X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=f1f78fa1d4fa450e9e7956f9e9ddeb5ad0f7c9fe;hb=HEAD;hp=3db148da094e2a99b852c264c73c64d40a018b25;hpb=c03d2649512cdc491a46dda1d1370273241b5253;p=jalview.git
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 3db148d..f1f78fa 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -1,13 +1,25 @@
-package jalview.gui;
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
-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;
+package jalview.gui;
import java.awt.BorderLayout;
import java.awt.CardLayout;
@@ -15,61 +27,45 @@ import java.awt.Color;
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.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.border.TitledBorder;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.io.cache.JvCacheableInputBox;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
-public class AnnotationColumnChooser extends AnnotationRowFilter implements
- ItemListener
+public class AnnotationColumnChooser extends AnnotationRowFilter
+ implements ItemListener
{
+ private JPanel switchableViewsPanel = new JPanel(new CardLayout());
- private ColumnSelection oldColumnSelection;
-
- private JComboBox annotations;
-
- JButton ok = new JButton();
+ private JPanel annotationComboBoxPanel = new JPanel();
- JButton cancel = new JButton();
+ private StructureFilterPanel gStructureFilterPanel;
- JPanel actionPanel = new JPanel();
-
- JPanel thresholdPanel = new JPanel();
-
- JPanel switchableViewsPanel = new JPanel(new CardLayout());
-
- CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
- .getLayout());
-
- JPanel noGraphFilterView = new JPanel();
-
- JPanel graphFilterView = new JPanel();
-
- JPanel annotationComboBoxPanel = new JPanel();
-
- StructureFilterPanel gStructureFilterPanel;
-
- StructureFilterPanel ngStructureFilterPanel;
+ private StructureFilterPanel ngStructureFilterPanel;
private StructureFilterPanel currentStructureFilterPanel;
- JLabel annotationLabel = new JLabel();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- private JComboBox threshold = new JComboBox();
-
private SearchPanel currentSearchPanel;
private SearchPanel gSearchPanel;
@@ -92,15 +88,30 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
private int actionOption = ACTION_OPTION_SELECT;
+ private HiddenColumns oldHiddenColumns;
+
+ protected static int MIN_WIDTH = (Platform.isJS() ? 370 : 420);
+
+ protected static int MIN_HEIGHT = (Platform.isJS() ? 370 : 430);
+
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
+ this(av, ap, null);
+ }
+
+ public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap,
+ AlignmentAnnotation selectedAnnotation)
+ {
super(av, ap);
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
- MessageManager.getString("label.select_by_annotation"), 520,
- 215);
+ MessageManager.getString("label.select_by_annotation"), 0, 0);
+ // BH note: MIGLayout ignores this completely,
+ // possibly creating a frame smaller than specified:
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
addSliderChangeListener();
addSliderMouseListeners();
@@ -109,26 +120,38 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
{
return;
}
- setOldColumnSelection(av.getColumnSelection());
+ setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
- setAnnotations(new JComboBox(getAnnotationItems(false)));
+ setAnnotations(new JComboBox<>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
-
- // restore the Object state from the previous session if one exists
- if (av.getAnnotationColumnSelectionState() != null)
+ AnnotationColumnChooser lastChooser = av
+ .getAnnotationColumnSelectionState();
+ // restore Object state from the previous session if one exists
+ 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());
+ }
+ if (selectedAnnotation != null)
+ {
+ try
+ {
+ setCurrentAnnotation(selectedAnnotation);
+ annotations.setSelectedItem(
+ getAnnotationMenuLabel(selectedAnnotation));
+ } catch (Exception x)
+ {
+ Console.error("Couldn't select annotation in column chooser", x);
+ }
}
try
@@ -144,85 +167,33 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
frame.pack();
}
- public AnnotationColumnChooser()
- {
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- 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);
- }
- });
- cancel.setOpaque(false);
- cancel.setText(MessageManager.getString("action.cancel"));
- cancel.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
+ super.jbInit();
- getAnnotations().addItemListener(this);
- getThreshold().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
-
- 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));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
-
- annotationLabel.setBackground(Color.white);
- annotationLabel.setFont(JvSwingUtils.getLabelFont());
- annotationLabel.setText("Select Annotation : ");
-
- thresholdPanel.setBorder(new TitledBorder("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());
- this.setLayout(borderLayout1);
+ 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);
+
annotationComboBoxPanel.setBackground(Color.white);
annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
@@ -233,10 +204,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
gStructureFilterPanel = new StructureFilterPanel(this);
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);
@@ -255,77 +226,63 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
AnnotationColumnChooser.NO_GRAPH_VIEW);
switchableViewsPanel.add(graphFilterView,
AnnotationColumnChooser.GRAPH_VIEW);
-
+ 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()
+ {
+ 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.getOldColumnSelection() != null)
+ 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 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.alignmentChanged();
- 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 getThreshold()
- {
- return threshold;
- }
-
- public void setThreshold(JComboBox threshold)
- {
- this.threshold = threshold;
- }
-
- public JComboBox getAnnotations()
- {
- return annotations;
- }
-
- public void setAnnotations(JComboBox annotations)
- {
- this.annotations = annotations;
- }
-
@Override
public void updateView()
{
@@ -337,76 +294,79 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
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(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.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);
}
@@ -414,56 +374,97 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
if (currentSearchPanel != null)
{
- if (!currentSearchPanel.getSearchString().isEmpty())
+ if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
{
- currentSearchPanel.getDescription().setEnabled(true);
- currentSearchPanel.getDisplayName().setEnabled(true);
- filterParams.setRegexString(currentSearchPanel.getSearchString());
- if (currentSearchPanel.isDisplayNameChecked())
+ filterParams.setRegexString(
+ currentSearchPanel.searchBox.getUserInput());
+ if (currentSearchPanel.displayName.isSelected())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
}
- if (currentSearchPanel.isDescriptionChecked())
+ if (currentSearchPanel.description.isSelected())
{
- filterParams
- .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+ filterParams.addRegexSearchField(
+ AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
}
}
- else
- {
- currentSearchPanel.getDescription().setEnabled(false);
- currentSearchPanel.getDisplayName().setEnabled(false);
- }
}
- filterAnnotations(getCurrentAnnotation().annotations, filterParams,
- av.getColumnSelection());
-
+ // 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();
- if (getActionOption() == ACTION_OPTION_HIDE)
+ av.getColumnSelection().filterAnnotations(currentAnnotation,
+ filterParams);
+
+ 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);
}
}
+ 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)
{
@@ -485,80 +486,394 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
}
}
-
@Override
public void itemStateChanged(ItemEvent e)
{
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;
}
- // else{
- // threshold.setSelectedIndex(AlignmentAnnotation.NO_GRAPH);
- // }
-
+ saveCache();
gSearchPanel.syncState();
gFurtherActionPanel.syncState();
- gFurtherActionPanel.syncState();
- gFurtherActionPanel.syncState();
+ gStructureFilterPanel.syncState();
ngSearchPanel.syncState();
ngFurtherActionPanel.syncState();
ngStructureFilterPanel.syncState();
- ngFurtherActionPanel.syncState();
+ CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
+ .getLayout();
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();
+
+ private JRadioButton selectOption = new JRadioButton();
+
+ private ButtonGroup optionsGroup = new ButtonGroup();
+
+ public FurtherActionPanel(AnnotationColumnChooser aColChooser)
+ {
+ this.aColChooser = aColChooser;
+ JvSwingUtils.jvInitComponent(selectOption, "action.select");
+ selectOption.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectRadioAction(actionEvent);
+ }
+ });
+
+ 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 SearchPanel getCurrentSearchPanel()
+ public class StructureFilterPanel extends JPanel
{
- return currentSearchPanel;
+ 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 setCurrentSearchPanel(SearchPanel currentSearchPanel)
+ public class SearchPanel extends JPanel
{
- this.currentSearchPanel = currentSearchPanel;
+ private AnnotationColumnChooser aColChooser;
+
+ private JCheckBox displayName = new JCheckBox();
+
+ private JCheckBox description = new JCheckBox();
+
+ private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
+
+ public JvCacheableInputBox 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")));
+
+ searchBox.getComponent().setToolTipText(
+ MessageManager.getString("info.enter_search_text_here"));
+ searchBox.addKeyListener(new java.awt.event.KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ e.consume();
+ searchStringAction();
+ }
+ }
+ });
+ searchBox.addFocusListener(new FocusAdapter()
+ {
+ @Override
+ public void focusLost(FocusEvent e)
+ {
+ searchStringAction();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(displayName, "label.label");
+ displayName.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ displayNameCheckboxAction();
+ }
+ });
+
+ JvSwingUtils.jvInitComponent(description, "label.description");
+ description.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ descriptionCheckboxAction();
+ }
+ });
+
+ syncState();
+ this.add(searchBox.getComponent());
+ this.add(displayName);
+ this.add(description);
+ }
+
+ public void displayNameCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void descriptionCheckboxAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ }
+
+ public void searchStringAction()
+ {
+ aColChooser.setCurrentSearchPanel(this);
+ aColChooser.updateView();
+ updateSearchPanelToolTips();
+ searchBox.updateCache();
+ }
+
+ 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.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);
+ }
}
- public int getActionOption()
+ @Override
+ public void ok_actionPerformed()
{
- return actionOption;
+ saveCache();
+ super.ok_actionPerformed();
}
- public void setActionOption(int actionOption)
+ @Override
+ public void cancel_actionPerformed()
{
- this.actionOption = actionOption;
+ saveCache();
+ super.cancel_actionPerformed();
}
- public StructureFilterPanel getCurrentStructureFilterPanel()
+ private void saveCache()
{
- return currentStructureFilterPanel;
+ gSearchPanel.searchBox.persistCache();
+ ngSearchPanel.searchBox.persistCache();
+ gSearchPanel.searchBox.updateCache();
+ ngSearchPanel.searchBox.updateCache();
}
- public void setCurrentStructureFilterPanel(
- StructureFilterPanel currentStructureFilterPanel)
+ public static void displayFor(AlignViewport av, AlignmentPanel ap,
+ AlignmentAnnotation alignmentAnnotation)
{
- this.currentStructureFilterPanel = currentStructureFilterPanel;
+ AnnotationColumnChooser colchooser = new AnnotationColumnChooser(av, ap,
+ alignmentAnnotation);
}
-
}