From: gmungoc Date: Tue, 23 Sep 2014 13:10:45 +0000 (+0100) Subject: JAL-1264 first cut of panel for annotation show/hide options X-Git-Tag: Jalview_2_9~169^2~22^2~30 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=76d3286a73053be49a8cfd6842fffba4db111e08;p=jalview.git JAL-1264 first cut of panel for annotation show/hide options --- diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 6736791..22754f8 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -54,8 +54,8 @@ action.right_justify_alignment = Right Justify Alignment action.boxes = Boxes action.text = Text action.by_pairwise_id = by Pairwise Identity -action.by_id = by Id action.by_length = by Length +action.by_id = by Id action.by_group = by Group action.remove = Remove action.remove_redundancy = Remove Redundancy... @@ -223,6 +223,7 @@ label.all_columns = All Columns label.all_sequences = All Sequences label.selected_columns = Selected Columns label.selected_sequences = Selected Sequences +label.except_selected_sequences = All except selected sequences label.all_but_selected_region = All but Selected Region (Shift+Ctrl+H) label.selected_region = Selected Region label.all_sequences_columns = All Sequences and Columns @@ -465,9 +466,9 @@ label.to_lower_case = To Lower Case label.toggle_case = Toggle Case label.edit_name_description = Edit Name/Description ... label.create_sequence_feature = Create Sequence Feature ... -label.edit_sequence = Edit Sequence label.edit_sequences = Edit Sequences label.sequence_details = Sequence Details +label.choose_annotations = Show/Hide Sequence Annotations label.jmol_help = Jmol Help label.all = All label.sort_by = Sort by @@ -738,3 +739,6 @@ label.select_columns_containing = Select columns containing label.select_columns_not_containing = Select columns that do not contain option.trim_retrieved_seqs = Trim retrieved sequences label.trim_retrieved_sequences = When the reference sequence is longer than the sequence that you are working with, only keep the relevant subsequences. +label.choose_annotations = Choose annotations to show or hide +label.show_selected_annotations = Show selected annotation types +label.hide_selected_annotations = Hide selected annotation types diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index b4cb3b1..17348c2 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -20,13 +20,18 @@ */ package jalview.datamodel; -import java.util.*; +import jalview.analysis.AAFrequency; +import jalview.analysis.Conservation; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; + +import java.awt.Color; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.Hashtable; import java.util.List; - -import java.awt.*; - -import jalview.analysis.*; -import jalview.schemes.*; +import java.util.Map; +import java.util.Vector; /** * Collects a set contiguous ranges on a set of sequences @@ -289,11 +294,13 @@ public class SequenceGroup implements AnnotatedCollectionI return eres; } + @Override public List getSequences() { return sequences; } + @Override public List getSequences( Map hiddenReps) { @@ -307,7 +314,7 @@ public class SequenceGroup implements AnnotatedCollectionI SequenceI seq; for (int i = 0; i < sequences.size(); i++) { - seq = (SequenceI) sequences.elementAt(i); + seq = sequences.elementAt(i); allSequences.addElement(seq); if (hiddenReps.containsKey(seq)) { @@ -635,6 +642,7 @@ public class SequenceGroup implements AnnotatedCollectionI * * @return the first column selected by this group. Runs from 0<=i 0) { - width = ((SequenceI) sequences.elementAt(0)).getLength(); + width = sequences.elementAt(0).getLength(); } for (int i = 1; i < sequences.size(); i++) { - SequenceI seq = (SequenceI) sequences.elementAt(i); + SequenceI seq = sequences.elementAt(i); if (seq.getLength() > width) { @@ -1211,7 +1221,7 @@ public class SequenceGroup implements AnnotatedCollectionI // TODO add in other methods like 'getAlignmentAnnotation(String label), // etc' ArrayList annot = new ArrayList(); - for (SequenceI seq : (Vector) sequences) + for (SequenceI seq : sequences) { AlignmentAnnotation[] aa = seq.getAnnotation(); if (aa != null) @@ -1250,6 +1260,27 @@ public class SequenceGroup implements AnnotatedCollectionI return aa; } + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param calcId + * @return + */ + public boolean hasAnnotation(String calcId) + { + if (calcId != null && !"".equals(calcId)) + { + for (AlignmentAnnotation a : getAlignmentAnnotation()) + { + if (a.getCalcId() == calcId) + { + return true; + } + } + } + return false; + } + public void clear() { sequences.clear(); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index e6b7af4..544a971 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -4025,6 +4025,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tm.setText(title);// tm.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { NewTreePanel(type, (String) pwtype, title); @@ -5313,6 +5314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); trimrs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); @@ -5703,6 +5705,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } } + + /** + * On menu option, open a panel to allow choice of annotation types to + * show/hide. + */ + @Override + protected void chooseAnnotations_actionPerformed() + { + new AnnotationChooser(this.alignPanel); + } } class PrintThread extends Thread diff --git a/src/jalview/gui/AnnotationChooser.java b/src/jalview/gui/AnnotationChooser.java new file mode 100644 index 0000000..bb940e8 --- /dev/null +++ b/src/jalview/gui/AnnotationChooser.java @@ -0,0 +1,564 @@ +package jalview.gui; + +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceGroup; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Checkbox; +import java.awt.CheckboxGroup; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.GridLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JPanel; + +/** + * A panel that allows the user to select which sequence-associated annotation + * rows to show or hide. + * + * @author gmcarstairs + * + */ +public class AnnotationChooser extends JPanel +{ + + private static final Font CHECKBOX_FONT = new Font("Serif", Font.BOLD, 12); + + private static final int MY_FRAME_WIDTH = 600; + + private static final int MY_FRAME_HEIGHT = 250; + + private JInternalFrame frame; + + private AlignmentPanel ap; + + private SequenceGroup sg; + + // all annotation rows' original visible state + private boolean[] resetState = null; + + // is 'Show' selected? + private boolean showSelected; + + // apply settings to selected (or all) sequences? + private boolean applyToSelectedSequences; + + // apply settings to unselected (or all) sequences? + private boolean applyToUnselectedSequences; + + // currently selected 'annotation type' checkboxes + private Map selectedTypes = new HashMap(); + + /** + * Constructor. + * + * @param alignPane + */ + public AnnotationChooser(AlignmentPanel alignPane) + { + super(); + this.ap = alignPane; + this.sg = alignPane.av.getSelectionGroup(); + saveResetState(alignPane.getAlignment()); + + try + { + jbInit(); + } catch (Exception ex) + { + ex.printStackTrace(); + } + showFrame(); + } + + /** + * Save the initial show/hide state of all annotations to allow a Cancel + * operation. + * + * @param alignment + */ + protected void saveResetState(AlignmentI alignment) + { + AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation(); + final int count = annotations.length; + this.resetState = new boolean[count]; + for (int i = 0; i < count; i++) + { + this.resetState[i] = annotations[i].visible; + } + } + + /** + * Populate this frame with: + *

+ * checkboxes for the types of annotation to show or hide (i.e. any annotation + * type shown for any sequence in the whole alignment) + *

+ * option to show or hide selected types + *

+ * option to show/hide for the currently selected group, or its inverse + *

+ * OK and Cancel (reset) buttons + */ + protected void jbInit() + { + setLayout(new GridLayout(3, 1)); + add(buildAnnotationTypesPanel()); + add(buildShowHideOptionsPanel()); + add(buildActionButtonsPanel()); + validate(); + } + + /** + * Construct the panel with checkboxes for annotation types. + * + * @return + */ + protected JPanel buildAnnotationTypesPanel() + { + JPanel jp = new JPanel(new FlowLayout(FlowLayout.LEFT)); + + List annotationTypes = getAnnotationTypes( + this.ap.getAlignment(), true); + + for (final String type : annotationTypes) + { + final JCheckBox check = new JCheckBox(type); + check.setFont(CHECKBOX_FONT); + check.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { + if (evt.getStateChange() == ItemEvent.SELECTED) + { + AnnotationChooser.this.selectedTypes.put(type, type); + } + else + { + AnnotationChooser.this.selectedTypes.remove(type); + } + repaintAnnotations(false); + } + }); + jp.add(check); + } + return jp; + } + + /** + * Set visibility flags on annotation rows then repaint the alignment panel. + *

+ * Optionally, update all rows, including those not in the 'apply to' scope. + * This makes more sense when switching between selected and unselected + * sequences. When selecting annotation types, or show/hide, we only apply the + * settings to the selected sequences. + *

+ * Note this only affects sequence-specific annotations, others are left + * unchanged. + */ + protected void repaintAnnotations(boolean updateAllRows) + { + for (AlignmentAnnotation aa : this.ap.getAlignment() + .getAlignmentAnnotation()) + { + if (aa.sequenceRef != null) + { + setAnnotationVisibility(aa, updateAllRows); + } + } + // copied from AnnotationLabel.actionPerformed (after show/hide row)... + // TODO should drive this functionality into AlignmentPanel + ap.updateAnnotation(); + this.ap.annotationPanel.adjustPanelHeight(); + this.ap.alabels.setSize(this.ap.alabels.getSize().width, + this.ap.annotationPanel.getSize().height); + this.ap.validate(); + this.ap.paintAlignment(true); + } + + /** + * Determine and set the visibility of the given annotation from the currently + * selected options. + *

+ * If its sequence is in the selected application scope + * (all/selected/unselected sequences), then we set its visibility. + *

+ * If the annotation type is one of those currently selected by checkbox, set + * its visibility to the selected value. If it is not currently selected, set + * it to the opposite value. So, unselecting an annotation type with 'hide' + * selected, will cause those annotations to be unhidden. + *

+ * If force update of all rows is wanted, then set rows not in the sequence + * selection scope to the opposite visibility to those in scope. + * + * @param aa + * @param updateAllRows + */ + protected void setAnnotationVisibility(AlignmentAnnotation aa, + boolean updateAllRows) + { + boolean setToVisible = false; + if (this.selectedTypes.containsKey(aa.label)) + { + setToVisible = this.showSelected; + } + else + { + setToVisible = !this.showSelected; + } + if (isInActionScope(aa)) + { + aa.visible = setToVisible; + } + else if (updateAllRows) + { + aa.visible = !setToVisible; + } + // TODO force not visible if associated sequence is hidden? + // currently hiding a sequence does not hide its annotation rows + } + + /** + * Answers true if the annotation falls in the current selection criteria for + * show/hide. + *

+ * It must be in the sequence selection group (for 'Apply to selection'), or + * not in it (for 'Apply except to selection'). No check needed for 'Apply to + * all'. + * + * @param aa + * @return + */ + protected boolean isInActionScope(AlignmentAnnotation aa) + { + boolean result = false; + if (this.applyToSelectedSequences && this.applyToUnselectedSequences) + { + // we don't care if the annotation's sequence is selected or not + result = true; + } + else if (this.sg.getSequences().contains(aa.sequenceRef)) + { + // annotation is for a member of the selection group + result = this.applyToSelectedSequences ? true : false; + } + else + { + // annotation is not associated with the selection group + result = this.applyToUnselectedSequences ? true : false; + } + return result; + } + + /** + * Get annotation 'types' for an alignment, optionally restricted to + * sequence-specific annotations only. The label is currently used for 'type'. + * + * TODO refactor to helper class. See + * AnnotationColourChooser.getAnnotationItems() for another client + * + * @param alignment + * @param sequenceSpecific + * @return + */ + public static List getAnnotationTypes(AlignmentI alignment, + boolean sequenceSpecificOnly) + { + // stub + List result = new ArrayList(); + for (AlignmentAnnotation aa : alignment.getAlignmentAnnotation()) + { + if (!sequenceSpecificOnly || aa.sequenceRef != null) + { + String label = aa.label; + if (!result.contains(label)) + { + result.add(label); + } + } + } + return result; + } + + /** + * Construct the panel with options to: + *

+ * show or hide the selected annotation types + *

+ * do this for the current selection group or its inverse + * + * @return + */ + protected JPanel buildShowHideOptionsPanel() + { + JPanel jp = new JPanel(); + jp.setLayout(new BorderLayout()); + + JPanel showHideOptions = buildShowHidePanel(); + jp.add(showHideOptions, BorderLayout.CENTER); + + JPanel applyToOptions = buildApplyToOptionsPanel(); + jp.add(applyToOptions, BorderLayout.SOUTH); + + return jp; + } + + /** + * Build a panel with radio buttons options for sequences to apply show/hide + * to. Options are all, current selection, all except current selection. + * Initial state has 'current selection' selected. + *

+ * If the sequence group is null, then we are acting on the whole alignment, + * and only 'all sequences' is enabled (and selected). + * + * @return + */ + protected JPanel buildApplyToOptionsPanel() + { + final boolean wholeAlignment = this.sg == null; + JPanel applyToOptions = new JPanel(new FlowLayout(FlowLayout.LEFT)); + CheckboxGroup actingOn = new CheckboxGroup(); + + String forAll = MessageManager.getString("label.all_sequences"); + final Checkbox allSequences = new Checkbox(forAll, actingOn, + wholeAlignment); + allSequences.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { + if (evt.getStateChange() == ItemEvent.SELECTED) { + AnnotationChooser.this.setApplyToSelectedSequences(true); + AnnotationChooser.this.setApplyToUnselectedSequences(true); + AnnotationChooser.this.repaintAnnotations(true); + } + } + }); + applyToOptions.add(allSequences); + + String forSelected = MessageManager + .getString("label.selected_sequences"); + final Checkbox selectedSequences = new Checkbox(forSelected, actingOn, + !wholeAlignment); + selectedSequences.setEnabled(!wholeAlignment); + selectedSequences.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { + if (evt.getStateChange() == ItemEvent.SELECTED) + { + AnnotationChooser.this.setApplyToSelectedSequences(true); + AnnotationChooser.this.setApplyToUnselectedSequences(false); + AnnotationChooser.this.repaintAnnotations(true); + } + } + }); + applyToOptions.add(selectedSequences); + + String exceptSelected = MessageManager + .getString("label.except_selected_sequences"); + final Checkbox unselectedSequences = new Checkbox(exceptSelected, actingOn, false); + unselectedSequences.setEnabled(!wholeAlignment); + unselectedSequences.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { + if (evt.getStateChange() == ItemEvent.SELECTED) + { + AnnotationChooser.this.setApplyToSelectedSequences(false); + AnnotationChooser.this.setApplyToUnselectedSequences(true); + AnnotationChooser.this.repaintAnnotations(true); + } + } + }); + applyToOptions.add(unselectedSequences); + + // set member variables to match the initial selection state + this.applyToSelectedSequences = selectedSequences.getState() + || allSequences.getState(); + this.applyToUnselectedSequences = unselectedSequences.getState() + || allSequences.getState(); + + return applyToOptions; + } + + /** + * Build a panel with radio buttons options to show or hide selected + * annotations. + * + * @return + */ + protected JPanel buildShowHidePanel() + { + JPanel showHideOptions = new JPanel(new FlowLayout(FlowLayout.LEFT)); + CheckboxGroup showOrHide = new CheckboxGroup(); + + /* + * Radio button 'Show selected annotations' - initially unselected + */ + String showLabel = MessageManager + .getString("label.show_selected_annotations"); + final Checkbox showOption = new Checkbox(showLabel, showOrHide, false); + showOption.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { + if (evt.getStateChange() == ItemEvent.SELECTED) { + AnnotationChooser.this.setShowSelected(true); + AnnotationChooser.this.repaintAnnotations(false); + } + } + }); + showHideOptions.add(showOption); + + /* + * Radio button 'hide selected annotations'- initially selected + */ + String hideLabel = MessageManager + .getString("label.hide_selected_annotations"); + final Checkbox hideOption = new Checkbox(hideLabel, showOrHide, true); + hideOption.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { + if (evt.getStateChange() == ItemEvent.SELECTED) + { + AnnotationChooser.this.setShowSelected(false); + AnnotationChooser.this.repaintAnnotations(false); + } + } + }); + showHideOptions.add(hideOption); + + /* + * Set member variable to match initial selection state + */ + this.showSelected = showOption.getState(); + + return showHideOptions; + } + + /** + * Construct the panel with OK and Cancel buttons. + * + * @return + */ + protected JPanel buildActionButtonsPanel() + { + JPanel jp = new JPanel(); + final Font labelFont = JvSwingUtils.getLabelFont(); + + JButton ok = new JButton(MessageManager.getString("action.ok")); + ok.setFont(labelFont); + ok.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + close_actionPerformed(); + } + }); + jp.add(ok); + + JButton cancel = new JButton(MessageManager.getString("action.cancel")); + cancel.setFont(labelFont); + cancel.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + cancel_actionPerformed(); + } + }); + jp.add(cancel); + + return jp; + } + + /** + * On 'Cancel' button, undo any changes. + */ + protected void cancel_actionPerformed() + { + resetOriginalState(); + this.ap.repaint(); + close_actionPerformed(); + } + + /** + * Restore annotation visibility to their state on entry here, and repaint + * alignment. + */ + protected void resetOriginalState() + { + int i = 0; + for (AlignmentAnnotation aa : this.ap.getAlignment() + .getAlignmentAnnotation()) + { + aa.visible = this.resetState[i++]; + } + } + + /** + * On 'Close' button, close the dialog. + */ + protected void close_actionPerformed() + { + try + { + this.frame.setClosed(true); + } catch (Exception exe) + { + } + } + + /** + * Render a frame containing this panel. + */ + private void showFrame() + { + frame = new JInternalFrame(); + frame.setContentPane(this); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + Desktop.addInternalFrame(frame, + MessageManager.getString("label.choose_annotations"), + MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true); + } + + protected void setShowSelected(boolean showSelected) + { + this.showSelected = showSelected; + } + + protected void setApplyToSelectedSequences( + boolean applyToSelectedSequences) + { + this.applyToSelectedSequences = applyToSelectedSequences; + } + + protected void setApplyToUnselectedSequences( + boolean applyToUnselectedSequences) + { + this.applyToUnselectedSequences = applyToUnselectedSequences; + } + +} diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 39f3a13..32e3f58 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -20,22 +20,38 @@ */ package jalview.gui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import javax.swing.*; -import javax.swing.event.*; - -import net.miginfocom.swing.MigLayout; - import jalview.bin.Cache; -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceGroup; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Color; import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.util.Hashtable; +import java.util.Vector; + +import javax.swing.BorderFactory; +import javax.swing.JButton; +import javax.swing.JCheckBox; +import javax.swing.JColorChooser; +import javax.swing.JComboBox; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JPanel; +import javax.swing.JSlider; +import javax.swing.JTextField; +import javax.swing.event.ChangeEvent; +import javax.swing.event.ChangeListener; + +import net.miginfocom.swing.MigLayout; public class AnnotationColourChooser extends JPanel { @@ -84,11 +100,12 @@ public class AnnotationColourChooser extends JPanel slider.addChangeListener(new ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { if (!adjusting) { - thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); + thresholdValue.setText((slider.getValue() / 1000f) + ""); valueChanged(!sliderDragging); } } @@ -109,6 +126,7 @@ public class AnnotationColourChooser extends JPanel super.mouseDragged(e); } + @Override public void mouseReleased(MouseEvent evt) { if (sliderDragging) @@ -213,7 +231,7 @@ public class AnnotationColourChooser extends JPanel if (!list.contains(label)) { anmap[list.size()] = i; - list.addElement(label); + list.add(label); } else @@ -221,13 +239,13 @@ public class AnnotationColourChooser extends JPanel if (!isSeqAssociated) { anmap[list.size()] = i; - list.addElement(label + "_" + (index++)); + list.add(label + "_" + (index++)); } } } seqAssociated.setEnabled(enableSeqAss); - annmap = new int[list.size()]; - System.arraycopy(anmap, 0, annmap, 0, annmap.length); + this.annmap = new int[list.size()]; + System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length); return list; } @@ -258,6 +276,7 @@ public class AnnotationColourChooser extends JPanel minColour.setToolTipText(MessageManager.getString("label.min_colour")); minColour.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { if (minColour.isEnabled()) @@ -272,6 +291,7 @@ public class AnnotationColourChooser extends JPanel maxColour.setToolTipText(MessageManager.getString("label.max_colour")); maxColour.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { if (maxColour.isEnabled()) @@ -284,6 +304,7 @@ public class AnnotationColourChooser extends JPanel ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); @@ -293,6 +314,7 @@ public class AnnotationColourChooser extends JPanel cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancel_actionPerformed(e); @@ -314,6 +336,7 @@ public class AnnotationColourChooser extends JPanel annotations.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { annotations_actionPerformed(e); @@ -321,6 +344,7 @@ public class AnnotationColourChooser extends JPanel }); threshold.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { threshold_actionPerformed(e); @@ -328,6 +352,7 @@ public class AnnotationColourChooser extends JPanel }); thresholdValue.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { thresholdValue_actionPerformed(e); @@ -347,6 +372,7 @@ public class AnnotationColourChooser extends JPanel .getString("label.use_original_colours")); currentColours.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { currentColours_actionPerformed(e); @@ -358,6 +384,7 @@ public class AnnotationColourChooser extends JPanel .getString("label.threshold_minmax")); thresholdIsMin.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { thresholdIsMin_actionPerformed(actionEvent); @@ -679,7 +706,7 @@ public class AnnotationColourChooser extends JPanel { changeColour(); } - currentAnnotation.threshold.value = (float) slider.getValue() / 1000f; + currentAnnotation.threshold.value = slider.getValue() / 1000f; propagateSeqAssociatedThreshold(updateAllAnnotation); ap.paintAlignment(false); } diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 0957d28..4ff525e 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -25,8 +25,6 @@ import jalview.analysis.Conservation; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.PDBEntry; @@ -60,7 +58,6 @@ import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.Hashtable; -import java.util.List; import java.util.Vector; import javax.swing.ButtonGroup; @@ -129,6 +126,8 @@ public class PopupMenu extends JPopupMenu JMenuItem sequenceSelDetails = new JMenuItem(); + JMenuItem chooseAnnotations = new JMenuItem(); + SequenceI sequence; JMenuItem createGroupMenuItem = new JMenuItem(); @@ -251,6 +250,7 @@ public class PopupMenu extends JPopupMenu item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -287,6 +287,7 @@ public class PopupMenu extends JPopupMenu menuItem.setText(pdb.getId()); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO re JAL-860: optionally open dialog or provide a menu entry @@ -337,6 +338,7 @@ public class PopupMenu extends JPopupMenu menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // System.out.println("1:"+structureLine); @@ -377,6 +379,7 @@ public class PopupMenu extends JPopupMenu { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence @@ -397,6 +400,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(false); @@ -412,6 +416,7 @@ public class PopupMenu extends JPopupMenu { seq.getName() })); menuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSequences(true); @@ -431,6 +436,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.reveal_sequences")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showSequence(index); @@ -452,6 +458,7 @@ public class PopupMenu extends JPopupMenu MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ap.av.showAllHiddenSeqs(); @@ -555,7 +562,7 @@ public class PopupMenu extends JPopupMenu SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { - Vector pes = (Vector) sq.getDatasetSequence() + Vector pes = sq.getDatasetSequence() .getPDBId(); if (pes != null && pes.size() > 0) { @@ -942,11 +949,13 @@ public class PopupMenu extends JPopupMenu { url })); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { showLink(url); @@ -982,11 +991,13 @@ public class PopupMenu extends JPopupMenu // TODO: put in info about what is being sent. item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { try @@ -1017,6 +1028,7 @@ public class PopupMenu extends JPopupMenu groupName.setText(MessageManager.getString("label.name")); groupName.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { groupName_actionPerformed(); @@ -1027,15 +1039,28 @@ public class PopupMenu extends JPopupMenu .getString("label.edit_name_description")); sequenceName.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceName_actionPerformed(); } }); + chooseAnnotations.setText(MessageManager + .getString("label.choose_annotations") + "..."); + chooseAnnotations + .addActionListener(new java.awt.event.ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + chooseAnnotations_actionPerformed(e); + } + }); sequenceDetails.setText(MessageManager .getString("label.sequence_details") + "..."); sequenceDetails.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceDetails_actionPerformed(); @@ -1046,6 +1071,7 @@ public class PopupMenu extends JPopupMenu sequenceSelDetails .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceSelectionDetails_actionPerformed(); @@ -1056,6 +1082,7 @@ public class PopupMenu extends JPopupMenu .setText(MessageManager.getString("action.remove_group")); unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { unGroupMenuItem_actionPerformed(); @@ -1066,6 +1093,7 @@ public class PopupMenu extends JPopupMenu createGroupMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createGroupMenuItem_actionPerformed(); @@ -1075,6 +1103,7 @@ public class PopupMenu extends JPopupMenu outline.setText(MessageManager.getString("action.border_colour")); outline.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outline_actionPerformed(); @@ -1084,6 +1113,7 @@ public class PopupMenu extends JPopupMenu .setText(MessageManager.getString("label.nucleotide")); nucleotideMenuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideMenuItem_actionPerformed(); @@ -1094,6 +1124,7 @@ public class PopupMenu extends JPopupMenu showBoxes.setState(true); showBoxes.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showBoxes_actionPerformed(); @@ -1103,6 +1134,7 @@ public class PopupMenu extends JPopupMenu showText.setState(true); showText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showText_actionPerformed(); @@ -1111,6 +1143,7 @@ public class PopupMenu extends JPopupMenu showColourText.setText(MessageManager.getString("label.colour_text")); showColourText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showColourText_actionPerformed(); @@ -1121,6 +1154,7 @@ public class PopupMenu extends JPopupMenu displayNonconserved.setState(true); displayNonconserved.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showNonconserved_actionPerformed(); @@ -1130,6 +1164,7 @@ public class PopupMenu extends JPopupMenu cut.setText(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(); @@ -1138,6 +1173,7 @@ public class PopupMenu extends JPopupMenu upperCase.setText(MessageManager.getString("label.to_upper_case")); upperCase.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); @@ -1146,6 +1182,7 @@ public class PopupMenu extends JPopupMenu copy.setText(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(); @@ -1154,6 +1191,7 @@ public class PopupMenu extends JPopupMenu lowerCase.setText(MessageManager.getString("label.to_lower_case")); lowerCase.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); @@ -1162,6 +1200,7 @@ public class PopupMenu extends JPopupMenu toggle.setText(MessageManager.getString("label.toggle_case")); toggle.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { changeCase(e); @@ -1172,6 +1211,7 @@ public class PopupMenu extends JPopupMenu pdbFromFile.setText(MessageManager.getString("label.from_file")); pdbFromFile.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pdbFromFile_actionPerformed(); @@ -1206,6 +1246,7 @@ public class PopupMenu extends JPopupMenu enterPDB.setText(MessageManager.getString("label.enter_pdb_id")); enterPDB.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { enterPDB_actionPerformed(); @@ -1214,6 +1255,7 @@ public class PopupMenu extends JPopupMenu discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids")); discoverPDB.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { discoverPDB_actionPerformed(); @@ -1225,6 +1267,7 @@ public class PopupMenu extends JPopupMenu .getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sequenceFeature_actionPerformed(); @@ -1233,6 +1276,7 @@ public class PopupMenu extends JPopupMenu textColour.setText(MessageManager.getString("label.text_colour")); textColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { textColour_actionPerformed(); @@ -1247,6 +1291,7 @@ public class PopupMenu extends JPopupMenu + "..."); editSequence.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { editSequence_actionPerformed(actionEvent); @@ -1263,6 +1308,7 @@ public class PopupMenu extends JPopupMenu add(groupMenu); add(sequenceMenu); this.add(structureMenu); + groupMenu.add(chooseAnnotations); groupMenu.add(editMenu); groupMenu.add(outputMenu); groupMenu.add(sequenceFeature); @@ -1303,6 +1349,7 @@ public class PopupMenu extends JPopupMenu JMenuItem item = new JMenuItem(userColours.nextElement().toString()); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -1342,6 +1389,7 @@ public class PopupMenu extends JPopupMenu noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(); @@ -1352,6 +1400,7 @@ public class PopupMenu extends JPopupMenu .getString("label.clustalx_colours")); clustalColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(); @@ -1360,6 +1409,7 @@ public class PopupMenu extends JPopupMenu zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { zappoColour_actionPerformed(); @@ -1368,6 +1418,7 @@ public class PopupMenu extends JPopupMenu taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { taylorColour_actionPerformed(); @@ -1378,6 +1429,7 @@ public class PopupMenu extends JPopupMenu hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(); @@ -1386,6 +1438,7 @@ public class PopupMenu extends JPopupMenu helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { helixColour_actionPerformed(); @@ -1395,6 +1448,7 @@ public class PopupMenu extends JPopupMenu .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(); @@ -1403,6 +1457,7 @@ public class PopupMenu extends JPopupMenu turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { turnColour_actionPerformed(); @@ -1411,6 +1466,7 @@ public class PopupMenu extends JPopupMenu buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { buriedColour_actionPerformed(); @@ -1420,6 +1476,7 @@ public class PopupMenu extends JPopupMenu .getString("label.above_identity_percentage")); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { abovePIDColour_actionPerformed(); @@ -1429,6 +1486,7 @@ public class PopupMenu extends JPopupMenu .getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { userDefinedColour_actionPerformed(e); @@ -1438,6 +1496,7 @@ public class PopupMenu extends JPopupMenu .setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { PIDColour_actionPerformed(); @@ -1446,6 +1505,7 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { BLOSUM62Colour_actionPerformed(); @@ -1456,6 +1516,7 @@ public class PopupMenu extends JPopupMenu purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(); @@ -1473,6 +1534,7 @@ public class PopupMenu extends JPopupMenu conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(); @@ -1721,6 +1783,17 @@ public class PopupMenu extends JPopupMenu } /** + * Open a panel where the user can choose which types of sequence annotation + * to show or hide. + * + * @param e + */ + protected void chooseAnnotations_actionPerformed(ActionEvent e) + { + // todo correct way to guard against opening a duplicate panel? + new AnnotationChooser(ap); + } + /** * DOCUMENT ME! * * @param e @@ -2171,6 +2244,7 @@ public class PopupMenu extends JPopupMenu : ap.av.getSequenceSelection()); Thread discpdb = new Thread(new Runnable() { + @Override public void run() { @@ -2255,7 +2329,7 @@ public class PopupMenu extends JPopupMenu if (sg != null) { if (sequence == null) - sequence = (Sequence) sg.getSequenceAt(0); + sequence = sg.getSequenceAt(0); EditNameDialog dialog = new EditNameDialog( sequence.getSequenceAsString(sg.getStartRes(), diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index d3154c7..3b8568c 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -186,6 +186,8 @@ public class GAlignFrame extends JInternalFrame public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem(); + JMenuItem chooseAnnotations = new JMenuItem(); + JMenuItem deleteGroups = new JMenuItem(); JMenuItem createGroup = new JMenuItem(); @@ -371,6 +373,7 @@ public class GAlignFrame extends JInternalFrame item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { outputText_actionPerformed(e); @@ -407,6 +410,7 @@ public class GAlignFrame extends JInternalFrame radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() @@ -431,6 +435,7 @@ public class GAlignFrame extends JInternalFrame { radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -442,6 +447,7 @@ public class GAlignFrame extends JInternalFrame }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -580,6 +586,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.SHIFT_MASK, false)); saveAs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { saveAs_actionPerformed(e); @@ -591,6 +598,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); closeMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { closeMenuItem_actionPerformed(false); @@ -609,6 +617,7 @@ public class GAlignFrame extends JInternalFrame selectAllSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { selectAllSequenceMenuItem_actionPerformed(e); @@ -621,6 +630,7 @@ public class GAlignFrame extends JInternalFrame deselectAllSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { deselectAllSequenceMenuItem_actionPerformed(e); @@ -634,6 +644,7 @@ public class GAlignFrame extends JInternalFrame invertSequenceMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { invertSequenceMenuItem_actionPerformed(e); @@ -643,6 +654,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.make_groups_selection")); grpsFromSelection.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { makeGrpsFromSelection_actionPerformed(e); @@ -668,6 +680,7 @@ public class GAlignFrame extends JInternalFrame remove2LeftMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { remove2LeftMenuItem_actionPerformed(e); @@ -681,6 +694,7 @@ public class GAlignFrame extends JInternalFrame remove2RightMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { remove2RightMenuItem_actionPerformed(e); @@ -694,6 +708,7 @@ public class GAlignFrame extends JInternalFrame removeGappedColumnMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { removeGappedColumnMenuItem_actionPerformed(e); @@ -708,6 +723,7 @@ public class GAlignFrame extends JInternalFrame removeAllGapsMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { removeAllGapsMenuItem_actionPerformed(e); @@ -718,6 +734,7 @@ public class GAlignFrame extends JInternalFrame justifyLeftMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { justifyLeftMenuItem_actionPerformed(e); @@ -728,6 +745,7 @@ public class GAlignFrame extends JInternalFrame justifyRightMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { justifyRightMenuItem_actionPerformed(e); @@ -737,6 +755,7 @@ public class GAlignFrame extends JInternalFrame viewBoxesMenuItem.setState(true); viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { viewBoxesMenuItem_actionPerformed(e); @@ -746,6 +765,7 @@ public class GAlignFrame extends JInternalFrame viewTextMenuItem.setState(true); viewTextMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { viewTextMenuItem_actionPerformed(e); @@ -757,6 +777,7 @@ public class GAlignFrame extends JInternalFrame showNonconservedMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showUnconservedMenuItem_actionPerformed(e); @@ -767,6 +788,7 @@ public class GAlignFrame extends JInternalFrame sortPairwiseMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortPairwiseMenuItem_actionPerformed(e); @@ -775,6 +797,7 @@ public class GAlignFrame extends JInternalFrame sortIDMenuItem.setText(MessageManager.getString("action.by_id")); sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortIDMenuItem_actionPerformed(e); @@ -785,6 +808,7 @@ public class GAlignFrame extends JInternalFrame sortLengthMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortLengthMenuItem_actionPerformed(e); @@ -793,6 +817,7 @@ public class GAlignFrame extends JInternalFrame sortGroupMenuItem.setText(MessageManager.getString("action.by_group")); sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortGroupMenuItem_actionPerformed(e); @@ -806,6 +831,7 @@ public class GAlignFrame extends JInternalFrame removeRedundancyMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { removeRedundancyMenuItem_actionPerformed(e); @@ -816,6 +842,7 @@ public class GAlignFrame extends JInternalFrame pairwiseAlignmentMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pairwiseAlignmentMenuItem_actionPerformed(e); @@ -825,6 +852,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.principal_component_analysis")); PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { PCAMenuItem_actionPerformed(e); @@ -835,6 +863,7 @@ public class GAlignFrame extends JInternalFrame averageDistanceTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { averageDistanceTreeMenuItem_actionPerformed(e); @@ -845,6 +874,7 @@ public class GAlignFrame extends JInternalFrame neighbourTreeMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { neighbourTreeMenuItem_actionPerformed(e); @@ -862,6 +892,7 @@ public class GAlignFrame extends JInternalFrame clustalColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { clustalColour_actionPerformed(e); @@ -870,6 +901,7 @@ public class GAlignFrame extends JInternalFrame zappoColour.setText(MessageManager.getString("label.zappo")); zappoColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { zappoColour_actionPerformed(e); @@ -878,6 +910,7 @@ public class GAlignFrame extends JInternalFrame taylorColour.setText(MessageManager.getString("label.taylor")); taylorColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { taylorColour_actionPerformed(e); @@ -888,6 +921,7 @@ public class GAlignFrame extends JInternalFrame hydrophobicityColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hydrophobicityColour_actionPerformed(e); @@ -896,6 +930,7 @@ public class GAlignFrame extends JInternalFrame helixColour.setText(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { helixColour_actionPerformed(e); @@ -905,6 +940,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.strand_propensity")); strandColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { strandColour_actionPerformed(e); @@ -913,6 +949,7 @@ public class GAlignFrame extends JInternalFrame turnColour.setText(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { turnColour_actionPerformed(e); @@ -921,6 +958,7 @@ public class GAlignFrame extends JInternalFrame buriedColour.setText(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { buriedColour_actionPerformed(e); @@ -930,6 +968,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.user_defined")); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { userDefinedColour_actionPerformed(e); @@ -939,6 +978,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("label.percentage_identity")); PIDColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { PIDColour_actionPerformed(e); @@ -948,6 +988,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("label.blosum62_score")); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { BLOSUM62Colour_actionPerformed(e); @@ -956,6 +997,7 @@ public class GAlignFrame extends JInternalFrame nucleotideColour.setText(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideColour_actionPerformed(e); @@ -967,6 +1009,7 @@ public class GAlignFrame extends JInternalFrame purinePyrimidineColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { purinePyrimidineColour_actionPerformed(e); @@ -977,6 +1020,7 @@ public class GAlignFrame extends JInternalFrame RNAInteractionColour .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { RNAInteractionColour_actionPerformed(e); @@ -994,6 +1038,7 @@ public class GAlignFrame extends JInternalFrame avDistanceTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { avTreeBlosumMenuItem_actionPerformed(e); @@ -1004,6 +1049,7 @@ public class GAlignFrame extends JInternalFrame njTreeBlosumMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { njTreeBlosumMenuItem_actionPerformed(e); @@ -1017,6 +1063,7 @@ public class GAlignFrame extends JInternalFrame annotationPanelMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { annotationPanelMenuItem_actionPerformed(e); @@ -1027,6 +1074,7 @@ public class GAlignFrame extends JInternalFrame colourTextMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { colourTextMenuItem_actionPerformed(e); @@ -1035,6 +1083,7 @@ public class GAlignFrame extends JInternalFrame htmlMenuItem.setText(MessageManager.getString("label.html")); htmlMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { htmlMenuItem_actionPerformed(e); @@ -1044,6 +1093,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.overview_window")); overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { overviewMenuItem_actionPerformed(e); @@ -1056,6 +1106,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); undoMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { undoMenuItem_actionPerformed(e); @@ -1068,6 +1119,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); redoMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { redoMenuItem_actionPerformed(e); @@ -1078,6 +1130,7 @@ public class GAlignFrame extends JInternalFrame conservationMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { conservationMenuItem_actionPerformed(e); @@ -1086,6 +1139,7 @@ public class GAlignFrame extends JInternalFrame noColourmenuItem.setText(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { noColourmenuItem_actionPerformed(e); @@ -1094,6 +1148,7 @@ public class GAlignFrame extends JInternalFrame wrapMenuItem.setText(MessageManager.getString("label.wrap")); wrapMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { wrapMenuItem_actionPerformed(e); @@ -1105,6 +1160,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); printMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { printMenuItem_actionPerformed(e); @@ -1116,6 +1172,7 @@ public class GAlignFrame extends JInternalFrame renderGapsMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { renderGapsMenuItem_actionPerformed(e); @@ -1127,6 +1184,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); findMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { findMenuItem_actionPerformed(e); @@ -1136,6 +1194,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.above_identity_threshold")); abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { abovePIDThreshold_actionPerformed(e); @@ -1145,11 +1204,22 @@ public class GAlignFrame extends JInternalFrame .getString("label.show_sequence_features")); showSeqFeatures.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { showSeqFeatures_actionPerformed(actionEvent); } }); + chooseAnnotations.setText(MessageManager + .getString("label.choose_annotations") + "..."); + chooseAnnotations.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent actionEvent) + { + chooseAnnotations_actionPerformed(); + } + }); /* * showSeqFeaturesHeight.setText("Vary Sequence Feature Height"); * showSeqFeaturesHeight.addActionListener(new ActionListener() { public @@ -1161,6 +1231,7 @@ public class GAlignFrame extends JInternalFrame showDbRefsMenuitem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showDbRefs_actionPerformed(e); @@ -1172,6 +1243,7 @@ public class GAlignFrame extends JInternalFrame showNpFeatsMenuitem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showNpFeats_actionPerformed(e); @@ -1183,6 +1255,7 @@ public class GAlignFrame extends JInternalFrame showGroupConservation.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showGroupConservation_actionPerformed(e); @@ -1195,6 +1268,7 @@ public class GAlignFrame extends JInternalFrame showGroupConsensus.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showGroupConsensus_actionPerformed(e); @@ -1206,6 +1280,7 @@ public class GAlignFrame extends JInternalFrame showConsensusHistogram.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showConsensusHistogram_actionPerformed(e); @@ -1217,6 +1292,7 @@ public class GAlignFrame extends JInternalFrame showSequenceLogo.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showSequenceLogo_actionPerformed(e); @@ -1228,6 +1304,7 @@ public class GAlignFrame extends JInternalFrame normaliseSequenceLogo.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { normaliseSequenceLogo_actionPerformed(e); @@ -1241,6 +1318,7 @@ public class GAlignFrame extends JInternalFrame applyAutoAnnotationSettings.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { applyAutoAnnotationSettings_actionPerformed(e); @@ -1251,6 +1329,7 @@ public class GAlignFrame extends JInternalFrame nucleotideColour.setText(MessageManager.getString("label.nucleotide")); nucleotideColour.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { nucleotideColour_actionPerformed(e); @@ -1276,6 +1355,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); deleteGroups.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { deleteGroups_actionPerformed(e); @@ -1287,6 +1367,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); createGroup.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createGroup_actionPerformed(e); @@ -1299,6 +1380,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.SHIFT_MASK, false)); unGroup.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { unGroup_actionPerformed(e); @@ -1311,6 +1393,7 @@ public class GAlignFrame extends JInternalFrame copy.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { copy_actionPerformed(e); @@ -1322,6 +1405,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); cut.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cut_actionPerformed(e); @@ -1332,6 +1416,7 @@ public class GAlignFrame extends JInternalFrame java.awt.event.KeyEvent.VK_BACK_SPACE, 0, false)); delete.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { delete_actionPerformed(e); @@ -1345,6 +1430,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.SHIFT_MASK, false)); pasteNew.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pasteNew_actionPerformed(e); @@ -1356,6 +1442,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); pasteThis.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pasteThis_actionPerformed(e); @@ -1365,6 +1452,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.apply_colour_to_all_groups")); applyToAllGroups.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { applyToAllGroups_actionPerformed(e); @@ -1372,6 +1460,7 @@ public class GAlignFrame extends JInternalFrame }); createPNG.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createPNG(null); @@ -1383,6 +1472,7 @@ public class GAlignFrame extends JInternalFrame font.setText(MessageManager.getString("action.font")); font.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { font_actionPerformed(e); @@ -1394,6 +1484,7 @@ public class GAlignFrame extends JInternalFrame seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true)); seqLimits.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { seqLimit_actionPerformed(e); @@ -1402,6 +1493,7 @@ public class GAlignFrame extends JInternalFrame epsFile.setText("EPS"); epsFile.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { createEPS(null); @@ -1413,6 +1505,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.load_associated_tree")); LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { LoadtreeMenuItem_actionPerformed(e); @@ -1423,6 +1516,7 @@ public class GAlignFrame extends JInternalFrame scaleAbove.setText(MessageManager.getString("action.scale_above")); scaleAbove.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { scaleAbove_actionPerformed(e); @@ -1433,6 +1527,7 @@ public class GAlignFrame extends JInternalFrame scaleLeft.setText(MessageManager.getString("action.scale_left")); scaleLeft.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { scaleLeft_actionPerformed(e); @@ -1443,6 +1538,7 @@ public class GAlignFrame extends JInternalFrame scaleRight.setText(MessageManager.getString("action.scale_right")); scaleRight.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { scaleRight_actionPerformed(e); @@ -1455,6 +1551,7 @@ public class GAlignFrame extends JInternalFrame centreColumnLabelsMenuItem .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { centreColumnLabels_actionPerformed(e); @@ -1467,6 +1564,7 @@ public class GAlignFrame extends JInternalFrame followHighlightMenuItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { followHighlight_actionPerformed(); @@ -1478,6 +1576,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.modify_identity_thereshold")); modifyPID.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { modifyPID_actionPerformed(e); @@ -1488,6 +1587,7 @@ public class GAlignFrame extends JInternalFrame modifyConservation .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { modifyConservation_actionPerformed(e); @@ -1498,15 +1598,18 @@ public class GAlignFrame extends JInternalFrame sort.setText(MessageManager.getString("action.sort")); sort.addMenuListener(new MenuListener() { + @Override public void menuSelected(MenuEvent e) { buildTreeMenu(); } + @Override public void menuDeselected(MenuEvent e) { } + @Override public void menuCanceled(MenuEvent e) { } @@ -1517,14 +1620,17 @@ public class GAlignFrame extends JInternalFrame sortByAnnotScore.addMenuListener(new javax.swing.event.MenuListener() { + @Override public void menuCanceled(MenuEvent e) { } + @Override public void menuDeselected(MenuEvent e) { } + @Override public void menuSelected(MenuEvent e) { buildSortByAnnotationScoresMenu(); @@ -1541,6 +1647,7 @@ public class GAlignFrame extends JInternalFrame .getDefault("PAD_GAPS", false)); padGapsMenuitem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { padGapsMenuitem_actionPerformed(e); @@ -1550,6 +1657,7 @@ public class GAlignFrame extends JInternalFrame vamsasStore.setText(MessageManager.getString("label.vamsas_store")); vamsasStore.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { vamsasStore_actionPerformed(e); @@ -1559,6 +1667,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.translate_cDNA")); showTranslation.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showTranslation_actionPerformed(e); @@ -1568,6 +1677,7 @@ public class GAlignFrame extends JInternalFrame + "..."); extractScores.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { extractScores_actionPerformed(e); @@ -1586,6 +1696,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.feature_settings")); openFeatureSettings.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { featureSettings_actionPerformed(e); @@ -1595,6 +1706,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("label.fetch_sequences")); fetchSequence.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { fetchSequence_actionPerformed(e); @@ -1605,6 +1717,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.by_annotation")); annotationColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { annotationColour_actionPerformed(e); @@ -1615,6 +1728,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.by_rna_helixes")); rnahelicesColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { rnahelicesColour_actionPerformed(e); @@ -1625,6 +1739,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.load_features_annotations")); associatedData.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { associatedData_actionPerformed(e); @@ -1636,6 +1751,7 @@ public class GAlignFrame extends JInternalFrame "AUTO_CALC_CONSENSUS", true)); autoCalculate.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { autoCalculate_actionPerformed(e); @@ -1651,6 +1767,7 @@ public class GAlignFrame extends JInternalFrame .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false)); sortByTree.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { sortByTreeOption_actionPerformed(e); @@ -1666,6 +1783,7 @@ public class GAlignFrame extends JInternalFrame listenToViewSelections.setState(false); listenToViewSelections.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { listenToViewSelections_actionPerformed(e); @@ -1677,6 +1795,7 @@ public class GAlignFrame extends JInternalFrame addFromFile.setText(MessageManager.getString("label.from_file")); addFromFile.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { addFromFile_actionPerformed(e); @@ -1685,6 +1804,7 @@ public class GAlignFrame extends JInternalFrame addFromText.setText(MessageManager.getString("label.from_textbox")); addFromText.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { addFromText_actionPerformed(e); @@ -1693,6 +1813,7 @@ public class GAlignFrame extends JInternalFrame addFromURL.setText(MessageManager.getString("label.from_url")); addFromURL.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { addFromURL_actionPerformed(e); @@ -1702,6 +1823,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.export_features")); exportFeatures.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { exportFeatures_actionPerformed(e); @@ -1711,6 +1833,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.export_annotations")); exportAnnotations.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { exportAnnotations_actionPerformed(e); @@ -1723,6 +1846,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_sequence_visibility")); showAllSeqs.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showAllSeqs_actionPerformed(e); @@ -1733,6 +1857,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_columns_visibility")); showAllColumns.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showAllColumns_actionPerformed(e); @@ -1745,6 +1870,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_sequence_visibility")); hideSelSequences.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSelSequences_actionPerformed(e); @@ -1756,6 +1882,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggle_columns_visibility")); hideSelColumns.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideSelColumns_actionPerformed(e); @@ -1765,6 +1892,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.selected_region")); hideAllSelection.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideAllSelection_actionPerformed(e); @@ -1775,6 +1903,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.all_but_selected_region")); hideAllButSelection.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hideAllButSelection_actionPerformed(e); @@ -1786,6 +1915,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.toggles_visibility_hidden_selected_regions")); showAllhidden.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { showAllhidden_actionPerformed(e); @@ -1796,6 +1926,7 @@ public class GAlignFrame extends JInternalFrame .getString("action.show_hidden_markers")); hiddenMarkers.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { hiddenMarkers_actionPerformed(e); @@ -1809,6 +1940,7 @@ public class GAlignFrame extends JInternalFrame | java.awt.event.KeyEvent.ALT_MASK, false)); invertColSel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { invertColSel_actionPerformed(e); @@ -1816,6 +1948,7 @@ public class GAlignFrame extends JInternalFrame }); tabbedPane.addChangeListener(new javax.swing.event.ChangeListener() { + @Override public void stateChanged(ChangeEvent evt) { JTabbedPane pane = (JTabbedPane) evt.getSource(); @@ -1825,6 +1958,7 @@ public class GAlignFrame extends JInternalFrame }); tabbedPane.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent e) { tabbedPane_mousePressed(e); @@ -1832,6 +1966,7 @@ public class GAlignFrame extends JInternalFrame }); tabbedPane.addFocusListener(new FocusAdapter() { + @Override public void focusGained(FocusEvent e) { tabbedPane_focusGained(e); @@ -1843,6 +1978,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); save.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { save_actionPerformed(e); @@ -1852,6 +1988,7 @@ public class GAlignFrame extends JInternalFrame reload.setText(MessageManager.getString("action.reload")); reload.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { reload_actionPerformed(e); @@ -1863,6 +2000,7 @@ public class GAlignFrame extends JInternalFrame .getMenuShortcutKeyMask(), false)); newView.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { newView_actionPerformed(e); @@ -1875,6 +2013,7 @@ public class GAlignFrame extends JInternalFrame + "..."); textColour.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { textColour_actionPerformed(e); @@ -1886,6 +2025,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.right_align_sequence_id")); idRightAlign.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { idRightAlign_actionPerformed(e); @@ -1897,6 +2037,7 @@ public class GAlignFrame extends JInternalFrame java.awt.event.KeyEvent.VK_G, 0, false)); gatherViews.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { gatherViews_actionPerformed(e); @@ -1908,6 +2049,7 @@ public class GAlignFrame extends JInternalFrame java.awt.event.KeyEvent.VK_X, 0, false)); expandViews.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { expandViews_actionPerformed(e); @@ -1917,6 +2059,7 @@ public class GAlignFrame extends JInternalFrame .setText(MessageManager.getString("action.page_setup") + "..."); pageSetup.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { pageSetup_actionPerformed(e); @@ -1926,6 +2069,7 @@ public class GAlignFrame extends JInternalFrame .getString("label.alignment_props") + "..."); alignmentProperties.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent actionEvent) { alignmentProperties(); @@ -1999,6 +2143,7 @@ public class GAlignFrame extends JInternalFrame viewMenu.add(autoAnnMenu); viewMenu.addSeparator(); viewMenu.add(showSeqFeatures); + viewMenu.add(chooseAnnotations); // viewMenu.add(showSeqFeaturesHeight); viewMenu.add(openFeatureSettings); @@ -2107,6 +2252,14 @@ public class GAlignFrame extends JInternalFrame // selectMenu.add(listenToViewSelections); } + /** + * Action on menu item "Show/hide sequence annotations..." + */ + protected void chooseAnnotations_actionPerformed() + { + + } + protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java new file mode 100644 index 0000000..161ebee --- /dev/null +++ b/test/jalview/gui/AnnotationChooserTest.java @@ -0,0 +1,44 @@ +package jalview.gui; + +import jalview.io.AppletFormatAdapter; +import jalview.io.FileLoader; + +import org.junit.Before; +import org.junit.Test; + +/** + * Unit tests for AnnotationChooser + * + * @author gmcarstairs + * + */ +public class AnnotationChooserTest +{ + final static String TEST_FILE = "./examples/uniref50.fa"; + AnnotationChooser testee; + + AlignFrame af; + + @Before + public void setUp() + { + FileLoader fl = new jalview.io.FileLoader(false); + af = fl.LoadFileWaitTillLoaded(TEST_FILE, + AppletFormatAdapter.FILE); + + } + + @Test + public void testAlignmentLoader() throws Exception + { + + AlignmentPanel parentPanel = new AlignmentPanel(af, af.getViewport()); + testee = new AnnotationChooser(parentPanel); + } + + @Test + public void testBuildFrame() + { + + } +}