src/jalview/jbgui/GStructureChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21
  22 package jalview.jbgui;
  23
  24 import java.awt.BorderLayout;
  25 import java.awt.CardLayout;
  26 import java.awt.Component;
  27 import java.awt.Dimension;
  28 import java.awt.FlowLayout;
  29 import java.awt.Font;
  30 import java.awt.GridBagConstraints;
  31 import java.awt.GridBagLayout;
  32 import java.awt.GridLayout;
  33 import java.awt.Insets;
  34 import java.awt.Point;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.awt.event.ItemEvent;
  38 import java.awt.event.ItemListener;
  39 import java.awt.event.KeyAdapter;
  40 import java.awt.event.KeyEvent;
  41 import java.awt.event.MouseAdapter;
  42 import java.awt.event.MouseEvent;
  43 import java.util.Arrays;
  44 import java.util.HashMap;
  45 import java.util.Map;
  46
  47 import javax.swing.ImageIcon;
  48 import javax.swing.JButton;
  49 import javax.swing.JCheckBox;
  50 import javax.swing.JComboBox;
  51 import javax.swing.JFrame;
  52 import javax.swing.JInternalFrame;
  53 import javax.swing.JLabel;
  54 import javax.swing.JList;
  55 import javax.swing.JPanel;
  56 import javax.swing.JScrollPane;
  57 import javax.swing.JSeparator;
  58 import javax.swing.JTabbedPane;
  59 import javax.swing.JTable;
  60 import javax.swing.JTextField;
  61 import javax.swing.ListCellRenderer;
  62 import javax.swing.SwingConstants;
  63 import javax.swing.Timer;
  64 import javax.swing.event.ChangeEvent;
  65 import javax.swing.event.ChangeListener;
  66 import javax.swing.event.DocumentEvent;
  67 import javax.swing.event.DocumentListener;
  68 import javax.swing.event.InternalFrameEvent;
  69 import javax.swing.table.TableColumn;
  70
  71 import jalview.datamodel.SequenceI;
  72 import jalview.fts.api.FTSDataColumnI;
  73 import jalview.fts.core.FTSDataColumnPreferences;
  74 import jalview.gui.AlignmentPanel;
  75 import jalview.gui.Desktop;
  76 import jalview.gui.JvSwingUtils;
  77 import jalview.gui.StructureViewer;
  78 import jalview.structure.StructureImportSettings;
  79 import jalview.structure.StructureImportSettings.TFType;
  80 import jalview.util.MessageManager;
  81 import jalview.util.Platform;
  82 import net.miginfocom.swing.MigLayout;
  83
  84 @SuppressWarnings("serial")
  85 /**
  86  * GUI layout for structure chooser
  87  *
  88  * @author tcnofoegbu
  89  *
  90  */
  91 public abstract class GStructureChooser extends JPanel
  92         implements ItemListener
  93 {
  94   private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
  95
  96   public static final String VIEWS_FILTER = "VIEWS_FILTER";
  97
  98   protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
  99
 100   protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
 101
 102   /*
 103    * 'cached' structure view
 104    */
 105   protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
 106
 107   protected JPanel statusPanel = new JPanel();
 108
 109   public JLabel statusBar = new JLabel();
 110
 111   protected String frameTitle = MessageManager
 112           .getString("label.structure_chooser");
 113
 114   protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
 115
 116   protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
 117
 118   protected AlignmentPanel ap;
 119
 120   protected StringBuilder errorWarning = new StringBuilder();
 121
 122   protected JButton btn_add;
 123
 124   protected JButton btn_newView;
 125
 126   protected JButton btn_pdbFromFile = new JButton();
 127
 128   protected JLabel lbl_chooseTempFacType = new JLabel();
 129
 130   protected JComboBox<StructureImportSettings.TFType> combo_tempFacAs = new JComboBox<>();
 131
 132   protected JButton btn_paeMatrixFile = new JButton();
 133
 134   // holder for icon and button
 135   protected JPanel pnl_queryTDB;
 136
 137   protected JButton btn_queryTDB = new JButton();
 138
 139   protected JCheckBox chk_superpose = new JCheckBox(
 140           MessageManager.getString("label.superpose_structures"));
 141
 142   protected JTextField txt_search = new JTextField(14);
 143
 144   protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
 145
 146   protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
 147           .getLayout());
 148
 149   protected JCheckBox chk_invertFilter = new JCheckBox(
 150           MessageManager.getString("label.invert"));
 151
 152   protected ImageIcon loadingImage = new ImageIcon(
 153           getClass().getResource("/images/loading.gif"));
 154
 155   protected ImageIcon goodImage = new ImageIcon(
 156           getClass().getResource("/images/good.png"));
 157
 158   protected ImageIcon errorImage = new ImageIcon(
 159           getClass().getResource("/images/error.png"));
 160
 161   protected ImageIcon warningImage = new ImageIcon(
 162           getClass().getResource("/images/warning.gif"));
 163
 164   protected ImageIcon tdbImage = new ImageIcon(getClass()
 165           .getResource("/images/3d-beacons-logo-transparent.png"));
 166
 167   protected JLabel lbl_loading = new JLabel(loadingImage);
 168
 169   protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
 170
 171   protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
 172
 173   protected AssociateSeqPanel idInputAssSeqPanel = new AssociateSeqPanel();
 174
 175   protected AssociateSeqPanel fileChooserAssSeqPanel = new AssociateSeqPanel();
 176
 177   protected JComboBox<StructureViewer> targetView = new JComboBox<>();
 178
 179   protected JTable tbl_local_pdb = new JTable();
 180
 181   protected JTabbedPane pnl_filter = new JTabbedPane();
 182
 183   protected abstract FTSDataColumnPreferences getFTSDocFieldPrefs();
 184
 185   protected abstract void setFTSDocFieldPrefs(
 186           FTSDataColumnPreferences newPrefs);
 187
 188   protected FTSDataColumnI[] previousWantedFields;
 189
 190   protected static Map<String, Integer> tempUserPrefs = new HashMap<>();
 191
 192   private JTable tbl_summary = new JTable()
 193   {
 194     private boolean inLayout;
 195
 196     @Override
 197     public boolean getScrollableTracksViewportWidth()
 198     {
 199       return hasExcessWidth();
 200
 201     }
 202
 203     @Override
 204     public void doLayout()
 205     {
 206       if (hasExcessWidth())
 207       {
 208         autoResizeMode = AUTO_RESIZE_SUBSEQUENT_COLUMNS;
 209       }
 210       inLayout = true;
 211       super.doLayout();
 212       inLayout = false;
 213       autoResizeMode = AUTO_RESIZE_OFF;
 214     }
 215
 216     protected boolean hasExcessWidth()
 217     {
 218       return getPreferredSize().width < getParent().getWidth();
 219     }
 220
 221     @Override
 222     public void columnMarginChanged(ChangeEvent e)
 223     {
 224       if (isEditing())
 225       {
 226         removeEditor();
 227       }
 228       TableColumn resizingColumn = getTableHeader().getResizingColumn();
 229       // Need to do this here, before the parent's
 230       // layout manager calls getPreferredSize().
 231       if (resizingColumn != null && autoResizeMode == AUTO_RESIZE_OFF
 232               && !inLayout)
 233       {
 234         resizingColumn.setPreferredWidth(resizingColumn.getWidth());
 235         String colHeader = resizingColumn.getHeaderValue().toString();
 236         tempUserPrefs.put(colHeader, resizingColumn.getWidth());
 237       }
 238       resizeAndRepaint();
 239     }
 240
 241     @Override
 242     public String getToolTipText(MouseEvent evt)
 243     {
 244       String toolTipText = null;
 245       java.awt.Point pnt = evt.getPoint();
 246       int rowIndex = rowAtPoint(pnt);
 247       int colIndex = columnAtPoint(pnt);
 248
 249       try
 250       {
 251         if (getValueAt(rowIndex, colIndex) == null)
 252         {
 253           return null;
 254         }
 255         toolTipText = getValueAt(rowIndex, colIndex).toString();
 256       } catch (Exception e)
 257       {
 258         // e.printStackTrace();
 259       }
 260       toolTipText = (toolTipText == null ? null
 261               : (toolTipText.length() > 500
 262                       ? JvSwingUtils.wrapTooltip(true,
 263                               "\"" + toolTipText.subSequence(0, 500)
 264                                       + "...\"")
 265                       : JvSwingUtils.wrapTooltip(true, toolTipText)));
 266       return toolTipText;
 267     }
 268   };
 269
 270   public GStructureChooser()
 271   {
 272   }
 273
 274   protected void initDialog()
 275   {
 276
 277     try
 278     {
 279       jbInit();
 280       mainFrame.setFrameIcon(null);
 281       mainFrame.setVisible(false);
 282       mainFrame.invalidate();
 283       mainFrame.pack();
 284     } catch (Exception e)
 285     {
 286       System.out.println(e); // for JavaScript TypeError
 287       e.printStackTrace();
 288     }
 289   }
 290
 291   // BH SwingJS optimization
 292   // (a) 100-ms interruptable timer for text entry -- BH 1/10/2019
 293   // (b) two-character minimum, at least for JavaScript.
 294
 295   private Timer timer;
 296
 297   protected void txt_search_ActionPerformedDelayed()
 298   {
 299     if (timer != null)
 300     {
 301       timer.stop();
 302     }
 303     timer = new Timer(300, new ActionListener()
 304     {
 305
 306       @Override
 307       public void actionPerformed(ActionEvent e)
 308       {
 309         txt_search_ActionPerformed();
 310       }
 311     });
 312     timer.setRepeats(false);
 313     timer.start();
 314   }
 315   //
 316
 317   /**
 318    * Initializes the GUI default properties
 319    *
 320    * @throws Exception
 321    */
 322   private void jbInit() throws Exception
 323   {
 324     Integer width = tempUserPrefs.get("structureChooser.width") == null
 325             ? 800
 326             : tempUserPrefs.get("structureChooser.width");
 327     Integer height = tempUserPrefs.get("structureChooser.height") == null
 328             ? 400
 329             : tempUserPrefs.get("structureChooser.height");
 330     tbl_summary.setAutoCreateRowSorter(true);
 331     tbl_summary.getTableHeader().setReorderingAllowed(false);
 332     tbl_summary.addMouseListener(new MouseAdapter()
 333     {
 334       @Override
 335       public void mousePressed(MouseEvent e)
 336       {
 337         if (!popupAction(e))
 338         {
 339           super.mousePressed(e);
 340         }
 341       }
 342
 343       @Override
 344       public void mouseClicked(MouseEvent e)
 345       {
 346         if (!popupAction(e))
 347         {
 348           validateSelections();
 349         }
 350       }
 351
 352       @Override
 353       public void mouseReleased(MouseEvent e)
 354       {
 355         if (!popupAction(e))
 356         {
 357           validateSelections();
 358         }
 359       }
 360
 361       boolean popupAction(MouseEvent e)
 362       {
 363         if (e.isPopupTrigger())
 364         {
 365           Point pt = e.getPoint();
 366           int selectedRow = tbl_summary.rowAtPoint(pt);
 367           if (showPopupFor(selectedRow, pt.x, pt.y))
 368           {
 369             return true;
 370           }
 371         }
 372         return false;
 373       }
 374     });
 375     tbl_summary.addKeyListener(new KeyAdapter()
 376     {
 377       @Override
 378       public void keyPressed(KeyEvent evt)
 379       {
 380         validateSelections();
 381         switch (evt.getKeyCode())
 382         {
 383         case KeyEvent.VK_ESCAPE: // escape key
 384           mainFrame.dispose();
 385           break;
 386         case KeyEvent.VK_ENTER: // enter key
 387           if (btn_add.isEnabled())
 388           {
 389             add_ActionPerformed();
 390           }
 391           break;
 392         case KeyEvent.VK_TAB: // tab key
 393           if (evt.isShiftDown())
 394           {
 395             pnl_filter.requestFocus();
 396           }
 397           else
 398           {
 399             btn_add.requestFocus();
 400           }
 401           evt.consume();
 402           break;
 403         default:
 404           return;
 405         }
 406       }
 407     });
 408
 409     JButton btn_cancel = new JButton(
 410             MessageManager.getString("action.cancel"));
 411     btn_cancel.setFont(VERDANA_12);
 412     btn_cancel.addActionListener(new java.awt.event.ActionListener()
 413     {
 414       @Override
 415       public void actionPerformed(ActionEvent e)
 416       {
 417         closeAction(pnl_filter.getHeight());
 418       }
 419     });
 420     btn_cancel.addKeyListener(new KeyAdapter()
 421     {
 422       @Override
 423       public void keyPressed(KeyEvent evt)
 424       {
 425         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 426         {
 427           closeAction(pnl_filter.getHeight());
 428         }
 429       }
 430     });
 431
 432     tbl_local_pdb.setAutoCreateRowSorter(true);
 433     tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
 434     tbl_local_pdb.addMouseListener(new MouseAdapter()
 435     {
 436       @Override
 437       public void mouseClicked(MouseEvent e)
 438       {
 439         validateSelections();
 440       }
 441
 442       @Override
 443       public void mouseReleased(MouseEvent e)
 444       {
 445         validateSelections();
 446       }
 447     });
 448     tbl_local_pdb.addKeyListener(new KeyAdapter()
 449     {
 450       @Override
 451       public void keyPressed(KeyEvent evt)
 452       {
 453         validateSelections();
 454         switch (evt.getKeyCode())
 455         {
 456         case KeyEvent.VK_ESCAPE: // escape key
 457           mainFrame.dispose();
 458           break;
 459         case KeyEvent.VK_ENTER: // enter key
 460           if (btn_add.isEnabled())
 461           {
 462             add_ActionPerformed();
 463           }
 464           break;
 465         case KeyEvent.VK_TAB: // tab key
 466           if (evt.isShiftDown())
 467           {
 468             cmb_filterOption.requestFocus();
 469           }
 470           else
 471           {
 472             if (btn_add.isEnabled())
 473             {
 474               btn_add.requestFocus();
 475             }
 476             else
 477             {
 478               btn_cancel.requestFocus();
 479             }
 480           }
 481           evt.consume();
 482           break;
 483         default:
 484           return;
 485         }
 486       }
 487     });
 488
 489     btn_newView = new JButton(
 490             MessageManager.formatMessage("action.new_structure_view_with",
 491                     StructureViewer.getViewerType().toString()));
 492     btn_newView.setFont(VERDANA_12);
 493     btn_newView.addActionListener(new java.awt.event.ActionListener()
 494     {
 495       @Override
 496       public void actionPerformed(ActionEvent e)
 497       {
 498         newView_ActionPerformed();
 499       }
 500     });
 501     btn_newView.addKeyListener(new KeyAdapter()
 502     {
 503       @Override
 504       public void keyPressed(KeyEvent evt)
 505       {
 506         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 507         {
 508           newView_ActionPerformed();
 509         }
 510       }
 511     });
 512
 513     // TODO: JAL-3898 - get list of available external programs to view
 514     // structures with
 515
 516     btn_add = new JButton(MessageManager.getString("action.add"));
 517     btn_add.setFont(VERDANA_12);
 518     btn_add.addActionListener(new java.awt.event.ActionListener()
 519     {
 520       @Override
 521       public void actionPerformed(ActionEvent e)
 522       {
 523         add_ActionPerformed();
 524       }
 525     });
 526     btn_add.addKeyListener(new KeyAdapter()
 527     {
 528       @Override
 529       public void keyPressed(KeyEvent evt)
 530       {
 531         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 532         {
 533           add_ActionPerformed();
 534         }
 535       }
 536     });
 537
 538     btn_pdbFromFile.setFont(VERDANA_12);
 539     String btn_title = MessageManager.getString("label.select_pdb_file");
 540     btn_pdbFromFile.setText(btn_title + "              ");
 541     btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
 542     {
 543       @Override
 544       public void actionPerformed(ActionEvent e)
 545       {
 546         pdbFromFile_actionPerformed();
 547       }
 548     });
 549     btn_pdbFromFile.addKeyListener(new KeyAdapter()
 550     {
 551       @Override
 552       public void keyPressed(KeyEvent evt)
 553       {
 554         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 555         {
 556           pdbFromFile_actionPerformed();
 557         }
 558       }
 559     });
 560
 561     lbl_chooseTempFacType.setText(new StringBuilder()
 562             .append(MessageManager.getString("label.choose_tempfac_type"))
 563             .append(" ").append(MessageManager.getString("label.optional"))
 564             .toString());
 565
 566     for (TFType t : TFType.values())
 567     {
 568       combo_tempFacAs.addItem(t);
 569     }
 570     // add changelistener
 571
 572     btn_paeMatrixFile.setText(new StringBuilder()
 573             .append(MessageManager.getString("label.add_pae_matrix_file"))
 574             .append(" ").append(MessageManager.getString("label.optional"))
 575             .toString());
 576     ;
 577     // add actionlistener
 578
 579     JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
 580     scrl_foundStructures.setPreferredSize(new Dimension(width, height));
 581
 582     JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
 583     scrl_localPDB.setPreferredSize(new Dimension(width, height));
 584     scrl_localPDB.setHorizontalScrollBarPolicy(
 585             JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 586
 587     chk_invertFilter.setFont(VERDANA_12);
 588     txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
 589             MessageManager.getString("label.enter_pdb_id_tip")));
 590     txt_search.getDocument().addDocumentListener(new DocumentListener()
 591     {
 592       @Override
 593       public void insertUpdate(DocumentEvent e)
 594       {
 595         txt_search_ActionPerformedDelayed();
 596       }
 597
 598       @Override
 599       public void removeUpdate(DocumentEvent e)
 600       {
 601         txt_search_ActionPerformedDelayed();
 602       }
 603
 604       @Override
 605       public void changedUpdate(DocumentEvent e)
 606       {
 607         txt_search_ActionPerformedDelayed();
 608       }
 609     });
 610
 611     cmb_filterOption.setFont(VERDANA_12);
 612     cmb_filterOption.setToolTipText(
 613             MessageManager.getString("info.select_filter_option"));
 614     cmb_filterOption.addItemListener(this);
 615     // add CustomComboSeparatorsRenderer to filter option combo-box
 616     cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
 617             (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
 618     {
 619       @Override
 620       protected boolean addSeparatorAfter(JList list, FilterOption value,
 621               int index)
 622       {
 623         return value.isAddSeparatorAfter();
 624       }
 625     });
 626
 627     chk_invertFilter.addItemListener(this);
 628     btn_queryTDB = new JButton();
 629     if (Platform.isMac())
 630     {
 631       // needed to make icon button have round corners in vaqua
 632       btn_queryTDB.putClientProperty("JButton.buttonType", "bevel");
 633     }
 634     btn_queryTDB.setMargin(new Insets(0, 16, 0, 20));
 635     btn_queryTDB
 636             .setText(MessageManager.getString("label.search_3dbeacons"));
 637     btn_queryTDB.setIconTextGap(12);
 638     btn_queryTDB.setIcon(tdbImage);
 639     btn_queryTDB.setVerticalTextPosition(SwingConstants.CENTER);
 640     btn_queryTDB.setHorizontalTextPosition(SwingConstants.TRAILING);
 641     btn_queryTDB.setFont(VERDANA_12);
 642     btn_queryTDB.setToolTipText(
 643             MessageManager.getString("label.find_models_from_3dbeacons"));
 644     // btn_queryTDB.setPreferredSize(new Dimension(200, 32));
 645     btn_queryTDB.setVisible(false);
 646
 647     targetView.setVisible(false);
 648
 649     JPanel actionsPanel = new JPanel(new MigLayout());
 650     actionsPanel.add(targetView, "left");
 651     actionsPanel.add(btn_add, "wrap");
 652     actionsPanel.add(chk_superpose, "left");
 653     actionsPanel.add(btn_newView);
 654     actionsPanel.add(btn_cancel, "right");
 655
 656     JPanel pnl_main = new JPanel(new BorderLayout());
 657     JPanel pnl_controls = new JPanel();
 658     pnl_queryTDB = new JPanel();
 659     pnl_queryTDB.setLayout(new FlowLayout(FlowLayout.CENTER, 4, 4));
 660     pnl_queryTDB.setBackground(getBackground());
 661     pnl_queryTDB.add(btn_queryTDB);
 662
 663     pnl_queryTDB.setVisible(false);
 664     pnl_main.add(pnl_queryTDB, BorderLayout.NORTH);
 665     pnl_controls.add(cmb_filterOption);
 666     pnl_controls.add(lbl_loading);
 667     pnl_controls.add(chk_invertFilter);
 668     pnl_main.add(pnl_controls, BorderLayout.CENTER);
 669     lbl_loading.setVisible(false);
 670
 671     JPanel pnl_fileChooser = new JPanel(new FlowLayout());
 672     pnl_fileChooser.add(btn_pdbFromFile);
 673     pnl_fileChooser.add(lbl_fromFileStatus);
 674
 675     JPanel pnl_fileOptions = new JPanel();
 676     pnl_fileOptions.setLayout(new GridBagLayout());
 677     GridBagConstraints gbc = new GridBagConstraints();
 678     gbc.gridx = 0;
 679     gbc.gridy = 0;
 680     gbc.weightx = 0.0;
 681     gbc.weighty = 0.0;
 682     gbc.insets = new Insets(0, 0, 18, 0);
 683     gbc.fill = GridBagConstraints.NONE;
 684     gbc.anchor = GridBagConstraints.FIRST_LINE_START;
 685     pnl_fileOptions.add(pnl_fileChooser, gbc);
 686     gbc.gridy++;
 687     gbc.insets = new Insets(0, 0, 2, 0);
 688     pnl_fileOptions.add(lbl_chooseTempFacType, gbc);
 689     gbc.gridy++;
 690     gbc.insets = new Insets(0, 0, 18, 0);
 691     pnl_fileOptions.add(combo_tempFacAs, gbc);
 692     gbc.gridy++;
 693     gbc.weighty = 1.0;
 694     pnl_fileOptions.add(btn_paeMatrixFile, gbc);
 695
 696     JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
 697     pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.PAGE_START);
 698     pnl_fileChooserBL.add(pnl_fileOptions, BorderLayout.CENTER);
 699
 700     JPanel pnl_idInput = new JPanel(new FlowLayout());
 701     pnl_idInput.add(txt_search);
 702     pnl_idInput.add(lbl_pdbManualFetchStatus);
 703
 704     JPanel pnl_idInputBL = new JPanel(new BorderLayout());
 705     pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
 706     pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
 707
 708     final String foundStructureSummary = MessageManager
 709             .getString("label.found_structures_summary");
 710     final String configureCols = MessageManager
 711             .getString("label.configure_displayed_columns");
 712     ChangeListener changeListener = new ChangeListener()
 713     {
 714       @Override
 715       public void stateChanged(ChangeEvent changeEvent)
 716       {
 717         JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
 718                 .getSource();
 719         int index = sourceTabbedPane.getSelectedIndex();
 720         btn_add.setVisible(targetView.isVisible());
 721         btn_newView.setVisible(true);
 722         btn_cancel.setVisible(true);
 723         if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
 724         {
 725           btn_add.setEnabled(false);
 726           btn_cancel.setEnabled(false);
 727           btn_add.setVisible(false);
 728           btn_newView.setEnabled(false);
 729           btn_cancel.setVisible(false);
 730           previousWantedFields = getFTSDocFieldPrefs()
 731                   .getStructureSummaryFields()
 732                   .toArray(new FTSDataColumnI[0]);
 733         }
 734         if (sourceTabbedPane.getTitleAt(index)
 735                 .equals(foundStructureSummary))
 736         {
 737           btn_cancel.setEnabled(true);
 738           if (wantedFieldsUpdated())
 739           {
 740             tabRefresh();
 741           }
 742           else
 743           {
 744             validateSelections();
 745           }
 746         }
 747       }
 748     };
 749     pnl_filter.addChangeListener(changeListener);
 750     pnl_filter.setPreferredSize(new Dimension(width, height));
 751     pnl_filter.add(foundStructureSummary, scrl_foundStructures);
 752     pnl_filter.add(configureCols, getFTSDocFieldPrefs());
 753
 754     JPanel pnl_locPDB = new JPanel(new BorderLayout());
 755     pnl_locPDB.add(scrl_localPDB);
 756
 757     pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
 758     pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
 759     pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
 760     pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
 761
 762     this.setLayout(new BorderLayout());
 763     this.add(pnl_main, java.awt.BorderLayout.NORTH);
 764     this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
 765     // this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
 766     statusPanel.setLayout(new GridLayout());
 767
 768     JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
 769     pnl_actionsAndStatus.add(actionsPanel, BorderLayout.CENTER);
 770     pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
 771     statusPanel.add(statusBar, null);
 772     this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
 773
 774     mainFrame.addInternalFrameListener(
 775             new javax.swing.event.InternalFrameAdapter()
 776             {
 777               @Override
 778               public void internalFrameClosing(InternalFrameEvent e)
 779               {
 780                 closeAction(pnl_filter.getHeight());
 781               }
 782             });
 783     mainFrame.setVisible(true);
 784     mainFrame.setContentPane(this);
 785     mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
 786     Integer x = tempUserPrefs.get("structureChooser.x");
 787     Integer y = tempUserPrefs.get("structureChooser.y");
 788     if (x != null && y != null)
 789     {
 790       mainFrame.setLocation(x, y);
 791     }
 792     Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
 793   }
 794
 795   protected abstract boolean showPopupFor(int selectedRow, int x, int y);
 796
 797   protected void closeAction(int preferredHeight)
 798   {
 799     // System.out.println(">>>>>>>>>> closing internal frame!!!");
 800     // System.out.println("width : " + mainFrame.getWidth());
 801     // System.out.println("heigh : " + mainFrame.getHeight());
 802     // System.out.println("x : " + mainFrame.getX());
 803     // System.out.println("y : " + mainFrame.getY());
 804     tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
 805     tempUserPrefs.put("structureChooser.height", preferredHeight);
 806     tempUserPrefs.put("structureChooser.x", mainFrame.getX());
 807     tempUserPrefs.put("structureChooser.y", mainFrame.getY());
 808     mainFrame.dispose();
 809   }
 810
 811   public boolean wantedFieldsUpdated()
 812   {
 813     if (previousWantedFields == null)
 814     {
 815       return true;
 816     }
 817
 818     FTSDataColumnI[] currentWantedFields = getFTSDocFieldPrefs()
 819             .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
 820     return Arrays.equals(currentWantedFields, previousWantedFields) ? false
 821             : true;
 822
 823   }
 824
 825   @Override
 826   /**
 827    * Event listener for the 'filter' combo-box and 'invert' check-box
 828    */
 829   public void itemStateChanged(ItemEvent e)
 830   {
 831     stateChanged(e);
 832   }
 833
 834   /**
 835    * This inner class provides the provides the data model for associate
 836    * sequence combo-box - cmb_assSeq
 837    *
 838    * @author tcnofoegbu
 839    *
 840    */
 841   public class AssociateSeqOptions
 842   {
 843     private SequenceI sequence;
 844
 845     private String name;
 846
 847     public AssociateSeqOptions(SequenceI seq)
 848     {
 849       this.sequence = seq;
 850       this.name = (seq.getName().length() >= 23)
 851               ? seq.getName().substring(0, 23)
 852               : seq.getName();
 853     }
 854
 855     public AssociateSeqOptions(String name, SequenceI seq)
 856     {
 857       this.name = name;
 858       this.sequence = seq;
 859     }
 860
 861     @Override
 862     public String toString()
 863     {
 864       return name;
 865     }
 866
 867     public String getName()
 868     {
 869       return name;
 870     }
 871
 872     public void setName(String name)
 873     {
 874       this.name = name;
 875     }
 876
 877     public SequenceI getSequence()
 878     {
 879       return sequence;
 880     }
 881
 882     public void setSequence(SequenceI sequence)
 883     {
 884       this.sequence = sequence;
 885     }
 886
 887   }
 888
 889   /**
 890    * This inner class holds the Layout and configuration of the panel which
 891    * handles association of manually fetched structures to a unique sequence
 892    * when more than one sequence selection is made
 893    *
 894    * @author tcnofoegbu
 895    *
 896    */
 897   public class AssociateSeqPanel extends JPanel implements ItemListener
 898   {
 899     private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
 900
 901     private JLabel lbl_associateSeq = new JLabel();
 902
 903     public AssociateSeqPanel()
 904     {
 905       this.setLayout(new FlowLayout());
 906       this.add(cmb_assSeq);
 907       this.add(lbl_associateSeq);
 908       cmb_assSeq.setToolTipText(
 909               MessageManager.getString("info.associate_wit_sequence"));
 910       cmb_assSeq.addItemListener(this);
 911     }
 912
 913     public void loadCmbAssSeq()
 914     {
 915       populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
 916     }
 917
 918     public JComboBox<AssociateSeqOptions> getCmb_assSeq()
 919     {
 920       return cmb_assSeq;
 921     }
 922
 923     public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)
 924     {
 925       this.cmb_assSeq = cmb_assSeq;
 926     }
 927
 928     @Override
 929     public void itemStateChanged(ItemEvent e)
 930     {
 931       if (e.getStateChange() == ItemEvent.SELECTED)
 932       {
 933         cmbAssSeqStateChanged();
 934       }
 935     }
 936   }
 937
 938   public JTable getResultTable()
 939   {
 940     return tbl_summary;
 941   }
 942
 943   public JComboBox<FilterOption> getCmbFilterOption()
 944   {
 945     return cmb_filterOption;
 946   }
 947
 948   /**
 949    * Custom ListCellRenderer for adding a separator between different categories
 950    * of structure chooser filter option drop-down.
 951    *
 952    * @author tcnofoegbu
 953    *
 954    */
 955   public abstract class CustomComboSeparatorsRenderer
 956           implements ListCellRenderer<Object>
 957   {
 958     private ListCellRenderer<Object> regent;
 959
 960     private JPanel separatorPanel = new JPanel(new BorderLayout());
 961
 962     private JSeparator jSeparator = new JSeparator();
 963
 964     public CustomComboSeparatorsRenderer(
 965             ListCellRenderer<Object> listCellRenderer)
 966     {
 967       this.regent = listCellRenderer;
 968     }
 969
 970     @Override
 971     public Component getListCellRendererComponent(JList list, Object value,
 972             int index, boolean isSelected, boolean cellHasFocus)
 973     {
 974
 975       Component comp = regent.getListCellRendererComponent(list, value,
 976               index, isSelected, cellHasFocus);
 977       if (index != -1
 978               && addSeparatorAfter(list, (FilterOption) value, index))
 979       {
 980         separatorPanel.removeAll();
 981         separatorPanel.add(comp, BorderLayout.CENTER);
 982         separatorPanel.add(jSeparator, BorderLayout.SOUTH);
 983         return separatorPanel;
 984       }
 985       else
 986       {
 987         return comp;
 988       }
 989     }
 990
 991     protected abstract boolean addSeparatorAfter(JList list,
 992             FilterOption value, int index);
 993   }
 994
 995   protected abstract void stateChanged(ItemEvent e);
 996
 997   protected abstract void add_ActionPerformed();
 998
 999   protected abstract void newView_ActionPerformed();
1000
1001   protected abstract void pdbFromFile_actionPerformed();
1002
1003   protected abstract void txt_search_ActionPerformed();
1004
1005   protected abstract void populateCmbAssociateSeqOptions(
1006           JComboBox<AssociateSeqOptions> cmb_assSeq,
1007           JLabel lbl_associateSeq);
1008
1009   protected abstract void cmbAssSeqStateChanged();
1010
1011   protected abstract void tabRefresh();
1012
1013   protected abstract void validateSelections();
1014
1015   public JInternalFrame getFrame()
1016   {
1017     return mainFrame;
1018   }
1019
1020   public void setPdbOptionsEnabled(boolean b)
1021   {
1022     lbl_chooseTempFacType.setEnabled(b);
1023     combo_tempFacAs.setEnabled(b);
1024     btn_paeMatrixFile.setEnabled(b);
1025   }
1026 }