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 java.awt.BorderLayout;
+import java.awt.CardLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.Iterator;
import javax.swing.JButton;
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 net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
-public class AnnotationColumnChooser extends AnnotationRowFilter
+public class AnnotationColumnChooser extends AnnotationRowFilter implements
+ ItemListener
{
private ColumnSelection oldColumnSelection;
JButton cancel = new JButton();
- JPanel jPanel1 = new JPanel();
+ JPanel actionPanel = new JPanel();
- JPanel jPanel2 = 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 currentStructureFilterPanel;
+
+ JLabel annotationLabel = new JLabel();
BorderLayout borderLayout1 = new BorderLayout();
private JComboBox<String> threshold = new JComboBox<String>();
+ 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;
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
{
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.select_by_annotation"), 520,
+ 215);
addSliderChangeListener();
addSliderMouseListeners();
setOldColumnSelection(av.getColumnSelection());
adjusting = true;
- setAnnotations(new JComboBox<String>(
- getAnnotationItems(seqAssociated.isSelected())));
+ setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
populateThresholdComboBox(threshold);
- if (av.getCurrentAnnotationColumnSelectionState() != null)
+ // restore the Object state from the previous session if one exists
+ if (av.getAnnotationColumnSelectionState() != null)
{
- annotations.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getAnnotations()
- .getSelectedIndex());
- threshold.setSelectedIndex(av
- .getCurrentAnnotationColumnSelectionState().getThreshold()
- .getSelectedIndex());
+ currentSearchPanel = av.getAnnotationColumnSelectionState()
+ .getCurrentSearchPanel();
+ currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+ .getCurrentStructureFilterPanel();
+ annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ .getAnnotations().getSelectedIndex());
+ threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
+ .getThreshold().getSelectedIndex());
+ actionOption = av.getAnnotationColumnSelectionState()
+ .getActionOption();
+
}
try
frame.pack();
}
-
public AnnotationColumnChooser()
{
try
}
});
- getAnnotations().addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
+ getAnnotations().addItemListener(this);
getThreshold().addActionListener(new ActionListener()
{
@Override
threshold_actionPerformed(e);
}
});
+
thresholdValue.addActionListener(new ActionListener()
{
@Override
slider.setPreferredSize(new Dimension(100, 32));
thresholdValue.setEnabled(false);
thresholdValue.setColumns(7);
- thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
- thresholdIsMin.setText(MessageManager
- .getString("label.threshold_minmax"));
- thresholdIsMin.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent actionEvent)
- {
- thresholdIsMin_actionPerformed(actionEvent);
- }
- });
- seqAssociated.setBackground(Color.white);
- seqAssociated.setFont(JvSwingUtils.getLabelFont());
- seqAssociated.setText(MessageManager
- .getString("label.per_sequence_only"));
- seqAssociated.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
- }
- });
+ annotationLabel.setBackground(Color.white);
+ annotationLabel.setFont(JvSwingUtils.getLabelFont());
+ annotationLabel.setText("Select Annotation : ");
+
+ thresholdPanel.setBorder(new TitledBorder("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);
- jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
- jPanel1.setBackground(Color.white);
- jPanel2.setBackground(Color.white);
-
- jPanel1.add(ok);
- jPanel1.add(cancel);
- jPanel2.add(getAnnotations(), "grow, wrap");
- jPanel2.add(seqAssociated, "wrap");
- jPanel2.add(getThreshold(), "grow, wrap");
- jPanel2.add(thresholdIsMin, "wrap");
- jPanel2.add(slider, "grow");
- jPanel2.add(thresholdValue, "grow");
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.CENTER);
+ 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());
+
+ 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.add(getThreshold());
+ thresholdPanel.add(thresholdValue, "wrap");
+ thresholdPanel.add(slider, "grow, span, wrap");
+
+ actionPanel.add(ok);
+ actionPanel.add(cancel);
+
+ graphFilterView.add(gSearchPanel, "grow, span, wrap");
+ graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
+ graphFilterView.add(thresholdPanel, "grow, span, wrap");
+ graphFilterView.add(gFurtherActionPanel);
+
+ noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
+ noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
+ noGraphFilterView.add(ngFurtherActionPanel);
+
+ annotationComboBoxPanel.add(getAnnotations());
+ switchableViewsPanel.add(noGraphFilterView,
+ AnnotationColumnChooser.NO_GRAPH_VIEW);
+ switchableViewsPanel.add(graphFilterView,
+ AnnotationColumnChooser.GRAPH_VIEW);
+
+ 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()
{
- av.getColumnSelection().clear();
- av.setColumnSelection(this.getOldColumnSelection());
+ 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<int[]> itr = oldSelection.getHiddenColumns()
+ .iterator(); itr.hasNext();)
+ {
+ int positions[] = itr.next();
+ av.hideColumns(positions[0], positions[1]);
+ }
+ }
+ av.setColumnSelection(oldSelection);
+ }
+ // ap.alignmentChanged();
+ ap.paintAlignment(true);
+ }
+
}
public void valueChanged(boolean updateAllAnnotation)
{
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
- updateView();
- propagateSeqAssociatedThreshold(updateAllAnnotation,
- getCurrentAnnotation());
- ap.paintAlignment(false);
+ if (slider.isEnabled())
+ {
+ getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ updateView();
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false);
+ }
}
public JComboBox<String> getThreshold()
@Override
public void updateView()
{
- changeColumnSelection();
- }
- void changeColumnSelection()
- {
// Check if combobox is still adjusting
if (adjusting)
{
return;
}
+ AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
+
setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
.getSelectedIndex()]]);
-
int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
.getSelectedIndex());
slider.setEnabled(true);
thresholdValue.setEnabled(true);
- thresholdIsMin.setEnabled(true);
if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
{
slider.setEnabled(false);
thresholdValue.setEnabled(false);
thresholdValue.setText("");
- thresholdIsMin.setEnabled(false);
+ // build filter params
}
- else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
- && getCurrentAnnotation().threshold == null)
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
{
- getCurrentAnnotation()
- .setThreshold(new jalview.datamodel.GraphLine(
- (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
- "Threshold", Color.black));
- }
+ if (getCurrentAnnotation().threshold == null)
+ {
+ getCurrentAnnotation()
+ .setThreshold(
+ new jalview.datamodel.GraphLine(
+ (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+ "Threshold", Color.black));
+ }
- if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
- {
adjusting = true;
float range = getCurrentAnnotation().graphMax * 1000
- getCurrentAnnotation().graphMin * 1000;
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
+
+ // build filter params
+ filterParams
+ .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+ if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+ {
+
+ 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.getAlphaHelix().isSelected())
+ {
+ filterParams.setFilterAlphaHelix(true);
+ }
+ if (currentStructureFilterPanel.getBetaStrand().isSelected())
+ {
+ filterParams.setFilterBetaSheet(true);
+ }
+ if (currentStructureFilterPanel.getTurn().isSelected())
+ {
+ filterParams.setFilterTurn(true);
+ }
+ }
+
+ if (currentSearchPanel != null)
+ {
+ if (!currentSearchPanel.getSearchString().isEmpty())
+ {
+ currentSearchPanel.getDescription().setEnabled(true);
+ currentSearchPanel.getDisplayName().setEnabled(true);
+ filterParams.setRegexString(currentSearchPanel.getSearchString());
+ if (currentSearchPanel.isDisplayNameChecked())
+ {
+ filterParams
+ .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+ }
+ if (currentSearchPanel.isDescriptionChecked())
+ {
+ filterParams
+ .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+ }
+ }
+ else
+ {
+ currentSearchPanel.getDescription().setEnabled(false);
+ currentSearchPanel.getDisplayName().setEnabled(false);
+ }
}
- markColumnsContaining(getCurrentAnnotation(), selectedThresholdItem);
- av.setCurrentAnnotationColumnSelectionState(this);
- ap.alignmentChanged();
+ filterAnnotations(getCurrentAnnotation().annotations, filterParams,
+ av.getColumnSelection());
+
+ av.showAllHiddenColumns();
+ if (getActionOption() == ACTION_OPTION_HIDE)
+ {
+ av.hideSelectedColumns();
+ }
+
+ filterParams = null;
+ av.setAnnotationColumnSelectionState(this);
ap.paintAlignment(true);
}
{
if (currentColumnSelection != null)
{
- this.oldColumnSelection = new ColumnSelection();
- this.oldColumnSelection.setElementsFrom(currentColumnSelection);
+ this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
}
}
+
+
+ public void select_action(ActionEvent actionEvent)
+ {
+ JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
+ if (radioButton.isSelected())
+ {
+ setActionOption(ACTION_OPTION_SELECT);
+ updateView();
+ }
+ }
+
+ public void hide_action(ActionEvent actionEvent)
+ {
+ JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
+ if (radioButton.isSelected())
+ {
+ setActionOption(ACTION_OPTION_HIDE);
+ updateView();
+ }
+ }
+
+
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ selectedAnnotationChanged();
+ }
+
+ public void selectedAnnotationChanged()
+ {
+ String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
+ if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+ {
+ currentView = AnnotationColumnChooser.GRAPH_VIEW;
+ }
+ // else{
+ // threshold.setSelectedIndex(AlignmentAnnotation.NO_GRAPH);
+ // }
+
+ gSearchPanel.syncState();
+ gFurtherActionPanel.syncState();
+ gFurtherActionPanel.syncState();
+ gFurtherActionPanel.syncState();
+
+ ngSearchPanel.syncState();
+ ngFurtherActionPanel.syncState();
+ ngStructureFilterPanel.syncState();
+ ngFurtherActionPanel.syncState();
+
+ switchableViewsLayout.show(switchableViewsPanel, currentView);
+ updateView();
+ }
+
+
+ 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;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff