src/jalview/jbgui/GStructureChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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 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.JvSummaryTable;
  32 import jalview.gui.JvSwingUtils;
  33 import jalview.util.MessageManager;
  34
  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;
  40 import java.awt.GridLayout;
  41 import java.awt.event.ActionEvent;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.KeyAdapter;
  45 import java.awt.event.KeyEvent;
  46 import java.awt.event.MouseAdapter;
  47 import java.awt.event.MouseEvent;
  48 import java.util.Arrays;
  49 import java.util.HashMap;
  50 import java.util.Map;
  51
  52 import javax.swing.ImageIcon;
  53 import javax.swing.JButton;
  54 import javax.swing.JCheckBox;
  55 import javax.swing.JComboBox;
  56 import javax.swing.JFrame;
  57 import javax.swing.JInternalFrame;
  58 import javax.swing.JLabel;
  59 import javax.swing.JList;
  60 import javax.swing.JPanel;
  61 import javax.swing.JScrollPane;
  62 import javax.swing.JSeparator;
  63 import javax.swing.JTabbedPane;
  64 import javax.swing.JTable;
  65 import javax.swing.JTextField;
  66 import javax.swing.ListCellRenderer;
  67 import javax.swing.event.ChangeEvent;
  68 import javax.swing.event.ChangeListener;
  69 import javax.swing.event.DocumentEvent;
  70 import javax.swing.event.DocumentListener;
  71 import javax.swing.event.InternalFrameEvent;
  72
  73 @SuppressWarnings("serial")
  74 /**
  75  * GUI layout for structure chooser
  76  * @author tcnofoegbu
  77  *
  78  */
  79 public abstract class GStructureChooser extends JPanel implements
  80         ItemListener
  81 {
  82   protected JPanel statusPanel = new JPanel();
  83
  84   public JLabel statusBar = new JLabel();
  85
  86   private JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
  87
  88   protected String frameTitle = MessageManager
  89           .getString("label.structure_chooser");
  90
  91   protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
  92
  93   protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<FilterOption>();
  94
  95   protected AlignmentPanel ap;
  96
  97   protected StringBuilder errorWarning = new StringBuilder();
  98
  99   protected JLabel lbl_result = new JLabel(
 100           MessageManager.getString("label.select"));
 101
 102   protected JButton btn_view = new JButton();
 103
 104   protected JButton btn_cancel = new JButton();
 105
 106   protected JButton btn_pdbFromFile = new JButton();
 107
 108   protected JButton btn_runPhyre2Prediction = new JButton();
 109
 110   protected JTextField txt_search = new JTextField(14);
 111
 112   private JPanel pnl_actions = new JPanel();
 113
 114   private JPanel pnl_main = new JPanel();
 115
 116   private JPanel pnl_idInput = new JPanel(new FlowLayout());
 117
 118   private JPanel pnl_fileChooser = new JPanel(new FlowLayout());
 119
 120   private JPanel pnl_phyre2Prediction = new JPanel(new FlowLayout());
 121
 122   private JPanel pnl_phyre2PredictionBL = new JPanel(new BorderLayout());
 123
 124   private JPanel pnl_idInputBL = new JPanel(new BorderLayout());
 125
 126   private JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
 127
 128   private JPanel pnl_locPDB = new JPanel(new BorderLayout());
 129
 130   protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
 131
 132   protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
 133           .getLayout());
 134
 135   private BorderLayout mainLayout = new BorderLayout();
 136
 137   protected JCheckBox chk_rememberSettings = new JCheckBox(
 138           MessageManager.getString("label.dont_ask_me_again"));
 139
 140   protected JCheckBox chk_invertFilter = new JCheckBox(
 141           MessageManager.getString("label.invert"));
 142
 143   protected ImageIcon loadingImage = new ImageIcon(getClass().getResource(
 144           "/images/loading.gif"));
 145
 146   protected ImageIcon goodImage = new ImageIcon(getClass().getResource(
 147           "/images/good.png"));
 148
 149   protected ImageIcon errorImage = new ImageIcon(getClass().getResource(
 150           "/images/error.png"));
 151
 152   protected ImageIcon warningImage = new ImageIcon(getClass().getResource(
 153           "/images/warning.gif"));
 154
 155   protected JLabel lbl_warning = new JLabel(warningImage);
 156
 157   protected JLabel lbl_loading = new JLabel(loadingImage);
 158
 159   protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
 160
 161   protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
 162
 163   protected AssciateSeqPanel phyre2InputAssSeqPanel = new AssciateSeqPanel();
 164
 165   protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
 166
 167   protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
 168
 169   protected static final String VIEWS_FILTER = "VIEWS_FILTER";
 170
 171   protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
 172
 173   protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
 174
 175   protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
 176
 177   protected static final String VIEWS_PHYRE2_PREDICTION = "VIEWS_PHYRE2_PREDICTION";
 178
 179   protected JTable tbl_local_pdb = new JTable();
 180
 181   protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
 182
 183   protected JTabbedPane pnl_filter = new JTabbedPane();
 184
 185   protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
 186           PreferenceSource.STRUCTURE_CHOOSER,
 187           PDBFTSRestClient.getInstance());
 188
 189   protected FTSDataColumnI[] previousWantedFields;
 190
 191   protected static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
 192
 193   private JTable tbl_summary = new JvSummaryTable(tempUserPrefs);
 194
 195
 196   protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
 197
 198   JPanel phyreResultPanel = new JPanel(new BorderLayout());
 199
 200   protected static Map<String, Integer> tempPrefsForPhyre = new HashMap<String, Integer>();
 201
 202   private JTable tbl_phyre2_summary = new JvSummaryTable(tempPrefsForPhyre);
 203
 204   protected JScrollPane scrl_phyre2Summary = new JScrollPane(
 205           tbl_phyre2_summary);
 206
 207   public GStructureChooser()
 208   {
 209     try
 210     {
 211       jbInit();
 212       mainFrame.setVisible(false);
 213       mainFrame.invalidate();
 214       mainFrame.pack();
 215     } catch (Exception e)
 216     {
 217       e.printStackTrace();
 218     }
 219   }
 220
 221   /**
 222    * Initializes the GUI default properties
 223    *
 224    * @throws Exception
 225    */
 226   @SuppressWarnings("unchecked")
 227   private void jbInit() throws Exception
 228   {
 229     Integer width = tempUserPrefs.get("structureChooser.width") == null ? 800
 230             : tempUserPrefs.get("structureChooser.width");
 231     Integer height = tempUserPrefs.get("structureChooser.height") == null ? 400
 232             : tempUserPrefs.get("structureChooser.height");
 233     tbl_summary.setAutoCreateRowSorter(true);
 234     tbl_summary.getTableHeader().setReorderingAllowed(false);
 235     tbl_summary.addMouseListener(new MouseAdapter()
 236     {
 237       @Override
 238       public void mouseClicked(MouseEvent e)
 239       {
 240         validateSelections();
 241       }
 242
 243       @Override
 244       public void mouseReleased(MouseEvent e)
 245       {
 246         validateSelections();
 247       }
 248     });
 249     tbl_summary.addKeyListener(new KeyAdapter()
 250     {
 251       @Override
 252       public void keyPressed(KeyEvent evt)
 253       {
 254         validateSelections();
 255         switch (evt.getKeyCode())
 256         {
 257         case KeyEvent.VK_ESCAPE: // escape key
 258           mainFrame.dispose();
 259           break;
 260         case KeyEvent.VK_ENTER: // enter key
 261           if (btn_view.isEnabled())
 262           {
 263             ok_ActionPerformed();
 264           }
 265           break;
 266         case KeyEvent.VK_TAB: // tab key
 267           if (evt.isShiftDown())
 268           {
 269             pnl_filter.requestFocus();
 270           }
 271           else
 272           {
 273             btn_view.requestFocus();
 274           }
 275           evt.consume();
 276           break;
 277         default:
 278           return;
 279         }
 280       }
 281     });
 282     tbl_local_pdb.setAutoCreateRowSorter(true);
 283     tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
 284     tbl_local_pdb.addMouseListener(new MouseAdapter()
 285     {
 286       @Override
 287       public void mouseClicked(MouseEvent e)
 288       {
 289         validateSelections();
 290       }
 291
 292       @Override
 293       public void mouseReleased(MouseEvent e)
 294       {
 295         validateSelections();
 296       }
 297     });
 298     tbl_local_pdb.addKeyListener(new KeyAdapter()
 299     {
 300       @Override
 301       public void keyPressed(KeyEvent evt)
 302       {
 303         validateSelections();
 304         switch (evt.getKeyCode())
 305         {
 306         case KeyEvent.VK_ESCAPE: // escape key
 307           mainFrame.dispose();
 308           break;
 309         case KeyEvent.VK_ENTER: // enter key
 310           if (btn_view.isEnabled())
 311           {
 312             ok_ActionPerformed();
 313           }
 314           break;
 315         case KeyEvent.VK_TAB: // tab key
 316           if (evt.isShiftDown())
 317           {
 318             cmb_filterOption.requestFocus();
 319           }
 320           else
 321           {
 322             if (btn_view.isEnabled())
 323             {
 324               btn_view.requestFocus();
 325             }
 326             else
 327             {
 328               btn_cancel.requestFocus();
 329             }
 330           }
 331           evt.consume();
 332           break;
 333         default:
 334           return;
 335         }
 336       }
 337     });
 338     btn_view.setFont(new java.awt.Font("Verdana", 0, 12));
 339     btn_view.setText(MessageManager.getString("action.view"));
 340     btn_view.addActionListener(new java.awt.event.ActionListener()
 341     {
 342       @Override
 343       public void actionPerformed(ActionEvent e)
 344       {
 345         ok_ActionPerformed();
 346       }
 347     });
 348     btn_view.addKeyListener(new KeyAdapter()
 349     {
 350       @Override
 351       public void keyPressed(KeyEvent evt)
 352       {
 353         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 354         {
 355           ok_ActionPerformed();
 356         }
 357       }
 358     });
 359
 360     btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
 361     btn_cancel.setText(MessageManager.getString("action.cancel"));
 362     btn_cancel.addActionListener(new java.awt.event.ActionListener()
 363     {
 364       @Override
 365       public void actionPerformed(ActionEvent e)
 366       {
 367         closeAction(pnl_filter.getHeight());
 368       }
 369     });
 370     btn_cancel.addKeyListener(new KeyAdapter()
 371     {
 372       @Override
 373       public void keyPressed(KeyEvent evt)
 374       {
 375         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 376         {
 377           closeAction(pnl_filter.getHeight());
 378         }
 379       }
 380     });
 381
 382     btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
 383     String btn_title = MessageManager.getString("label.select_pdb_file");
 384     btn_pdbFromFile.setText(btn_title + "              ");
 385     btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
 386     {
 387       @Override
 388       public void actionPerformed(ActionEvent e)
 389       {
 390         pdbFromFile_actionPerformed();
 391       }
 392     });
 393     btn_pdbFromFile.addKeyListener(new KeyAdapter()
 394     {
 395       @Override
 396       public void keyPressed(KeyEvent evt)
 397       {
 398         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 399         {
 400           pdbFromFile_actionPerformed();
 401         }
 402       }
 403     });
 404
 405     btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
 406     tbl_phyre2_summary.setAutoCreateRowSorter(true);
 407     tbl_phyre2_summary.getTableHeader().setReorderingAllowed(false);
 408
 409     tbl_phyre2_summary.addMouseListener(new MouseAdapter()
 410     {
 411       @Override
 412       public void mouseClicked(MouseEvent e)
 413       {
 414         validateSelections();
 415       }
 416
 417       @Override
 418       public void mouseReleased(MouseEvent e)
 419       {
 420         validateSelections();
 421       }
 422     });
 423     tbl_phyre2_summary.addKeyListener(new KeyAdapter()
 424     {
 425       @Override
 426       public void keyPressed(KeyEvent evt)
 427       {
 428         validateSelections();
 429         switch (evt.getKeyCode())
 430         {
 431         case KeyEvent.VK_ESCAPE: // escape key
 432           mainFrame.dispose();
 433           break;
 434         case KeyEvent.VK_ENTER: // enter key
 435           if (btn_view.isEnabled())
 436           {
 437             ok_ActionPerformed();
 438           }
 439           break;
 440         case KeyEvent.VK_TAB: // tab key
 441           if (evt.isShiftDown())
 442           {
 443             cmb_filterOption.requestFocus();
 444           }
 445           else
 446           {
 447             if (btn_view.isEnabled())
 448             {
 449               btn_view.requestFocus();
 450             }
 451             else
 452             {
 453               btn_cancel.requestFocus();
 454             }
 455           }
 456           evt.consume();
 457           break;
 458         default:
 459           return;
 460         }
 461       }
 462     });
 463
 464     String btn_runPhyre2Prediction_title = MessageManager
 465             .getString("label.run_phyre2_prediction");
 466     btn_runPhyre2Prediction
 467             .setText(btn_runPhyre2Prediction_title + "     ");
 468     btn_runPhyre2Prediction
 469             .addActionListener(new java.awt.event.ActionListener()
 470             {
 471               @Override
 472               public void actionPerformed(ActionEvent e)
 473               {
 474                 predict3DModelWithPhyre2();
 475               }
 476             });
 477     btn_runPhyre2Prediction.addKeyListener(new KeyAdapter()
 478     {
 479       @Override
 480       public void keyPressed(KeyEvent evt)
 481       {
 482         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
 483         {
 484           predict3DModelWithPhyre2();
 485         }
 486       }
 487     });
 488
 489     scrl_foundStructures.setPreferredSize(new Dimension(width, height));
 490
 491     scrl_localPDB.setPreferredSize(new Dimension(width, height));
 492     scrl_localPDB
 493             .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 494
 495     cmb_filterOption.setFont(new java.awt.Font("Verdana", 0, 12));
 496     chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
 497     chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
 498     chk_rememberSettings.setVisible(false);
 499     txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
 500             MessageManager.getString("label.enter_pdb_id")));
 501     cmb_filterOption.setToolTipText(MessageManager
 502             .getString("info.select_filter_option"));
 503     txt_search.getDocument().addDocumentListener(new DocumentListener()
 504     {
 505       @Override
 506       public void insertUpdate(DocumentEvent e)
 507       {
 508         txt_search_ActionPerformed();
 509       }
 510
 511       @Override
 512       public void removeUpdate(DocumentEvent e)
 513       {
 514         txt_search_ActionPerformed();
 515       }
 516
 517       @Override
 518       public void changedUpdate(DocumentEvent e)
 519       {
 520         txt_search_ActionPerformed();
 521       }
 522     });
 523
 524     cmb_filterOption.addItemListener(this);
 525
 526     // add CustomComboSeparatorsRenderer to filter option combo-box
 527     cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
 528             (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
 529     {
 530       @Override
 531       protected boolean addSeparatorAfter(JList list, FilterOption value,
 532               int index)
 533       {
 534         return value.isAddSeparatorAfter();
 535       }
 536     });
 537
 538     chk_invertFilter.addItemListener(this);
 539
 540     pnl_actions.add(chk_rememberSettings);
 541     pnl_actions.add(btn_view);
 542     pnl_actions.add(btn_cancel);
 543
 544     // pnl_filter.add(lbl_result);
 545     pnl_main.add(cmb_filterOption);
 546     pnl_main.add(lbl_loading);
 547     pnl_main.add(chk_invertFilter);
 548     lbl_loading.setVisible(false);
 549
 550     pnl_fileChooser.add(btn_pdbFromFile);
 551     pnl_fileChooser.add(lbl_fromFileStatus);
 552     pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
 553     pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
 554
 555     scrl_phyre2Summary.setPreferredSize(new Dimension(width, height));
 556     scrl_phyre2Summary
 557             .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 558
 559     phyreResultPanel.add(pnl_phyre2Prediction, BorderLayout.NORTH);
 560     phyreResultPanel.add(scrl_phyre2Summary, BorderLayout.CENTER);
 561
 562     pnl_phyre2Prediction.add(btn_runPhyre2Prediction);
 563     pnl_phyre2PredictionBL.add(phyre2InputAssSeqPanel, BorderLayout.NORTH);
 564     pnl_phyre2PredictionBL.add(phyreResultPanel, BorderLayout.CENTER);
 565
 566     pnl_idInput.add(txt_search);
 567     pnl_idInput.add(lbl_pdbManualFetchStatus);
 568     pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
 569     pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
 570
 571     final String foundStructureSummary = MessageManager
 572             .getString("label.found_structures_summary");
 573     final String configureCols = MessageManager
 574             .getString("label.configure_displayed_columns");
 575     ChangeListener changeListener = new ChangeListener()
 576     {
 577       @Override
 578       public void stateChanged(ChangeEvent changeEvent)
 579       {
 580         JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
 581                 .getSource();
 582         int index = sourceTabbedPane.getSelectedIndex();
 583         btn_view.setVisible(true);
 584         btn_cancel.setVisible(true);
 585         if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
 586         {
 587           btn_view.setEnabled(false);
 588           btn_cancel.setEnabled(false);
 589           btn_view.setVisible(false);
 590           btn_cancel.setVisible(false);
 591           previousWantedFields = pdbDocFieldPrefs
 592                   .getStructureSummaryFields().toArray(
 593                           new FTSDataColumnI[0]);
 594         }
 595         if (sourceTabbedPane.getTitleAt(index)
 596                 .equals(foundStructureSummary))
 597         {
 598           btn_cancel.setEnabled(true);
 599           if (wantedFieldsUpdated())
 600           {
 601             tabRefresh();
 602           }
 603           else
 604           {
 605             validateSelections();
 606           }
 607         }
 608       }
 609     };
 610     pnl_filter.addChangeListener(changeListener);
 611     pnl_filter.setPreferredSize(new Dimension(width, height));
 612     pnl_filter.add(foundStructureSummary, scrl_foundStructures);
 613     pnl_filter.add(configureCols, pdbDocFieldPrefs);
 614
 615     pnl_locPDB.add(scrl_localPDB);
 616
 617     pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
 618     pnl_switchableViews.add(pnl_idInputBL, VIEWS_ENTER_ID);
 619     pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
 620     pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
 621     pnl_switchableViews
 622             .add(pnl_phyre2PredictionBL, VIEWS_PHYRE2_PREDICTION);
 623
 624     this.setLayout(mainLayout);
 625     this.add(pnl_main, java.awt.BorderLayout.NORTH);
 626     this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
 627     // this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
 628     statusPanel.setLayout(new GridLayout());
 629     pnl_actionsAndStatus.add(pnl_actions, BorderLayout.CENTER);
 630     pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
 631     statusPanel.add(statusBar, null);
 632     this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
 633
 634     mainFrame
 635             .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 636             {
 637               @Override
 638               public void internalFrameClosing(InternalFrameEvent e)
 639               {
 640                 closeAction(pnl_filter.getHeight());
 641               }
 642             });
 643     mainFrame.setVisible(true);
 644     mainFrame.setContentPane(this);
 645     mainFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
 646     Integer x = tempUserPrefs.get("structureChooser.x");
 647     Integer y = tempUserPrefs.get("structureChooser.y");
 648     if (x != null && y != null)
 649     {
 650       mainFrame.setLocation(x, y);
 651     }
 652     Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
 653   }
 654
 655   protected void closeAction(int preferredHeight)
 656   {
 657     // System.out.println(">>>>>>>>>> closing internal frame!!!");
 658     // System.out.println("width : " + mainFrame.getWidth());
 659     // System.out.println("heigh : " + mainFrame.getHeight());
 660     // System.out.println("x : " + mainFrame.getX());
 661     // System.out.println("y : " + mainFrame.getY());
 662     tempUserPrefs.put("structureChooser.width", pnl_filter.getWidth());
 663     tempUserPrefs.put("structureChooser.height", preferredHeight);
 664     tempUserPrefs.put("structureChooser.x", mainFrame.getX());
 665     tempUserPrefs.put("structureChooser.y", mainFrame.getY());
 666     mainFrame.dispose();
 667   }
 668
 669   public boolean wantedFieldsUpdated()
 670   {
 671     if (previousWantedFields == null)
 672     {
 673       return true;
 674     }
 675
 676     FTSDataColumnI[] currentWantedFields = pdbDocFieldPrefs
 677             .getStructureSummaryFields().toArray(new FTSDataColumnI[0]);
 678     return Arrays.equals(currentWantedFields, previousWantedFields) ? false
 679             : true;
 680
 681   }
 682
 683   @Override
 684   /**
 685    * Event listener for the 'filter' combo-box and 'invert' check-box
 686    */
 687   public void itemStateChanged(ItemEvent e)
 688   {
 689     stateChanged(e);
 690   }
 691
 692   /**
 693    * This inner class provides the data model for the structure filter combo-box
 694    *
 695    * @author tcnofoegbu
 696    *
 697    */
 698   public class FilterOption
 699   {
 700     private String name;
 701
 702     private String value;
 703
 704     private String view;
 705
 706     private boolean addSeparatorAfter;
 707
 708     public FilterOption(String name, String value, String view,
 709             boolean addSeparatorAfter)
 710     {
 711       this.name = name;
 712       this.value = value;
 713       this.view = view;
 714       this.addSeparatorAfter = addSeparatorAfter;
 715     }
 716
 717     public String getName()
 718     {
 719       return name;
 720     }
 721
 722     public void setName(String name)
 723     {
 724       this.name = name;
 725     }
 726
 727     public String getValue()
 728     {
 729       return value;
 730     }
 731
 732     public void setValue(String value)
 733     {
 734       this.value = value;
 735     }
 736
 737     public String getView()
 738     {
 739       return view;
 740     }
 741
 742     public void setView(String view)
 743     {
 744       this.view = view;
 745     }
 746
 747     @Override
 748     public String toString()
 749     {
 750       return this.name;
 751     }
 752
 753     public boolean isAddSeparatorAfter()
 754     {
 755       return addSeparatorAfter;
 756     }
 757
 758     public void setAddSeparatorAfter(boolean addSeparatorAfter)
 759     {
 760       this.addSeparatorAfter = addSeparatorAfter;
 761     }
 762   }
 763
 764   /**
 765    * This inner class provides the provides the data model for associate
 766    * sequence combo-box - cmb_assSeq
 767    *
 768    * @author tcnofoegbu
 769    *
 770    */
 771   public class AssociateSeqOptions
 772   {
 773     private SequenceI sequence;
 774
 775     private String name;
 776
 777     public AssociateSeqOptions(SequenceI seq)
 778     {
 779       this.sequence = seq;
 780       this.name = (seq.getName().length() >= 23) ? seq.getName().substring(
 781               0, 23) : seq.getName();
 782     }
 783
 784     public AssociateSeqOptions(String name, SequenceI seq)
 785     {
 786       this.name = name;
 787       this.sequence = seq;
 788     }
 789
 790     @Override
 791     public String toString()
 792     {
 793       return name;
 794     }
 795
 796     public String getName()
 797     {
 798       return name;
 799     }
 800
 801     public void setName(String name)
 802     {
 803       this.name = name;
 804     }
 805
 806     public SequenceI getSequence()
 807     {
 808       return sequence;
 809     }
 810
 811     public void setSequence(SequenceI sequence)
 812     {
 813       this.sequence = sequence;
 814     }
 815
 816   }
 817
 818   /**
 819    * This inner class holds the Layout and configuration of the panel which
 820    * handles association of manually fetched structures to a unique sequence
 821    * when more than one sequence selection is made
 822    *
 823    * @author tcnofoegbu
 824    *
 825    */
 826   public class AssciateSeqPanel extends JPanel implements ItemListener
 827   {
 828     private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<AssociateSeqOptions>();
 829
 830     private JLabel lbl_associateSeq = new JLabel();
 831
 832     public AssciateSeqPanel()
 833     {
 834       this.setLayout(new FlowLayout());
 835       this.add(cmb_assSeq);
 836       this.add(lbl_associateSeq);
 837       cmb_assSeq.setToolTipText(MessageManager
 838               .getString("info.associate_wit_sequence"));
 839       cmb_assSeq.addItemListener(this);
 840     }
 841
 842     public void loadCmbAssSeq()
 843     {
 844       populateCmbAssociateSeqOptions(cmb_assSeq, lbl_associateSeq);
 845     }
 846
 847     public JComboBox<AssociateSeqOptions> getCmb_assSeq()
 848     {
 849       return cmb_assSeq;
 850     }
 851
 852     public void setCmb_assSeq(JComboBox<AssociateSeqOptions> cmb_assSeq)
 853     {
 854       this.cmb_assSeq = cmb_assSeq;
 855     }
 856
 857     @Override
 858     public void itemStateChanged(ItemEvent e)
 859     {
 860       if (e.getStateChange() == ItemEvent.SELECTED)
 861       {
 862         cmbAssSeqStateChanged();
 863       }
 864     }
 865   }
 866
 867   public JTable getResultTable()
 868   {
 869     return tbl_summary;
 870   }
 871
 872   public JComboBox<FilterOption> getCmbFilterOption()
 873   {
 874     return cmb_filterOption;
 875   }
 876
 877
 878   public JTable getPhyreResultTable()
 879   {
 880     return tbl_phyre2_summary;
 881   }
 882
 883   public abstract class CustomComboSeparatorsRenderer implements
 884           ListCellRenderer<Object>
 885   {
 886     private ListCellRenderer<Object> regent;
 887
 888     private JPanel separatorPanel = new JPanel(new BorderLayout());
 889
 890     private JSeparator jSeparator = new JSeparator();
 891
 892     public CustomComboSeparatorsRenderer(ListCellRenderer<Object> listCellRenderer)
 893     {
 894       this.regent = listCellRenderer;
 895     }
 896
 897     @Override
 898     public Component getListCellRendererComponent(JList list,
 899             Object value,
 900             int index, boolean isSelected, boolean cellHasFocus)
 901     {
 902
 903       Component comp = regent.getListCellRendererComponent(list, value,
 904               index, isSelected, cellHasFocus);
 905       if (index != -1
 906               && addSeparatorAfter(list, (FilterOption) value, index))
 907       {
 908         separatorPanel.removeAll();
 909         separatorPanel.add(comp, BorderLayout.CENTER);
 910         separatorPanel.add(jSeparator, BorderLayout.SOUTH);
 911         return separatorPanel;
 912       }
 913       else
 914       {
 915         return comp;
 916       }
 917     }
 918
 919     protected abstract boolean addSeparatorAfter(JList list,
 920             FilterOption value,
 921             int index);
 922   }
 923
 924   protected abstract void stateChanged(ItemEvent e);
 925
 926   protected abstract void ok_ActionPerformed();
 927
 928   protected abstract void pdbFromFile_actionPerformed();
 929
 930   protected abstract void txt_search_ActionPerformed();
 931
 932   public abstract void populateCmbAssociateSeqOptions(
 933           JComboBox<AssociateSeqOptions> cmb_assSeq, JLabel lbl_associateSeq);
 934
 935   public abstract void cmbAssSeqStateChanged();
 936
 937   public abstract void tabRefresh();
 938
 939   public abstract void validateSelections();
 940
 941   public abstract void predict3DModelWithPhyre2();
 942
 943 }