X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=5adecad0a226dbe24e45a7c72c9ee25177844a18;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=6cf359b700dbdb817e685eab58ce444937cc8bc3;hpb=14985603cea28569e295ddabb219da8034f1c7b2;p=jalview.git diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java index 6cf359b..5adecad 100644 --- a/src/jalview/gui/AnnotationColumnChooser.java +++ b/src/jalview/gui/AnnotationColumnChooser.java @@ -21,8 +21,8 @@ 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.viewmodel.annotationfilter.AnnotationFilterParameter; @@ -30,11 +30,14 @@ import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; 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.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; @@ -43,16 +46,13 @@ import javax.swing.JInternalFrame; 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 JPanel switchableViewsPanel = new JPanel(new CardLayout()); @@ -88,6 +88,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements private HiddenColumns oldHiddenColumns; + protected int MIN_WIDTH = 420; + + protected int MIN_HEIGHT = 430; + public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap) { super(av, ap); @@ -97,6 +101,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements Desktop.addInternalFrame(frame, MessageManager.getString("label.select_by_annotation"), 520, 215); + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); addSliderChangeListener(); addSliderMouseListeners(); @@ -108,22 +113,23 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements setOldHiddenColumns(av.getAlignment().getHiddenColumns()); adjusting = true; - setAnnotations(new JComboBox(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 @@ -145,12 +151,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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]", "[][]")); + percentThreshold.setBackground(Color.white); + percentThreshold.setFont(JvSwingUtils.getLabelFont()); + JPanel actionPanel = new JPanel(); actionPanel.setBackground(Color.white); actionPanel.setFont(JvSwingUtils.getLabelFont()); @@ -174,8 +183,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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); @@ -230,24 +240,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements if (av.getAnnotationColumnSelectionState() != null) { - HiddenColumns oldHidden = av - .getAnnotationColumnSelectionState() + HiddenColumns oldHidden = av.getAnnotationColumnSelectionState() .getOldHiddenColumns(); - if (oldHidden != null && oldHidden.getHiddenRegions() != null - && !oldHidden.getHiddenRegions().isEmpty()) - { - for (Iterator itr = oldHidden.getHiddenRegions() - .iterator(); itr.hasNext();) - { - int positions[] = itr.next(); - av.hideColumns(positions[0], positions[1]); - } - } av.getAlignment().setHiddenColumns(oldHidden); } - ap.paintAlignment(true); + av.sendSelection(); + ap.paintAlignment(true, true); } - } @Override @@ -259,7 +258,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements updateView(); propagateSeqAssociatedThreshold(updateAllAnnotation, getCurrentAnnotation()); - ap.paintAlignment(false); + ap.paintAlignment(false, false); } } @@ -274,31 +273,33 @@ 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); 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) { - getCurrentAnnotation() - .setThreshold( - new jalview.datamodel.GraphLine( - (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f, - "Threshold", Color.black)); + getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine( + (getCurrentAnnotation().graphMax + - getCurrentAnnotation().graphMin) / 2f, + "Threshold", Color.black)); } adjusting = true; @@ -307,30 +308,33 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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.setValue( + (int) (getCurrentAnnotation().threshold.value * 1000)); + + 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().graph != AlignmentAnnotation.NO_GRAPH) + filterParams.setThresholdType( + AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); + if (getCurrentAnnotation().isQuantitative()) { filterParams .setThresholdValue(getCurrentAnnotation().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); } } } @@ -354,42 +358,41 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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); - 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 HiddenColumns getOldHiddenColumns() @@ -478,11 +481,11 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements { 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(); @@ -555,7 +558,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements public void syncState() { - if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE) + if (aColChooser + .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE) { this.optionsGroup.setSelected(this.hideOption.getModel(), true); } @@ -622,8 +626,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } }); - this.setBorder(new TitledBorder(MessageManager - .getString("label.structures_filter"))); + this.setBorder(new TitledBorder( + MessageManager.getString("label.structures_filter"))); JvSwingUtils.jvInitComponent(this); this.add(all); @@ -713,42 +717,46 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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 searchBox = new JvCacheableInputBox<>( + FILTER_BY_ANN_CACHE_KEY); public SearchPanel(AnnotationColumnChooser aColChooser) { this.aColChooser = aColChooser; JvSwingUtils.jvInitComponent(this); - this.setBorder(new TitledBorder(MessageManager - .getString("label.search_filter"))); - - JvSwingUtils.jvInitComponent(searchBox); - searchBox.setToolTipText(MessageManager - .getString("info.enter_search_text_here")); - searchBox.getDocument().addDocumentListener(new DocumentListener() + 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() + { + @Override + public void keyPressed(KeyEvent e) + { + if (e.getKeyCode() == KeyEvent.VK_ENTER) + { + e.consume(); + searchStringAction(); + } + } + }); + searchBox.getEditor().getEditorComponent() + .addFocusListener(new FocusAdapter() { @Override - public void insertUpdate(DocumentEvent e) - { - searchStringAction(); - } - - @Override - public void removeUpdate(DocumentEvent e) - { - searchStringAction(); - } - - @Override - public void changedUpdate(DocumentEvent e) + public void focusLost(FocusEvent e) { searchStringAction(); } }); JvSwingUtils.jvInitComponent(displayName, "label.label"); - displayName.setEnabled(false); displayName.addActionListener(new ActionListener() { @Override @@ -759,13 +767,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements }); JvSwingUtils.jvInitComponent(description, "label.description"); - description.setEnabled(false); description.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { - discriptionCheckboxAction(); + descriptionCheckboxAction(); } }); @@ -781,7 +788,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements aColChooser.updateView(); } - public void discriptionCheckboxAction() + public void descriptionCheckboxAction() { aColChooser.setCurrentSearchPanel(this); aColChooser.updateView(); @@ -792,6 +799,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements aColChooser.setCurrentSearchPanel(this); aColChooser.updateView(); updateSearchPanelToolTips(); + searchBox.updateCache(); } public void syncState() @@ -805,7 +813,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements displayName.setEnabled(sp.displayName.isEnabled()); displayName.setSelected(sp.displayName.isSelected()); - searchBox.setText(sp.searchBox.getText()); + searchBox.setSelectedItem(sp.searchBox.getUserInput()); } updateSearchPanelToolTips(); } @@ -815,16 +823,37 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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); } } + @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(); + } }