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.fts.core;
24 import jalview.fts.api.FTSDataColumnI;
25 import jalview.fts.api.GFTSPanelI;
26 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
27 import jalview.gui.Desktop;
28 import jalview.gui.IProgressIndicator;
29 import jalview.gui.JvSwingUtils;
30 import jalview.gui.SequenceFetcher;
31 import jalview.util.MessageManager;
33 import java.awt.BorderLayout;
34 import java.awt.CardLayout;
35 import java.awt.Dimension;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.ActionListener;
38 import java.awt.event.FocusEvent;
39 import java.awt.event.FocusListener;
40 import java.awt.event.KeyAdapter;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.MouseAdapter;
43 import java.awt.event.MouseEvent;
44 import java.text.DecimalFormat;
45 import java.util.ArrayList;
46 import java.util.Arrays;
47 import java.util.Collection;
48 import java.util.Collections;
49 import java.util.Comparator;
50 import java.util.HashSet;
51 import java.util.List;
53 import javax.swing.ImageIcon;
54 import javax.swing.JButton;
55 import javax.swing.JComboBox;
56 import javax.swing.JFrame;
57 import javax.swing.JInternalFrame;
58 import javax.swing.JLabel;
59 import javax.swing.JPanel;
60 import javax.swing.JScrollPane;
61 import javax.swing.JTabbedPane;
62 import javax.swing.JTable;
63 import javax.swing.JTextField;
64 import javax.swing.Timer;
65 import javax.swing.event.ChangeEvent;
66 import javax.swing.event.ChangeListener;
67 import javax.swing.event.DocumentEvent;
68 import javax.swing.event.DocumentListener;
69 import javax.swing.table.DefaultTableModel;
70 import javax.swing.table.TableColumn;
73 * This class provides the swing GUI layout for FTS Panel and implements most of
74 * the contracts defined in GFSPanelI
80 @SuppressWarnings("serial")
81 public abstract class GFTSPanel extends JPanel implements GFTSPanelI
83 protected JInternalFrame mainFrame = new JInternalFrame(
86 protected IProgressIndicator progressIdicator;
88 protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<FTSDataColumnI>();
90 protected JButton btn_ok = new JButton();
92 protected JButton btn_back = new JButton();
94 protected JButton btn_cancel = new JButton();
96 protected JTextField txt_search = new JTextField(30);
98 protected SequenceFetcher seqFetcher;
100 protected Collection<FTSDataColumnI> wantedFields;
102 private String lastSearchTerm = "";
104 protected JButton btn_next_page = new JButton();
106 protected JButton btn_prev_page = new JButton();
108 protected StringBuilder errorWarning = new StringBuilder();
110 protected ImageIcon warningImage = new ImageIcon(getClass().getResource(
111 "/images/warning.gif"));
113 protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
114 "/images/loading.gif"));
116 protected ImageIcon balnkPlaceholderImage = new ImageIcon(getClass()
117 .getResource("/images/blank_16x16_placeholder.png"));
119 protected JLabel lbl_warning = new JLabel(warningImage);
121 protected JLabel lbl_loading = new JLabel(loadingImage);
123 protected JLabel lbl_blank = new JLabel(balnkPlaceholderImage);
125 private JTabbedPane tabbedPane = new JTabbedPane();
127 private JPanel pnl_actions = new JPanel();
129 private JPanel pnl_results = new JPanel(new CardLayout());
131 private JPanel pnl_inputs = new JPanel();
133 private BorderLayout mainLayout = new BorderLayout();
135 protected Object[] previousWantedFields;
137 protected int resultSetCount;
139 protected int totalResultSetCount;
141 protected int offSet;
143 protected int pageLimit;
145 protected HashSet<String> paginatorCart = new HashSet<String>();
147 protected static final DecimalFormat totalNumberformatter = new DecimalFormat(
150 private JTable tbl_summary = new JTable()
152 private boolean inLayout;
155 public boolean getScrollableTracksViewportWidth()
157 return hasExcessWidth();
162 public void doLayout()
164 if (hasExcessWidth())
166 autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS;
171 autoResizeMode = AUTO_RESIZE_OFF;
174 protected boolean hasExcessWidth()
176 return getPreferredSize().width < getParent().getWidth();
180 public void columnMarginChanged(ChangeEvent e)
186 TableColumn resizingColumn = getTableHeader().getResizingColumn();
187 // Need to do this here, before the parent's
188 // layout manager calls getPreferredSize().
189 if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF
192 resizingColumn.setPreferredWidth(resizingColumn.getWidth());
198 public String getToolTipText(MouseEvent evt)
200 String toolTipText = null;
201 java.awt.Point pnt = evt.getPoint();
202 int rowIndex = rowAtPoint(pnt);
203 int colIndex = columnAtPoint(pnt);
207 if (getValueAt(rowIndex, colIndex) == null)
211 toolTipText = getValueAt(rowIndex, colIndex).toString();
213 } catch (Exception e)
217 toolTipText = (toolTipText == null ? null
218 : (toolTipText.length() > 500 ? JvSwingUtils.wrapTooltip(
219 true, toolTipText.subSequence(0, 500) + "...")
220 : JvSwingUtils.wrapTooltip(true, toolTipText)));
225 protected JScrollPane scrl_searchResult = new JScrollPane(tbl_summary);
232 mainFrame.invalidate();
234 } catch (Exception e)
241 * Initializes the GUI default properties
245 private void jbInit() throws Exception
247 lbl_warning.setVisible(false);
248 lbl_warning.setFont(new java.awt.Font("Verdana", 0, 12));
249 lbl_loading.setVisible(false);
250 lbl_loading.setFont(new java.awt.Font("Verdana", 0, 12));
251 lbl_blank.setVisible(true);
252 lbl_blank.setFont(new java.awt.Font("Verdana", 0, 12));
254 tbl_summary.setAutoCreateRowSorter(true);
255 tbl_summary.getTableHeader().setReorderingAllowed(false);
256 tbl_summary.addMouseListener(new MouseAdapter()
259 public void mouseClicked(MouseEvent e)
265 public void mouseReleased(MouseEvent e)
270 tbl_summary.addKeyListener(new KeyAdapter()
273 public void keyPressed(KeyEvent evt)
276 switch (evt.getKeyCode())
278 case KeyEvent.VK_ESCAPE: // escape key
279 btn_back_ActionPerformed();
281 case KeyEvent.VK_ENTER: // enter key
282 if (btn_ok.isEnabled())
288 case KeyEvent.VK_TAB: // tab key
289 if (evt.isShiftDown())
291 tabbedPane.requestFocus();
295 btn_back.requestFocus();
305 btn_back.setFont(new java.awt.Font("Verdana", 0, 12));
306 btn_back.setText(MessageManager.getString("action.back"));
307 btn_back.addActionListener(new java.awt.event.ActionListener()
310 public void actionPerformed(ActionEvent e)
312 btn_back_ActionPerformed();
315 btn_back.addKeyListener(new KeyAdapter()
318 public void keyPressed(KeyEvent evt)
320 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
322 btn_back_ActionPerformed();
327 btn_ok.setEnabled(false);
328 btn_ok.setFont(new java.awt.Font("Verdana", 0, 12));
329 btn_ok.setText(MessageManager.getString("action.ok"));
330 btn_ok.addActionListener(new java.awt.event.ActionListener()
333 public void actionPerformed(ActionEvent e)
338 btn_ok.addKeyListener(new KeyAdapter()
341 public void keyPressed(KeyEvent evt)
343 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
349 btn_next_page.setEnabled(false);
350 btn_next_page.setToolTipText(MessageManager
351 .getString("label.next_page_tooltop"));
352 btn_next_page.setFont(new java.awt.Font("Verdana", 0, 12));
353 btn_next_page.setText(MessageManager.getString("action.next_page"));
354 btn_next_page.addActionListener(new java.awt.event.ActionListener()
357 public void actionPerformed(ActionEvent e)
362 btn_next_page.addKeyListener(new KeyAdapter()
365 public void keyPressed(KeyEvent evt)
367 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
374 btn_prev_page.setEnabled(false);
375 btn_prev_page.setToolTipText(MessageManager
376 .getString("label.prev_page_tooltop"));
377 btn_prev_page.setFont(new java.awt.Font("Verdana", 0, 12));
378 btn_prev_page.setText(MessageManager.getString("action.prev_page"));
379 btn_prev_page.addActionListener(new java.awt.event.ActionListener()
382 public void actionPerformed(ActionEvent e)
387 btn_prev_page.addKeyListener(new KeyAdapter()
390 public void keyPressed(KeyEvent evt)
392 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
399 if (isPaginationEnabled())
401 btn_prev_page.setVisible(true);
402 btn_next_page.setVisible(true);
406 btn_prev_page.setVisible(false);
407 btn_next_page.setVisible(false);
410 btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
411 btn_cancel.setText(MessageManager.getString("action.cancel"));
412 btn_cancel.addActionListener(new java.awt.event.ActionListener()
415 public void actionPerformed(ActionEvent e)
417 btn_cancel_ActionPerformed();
420 btn_cancel.addKeyListener(new KeyAdapter()
423 public void keyPressed(KeyEvent evt)
425 if (evt.getKeyCode() == KeyEvent.VK_ENTER)
427 btn_cancel_ActionPerformed();
431 scrl_searchResult.setPreferredSize(new Dimension(800, 400));
433 cmb_searchTarget.setFont(new java.awt.Font("Verdana", 0, 12));
434 cmb_searchTarget.addActionListener(new ActionListener()
437 public void actionPerformed(ActionEvent e)
440 if ("all".equalsIgnoreCase(getCmbSearchTarget().getSelectedItem()
443 tooltipText = MessageManager.getString("label.search_all");
445 else if ("pdb id".equalsIgnoreCase(getCmbSearchTarget()
446 .getSelectedItem().toString()))
448 tooltipText = MessageManager
449 .getString("label.separate_multiple_accession_ids");
453 tooltipText = MessageManager.formatMessage(
454 "label.separate_multiple_query_values",
455 new Object[] { getCmbSearchTarget().getSelectedItem()
458 txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
464 populateCmbSearchTargetOptions();
466 txt_search.setFont(new java.awt.Font("Verdana", 0, 12));
468 txt_search.addKeyListener(new KeyAdapter()
471 public void keyPressed(KeyEvent e)
473 if (e.getKeyCode() == KeyEvent.VK_ENTER)
475 if (txt_search.getText() == null
476 || txt_search.getText().isEmpty())
480 String primaryKeyName = getFTSRestClient().getPrimaryKeyColumn()
482 if (primaryKeyName.equalsIgnoreCase(getCmbSearchTarget()
483 .getSelectedItem().toString()))
485 transferToSequenceFetcher(txt_search.getText());
491 final DeferredTextInputListener listener = new DeferredTextInputListener(
496 public void actionPerformed(ActionEvent e)
498 if (!getTypedText().equalsIgnoreCase(lastSearchTerm))
501 paginatorCart.clear();
502 lastSearchTerm = getTypedText();
506 txt_search.getDocument().addDocumentListener(listener);
507 txt_search.addFocusListener(new FocusListener()
510 public void focusGained(FocusEvent e)
516 public void focusLost(FocusEvent e)
522 final String searchTabTitle = MessageManager
523 .getString("label.search_result");
524 final String configureCols = MessageManager
525 .getString("label.configure_displayed_columns");
526 ChangeListener changeListener = new ChangeListener()
529 public void stateChanged(ChangeEvent changeEvent)
531 JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
533 int index = sourceTabbedPane.getSelectedIndex();
535 btn_back.setVisible(true);
536 btn_cancel.setVisible(true);
537 btn_ok.setVisible(true);
538 if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
540 btn_back.setVisible(false);
541 btn_cancel.setVisible(false);
542 btn_ok.setVisible(false);
543 btn_back.setEnabled(false);
544 btn_cancel.setEnabled(false);
545 btn_ok.setEnabled(false);
546 btn_next_page.setEnabled(false);
547 btn_prev_page.setEnabled(false);
548 txt_search.setEnabled(false);
549 cmb_searchTarget.setEnabled(false);
550 previousWantedFields = getFTSRestClient()
551 .getAllDefaulDisplayedDataColumns()
552 .toArray(new Object[0]);
554 if (sourceTabbedPane.getTitleAt(index).equals(searchTabTitle))
556 btn_back.setEnabled(true);
557 btn_cancel.setEnabled(true);
558 refreshPaginatorState();
559 txt_search.setEnabled(true);
560 cmb_searchTarget.setEnabled(true);
561 if (wantedFieldsUpdated())
564 paginatorCart.clear();
573 tabbedPane.addChangeListener(changeListener);
574 tabbedPane.setPreferredSize(new Dimension(800, 400));
575 tabbedPane.add(searchTabTitle, scrl_searchResult);
576 tabbedPane.add(configureCols, new FTSDataColumnPreferences(
577 PreferenceSource.SEARCH_SUMMARY, getFTSRestClient()));
579 pnl_actions.add(btn_back);
580 pnl_actions.add(btn_ok);
581 pnl_actions.add(btn_cancel);
583 pnl_results.add(tabbedPane);
584 pnl_inputs.add(cmb_searchTarget);
585 pnl_inputs.add(txt_search);
586 pnl_inputs.add(lbl_loading);
587 pnl_inputs.add(lbl_warning);
588 pnl_inputs.add(lbl_blank);
589 pnl_inputs.add(btn_prev_page);
590 pnl_inputs.add(btn_next_page);
592 this.setLayout(mainLayout);
593 this.add(pnl_inputs, java.awt.BorderLayout.NORTH);
594 this.add(pnl_results, java.awt.BorderLayout.CENTER);
595 this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
596 mainFrame.setVisible(true);
597 mainFrame.setContentPane(this);
598 mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
599 Desktop.addInternalFrame(mainFrame, getFTSFrameTitle(), 900, 500);
602 public class DeferredTextInputListener implements DocumentListener
604 private final Timer swingTimer;
606 public DeferredTextInputListener(int timeOut, ActionListener listener,
609 swingTimer = new Timer(timeOut, listener);
610 swingTimer.setRepeats(repeats);
624 public void insertUpdate(DocumentEvent e)
626 swingTimer.restart();
630 public void removeUpdate(DocumentEvent e)
632 swingTimer.restart();
636 public void changedUpdate(DocumentEvent e)
638 swingTimer.restart();
643 public boolean wantedFieldsUpdated()
645 if (previousWantedFields == null)
650 return Arrays.equals(getFTSRestClient()
651 .getAllDefaulDisplayedDataColumns()
652 .toArray(new Object[0]), previousWantedFields) ? false
657 public void validateSelection()
659 if (tbl_summary.getSelectedRows().length > 0
660 || !paginatorCart.isEmpty())
662 btn_ok.setEnabled(true);
666 btn_ok.setEnabled(false);
670 public JComboBox<FTSDataColumnI> getCmbSearchTarget()
672 return cmb_searchTarget;
675 public JTextField getTxtSearch()
680 public JInternalFrame getMainFrame()
685 protected void delayAndEnableActionButtons()
695 } catch (InterruptedException e)
699 btn_ok.setEnabled(true);
700 btn_back.setEnabled(true);
701 btn_cancel.setEnabled(true);
706 protected void checkForErrors()
708 lbl_warning.setVisible(false);
709 lbl_blank.setVisible(true);
710 if (errorWarning.length() > 0)
712 lbl_loading.setVisible(false);
713 lbl_blank.setVisible(false);
714 lbl_warning.setToolTipText(JvSwingUtils.wrapTooltip(true,
715 errorWarning.toString()));
716 lbl_warning.setVisible(true);
720 protected void btn_back_ActionPerformed()
723 new SequenceFetcher(progressIdicator);
726 protected void disableActionButtons()
728 btn_ok.setEnabled(false);
729 btn_back.setEnabled(false);
730 btn_cancel.setEnabled(false);
733 protected void btn_cancel_ActionPerformed()
739 * Populates search target combo-box options
741 public void populateCmbSearchTargetOptions()
743 List<FTSDataColumnI> searchableTargets = new ArrayList<FTSDataColumnI>();
746 Collection<FTSDataColumnI> foundFTSTargets = getFTSRestClient()
747 .getSearchableDataColumns();
748 searchableTargets.addAll(foundFTSTargets);
749 } catch (Exception e)
754 Collections.sort(searchableTargets, new Comparator<FTSDataColumnI>()
757 public int compare(FTSDataColumnI o1, FTSDataColumnI o2)
759 return o1.getName().compareTo(o2.getName());
763 for (FTSDataColumnI searchTarget : searchableTargets)
765 cmb_searchTarget.addItem(searchTarget);
770 public void transferToSequenceFetcher(String ids)
772 // mainFrame.dispose();
773 seqFetcher.getTextArea().setText(ids);
774 Thread worker = new Thread(seqFetcher);
779 public String getTypedText()
781 return txt_search.getText().trim();
785 public JTable getResultTable()
792 lbl_loading.setVisible(false);
793 errorWarning.setLength(0);
794 lbl_warning.setVisible(false);
795 lbl_blank.setVisible(true);
796 btn_ok.setEnabled(false);
797 mainFrame.setTitle(getFTSFrameTitle());
799 tbl_summary.setModel(new DefaultTableModel());
800 tbl_summary.setVisible(false);
804 public void setPrevPageButtonEnabled(boolean isEnabled)
806 btn_prev_page.setEnabled(isEnabled);
810 public void setNextPageButtonEnabled(boolean isEnabled)
812 btn_next_page.setEnabled(isEnabled);
816 public void setErrorMessage(String message)
818 errorWarning.append(message);
822 public void updateSearchFrameTitle(String title)
824 mainFrame.setTitle(title);
828 public void setSearchInProgress(Boolean isSearchInProgress)
830 lbl_blank.setVisible(!isSearchInProgress);
831 lbl_loading.setVisible(isSearchInProgress);
835 public void prevPageAction()
837 updatePaginatorCart();
838 if (offSet >= pageLimit)
840 offSet = offSet - pageLimit;
845 refreshPaginatorState();
850 public void nextPageAction()
852 updatePaginatorCart();
853 offSet = offSet + pageLimit;
857 public void updatePaginatorCart()
859 int primaryKeyColIndex = 0;
860 JTable resultTable = getResultTable();
861 int totalRows = resultTable.getRowCount();
864 primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
865 wantedFields, false);
866 } catch (Exception e)
871 for (int row = 0; row < totalRows; row++)
873 String id = (String) resultTable.getValueAt(row, primaryKeyColIndex);
874 if (paginatorCart.contains(id))
876 paginatorCart.remove(id);
879 int[] selectedRows = resultTable.getSelectedRows();
880 for (int summaryRow : selectedRows)
882 String idStr = resultTable.getValueAt(summaryRow,
883 primaryKeyColIndex).toString();
884 paginatorCart.add(idStr);
886 // System.out.println("Paginator shopping cart size : "
887 // + paginatorCart.size());
890 public void updateSummaryTableSelections()
892 JTable resultTable = getResultTable();
893 if (paginatorCart.isEmpty())
897 int primaryKeyColIndex = 0;
900 primaryKeyColIndex = getFTSRestClient().getPrimaryKeyColumIndex(
901 wantedFields, false);
902 } catch (Exception e)
906 // System.out.println(">>>>>> got here : 1");
907 int totalRows = resultTable.getRowCount();
908 // resultTable.clearSelection();
909 for (int row = 0; row < totalRows; row++)
911 String id = (String) resultTable.getValueAt(row, primaryKeyColIndex);
912 if (paginatorCart.contains(id))
914 resultTable.addRowSelectionInterval(row, row);
919 public void refreshPaginatorState()
921 // System.out.println("resultSet count : " + resultSetCount);
922 // System.out.println("offSet : " + offSet);
923 // System.out.println("page limit : " + pageLimit);
924 setPrevPageButtonEnabled(false);
925 setNextPageButtonEnabled(false);
926 if (resultSetCount == 0 && pageLimit == 0)
930 if (resultSetCount >= pageLimit)
932 setNextPageButtonEnabled(true);
934 if (offSet >= pageLimit)
936 setPrevPageButtonEnabled(true);
939 public void referesh()
941 mainFrame.setTitle(getFTSFrameTitle());