package jalview.appletgui; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.ColumnSelection; import jalview.schemes.AnnotationColourGradient; import jalview.util.MessageManager; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; import java.awt.BorderLayout; import java.awt.CardLayout; import java.awt.Checkbox; import java.awt.Choice; import java.awt.Color; import java.awt.Dimension; import java.awt.Frame; import java.awt.Panel; import java.awt.TextField; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.TextEvent; import java.awt.event.TextListener; import java.util.Iterator; import java.util.Vector; import javax.swing.JPanel; //import net.miginfocom.swing.MigLayout; public class AnnotationColumnChooser extends AnnotationRowFilter implements ActionListener, AdjustmentListener, ItemListener, MouseListener { private Choice annotations = new Choice(); private Panel actionPanel = new Panel(); private TitledPanel thresholdPanel = new TitledPanel(); private Panel switchableViewsPanel = new Panel(new CardLayout()); private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel .getLayout()); private Panel noGraphFilterView = new Panel(); private Panel graphFilterView = new Panel(); private Panel annotationComboBoxPanel = new Panel(); private BorderLayout borderLayout1 = new BorderLayout(); private BorderLayout gBorderLayout = new BorderLayout(); private BorderLayout ngBorderLayout = new BorderLayout(); private Choice threshold = new Choice(); private StructureFilterPanel gStructureFilterPanel; private StructureFilterPanel ngStructureFilterPanel; private StructureFilterPanel currentStructureFilterPanel; private SearchPanel currentSearchPanel; private SearchPanel gSearchPanel; private SearchPanel ngSearchPanel; private FurtherActionPanel currentFurtherActionPanel; private FurtherActionPanel gFurtherActionPanel; private FurtherActionPanel ngFurtherActionPanel; public static final int ACTION_OPTION_SELECT = 1; public static int ACTION_OPTION_HIDE = 2; public static String NO_GRAPH_VIEW = "0"; public static String GRAPH_VIEW = "1"; 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); frame = new Frame(); frame.add(this); jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.select_by_annotation"), 520, 215); slider.addAdjustmentListener(this); slider.addMouseListener(this); if (av.getAlignment().getAlignmentAnnotation() == null) { return; } setOldColumnSelection(av.getColumnSelection()); adjusting = true; Vector list = new Vector(); int index = 1; for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) { String label = av.getAlignment().getAlignmentAnnotation()[i].label; if (!list.contains(label)) { list.addElement(label); } else { list.addElement(label + "_" + (index++)); } } for (int i = 0; i < list.size(); i++) { annotations.addItem(list.elementAt(i).toString()); } populateThresholdComboBox(threshold); // restore Object state from the previous session if one exists if (av.getAnnotationColumnSelectionState() != null) { currentSearchPanel = av.getAnnotationColumnSelectionState() .getCurrentSearchPanel(); currentStructureFilterPanel = av.getAnnotationColumnSelectionState() .getCurrentStructureFilterPanel(); annotations.select(av.getAnnotationColumnSelectionState() .getAnnotations().getSelectedIndex()); threshold.select(av.getAnnotationColumnSelectionState() .getThreshold().getSelectedIndex()); actionOption = av.getAnnotationColumnSelectionState() .getActionOption(); } try { jbInit(); } catch (Exception ex) { } adjusting = false; updateView(); frame.invalidate(); frame.pack(); } private void jbInit() throws Exception { ok.setLabel(MessageManager.getString("action.ok")); cancel.setLabel(MessageManager.getString("action.cancel")); thresholdValue.setEnabled(false); thresholdValue.setColumns(7); ok.addActionListener(this); cancel.addActionListener(this); annotations.addItemListener(this); thresholdValue.addActionListener(this); threshold.addItemListener(this); slider.setBackground(Color.white); slider.setEnabled(false); slider.setPreferredSize(new Dimension(100, 32)); thresholdPanel.setBackground(Color.white); // thresholdPanel.setFont(JvSwingUtils.getLabelFont()); // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]")); actionPanel.setBackground(Color.white); // actionPanel.setFont(JvSwingUtils.getLabelFont()); graphFilterView.setLayout(gBorderLayout); graphFilterView.setBackground(Color.white); noGraphFilterView.setLayout(ngBorderLayout); noGraphFilterView.setBackground(Color.white); annotationComboBoxPanel.setBackground(Color.white); // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont()); gSearchPanel = new SearchPanel(this); ngSearchPanel = new SearchPanel(this); gFurtherActionPanel = new FurtherActionPanel(this); ngFurtherActionPanel = new FurtherActionPanel(this); gStructureFilterPanel = new StructureFilterPanel(this); ngStructureFilterPanel = new StructureFilterPanel(this); thresholdPanel.setTitle("Threshold Filter"); thresholdPanel.add(getThreshold()); thresholdPanel.add(slider); thresholdPanel.add(thresholdValue); actionPanel.add(ok); actionPanel.add(cancel); JPanel staticPanel = new JPanel(); staticPanel.setLayout(new BorderLayout()); staticPanel.setBackground(Color.white); staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH); staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH); graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH); graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER); graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH); noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START); noGraphFilterView.add(ngStructureFilterPanel, java.awt.BorderLayout.CENTER); noGraphFilterView.add(ngFurtherActionPanel, java.awt.BorderLayout.CENTER); annotationComboBoxPanel.add(getAnnotations()); switchableViewsPanel.add(noGraphFilterView, AnnotationColumnChooser.NO_GRAPH_VIEW); 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(); this.validate(); } @SuppressWarnings("unchecked") public void reset() { if (this.getOldColumnSelection() != 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); } ap.paintAlignment(true); } } public void adjustmentValueChanged(AdjustmentEvent evt) { if (!adjusting) { thresholdValue.setText((slider.getValue() / 1000f) + ""); valueChanged(!sliderDragging); } } protected void addSliderMouseListeners() { slider.addMouseListener(new MouseAdapter() { @Override public void mousePressed(MouseEvent e) { sliderDragging = true; super.mousePressed(e); } @Override public void mouseDragged(MouseEvent e) { sliderDragging = true; super.mouseDragged(e); } @Override public void mouseReleased(MouseEvent evt) { if (sliderDragging) { sliderDragging = false; valueChanged(true); } ap.paintAlignment(true); } }); } public void valueChanged(boolean updateAllAnnotation) { if (slider.isEnabled()) { getCurrentAnnotation().threshold.value = slider.getValue() / 1000f; updateView(); ap.paintAlignment(false); } } public Choice getThreshold() { return threshold; } public void setThreshold(Choice threshold) { this.threshold = threshold; } public Choice getAnnotations() { return annotations; } public void setAnnotations(Choice annotations) { this.annotations = annotations; } @Override public void updateView() { // Check if combobox is still adjusting if (adjusting) { return; } AnnotationFilterParameter filterParams = new AnnotationFilterParameter(); setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations() .getSelectedIndex()]); int selectedThresholdItem = getSelectedThresholdItem(getThreshold() .getSelectedIndex()); slider.setEnabled(true); thresholdValue.setEnabled(true); if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD) { slider.setEnabled(false); thresholdValue.setEnabled(false); thresholdValue.setText(""); // build filter params } else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD) { if (getCurrentAnnotation().threshold == null) { getCurrentAnnotation() .setThreshold( new jalview.datamodel.GraphLine( (getCurrentAnnotation().graphMax - getCurrentAnnotation().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)); slider.setEnabled(true); thresholdValue.setEnabled(true); adjusting = false; // build filter params filterParams .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH) { filterParams .setThresholdValue(getCurrentAnnotation().threshold.value); if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD) { filterParams .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD); } else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD) { filterParams .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD); } } } if (currentStructureFilterPanel != null) { if (currentStructureFilterPanel.alphaHelix.getState()) { filterParams.setFilterAlphaHelix(true); } if (currentStructureFilterPanel.betaStrand.getState()) { filterParams.setFilterBetaSheet(true); } if (currentStructureFilterPanel.turn.getState()) { filterParams.setFilterTurn(true); } } if (currentSearchPanel != null) { if (!currentSearchPanel.searchBox.getText().isEmpty()) { currentSearchPanel.description.setEnabled(true); currentSearchPanel.displayName.setEnabled(true); filterParams.setRegexString(currentSearchPanel.searchBox.getText()); if (currentSearchPanel.displayName.getState()) { filterParams .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING); } if (currentSearchPanel.description.getState()) { filterParams .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION); } } else { currentSearchPanel.description.setEnabled(false); currentSearchPanel.displayName.setEnabled(false); } } av.getColumnSelection().filterAnnotations( getCurrentAnnotation().annotations, filterParams); av.showAllHiddenColumns(); if (getActionOption() == ACTION_OPTION_HIDE) { av.hideSelectedColumns(); } filterParams = null; av.setAnnotationColumnSelectionState(this); ap.paintAlignment(true); } public ColumnSelection getOldColumnSelection() { return oldColumnSelection; } public void setOldColumnSelection(ColumnSelection currentColumnSelection) { if (currentColumnSelection != null) { this.oldColumnSelection = new ColumnSelection(currentColumnSelection); } } 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; } @Override public void itemStateChanged(ItemEvent e) { if (e.getSource() == annotations) { selectedAnnotationChanged(); } else if (e.getSource() == threshold) { threshold_actionPerformed(null); } } public void selectedAnnotationChanged() { String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW; if (av.getAlignment().getAlignmentAnnotation()[getAnnotations() .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH) { currentView = AnnotationColumnChooser.GRAPH_VIEW; } gSearchPanel.syncState(); gFurtherActionPanel.syncState(); gStructureFilterPanel.syncState(); ngSearchPanel.syncState(); ngFurtherActionPanel.syncState(); ngStructureFilterPanel.syncState(); switchableViewsLayout.show(switchableViewsPanel, currentView); updateView(); } public class FurtherActionPanel extends Panel implements ItemListener { private AnnotationColumnChooser aColChooser; private Choice furtherAction = new Choice(); public FurtherActionPanel(AnnotationColumnChooser aColChooser) { this.aColChooser = aColChooser; furtherAction.addItem("Select"); furtherAction.addItem("Hide"); furtherAction.addItemListener(this); syncState(); // this.setTitle("Filter Actions"); // this.setFont(JvSwingUtils.getLabelFont()); this.add(furtherAction); } public void syncState() { if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE) { furtherAction.select("Hide"); } else { furtherAction.select("Select"); } } @Override public void itemStateChanged(ItemEvent e) { aColChooser.setCurrentFutherActionPanel(this); if (furtherAction.getSelectedItem().equalsIgnoreCase("Select")) { setActionOption(ACTION_OPTION_SELECT); updateView(); } else { setActionOption(ACTION_OPTION_HIDE); updateView(); } } } public class StructureFilterPanel extends TitledPanel implements ItemListener { private AnnotationColumnChooser aColChooser; private Checkbox alphaHelix = new Checkbox(); private Checkbox betaStrand = new Checkbox(); private Checkbox turn = new Checkbox(); private Checkbox all = new Checkbox(); public StructureFilterPanel(AnnotationColumnChooser aColChooser) { this.aColChooser = aColChooser; alphaHelix.setLabel(MessageManager.getString("label.alpha_helix")); alphaHelix.setBackground(Color.white); alphaHelix.addItemListener(this); betaStrand.setLabel(MessageManager.getString("label.beta_strand")); betaStrand.setBackground(Color.white); betaStrand.addItemListener(this); turn.setLabel(MessageManager.getString("label.turn")); turn.setBackground(Color.white); turn.addItemListener(this); all.setLabel(MessageManager.getString("label.select_all")); all.setBackground(Color.white); all.addItemListener(this); this.setBackground(Color.white); this.setTitle("Structure Filter"); // this.setFont(JvSwingUtils.getLabelFont()); 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.getState()) { alphaHelix.setState(true); betaStrand.setState(true); turn.setState(true); } else { alphaHelix.setState(false); betaStrand.setState(false); turn.setState(false); } aColChooser.setCurrentStructureFilterPanel(this); aColChooser.updateView(); } public void updateSelectAllState() { if (alphaHelix.getState() && betaStrand.getState() && turn.getState()) { all.setState(true); } else { all.setState(false); } } public void syncState() { StructureFilterPanel sfp = aColChooser .getCurrentStructureFilterPanel(); if (sfp != null) { alphaHelix.setState(sfp.alphaHelix.getState()); betaStrand.setState(sfp.betaStrand.getState()); turn.setState(sfp.turn.getState()); if (sfp.all.getState()) { all.setState(true); alphaHelix.setState(true); betaStrand.setState(true); turn.setState(true); } } } @Override public void itemStateChanged(ItemEvent e) { if (e.getSource() == alphaHelix) { alphaHelix_actionPerformed(); } else if (e.getSource() == betaStrand) { betaStrand_actionPerformed(); } else if (e.getSource() == turn) { turn_actionPerformed(); } else if (e.getSource() == all) { all_actionPerformed(); } } } public class SearchPanel extends TitledPanel implements ItemListener { private AnnotationColumnChooser aColChooser; private Checkbox displayName = new Checkbox(); private Checkbox description = new Checkbox(); private TextField searchBox = new TextField(10); public SearchPanel(AnnotationColumnChooser aColChooser) { this.aColChooser = aColChooser; searchBox.addTextListener(new TextListener() { @Override public void textValueChanged(TextEvent e) { searchStringAction(); } }); displayName.setLabel(MessageManager.getString("label.display_name")); displayName.setEnabled(false); displayName.addItemListener(this); description.setLabel(MessageManager.getString("label.description")); description.setEnabled(false); description.addItemListener(this); this.setTitle("Search Filter"); // this.setFont(JvSwingUtils.getLabelFont()); 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(); } public void syncState() { SearchPanel sp = aColChooser.getCurrentSearchPanel(); if (sp != null) { description.setEnabled(sp.description.isEnabled()); description.setState(sp.description.getState()); displayName.setEnabled(sp.displayName.isEnabled()); displayName.setState(sp.displayName.getState()); searchBox.setText(sp.searchBox.getText()); } } @Override public void itemStateChanged(ItemEvent e) { if (e.getSource() == displayName) { displayNameCheckboxAction(); } else if (e.getSource() == description) { discriptionCheckboxAction(); } } } public void actionPerformed(ActionEvent evt) { if (evt.getSource() == thresholdValue) { try { float f = new Float(thresholdValue.getText()).floatValue(); slider.setValue((int) (f * 1000)); adjustmentValueChanged(null); } catch (NumberFormatException ex) { } } else if (evt.getSource() == ok) { ok_actionPerformed(null); } else if (evt.getSource() == cancel) { cancel_actionPerformed(null); } else if (evt.getSource() == thresholdValue) { thresholdValue_actionPerformed(null); } else { updateView(); } } @Override public void mouseClicked(MouseEvent e) { // TODO Auto-generated method stub } @Override public void mousePressed(MouseEvent e) { if (e.getSource() == slider) { updateView(); } } @Override public void mouseReleased(MouseEvent e) { if (e.getSource() == slider) { updateView(); } } @Override public void mouseEntered(MouseEvent e) { if (e.getSource() == slider) { updateView(); } } @Override public void mouseExited(MouseEvent e) { if (e.getSource() == slider) { updateView(); } } }