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.event.ActionEvent;
43 import java.awt.event.ActionListener;
44 import java.awt.event.ItemEvent;
45 import java.awt.event.ItemListener;
46 import java.awt.event.KeyAdapter;
47 import java.awt.event.KeyEvent;
48 import java.awt.event.MouseAdapter;
49 import java.awt.event.MouseEvent;
50 import java.util.Arrays;
51 import java.util.HashMap;
54 import javax.swing.ImageIcon;
55 import javax.swing.JButton;
56 import javax.swing.JCheckBox;
57 import javax.swing.JComboBox;
58 import javax.swing.JFrame;
59 import javax.swing.JInternalFrame;
60 import javax.swing.JLabel;
61 import javax.swing.JList;
62 import javax.swing.JPanel;
63 import javax.swing.JScrollPane;
64 import javax.swing.JSeparator;
65 import javax.swing.JTabbedPane;
66 import javax.swing.JTable;
67 import javax.swing.JTextField;
68 import javax.swing.ListCellRenderer;
69 import javax.swing.Timer;
70 import javax.swing.event.ChangeEvent;
71 import javax.swing.event.ChangeListener;
72 import javax.swing.event.DocumentEvent;
73 import javax.swing.event.DocumentListener;
74 import javax.swing.event.InternalFrameEvent;
75 import javax.swing.table.TableColumn;
77 import net.miginfocom.swing.MigLayout;
79 @SuppressWarnings("serial")
81 * GUI layout for structure chooser
86 public abstract class GStructureChooser extends JPanel
87 implements ItemListener
89 private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
91 public static final String VIEWS_FILTER = "VIEWS_FILTER";
93 protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
95 protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
98 * 'cached' structure view
100 protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
102 protected JPanel statusPanel = new JPanel();
104 public JLabel statusBar = new JLabel();
106 protected String frameTitle = MessageManager
107 .getString("label.structure_chooser");
109 protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
111 protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
113 protected AlignmentPanel ap;
115 protected StringBuilder errorWarning = new StringBuilder();
117 protected JButton btn_add;
119 protected JButton btn_newView;
121 protected JButton btn_pdbFromFile = new JButton();
123 protected JCheckBox chk_superpose = new JCheckBox(
124 MessageManager.getString("label.superpose_structures"));
126 protected JTextField txt_search = new JTextField(14);
128 protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
130 protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
133 protected JCheckBox chk_invertFilter = new JCheckBox(
134 MessageManager.getString("label.invert"));
136 protected ImageIcon loadingImage = new ImageIcon(
137 getClass().getResource("/images/loading.gif"));
139 protected ImageIcon goodImage = new ImageIcon(
140 getClass().getResource("/images/good.png"));
142 protected ImageIcon errorImage = new ImageIcon(
143 getClass().getResource("/images/error.png"));
145 protected ImageIcon warningImage = new ImageIcon(
146 getClass().getResource("/images/warning.gif"));
148 protected JLabel lbl_loading = new JLabel(loadingImage);
150 protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
152 protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
154 protected AssociateSeqPanel idInputAssSeqPanel = new AssociateSeqPanel();
156 protected AssociateSeqPanel fileChooserAssSeqPanel = new AssociateSeqPanel();
158 protected JComboBox<StructureViewer> targetView = new JComboBox<>();
160 protected JTable tbl_local_pdb = new JTable();
162 protected JTabbedPane pnl_filter = new JTabbedPane();
164 protected abstract FTSDataColumnPreferences getFTSDocFieldPrefs();
165 protected abstract void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs);
168 protected FTSDataColumnI[] previousWantedFields;
170 protected static Map<String, Integer> tempUserPrefs = new HashMap<>();
172 private JTable tbl_summary = new JTable()
174 private boolean inLayout;
177 public boolean getScrollableTracksViewportWidth()
179 return hasExcessWidth();
184 public void doLayout()
186 if (hasExcessWidth())
188 autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS;
193 autoResizeMode = AUTO_RESIZE_OFF;
196 protected boolean hasExcessWidth()
198 return getPreferredSize().width < getParent().getWidth();
202 public void columnMarginChanged(ChangeEvent e)
208 TableColumn resizingColumn = getTableHeader().getResizingColumn();
209 // Need to do this here, before the parent's
210 // layout manager calls getPreferredSize().
211 if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF
214 resizingColumn.setPreferredWidth(resizingColumn.getWidth());
215 String colHeader = resizingColumn.getHeaderValue().toString();
216 tempUserPrefs.put(colHeader, resizingColumn.getWidth());
222 public String getToolTipText(MouseEvent evt)
224 String toolTipText = null;
225 java.awt.Point pnt = evt.getPoint();
226 int rowIndex = rowAtPoint(pnt);
227 int colIndex = columnAtPoint(pnt);
231 if (getValueAt(rowIndex, colIndex) == null)
235 toolTipText = getValueAt(rowIndex, colIndex).toString();
236 } catch (Exception e)
238 // e.printStackTrace();
240 toolTipText = (toolTipText == null ? null
241 : (toolTipText.length() > 500
242 ? JvSwingUtils.wrapTooltip(true,
243 "\"" + toolTipText.subSequence(0, 500)
245 : JvSwingUtils.wrapTooltip(true, toolTipText)));
250 public GStructureChooser()
253 protected void initDialog()
259 mainFrame.setVisible(false);
260 mainFrame.invalidate();
262 } catch (Exception e)
264 System.out.println(e); // for JavaScript TypeError
269 // BH SwingJS optimization
270 // (a) 100-ms interruptable timer for text entry -- BH 1/10/2019
271 // (b) two-character minimum, at least for JavaScript.
275 protected void txt_search_ActionPerformedDelayed() {
279 timer = new Timer(300, new ActionListener() {
282 public void actionPerformed(ActionEvent e) {
283 txt_search_ActionPerformed();
286 timer.setRepeats(false);
292 * Initializes the GUI default properties
296 private void jbInit() throws Exception
298 Integer width = tempUserPrefs.get("structureChooser.width") == null
300 : tempUserPrefs.get("structureChooser.width");
301 Integer height = tempUserPrefs.get("structureChooser.height") == null
303 : tempUserPrefs.get("structureChooser.height");
304 tbl_summary.setAutoCreateRowSorter(true);
305 tbl_summary.getTableHeader().setReorderingAllowed(false);
306 tbl_summary.addMouseListener(new MouseAdapter()
309 public void mouseClicked(MouseEvent e)
311 validateSelections();
315 public void mouseReleased(MouseEvent e)
317 validateSelections();
320 tbl_summary.addKeyListener(new KeyAdapter()
323 public void keyPressed(KeyEvent evt)
325 validateSelections();
326 switch (evt.getKeyCode())
328 case KeyEvent.VK_ESCAPE: // escape key
331 case KeyEvent.VK_ENTER: // enter key
332 if (btn_add.isEnabled())
334 add_ActionPerformed();
337 case KeyEvent.VK_TAB: // tab key
338 if (evt.isShiftDown())
340 pnl_filter.requestFocus();
344 btn_add.requestFocus();
354 JButton btn_cancel = new JButton(
355 MessageManager.getString("action.cancel"));
356 btn_cancel.setFont(VERDANA_12);
357 btn_cancel.addActionListener(new java.awt.event.ActionListener()
360 public void actionPerformed(ActionEvent e)
362 closeAction(pnl_filter.getHeight());
365 btn_cancel.addKeyListener(new KeyAdapter()
368 public void keyPressed(KeyEvent evt)
370 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
372 closeAction(pnl_filter.getHeight());
377 tbl_local_pdb.setAutoCreateRowSorter(true);
378 tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
379 tbl_local_pdb.addMouseListener(new MouseAdapter()
382 public void mouseClicked(MouseEvent e)
384 validateSelections();
388 public void mouseReleased(MouseEvent e)
390 validateSelections();
393 tbl_local_pdb.addKeyListener(new KeyAdapter()
396 public void keyPressed(KeyEvent evt)
398 validateSelections();
399 switch (evt.getKeyCode())
401 case KeyEvent.VK_ESCAPE: // escape key
404 case KeyEvent.VK_ENTER: // enter key
405 if (btn_add.isEnabled())
407 add_ActionPerformed();
410 case KeyEvent.VK_TAB: // tab key
411 if (evt.isShiftDown())
413 cmb_filterOption.requestFocus();
417 if (btn_add.isEnabled())
419 btn_add.requestFocus();
423 btn_cancel.requestFocus();
434 btn_newView = new JButton(MessageManager.getString("action.new_view"));
435 btn_newView.setFont(VERDANA_12);
436 btn_newView.addActionListener(new java.awt.event.ActionListener()
439 public void actionPerformed(ActionEvent e)
441 newView_ActionPerformed();
444 btn_newView.addKeyListener(new KeyAdapter()
447 public void keyPressed(KeyEvent evt)
449 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
451 newView_ActionPerformed();
456 btn_add = new JButton(MessageManager.getString("action.add"));
457 btn_add.setFont(VERDANA_12);
458 btn_add.addActionListener(new java.awt.event.ActionListener()
461 public void actionPerformed(ActionEvent e)
463 add_ActionPerformed();
466 btn_add.addKeyListener(new KeyAdapter()
469 public void keyPressed(KeyEvent evt)
471 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
473 add_ActionPerformed();
478 btn_pdbFromFile.setFont(VERDANA_12);
479 String btn_title = MessageManager.getString("label.select_pdb_file");
480 btn_pdbFromFile.setText(btn_title + " ");
481 btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
484 public void actionPerformed(ActionEvent e)
486 pdbFromFile_actionPerformed();
489 btn_pdbFromFile.addKeyListener(new KeyAdapter()
492 public void keyPressed(KeyEvent evt)
494 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
496 pdbFromFile_actionPerformed();
501 JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
502 scrl_foundStructures.setPreferredSize(new Dimension(width, height));
504 JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
505 scrl_localPDB.setPreferredSize(new Dimension(width, height));
506 scrl_localPDB.setHorizontalScrollBarPolicy(
507 JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
509 chk_invertFilter.setFont(VERDANA_12);
510 txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
511 MessageManager.getString("label.enter_pdb_id_tip")));
512 txt_search.getDocument().addDocumentListener(new DocumentListener()
515 public void insertUpdate(DocumentEvent e)
517 txt_search_ActionPerformedDelayed();
521 public void removeUpdate(DocumentEvent e)
523 txt_search_ActionPerformedDelayed();
527 public void changedUpdate(DocumentEvent e)
529 txt_search_ActionPerformedDelayed();
533 cmb_filterOption.setFont(VERDANA_12);
534 cmb_filterOption.setToolTipText(
535 MessageManager.getString("info.select_filter_option"));
536 cmb_filterOption.addItemListener(this);
537 // add CustomComboSeparatorsRenderer to filter option combo-box
538 cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
539 (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
542 protected boolean addSeparatorAfter(JList list, FilterOption value,
545 return value.isAddSeparatorAfter();
549 chk_invertFilter.addItemListener(this);
551 targetView.setVisible(false);
553 JPanel actionsPanel = new JPanel(new MigLayout());
554 actionsPanel.add(targetView, "left");
555 actionsPanel.add(btn_add, "wrap");
556 actionsPanel.add(chk_superpose, "left");
557 actionsPanel.add(btn_newView);
558 actionsPanel.add(btn_cancel, "right");
560 JPanel pnl_main = new JPanel();
561 pnl_main.add(cmb_filterOption);
562 pnl_main.add(lbl_loading);
563 pnl_main.add(chk_invertFilter);
564 lbl_loading.setVisible(false);
566 JPanel pnl_fileChooser = new JPanel(new FlowLayout());
567 pnl_fileChooser.add(btn_pdbFromFile);
568 pnl_fileChooser.add(lbl_fromFileStatus);
569 JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
570 pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
571 pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
573 JPanel pnl_idInput = new JPanel(new FlowLayout());
574 pnl_idInput.add(txt_search);
575 pnl_idInput.add(lbl_pdbManualFetchStatus);
577 JPanel pnl_idInputBL = new JPanel(new BorderLayout());
578 pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
579 pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
581 final String foundStructureSummary = MessageManager
582 .getString("label.found_structures_summary");
583 final String configureCols = MessageManager
584 .getString("label.configure_displayed_columns");
585 ChangeListener changeListener = new ChangeListener()
588 public void stateChanged(ChangeEvent changeEvent)
590 JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
592 int index = sourceTabbedPane.getSelectedIndex();
593 btn_add.setVisible(targetView.isVisible());
594 btn_newView.setVisible(true);
595 btn_cancel.setVisible(true);
596 if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
598 btn_add.setEnabled(false);
599 btn_cancel.setEnabled(false);
600 btn_add.setVisible(false);
601 btn_newView.setEnabled(false);
602 btn_cancel.setVisible(false);
603 previousWantedFields = getFTSDocFieldPrefs()
604 .getStructureSummaryFields()
605 .toArray(new FTSDataColumnI[0]);
607 if (sourceTabbedPane.getTitleAt(index)
608 .equals(foundStructureSummary))
610 btn_cancel.setEnabled(true);
611 if (wantedFieldsUpdated())
617 validateSelections();
622 pnl_filter.addChangeListener(changeListener);
623 pnl_filter.setPreferredSize(new Dimension(width, height));
624 pnl_filter.add(foundStructureSummary, scrl_foundStructures);
625 pnl_filter.add(configureCols, getFTSDocFieldPrefs());
627 JPanel pnl_locPDB = new JPanel(new BorderLayout());
628 pnl_locPDB.add(scrl_localPDB);
630 pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
631 pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
632 pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
633 pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
635 this.setLayout(new BorderLayout());
636 this.add(pnl_main, java.awt.BorderLayout.NORTH);
637 this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
638 // this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
639 statusPanel.setLayout(new GridLayout());
641 JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
642 pnl_actionsAndStatus.add(actionsPanel, BorderLayout.CENTER);
643 pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
644 statusPanel.add(statusBar, null);
645 this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
647 mainFrame.addInternalFrameListener(
648 new javax.swing.event.InternalFrameAdapter()
651 public void internalFrameClosing(InternalFrameEvent e)
653 closeAction(pnl_filter.getHeight());
656 mainFrame.setVisible(true);
657 mainFrame.setContentPane(this);
658 mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
659 Integer x = tempUserPrefs.get("structureChooser.x");
660 Integer y = tempUserPrefs.get("structureChooser.y");
661 if (x != null && y != null)
663 mainFrame.setLocation(x, y);
665 Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
669 protected void closeAction(int preferredHeight)
671 // System.out.println(">>>>>>>>>> closing internal frame!!!");
672 // System.out.println("width : " + mainFrame.getWidth());
673 // System.out.println("heigh : " + mainFrame.getHeight());
674 // System.out.println("x : " + mainFrame.getX());
675 // System.out.println("y : " + mainFrame.getY());
676 tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
677 tempUserPrefs.put("structureChooser.height", preferredHeight);
678 tempUserPrefs.put("structureChooser.x", mainFrame.getX());
679 tempUserPrefs.put("structureChooser.y", mainFrame.getY());
683 public boolean wantedFieldsUpdated()
685 if (previousWantedFields == null)
690 FTSDataColumnI[] currentWantedFields = getFTSDocFieldPrefs()
691 .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
692 return Arrays.equals(currentWantedFields, previousWantedFields) ? false
699 * Event listener for the 'filter' combo-box and 'invert' check-box
701 public void itemStateChanged(ItemEvent e)
707 * This inner class provides the provides the data model for associate
708 * sequence combo-box - cmb_assSeq
713 public class AssociateSeqOptions
715 private SequenceI sequence;
719 public AssociateSeqOptions(SequenceI seq)
722 this.name = (seq.getName().length() >= 23)
723 ? seq.getName().substring(0, 23)
727 public AssociateSeqOptions(String name, SequenceI seq)
734 public String toString()
739 public String getName()
744 public void setName(String name)
749 public SequenceI getSequence()
754 public void setSequence(SequenceI sequence)
756 this.sequence = sequence;
762 * This inner class holds the Layout and configuration of the panel which
763 * handles association of manually fetched structures to a unique sequence
764 * when more than one sequence selection is made
769 public class AssociateSeqPanel extends JPanel implements ItemListener
771 private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
773 private JLabel lbl_associateSeq = new JLabel();
775 public AssociateSeqPanel()
777 this.setLayout(new FlowLayout());
778 this.add(cmb_assSeq);
779 this.add(lbl_associateSeq);
780 cmb_assSeq.setToolTipText(
781 MessageManager.getString("info.associate_wit_sequence"));
782 cmb_assSeq.addItemListener(this);
785 public void loadCmbAssSeq()
787 populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
790 public JComboBox<AssociateSeqOptions> getCmb_assSeq()
795 public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)
797 this.cmb_assSeq = cmb_assSeq;
801 public void itemStateChanged(ItemEvent e)
803 if (e.getStateChange() == ItemEvent.SELECTED)
805 cmbAssSeqStateChanged();
810 public JTable getResultTable()
815 public JComboBox<FilterOption> getCmbFilterOption()
817 return cmb_filterOption;
821 * Custom ListCellRenderer for adding a separator between different categories
822 * of structure chooser filter option drop-down.
827 public abstract class CustomComboSeparatorsRenderer
828 implements ListCellRenderer<Object>
830 private ListCellRenderer<Object> regent;
832 private JPanel separatorPanel = new JPanel(new BorderLayout());
834 private JSeparator jSeparator = new JSeparator();
836 public CustomComboSeparatorsRenderer(
837 ListCellRenderer<Object> listCellRenderer)
839 this.regent = listCellRenderer;
843 public Component getListCellRendererComponent(JList list, Object value,
844 int index, boolean isSelected, boolean cellHasFocus)
847 Component comp = regent.getListCellRendererComponent(list, value,
848 index, isSelected, cellHasFocus);
850 && addSeparatorAfter(list, (FilterOption) value, index))
852 separatorPanel.removeAll();
853 separatorPanel.add(comp, BorderLayout.CENTER);
854 separatorPanel.add(jSeparator, BorderLayout.SOUTH);
855 return separatorPanel;
863 protected abstract boolean addSeparatorAfter(JList list,
864 FilterOption value, int index);
867 protected abstract void stateChanged(ItemEvent e);
869 protected abstract void add_ActionPerformed();
871 protected abstract void newView_ActionPerformed();
873 protected abstract void pdbFromFile_actionPerformed();
875 protected abstract void txt_search_ActionPerformed();
877 protected abstract void populateCmbAssociateSeqOptions(
878 JComboBox<AssociateSeqOptions> cmb_assSeq,
879 JLabel lbl_associateSeq);
881 protected abstract void cmbAssSeqStateChanged();
883 protected abstract void tabRefresh();
885 protected abstract void validateSelections();