2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 package jalview.jbgui;
24 import jalview.datamodel.SequenceI;
25 import jalview.fts.api.FTSDataColumnI;
26 import jalview.fts.core.FTSDataColumnPreferences;
27 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
28 import jalview.fts.service.pdb.PDBFTSRestClient;
29 import jalview.gui.AlignmentPanel;
30 import jalview.gui.Desktop;
31 import jalview.gui.JvSwingUtils;
32 import jalview.gui.StructureViewer;
33 import jalview.util.MessageManager;
35 import java.awt.BorderLayout;
36 import java.awt.CardLayout;
37 import java.awt.Component;
38 import java.awt.Dimension;
39 import java.awt.FlowLayout;
41 import java.awt.GridLayout;
42 import java.awt.Point;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.ItemEvent;
46 import java.awt.event.ItemListener;
47 import java.awt.event.KeyAdapter;
48 import java.awt.event.KeyEvent;
49 import java.awt.event.MouseAdapter;
50 import java.awt.event.MouseEvent;
51 import java.util.Arrays;
52 import java.util.HashMap;
55 import javax.swing.ImageIcon;
56 import javax.swing.JButton;
57 import javax.swing.JCheckBox;
58 import javax.swing.JComboBox;
59 import javax.swing.JFrame;
60 import javax.swing.JInternalFrame;
61 import javax.swing.JLabel;
62 import javax.swing.JList;
63 import javax.swing.JPanel;
64 import javax.swing.JScrollPane;
65 import javax.swing.JSeparator;
66 import javax.swing.JTabbedPane;
67 import javax.swing.JTable;
68 import javax.swing.JTextField;
69 import javax.swing.ListCellRenderer;
70 import javax.swing.Timer;
71 import javax.swing.event.ChangeEvent;
72 import javax.swing.event.ChangeListener;
73 import javax.swing.event.DocumentEvent;
74 import javax.swing.event.DocumentListener;
75 import javax.swing.event.InternalFrameEvent;
76 import javax.swing.table.TableColumn;
78 import net.miginfocom.swing.MigLayout;
80 @SuppressWarnings("serial")
82 * GUI layout for structure chooser
87 public abstract class GStructureChooser extends JPanel
88 implements ItemListener
90 private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
92 public static final String VIEWS_FILTER = "VIEWS_FILTER";
94 protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
96 protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
99 * 'cached' structure view
101 protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
103 protected JPanel statusPanel = new JPanel();
105 public JLabel statusBar = new JLabel();
107 protected String frameTitle = MessageManager
108 .getString("label.structure_chooser");
110 protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
112 protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
114 protected AlignmentPanel ap;
116 protected StringBuilder errorWarning = new StringBuilder();
118 protected JButton btn_add;
120 protected JButton btn_newView;
122 protected JButton btn_pdbFromFile = new JButton();
124 protected JCheckBox chk_superpose = new JCheckBox(
125 MessageManager.getString("label.superpose_structures"));
127 protected JTextField txt_search = new JTextField(14);
129 protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
131 protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
134 protected JCheckBox chk_invertFilter = new JCheckBox(
135 MessageManager.getString("label.invert"));
137 protected ImageIcon loadingImage = new ImageIcon(
138 getClass().getResource("/images/loading.gif"));
140 protected ImageIcon goodImage = new ImageIcon(
141 getClass().getResource("/images/good.png"));
143 protected ImageIcon errorImage = new ImageIcon(
144 getClass().getResource("/images/error.png"));
146 protected ImageIcon warningImage = new ImageIcon(
147 getClass().getResource("/images/warning.gif"));
149 protected JLabel lbl_loading = new JLabel(loadingImage);
151 protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
153 protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
155 protected AssociateSeqPanel idInputAssSeqPanel = new AssociateSeqPanel();
157 protected AssociateSeqPanel fileChooserAssSeqPanel = new AssociateSeqPanel();
159 protected JComboBox<StructureViewer> targetView = new JComboBox<>();
161 protected JTable tbl_local_pdb = new JTable();
163 protected JTabbedPane pnl_filter = new JTabbedPane();
165 protected abstract FTSDataColumnPreferences getFTSDocFieldPrefs();
166 protected abstract void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs);
169 protected FTSDataColumnI[] previousWantedFields;
171 protected static Map<String, Integer> tempUserPrefs = new HashMap<>();
173 private JTable tbl_summary = new JTable()
175 private boolean inLayout;
178 public boolean getScrollableTracksViewportWidth()
180 return hasExcessWidth();
185 public void doLayout()
187 if (hasExcessWidth())
189 autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS;
194 autoResizeMode = AUTO_RESIZE_OFF;
197 protected boolean hasExcessWidth()
199 return getPreferredSize().width < getParent().getWidth();
203 public void columnMarginChanged(ChangeEvent e)
209 TableColumn resizingColumn = getTableHeader().getResizingColumn();
210 // Need to do this here, before the parent's
211 // layout manager calls getPreferredSize().
212 if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF
215 resizingColumn.setPreferredWidth(resizingColumn.getWidth());
216 String colHeader = resizingColumn.getHeaderValue().toString();
217 tempUserPrefs.put(colHeader, resizingColumn.getWidth());
223 public String getToolTipText(MouseEvent evt)
225 String toolTipText = null;
226 java.awt.Point pnt = evt.getPoint();
227 int rowIndex = rowAtPoint(pnt);
228 int colIndex = columnAtPoint(pnt);
232 if (getValueAt(rowIndex, colIndex) == null)
236 toolTipText = getValueAt(rowIndex, colIndex).toString();
237 } catch (Exception e)
239 // e.printStackTrace();
241 toolTipText = (toolTipText == null ? null
242 : (toolTipText.length() > 500
243 ? JvSwingUtils.wrapTooltip(true,
244 "\"" + toolTipText.subSequence(0, 500)
246 : JvSwingUtils.wrapTooltip(true, toolTipText)));
251 public GStructureChooser()
254 protected void initDialog()
260 mainFrame.setVisible(false);
261 mainFrame.invalidate();
263 } catch (Exception e)
265 System.out.println(e); // for JavaScript TypeError
270 // BH SwingJS optimization
271 // (a) 100-ms interruptable timer for text entry -- BH 1/10/2019
272 // (b) two-character minimum, at least for JavaScript.
276 protected void txt_search_ActionPerformedDelayed() {
280 timer = new Timer(300, new ActionListener() {
283 public void actionPerformed(ActionEvent e) {
284 txt_search_ActionPerformed();
287 timer.setRepeats(false);
293 * Initializes the GUI default properties
297 private void jbInit() throws Exception
299 Integer width = tempUserPrefs.get("structureChooser.width") == null
301 : tempUserPrefs.get("structureChooser.width");
302 Integer height = tempUserPrefs.get("structureChooser.height") == null
304 : tempUserPrefs.get("structureChooser.height");
305 tbl_summary.setAutoCreateRowSorter(true);
306 tbl_summary.getTableHeader().setReorderingAllowed(false);
307 tbl_summary.addMouseListener(new MouseAdapter()
310 public void mousePressed(MouseEvent e)
314 super.mousePressed(e);
318 public void mouseClicked(MouseEvent e)
322 validateSelections();
327 public void mouseReleased(MouseEvent e)
331 validateSelections();
334 boolean popupAction(MouseEvent e)
336 if (e.isPopupTrigger())
338 Point pt = e.getPoint();
339 int selectedRow = tbl_summary.rowAtPoint(pt);
340 if (showPopupFor(selectedRow,pt.x,pt.y))
348 tbl_summary.addKeyListener(new KeyAdapter()
351 public void keyPressed(KeyEvent evt)
353 validateSelections();
354 switch (evt.getKeyCode())
356 case KeyEvent.VK_ESCAPE: // escape key
359 case KeyEvent.VK_ENTER: // enter key
360 if (btn_add.isEnabled())
362 add_ActionPerformed();
365 case KeyEvent.VK_TAB: // tab key
366 if (evt.isShiftDown())
368 pnl_filter.requestFocus();
372 btn_add.requestFocus();
382 JButton btn_cancel = new JButton(
383 MessageManager.getString("action.cancel"));
384 btn_cancel.setFont(VERDANA_12);
385 btn_cancel.addActionListener(new java.awt.event.ActionListener()
388 public void actionPerformed(ActionEvent e)
390 closeAction(pnl_filter.getHeight());
393 btn_cancel.addKeyListener(new KeyAdapter()
396 public void keyPressed(KeyEvent evt)
398 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
400 closeAction(pnl_filter.getHeight());
405 tbl_local_pdb.setAutoCreateRowSorter(true);
406 tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
407 tbl_local_pdb.addMouseListener(new MouseAdapter()
410 public void mouseClicked(MouseEvent e)
412 validateSelections();
416 public void mouseReleased(MouseEvent e)
418 validateSelections();
421 tbl_local_pdb.addKeyListener(new KeyAdapter()
424 public void keyPressed(KeyEvent evt)
426 validateSelections();
427 switch (evt.getKeyCode())
429 case KeyEvent.VK_ESCAPE: // escape key
432 case KeyEvent.VK_ENTER: // enter key
433 if (btn_add.isEnabled())
435 add_ActionPerformed();
438 case KeyEvent.VK_TAB: // tab key
439 if (evt.isShiftDown())
441 cmb_filterOption.requestFocus();
445 if (btn_add.isEnabled())
447 btn_add.requestFocus();
451 btn_cancel.requestFocus();
462 btn_newView = new JButton(MessageManager.getString("action.new_view"));
463 btn_newView.setFont(VERDANA_12);
464 btn_newView.addActionListener(new java.awt.event.ActionListener()
467 public void actionPerformed(ActionEvent e)
469 newView_ActionPerformed();
472 btn_newView.addKeyListener(new KeyAdapter()
475 public void keyPressed(KeyEvent evt)
477 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
479 newView_ActionPerformed();
484 btn_add = new JButton(MessageManager.getString("action.add"));
485 btn_add.setFont(VERDANA_12);
486 btn_add.addActionListener(new java.awt.event.ActionListener()
489 public void actionPerformed(ActionEvent e)
491 add_ActionPerformed();
494 btn_add.addKeyListener(new KeyAdapter()
497 public void keyPressed(KeyEvent evt)
499 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
501 add_ActionPerformed();
506 btn_pdbFromFile.setFont(VERDANA_12);
507 String btn_title = MessageManager.getString("label.select_pdb_file");
508 btn_pdbFromFile.setText(btn_title + " ");
509 btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
512 public void actionPerformed(ActionEvent e)
514 pdbFromFile_actionPerformed();
517 btn_pdbFromFile.addKeyListener(new KeyAdapter()
520 public void keyPressed(KeyEvent evt)
522 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
524 pdbFromFile_actionPerformed();
529 JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
530 scrl_foundStructures.setPreferredSize(new Dimension(width, height));
532 JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
533 scrl_localPDB.setPreferredSize(new Dimension(width, height));
534 scrl_localPDB.setHorizontalScrollBarPolicy(
535 JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
537 chk_invertFilter.setFont(VERDANA_12);
538 txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
539 MessageManager.getString("label.enter_pdb_id_tip")));
540 txt_search.getDocument().addDocumentListener(new DocumentListener()
543 public void insertUpdate(DocumentEvent e)
545 txt_search_ActionPerformedDelayed();
549 public void removeUpdate(DocumentEvent e)
551 txt_search_ActionPerformedDelayed();
555 public void changedUpdate(DocumentEvent e)
557 txt_search_ActionPerformedDelayed();
561 cmb_filterOption.setFont(VERDANA_12);
562 cmb_filterOption.setToolTipText(
563 MessageManager.getString("info.select_filter_option"));
564 cmb_filterOption.addItemListener(this);
565 // add CustomComboSeparatorsRenderer to filter option combo-box
566 cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
567 (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
570 protected boolean addSeparatorAfter(JList list, FilterOption value,
573 return value.isAddSeparatorAfter();
577 chk_invertFilter.addItemListener(this);
579 targetView.setVisible(false);
581 JPanel actionsPanel = new JPanel(new MigLayout());
582 actionsPanel.add(targetView, "left");
583 actionsPanel.add(btn_add, "wrap");
584 actionsPanel.add(chk_superpose, "left");
585 actionsPanel.add(btn_newView);
586 actionsPanel.add(btn_cancel, "right");
588 JPanel pnl_main = new JPanel();
589 pnl_main.add(cmb_filterOption);
590 pnl_main.add(lbl_loading);
591 pnl_main.add(chk_invertFilter);
592 lbl_loading.setVisible(false);
594 JPanel pnl_fileChooser = new JPanel(new FlowLayout());
595 pnl_fileChooser.add(btn_pdbFromFile);
596 pnl_fileChooser.add(lbl_fromFileStatus);
597 JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
598 pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
599 pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
601 JPanel pnl_idInput = new JPanel(new FlowLayout());
602 pnl_idInput.add(txt_search);
603 pnl_idInput.add(lbl_pdbManualFetchStatus);
605 JPanel pnl_idInputBL = new JPanel(new BorderLayout());
606 pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
607 pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
609 final String foundStructureSummary = MessageManager
610 .getString("label.found_structures_summary");
611 final String configureCols = MessageManager
612 .getString("label.configure_displayed_columns");
613 ChangeListener changeListener = new ChangeListener()
616 public void stateChanged(ChangeEvent changeEvent)
618 JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
620 int index = sourceTabbedPane.getSelectedIndex();
621 btn_add.setVisible(targetView.isVisible());
622 btn_newView.setVisible(true);
623 btn_cancel.setVisible(true);
624 if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
626 btn_add.setEnabled(false);
627 btn_cancel.setEnabled(false);
628 btn_add.setVisible(false);
629 btn_newView.setEnabled(false);
630 btn_cancel.setVisible(false);
631 previousWantedFields = getFTSDocFieldPrefs()
632 .getStructureSummaryFields()
633 .toArray(new FTSDataColumnI[0]);
635 if (sourceTabbedPane.getTitleAt(index)
636 .equals(foundStructureSummary))
638 btn_cancel.setEnabled(true);
639 if (wantedFieldsUpdated())
645 validateSelections();
650 pnl_filter.addChangeListener(changeListener);
651 pnl_filter.setPreferredSize(new Dimension(width, height));
652 pnl_filter.add(foundStructureSummary, scrl_foundStructures);
653 pnl_filter.add(configureCols, getFTSDocFieldPrefs());
655 JPanel pnl_locPDB = new JPanel(new BorderLayout());
656 pnl_locPDB.add(scrl_localPDB);
658 pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
659 pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
660 pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
661 pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
663 this.setLayout(new BorderLayout());
664 this.add(pnl_main, java.awt.BorderLayout.NORTH);
665 this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
666 // this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
667 statusPanel.setLayout(new GridLayout());
669 JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
670 pnl_actionsAndStatus.add(actionsPanel, BorderLayout.CENTER);
671 pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
672 statusPanel.add(statusBar, null);
673 this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
675 mainFrame.addInternalFrameListener(
676 new javax.swing.event.InternalFrameAdapter()
679 public void internalFrameClosing(InternalFrameEvent e)
681 closeAction(pnl_filter.getHeight());
684 mainFrame.setVisible(true);
685 mainFrame.setContentPane(this);
686 mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
687 Integer x = tempUserPrefs.get("structureChooser.x");
688 Integer y = tempUserPrefs.get("structureChooser.y");
689 if (x != null && y != null)
691 mainFrame.setLocation(x, y);
693 Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
697 protected abstract boolean showPopupFor(int selectedRow, int x, int y);
698 protected void closeAction(int preferredHeight)
700 // System.out.println(">>>>>>>>>> closing internal frame!!!");
701 // System.out.println("width : " + mainFrame.getWidth());
702 // System.out.println("heigh : " + mainFrame.getHeight());
703 // System.out.println("x : " + mainFrame.getX());
704 // System.out.println("y : " + mainFrame.getY());
705 tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
706 tempUserPrefs.put("structureChooser.height", preferredHeight);
707 tempUserPrefs.put("structureChooser.x", mainFrame.getX());
708 tempUserPrefs.put("structureChooser.y", mainFrame.getY());
712 public boolean wantedFieldsUpdated()
714 if (previousWantedFields == null)
719 FTSDataColumnI[] currentWantedFields = getFTSDocFieldPrefs()
720 .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
721 return Arrays.equals(currentWantedFields, previousWantedFields) ? false
728 * Event listener for the 'filter' combo-box and 'invert' check-box
730 public void itemStateChanged(ItemEvent e)
736 * This inner class provides the provides the data model for associate
737 * sequence combo-box - cmb_assSeq
742 public class AssociateSeqOptions
744 private SequenceI sequence;
748 public AssociateSeqOptions(SequenceI seq)
751 this.name = (seq.getName().length() >= 23)
752 ? seq.getName().substring(0, 23)
756 public AssociateSeqOptions(String name, SequenceI seq)
763 public String toString()
768 public String getName()
773 public void setName(String name)
778 public SequenceI getSequence()
783 public void setSequence(SequenceI sequence)
785 this.sequence = sequence;
791 * This inner class holds the Layout and configuration of the panel which
792 * handles association of manually fetched structures to a unique sequence
793 * when more than one sequence selection is made
798 public class AssociateSeqPanel extends JPanel implements ItemListener
800 private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
802 private JLabel lbl_associateSeq = new JLabel();
804 public AssociateSeqPanel()
806 this.setLayout(new FlowLayout());
807 this.add(cmb_assSeq);
808 this.add(lbl_associateSeq);
809 cmb_assSeq.setToolTipText(
810 MessageManager.getString("info.associate_wit_sequence"));
811 cmb_assSeq.addItemListener(this);
814 public void loadCmbAssSeq()
816 populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
819 public JComboBox<AssociateSeqOptions> getCmb_assSeq()
824 public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)
826 this.cmb_assSeq = cmb_assSeq;
830 public void itemStateChanged(ItemEvent e)
832 if (e.getStateChange() == ItemEvent.SELECTED)
834 cmbAssSeqStateChanged();
839 public JTable getResultTable()
844 public JComboBox<FilterOption> getCmbFilterOption()
846 return cmb_filterOption;
850 * Custom ListCellRenderer for adding a separator between different categories
851 * of structure chooser filter option drop-down.
856 public abstract class CustomComboSeparatorsRenderer
857 implements ListCellRenderer<Object>
859 private ListCellRenderer<Object> regent;
861 private JPanel separatorPanel = new JPanel(new BorderLayout());
863 private JSeparator jSeparator = new JSeparator();
865 public CustomComboSeparatorsRenderer(
866 ListCellRenderer<Object> listCellRenderer)
868 this.regent = listCellRenderer;
872 public Component getListCellRendererComponent(JList list, Object value,
873 int index, boolean isSelected, boolean cellHasFocus)
876 Component comp = regent.getListCellRendererComponent(list, value,
877 index, isSelected, cellHasFocus);
879 && addSeparatorAfter(list, (FilterOption) value, index))
881 separatorPanel.removeAll();
882 separatorPanel.add(comp, BorderLayout.CENTER);
883 separatorPanel.add(jSeparator, BorderLayout.SOUTH);
884 return separatorPanel;
892 protected abstract boolean addSeparatorAfter(JList list,
893 FilterOption value, int index);
896 protected abstract void stateChanged(ItemEvent e);
898 protected abstract void add_ActionPerformed();
900 protected abstract void newView_ActionPerformed();
902 protected abstract void pdbFromFile_actionPerformed();
904 protected abstract void txt_search_ActionPerformed();
906 protected abstract void populateCmbAssociateSeqOptions(
907 JComboBox<AssociateSeqOptions> cmb_assSeq,
908 JLabel lbl_associateSeq);
910 protected abstract void cmbAssSeqStateChanged();
912 protected abstract void tabRefresh();
914 protected abstract void validateSelections();