X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=020e027af438ac784585d2580cebf39df8b46107;hb=106a3890f956e2aa7780b2985f4326655912a558;hp=a95d0c0842025da7710cfbbb88c6173aa013bb49;hpb=84a135ae1933c4b497578fd4459de95424a007b9;p=jalview.git diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java index a95d0c0..020e027 100644 --- a/src/jalview/gui/AnnotationColumnChooser.java +++ b/src/jalview/gui/AnnotationColumnChooser.java @@ -36,7 +36,7 @@ import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.KeyEvent; -import java.util.Iterator; +import java.util.ArrayList; import javax.swing.ButtonGroup; import javax.swing.JCheckBox; @@ -50,8 +50,8 @@ import javax.swing.border.TitledBorder; 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()); @@ -119,18 +119,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements // 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 @@ -152,8 +150,8 @@ 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]", "[][]")); @@ -241,24 +239,23 @@ 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()) + if (oldHidden != null) { - for (Iterator itr = oldHidden.getHiddenRegions() - .iterator(); itr.hasNext();) + ArrayList regions = oldHidden.getHiddenColumnsCopy(); + for (int[] positions : regions) { - int positions[] = itr.next(); 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); } - ap.paintAlignment(true); + av.sendSelection(); + ap.paintAlignment(true, true); } - } @Override @@ -270,7 +267,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements updateView(); propagateSeqAssociatedThreshold(updateAllAnnotation, getCurrentAnnotation()); - ap.paintAlignment(false); + ap.paintAlignment(false, false); } } @@ -285,11 +282,12 @@ 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); @@ -307,11 +305,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements { 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; @@ -320,8 +317,9 @@ 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)); - + slider.setValue( + (int) (getCurrentAnnotation().threshold.value * 1000)); + setThresholdValueText(); slider.setMajorTickSpacing((int) (range / 10f)); @@ -330,8 +328,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements adjusting = false; // build filter params - filterParams - .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); + filterParams.setThresholdType( + AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); if (getCurrentAnnotation().isQuantitative()) { filterParams @@ -339,13 +337,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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); } } } @@ -371,17 +369,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements { 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); } } } @@ -393,7 +391,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements av.getColumnSelection().filterAnnotations( getCurrentAnnotation().annotations, filterParams); - if (getActionOption() == ACTION_OPTION_HIDE) + boolean hideCols = getActionOption() == ACTION_OPTION_HIDE; + if (hideCols) { av.hideSelectedColumns(); } @@ -401,7 +400,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements filterParams = null; av.setAnnotationColumnSelectionState(this); - ap.paintAlignment(true); + // only update overview and structures if columns were hidden + ap.paintAlignment(hideCols, hideCols); } public HiddenColumns getOldHiddenColumns() @@ -489,8 +489,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements 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; @@ -568,7 +567,8 @@ 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); } @@ -635,8 +635,8 @@ 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); @@ -728,7 +728,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT"; - public JvCacheableInputBox searchBox = new JvCacheableInputBox( + public JvCacheableInputBox searchBox = new JvCacheableInputBox<>( FILTER_BY_ANN_CACHE_KEY); public SearchPanel(AnnotationColumnChooser aColChooser) @@ -736,12 +736,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements this.aColChooser = aColChooser; JvSwingUtils.jvInitComponent(this); - this.setBorder(new TitledBorder(MessageManager - .getString("label.search_filter"))); + this.setBorder(new TitledBorder( + MessageManager.getString("label.search_filter"))); searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX"); - searchBox.setToolTipText(MessageManager - .getString("info.enter_search_text_here")); + searchBox.setToolTipText( + MessageManager.getString("info.enter_search_text_here")); searchBox.getEditor().getEditorComponent() .addKeyListener(new java.awt.event.KeyAdapter() { @@ -756,8 +756,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } }); - - JvSwingUtils.jvInitComponent(displayName, "label.label"); displayName.addActionListener(new ActionListener() { @@ -825,15 +823,15 @@ 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); } }