setAnnotations(new JComboBox<>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
-
+ AnnotationColumnChooser lastChooser = av
+ .getAnnotationColumnSelectionState();
// restore Object state from the previous session if one exists
- if (av.getAnnotationColumnSelectionState() != null)
+ if (lastChooser != null)
{
- currentSearchPanel = av.getAnnotationColumnSelectionState()
- .getCurrentSearchPanel();
- currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+ currentSearchPanel = lastChooser.getCurrentSearchPanel();
+ currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
- annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
- .getAnnotations().getSelectedIndex());
- threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
- .getThreshold().getSelectedIndex());
- actionOption = av.getAnnotationColumnSelectionState()
- .getActionOption();
+ annotations.setSelectedIndex(
+ lastChooser.getAnnotations().getSelectedIndex());
+ threshold.setSelectedIndex(
+ lastChooser.getThreshold().getSelectedIndex());
+ actionOption = lastChooser.getActionOption();
+ percentThreshold
+ .setSelected(lastChooser.percentThreshold.isSelected());
}
try
frame.pack();
}
- private void jbInit() throws Exception
+ @Override
+ protected void jbInit()
{
- ok.setOpaque(false);
- ok.setText(MessageManager.getString("action.ok"));
- ok.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
+ super.jbInit();
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
-
- annotations.addItemListener(this);
- threshold.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
-
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- thresholdValue.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- 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));
-
- thresholdPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.threshold_filter")));
+ JPanel thresholdPanel = new JPanel();
+ thresholdPanel.setBorder(new TitledBorder(
+ MessageManager.getString("label.threshold_filter")));
thresholdPanel.setBackground(Color.white);
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+ percentThreshold.setBackground(Color.white);
+ percentThreshold.setFont(JvSwingUtils.getLabelFont());
+
+ JPanel actionPanel = new JPanel();
actionPanel.setBackground(Color.white);
actionPanel.setFont(JvSwingUtils.getLabelFont());
+ JPanel graphFilterView = new JPanel();
graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
graphFilterView.setBackground(Color.white);
+ JPanel noGraphFilterView = new JPanel();
noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
noGraphFilterView.setBackground(Color.white);
ngStructureFilterPanel = new StructureFilterPanel(this);
thresholdPanel.add(getThreshold());
- thresholdPanel.add(thresholdValue, "wrap");
- thresholdPanel.add(slider, "grow, span, wrap");
+ thresholdPanel.add(percentThreshold, "wrap");
+ thresholdPanel.add(slider, "grow");
+ thresholdPanel.add(thresholdValue, "span, wrap");
actionPanel.add(ok);
actionPanel.add(cancel);
switchableViewsPanel.add(graphFilterView,
AnnotationColumnChooser.GRAPH_VIEW);
- this.setLayout(borderLayout1);
+ this.setLayout(new BorderLayout());
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 reset()
+ protected void updateThresholdPanelToolTip()
{
- if (this.getOldColumnSelection() != null)
+ thresholdValue.setToolTipText("");
+ slider.setToolTipText("");
+
+ String defaultTtip = MessageManager
+ .getString("info.change_threshold_mode_to_enable");
+
+ String thresh = getThreshold().getSelectedItem().toString();
+ if (thresh.equalsIgnoreCase("No Threshold"))
+ {
+ thresholdValue.setToolTipText(defaultTtip);
+ slider.setToolTipText(defaultTtip);
+ }
+ }
+
+ @Override
+ protected void reset()
+ {
+ if (this.getOldHiddenColumns() != null)
{
av.getColumnSelection().clear();
if (av.getAnnotationColumnSelectionState() != null)
{
- ColumnSelection oldSelection = av
- .getAnnotationColumnSelectionState()
- .getOldColumnSelection();
- if (oldSelection != null && oldSelection.getHiddenColumns() != null
- && !oldSelection.getHiddenColumns().isEmpty())
- {
- for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
- .iterator(); itr.hasNext();)
- {
- int positions[] = itr.next();
- av.hideColumns(positions[0], positions[1]);
- }
- }
- av.setColumnSelection(oldSelection);
+ HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
+ .getOldHiddenColumns();
+ av.getAlignment().setHiddenColumns(oldHidden);
}
- ap.paintAlignment(true);
+ av.sendSelection();
+ ap.paintAlignment(true, true);
}
-
}
+ @Override
public void valueChanged(boolean updateAllAnnotation)
{
if (slider.isEnabled())
{
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ getCurrentAnnotation().threshold.value = getSliderValue();
updateView();
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
- public JComboBox<String> getThreshold()
- {
- return threshold;
- }
-
- public void setThreshold(JComboBox<String> threshold)
- {
- this.threshold = threshold;
- }
-
- public JComboBox<String> getAnnotations()
- {
- return annotations;
- }
-
- public void setAnnotations(JComboBox<String> annotations)
- {
- this.annotations = annotations;
- }
-
@Override
public void updateView()
{
AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
- setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]]);
+ setCurrentAnnotation(av.getAlignment()
+ .getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]]);
- int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
- .getSelectedIndex());
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
+ percentThreshold.setEnabled(true);
+ final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
+ percentThreshold.setEnabled(false);
// build filter params
}
else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
- if (getCurrentAnnotation().threshold == null)
+ if (currentAnnotation.threshold == null)
{
- getCurrentAnnotation()
- .setThreshold(
- new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
+ currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
+ (currentAnnotation.graphMax
+ - currentAnnotation.graphMin) / 2f,
+ "Threshold", Color.black));
}
adjusting = true;
- float range = getCurrentAnnotation().graphMax * 1000
- - getCurrentAnnotation().graphMin * 1000;
-
- slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
- slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
- slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
- thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
- slider.setMajorTickSpacing((int) (range / 10f));
+
+ setSliderModel(currentAnnotation.graphMin,
+ currentAnnotation.graphMax,
+ currentAnnotation.threshold.value);
+
+ setThresholdValueText();
+
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
// build filter params
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
- if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+ if (currentAnnotation.isQuantitative())
{
filterParams
- .setThresholdValue(getCurrentAnnotation().threshold.value);
+ .setThresholdValue(currentAnnotation.threshold.value);
if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
{
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
}
else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
{
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
+ filterParams.setThresholdType(
+ AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
}
}
}
+ updateThresholdPanelToolTip();
if (currentStructureFilterPanel != null)
{
if (currentStructureFilterPanel.alphaHelix.isSelected())
if (currentSearchPanel != null)
{
-
- if (!currentSearchPanel.searchBox.getText().isEmpty())
+ if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
{
- currentSearchPanel.description.setEnabled(true);
- currentSearchPanel.displayName.setEnabled(true);
- filterParams.setRegexString(currentSearchPanel.searchBox.getText());
+ filterParams.setRegexString(
+ currentSearchPanel.searchBox.getUserInput());
if (currentSearchPanel.displayName.isSelected())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
}
if (currentSearchPanel.description.isSelected())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
}
}
- else
- {
- currentSearchPanel.description.setEnabled(false);
- currentSearchPanel.displayName.setEnabled(false);
- }
}
+ // show hidden columns here, before changing the column selection in
+ // filterAnnotations, because showing hidden columns has the side effect of
+ // adding them to the selection
+ av.showAllHiddenColumns();
av.getColumnSelection().filterAnnotations(
- getCurrentAnnotation().annotations, filterParams);
+ currentAnnotation.annotations, filterParams);
- av.showAllHiddenColumns();
- if (getActionOption() == ACTION_OPTION_HIDE)
+ boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
+ if (hideCols)
{
av.hideSelectedColumns();
}
+ av.sendSelection();
filterParams = null;
av.setAnnotationColumnSelectionState(this);
- ap.paintAlignment(true);
+ // only update overview and structures if columns were hidden
+ ap.paintAlignment(hideCols, hideCols);
}
- public ColumnSelection getOldColumnSelection()
+ public HiddenColumns getOldHiddenColumns()
{
- return oldColumnSelection;
+ return oldHiddenColumns;
}
- public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+ public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
{
- if (currentColumnSelection != null)
+ if (currentHiddenColumns != null)
{
- this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+ this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
}
}
selectedAnnotationChanged();
}
+ @Override
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+ .getSelectedIndex()]].isQuantitative())
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}
-
+ saveCache();
gSearchPanel.syncState();
gFurtherActionPanel.syncState();
gStructureFilterPanel.syncState();
ngFurtherActionPanel.syncState();
ngStructureFilterPanel.syncState();
+ CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
+ .getLayout();
switchableViewsLayout.show(switchableViewsPanel, currentView);
updateView();
}
-
public class FurtherActionPanel extends JPanel
{
private AnnotationColumnChooser aColChooser;
public void syncState()
{
- if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+ if (aColChooser
+ .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
{
- this.optionsGroup.setSelected(this.hideOption.getModel(),
- true);
+ this.optionsGroup.setSelected(this.hideOption.getModel(), true);
}
else
{
}
});
- this.setBorder(new TitledBorder(MessageManager
- .getString("label.structures_filter")));
+ this.setBorder(new TitledBorder(
+ MessageManager.getString("label.structures_filter")));
JvSwingUtils.jvInitComponent(this);
this.add(all);
private JCheckBox description = new JCheckBox();
- private JTextField searchBox = new JTextField(10);
+ private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
+
+ public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
+ FILTER_BY_ANN_CACHE_KEY, 23);
public SearchPanel(AnnotationColumnChooser aColChooser)
{
this.aColChooser = aColChooser;
JvSwingUtils.jvInitComponent(this);
- this.setBorder(new TitledBorder(MessageManager
- .getString("label.search_filter")));
+ this.setBorder(new TitledBorder(
+ MessageManager.getString("label.search_filter")));
- JvSwingUtils.jvInitComponent(searchBox);
- searchBox.getDocument().addDocumentListener(
- new DocumentListener()
+ searchBox.setToolTipText(
+ MessageManager.getString("info.enter_search_text_here"));
+ searchBox.getEditor().getEditorComponent()
+ .addKeyListener(new java.awt.event.KeyAdapter()
{
@Override
- public void insertUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
-
- @Override
- public void removeUpdate(DocumentEvent e)
- {
- searchStringAction();
- }
-
- @Override
- public void changedUpdate(DocumentEvent e)
+ public void keyPressed(KeyEvent e)
{
- searchStringAction();
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ e.consume();
+ searchStringAction();
+ }
}
});
+ searchBox.getEditor().getEditorComponent()
+ .addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ searchStringAction();
+ }
+ });
- JvSwingUtils.jvInitComponent(displayName, "label.display_name");
- displayName.setEnabled(false);
+ JvSwingUtils.jvInitComponent(displayName, "label.label");
displayName.addActionListener(new ActionListener()
{
@Override
});
JvSwingUtils.jvInitComponent(description, "label.description");
- description.setEnabled(false);
description.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent actionEvent)
{
- discriptionCheckboxAction();
+ descriptionCheckboxAction();
}
});
aColChooser.updateView();
}
- public void discriptionCheckboxAction()
+ public void descriptionCheckboxAction()
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
+ updateSearchPanelToolTips();
+ searchBox.updateCache();
}
public void syncState()
displayName.setEnabled(sp.displayName.isEnabled());
displayName.setSelected(sp.displayName.isSelected());
- searchBox.setText(sp.searchBox.getText());
+ searchBox.setSelectedItem(sp.searchBox.getUserInput());
}
+ 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);
+ }
+ }
+
+ @Override
+ public void ok_actionPerformed()
+ {
+ saveCache();
+ super.ok_actionPerformed();
}
+ @Override
+ public void cancel_actionPerformed()
+ {
+ saveCache();
+ super.cancel_actionPerformed();
+ }
+
+ private void saveCache()
+ {
+ gSearchPanel.searchBox.persistCache();
+ ngSearchPanel.searchBox.persistCache();
+ gSearchPanel.searchBox.updateCache();
+ ngSearchPanel.searchBox.updateCache();
+ }
}
git://source.jalview.org / jalview.git / blobdiff