package jalview.gui;
+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 java.awt.BorderLayout;
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.awt.event.KeyEvent;
-import java.util.ArrayList;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBox;
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 HiddenColumns oldHiddenColumns;
- protected int MIN_WIDTH = 420;
-
- protected int MIN_HEIGHT = 430;
+ 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)
{
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();
// restore Object state from the previous session if one exists
if (lastChooser != null)
{
- currentSearchPanel = lastChooser
- .getCurrentSearchPanel();
+ currentSearchPanel = lastChooser.getCurrentSearchPanel();
currentStructureFilterPanel = lastChooser
.getCurrentStructureFilterPanel();
- annotations.setSelectedIndex(lastChooser
- .getAnnotations().getSelectedIndex());
- threshold.setSelectedIndex(lastChooser
- .getThreshold().getSelectedIndex());
- actionOption = lastChooser
- .getActionOption();
- percentThreshold.setSelected(lastChooser.percentThreshold
- .isSelected());
+ annotations.setSelectedIndex(
+ lastChooser.getAnnotations().getSelectedIndex());
+ threshold.setSelectedIndex(
+ lastChooser.getThreshold().getSelectedIndex());
+ actionOption = lastChooser.getActionOption();
+ percentThreshold
+ .setSelected(lastChooser.percentThreshold.isSelected());
}
try
super.jbInit();
JPanel thresholdPanel = new JPanel();
- thresholdPanel.setBorder(new TitledBorder(MessageManager
- .getString("label.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]", "[][]"));
+ thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]") );
percentThreshold.setBackground(Color.white);
percentThreshold.setFont(JvSwingUtils.getLabelFont());
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);
if (av.getAnnotationColumnSelectionState() != null)
{
- HiddenColumns oldHidden = av
- .getAnnotationColumnSelectionState()
+ HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
.getOldHiddenColumns();
- if (oldHidden != null)
- {
- ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
- for (int[] positions : regions)
- {
- av.hideColumns(positions[0], positions[1]);
- }
- }
- // TODO not clear why we need to hide all the columns (above) if we are
- // going to copy the hidden columns over wholesale anyway
av.getAlignment().setHiddenColumns(oldHidden);
}
av.sendSelection();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
{
if (slider.isEnabled())
{
- getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+ getCurrentAnnotation().threshold.value = getSliderValue();
updateView();
propagateSeqAssociatedThreshold(updateAllAnnotation,
getCurrentAnnotation());
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
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);
}
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));
-
+ setSliderModel(currentAnnotation.graphMin,
+ currentAnnotation.graphMax,
+ currentAnnotation.threshold.value);
+
setThresholdValueText();
- slider.setMajorTickSpacing((int) (range / 10f));
slider.setEnabled(true);
thresholdValue.setEnabled(true);
adjusting = false;
// build filter params
- filterParams
- .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
- if (getCurrentAnnotation().isQuantitative())
+ 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);
}
}
}
{
if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
{
- filterParams.setRegexString(currentSearchPanel.searchBox
- .getUserInput());
+ 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);
}
}
}
// adding them to the selection
av.showAllHiddenColumns();
av.getColumnSelection().filterAnnotations(
- getCurrentAnnotation().annotations, filterParams);
+ currentAnnotation.annotations, filterParams);
- if (getActionOption() == ACTION_OPTION_HIDE)
+ boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
+ if (hideCols)
{
av.hideSelectedColumns();
}
filterParams = null;
av.setAnnotationColumnSelectionState(this);
- ap.paintAlignment(true);
+ // only update overview and structures if columns were hidden
+ ap.paintAlignment(hideCols, hideCols);
}
public HiddenColumns getOldHiddenColumns()
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
- if (av.getAlignment()
- .getAlignmentAnnotation()[annmap[getAnnotations()
+ if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
.getSelectedIndex()]].isQuantitative())
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
.getLayout();
- switchableViewsLayout.show(switchableViewsPanel, currentView);
+ switchableViewsLayout.show(switchableViewsPanel, currentView);
updateView();
}
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.setBorder(new TitledBorder(MessageManager
- .getString("label.structures_filter")));
+ this.setBorder(new TitledBorder(
+ MessageManager.getString("label.structures_filter")));
JvSwingUtils.jvInitComponent(this);
this.add(all);
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);
+ 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.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
- searchBox.setToolTipText(MessageManager
- .getString("info.enter_search_text_here"));
- searchBox.getEditor().getEditorComponent()
- .addKeyListener(new java.awt.event.KeyAdapter()
+ 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)
}
}
});
-
-
+ 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)
{
- discriptionCheckboxAction();
+ descriptionCheckboxAction();
}
});
syncState();
- this.add(searchBox);
+ this.add(searchBox.getComponent());
this.add(displayName);
this.add(description);
}
aColChooser.updateView();
}
- public void discriptionCheckboxAction()
+ public void descriptionCheckboxAction()
{
aColChooser.setCurrentSearchPanel(this);
aColChooser.updateView();
String defaultTtip = MessageManager
.getString("info.enter_search_text_to_enable");
String labelTtip = MessageManager.formatMessage(
- "info.search_in_annotation_label", annotations
- .getSelectedItem().toString());
+ "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);
+ "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