Coverage Report
File CalculationChooser.java
Coverage histogram
59% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| CalculationChooser | 80 | 252 | 87 |
Contributing tests
This file is covered by 1 test.
.
Source view
| 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 | package jalview.gui; | |
| 22 | ||
| 23 | import jalview.analysis.TreeBuilder; | |
| 24 | import jalview.analysis.scoremodels.ScoreModels; | |
| 25 | import jalview.analysis.scoremodels.SimilarityParams; | |
| 26 | import jalview.api.analysis.ScoreModelI; | |
| 27 | import jalview.api.analysis.SimilarityParamsI; | |
| 28 | import jalview.bin.Cache; | |
| 29 | import jalview.datamodel.SequenceGroup; | |
| 30 | import jalview.util.MessageManager; | |
| 31 | import jalview.util.Platform; | |
| 32 | import jalview.viewmodel.AlignmentViewport; | |
| 33 | import java.awt.BorderLayout; | |
| 34 | import java.awt.Color; | |
| 35 | import java.awt.Component; | |
| 36 | import java.awt.Dimension; | |
| 37 | import java.awt.FlowLayout; | |
| 38 | import java.awt.Font; | |
| 39 | import java.awt.GridLayout; | |
| 40 | import java.awt.Insets; | |
| 41 | import java.awt.event.ActionEvent; | |
| 42 | import java.awt.event.ActionListener; | |
| 43 | import java.awt.event.FocusEvent; | |
| 44 | import java.awt.event.FocusListener; | |
| 45 | import java.awt.event.MouseAdapter; | |
| 46 | import java.awt.event.MouseEvent; | |
| 47 | import java.beans.PropertyVetoException; | |
| 48 | import java.util.ArrayList; | |
| 49 | import java.util.List; | |
| 50 | ||
| 51 | import javax.swing.BorderFactory; | |
| 52 | import javax.swing.ButtonGroup; | |
| 53 | import javax.swing.DefaultComboBoxModel; | |
| 54 | import javax.swing.JButton; | |
| 55 | import javax.swing.JCheckBox; | |
| 56 | import javax.swing.JComboBox; | |
| 57 | import javax.swing.JInternalFrame; | |
| 58 | import javax.swing.JLabel; | |
| 59 | import javax.swing.JLayeredPane; | |
| 60 | import javax.swing.JPanel; | |
| 61 | import javax.swing.JRadioButton; | |
| 62 | import javax.swing.event.InternalFrameAdapter; | |
| 63 | import javax.swing.event.InternalFrameEvent; | |
| 64 | ||
| 65 | import jalview.analysis.AlignmentUtils; | |
| 66 | import jalview.analysis.TreeBuilder; | |
| 67 | import jalview.analysis.scoremodels.ScoreMatrix; | |
| 68 | import jalview.analysis.scoremodels.ScoreModels; | |
| 69 | import jalview.analysis.scoremodels.SimilarityParams; | |
| 70 | import jalview.api.analysis.ScoreModelI; | |
| 71 | import jalview.api.analysis.SimilarityParamsI; | |
| 72 | import jalview.bin.Cache; | |
| 73 | import jalview.datamodel.AlignmentAnnotation; | |
| 74 | import jalview.datamodel.SequenceGroup; | |
| 75 | import jalview.util.MessageManager; | |
| 76 | ||
| 77 | /** | |
| 78 | * A dialog where a user can choose and action Tree or PCA calculation options | |
| 79 | */ | |
| 80 | public class CalculationChooser extends JPanel | |
| 81 | { | |
| 82 | /* | |
| 83 | * flag for whether gap matches residue in the PID calculation for a Tree | |
| 84 | * - true gives Jalview 2.10.1 behaviour | |
| 85 | * - set to false (using Groovy) for a more correct tree | |
| 86 | * (JAL-374) | |
| 87 | */ | |
| 88 | private static boolean treeMatchGaps = true; | |
| 89 | ||
| 90 | private static final Font VERDANA_11PT = new Font("Verdana", 0, 11); | |
| 91 | ||
| 92 | private static final int MIN_PAIRWISE_SELECTION = 2; | |
| 93 | ||
| 94 | private static final int MIN_TREE_SELECTION = 3; | |
| 95 | ||
| 96 | private static final int MIN_PCA_SELECTION = 4; | |
| 97 | ||
| 98 | private String secondaryStructureModelName; | |
| 99 | ||
| 100 | 0 |  private void getSecondaryStructureModelName() |
| 101 | { | |
| 102 | ||
| 103 | 0 | ScoreModels scoreModels = ScoreModels.getInstance(); |
| 104 | 0 | for (ScoreModelI sm : scoreModels.getModels()) |
| 105 | { | |
| 106 | 0 | if (sm.isSecondaryStructure()) |
| 107 | { | |
| 108 | 0 | secondaryStructureModelName = sm.getName(); |
| 109 | } | |
| 110 | } | |
| 111 | ||
| 112 | } | |
| 113 | ||
| 114 | /** | |
| 115 | * minimum number of sequences needed for PASIMAP is 9 (so each has 8 | |
| 116 | * connections) | |
| 117 | */ | |
| 118 | private static final int MIN_PASIMAP_SELECTION = 9; | |
| 119 | ||
| 120 | AlignFrame af; | |
| 121 | ||
| 122 | JRadioButton pairwise; | |
| 123 | ||
| 124 | JRadioButton pca; | |
| 125 | ||
| 126 | JRadioButton pasimap; | |
| 127 | ||
| 128 | JRadioButton neighbourJoining; | |
| 129 | ||
| 130 | JRadioButton averageDistance; | |
| 131 | ||
| 132 | JComboBox<String> modelNames; | |
| 133 | ||
| 134 | JComboBox<String> ssSourceDropdown; | |
| 135 | ||
| 136 | JButton calculate; | |
| 137 | ||
| 138 | private JInternalFrame frame; | |
| 139 | ||
| 140 | private JCheckBox includeGaps; | |
| 141 | ||
| 142 | private JCheckBox matchGaps; | |
| 143 | ||
| 144 | private JCheckBox includeGappedColumns; | |
| 145 | ||
| 146 | private JCheckBox shorterSequence; | |
| 147 | ||
| 148 | final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer(); | |
| 149 | ||
| 150 | List<String> tips = new ArrayList<>(); | |
| 151 | ||
| 152 | /* | |
| 153 | * the most recently opened PCA results panel | |
| 154 | */ | |
| 155 | private PCAPanel pcaPanel; | |
| 156 | ||
| 157 | private PaSiMapPanel pasimapPanel; | |
| 158 | ||
| 159 | /** | |
| 160 | * Constructor | |
| 161 | * | |
| 162 | * @param af | |
| 163 | */ | |
| 164 | 0 | public CalculationChooser(AlignFrame alignFrame) |
| 165 | { | |
| 166 | 0 | this.af = alignFrame; |
| 167 | 0 | init(); |
| 168 | 0 | af.alignPanel.setCalculationDialog(this); |
| 169 | ||
| 170 | } | |
| 171 | ||
| 172 | /** | |
| 173 | * Lays out the panel and adds it to the desktop | |
| 174 | */ | |
| 175 | 0 | void init() |
| 176 | { | |
| 177 | 0 | getSecondaryStructureModelName(); |
| 178 | 0 | setLayout(new BorderLayout()); |
| 179 | 0 | frame = new JInternalFrame(); |
| 180 | 0 | frame.setFrameIcon(null); |
| 181 | 0 | frame.setContentPane(this); |
| 182 | 0 | this.setBackground(Color.white); |
| 183 | 0 | frame.addFocusListener(new FocusListener() |
| 184 | { | |
| 185 | ||
| 186 | 0 | @Override |
| 187 | public void focusLost(FocusEvent e) | |
| 188 | { | |
| 189 | } | |
| 190 | ||
| 191 | 0 | @Override |
| 192 | public void focusGained(FocusEvent e) | |
| 193 | { | |
| 194 | 0 | validateCalcTypes(); |
| 195 | } | |
| 196 | }); | |
| 197 | /* | |
| 198 | * Layout consists of 3 or 4 panels: | |
| 199 | * - first with choice of PCA or tree method NJ or AV | |
| 200 | * - second with choice of score model | |
| 201 | * - third with score model parameter options [suppressed] | |
| 202 | * - fourth with OK and Cancel | |
| 203 | */ | |
| 204 | 0 | pca = new JRadioButton( |
| 205 | MessageManager.getString("label.principal_component_analysis")); | |
| 206 | 0 | pca.setOpaque(false); |
| 207 | ||
| 208 | 0 | pasimap = new JRadioButton( // create the JRadioButton for pasimap with |
| 209 | // label.pasimap as its text | |
| 210 | MessageManager.getString("label.pasimap")); | |
| 211 | 0 | pasimap.setOpaque(false); |
| 212 | ||
| 213 | 0 | neighbourJoining = new JRadioButton( |
| 214 | MessageManager.getString("label.tree_calc_nj")); | |
| 215 | 0 | neighbourJoining.setSelected(true); |
| 216 | 0 | neighbourJoining.setOpaque(false); |
| 217 | ||
| 218 | 0 | averageDistance = new JRadioButton( |
| 219 | MessageManager.getString("label.tree_calc_av")); | |
| 220 | 0 | averageDistance.setOpaque(false); |
| 221 | ||
| 222 | 0 | pairwise = new JRadioButton( |
| 223 | MessageManager.getString("action.pairwise_alignment")); | |
| 224 | 0 | pairwise.setOpaque(false); |
| 225 | ||
| 226 | 0 | JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); |
| 227 | 0 | calcChoicePanel.setOpaque(false); |
| 228 | ||
| 229 | // first create the Tree calculation's border panel | |
| 230 | 0 | JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT)); |
| 231 | 0 | treePanel.setOpaque(false); |
| 232 | ||
| 233 | 0 | JvSwingUtils.createTitledBorder(treePanel, |
| 234 | MessageManager.getString("label.tree"), true); | |
| 235 | ||
| 236 | // then copy the inset dimensions for the border-less PCA panel | |
| 237 | 0 | JPanel pcaBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT)); |
| 238 | 0 | Insets b = treePanel.getBorder().getBorderInsets(treePanel); |
| 239 | 0 | pcaBorderless.setBorder( |
| 240 | BorderFactory.createEmptyBorder(2, b.left, 2, b.right)); | |
| 241 | 0 | pcaBorderless.setOpaque(false); |
| 242 | ||
| 243 | 0 | pcaBorderless.add(pca, FlowLayout.LEFT); |
| 244 | 0 | calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT); |
| 245 | ||
| 246 | // create pasimap panel | |
| 247 | 0 | JPanel pasimapBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT)); // create |
| 248 | // new | |
| 249 | // JPanel | |
| 250 | // (button) | |
| 251 | // for | |
| 252 | // pasimap | |
| 253 | 0 | pasimapBorderless.setBorder( |
| 254 | BorderFactory.createEmptyBorder(2, b.left, 2, b.right)); // set | |
| 255 | // border | |
| 256 | // (margin) | |
| 257 | // for | |
| 258 | // button | |
| 259 | // (same as | |
| 260 | // treePanel | |
| 261 | // and pca) | |
| 262 | 0 | pasimapBorderless.setOpaque(false); // false -> stops every pixel inside |
| 263 | // border from being painted | |
| 264 | 0 | pasimapBorderless.add(pasimap, FlowLayout.LEFT); // add pasimap button to |
| 265 | // the JPanel | |
| 266 | 0 | if (!Platform.isJS()) |
| 267 | { | |
| 268 | // FIXME JAL-4443 | |
| 269 | 0 | calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button |
| 270 | // with | |
| 271 | // border and | |
| 272 | // everything to | |
| 273 | // the overall | |
| 274 | // ChoicePanel | |
| 275 | } | |
| 276 | ||
| 277 | 0 | treePanel.add(neighbourJoining); |
| 278 | 0 | treePanel.add(averageDistance); |
| 279 | ||
| 280 | 0 | calcChoicePanel.add(treePanel); |
| 281 | 0 | calcChoicePanel.add(pairwise, FlowLayout.CENTER); |
| 282 | ||
| 283 | 0 | ButtonGroup calcTypes = new ButtonGroup(); |
| 284 | 0 | calcTypes.add(pca); |
| 285 | 0 | if (!Platform.isJS()) |
| 286 | { | |
| 287 | // FIXME JAL-4443 | |
| 288 | 0 | calcTypes.add(pasimap); |
| 289 | } | |
| 290 | 0 | calcTypes.add(neighbourJoining); |
| 291 | 0 | calcTypes.add(averageDistance); |
| 292 | 0 | calcTypes.add(pairwise); |
| 293 | ||
| 294 | 0 | ActionListener calcChanged = new ActionListener() |
| 295 | { | |
| 296 | 0 | @Override |
| 297 | public void actionPerformed(ActionEvent e) | |
| 298 | { | |
| 299 | 0 | validateCalcTypes(); |
| 300 | } | |
| 301 | }; | |
| 302 | 0 | pca.addActionListener(calcChanged); |
| 303 | 0 | pasimap.addActionListener(calcChanged); // add the calcChanged |
| 304 | // ActionListener to pasimap --> | |
| 305 | // <++> idk | |
| 306 | 0 | neighbourJoining.addActionListener(calcChanged); |
| 307 | 0 | averageDistance.addActionListener(calcChanged); |
| 308 | ||
| 309 | // to do | |
| 310 | 0 | ssSourceDropdown = buildSSSourcesOptionsList(); |
| 311 | 0 | ssSourceDropdown.setVisible(false); // Initially hide the dropdown |
| 312 | 0 | pairwise.addActionListener(calcChanged); |
| 313 | /* | |
| 314 | * score models drop-down - with added tooltips! | |
| 315 | */ | |
| 316 | 0 | modelNames = buildModelOptionsList(); |
| 317 | ||
| 318 | // Step 3: Show or Hide Dropdown Based on Selection | |
| 319 | 0 | modelNames.addActionListener(new ActionListener() |
| 320 | { | |
| 321 | 0 | @Override |
| 322 | public void actionPerformed(ActionEvent e) | |
| 323 | { | |
| 324 | 0 | String selectedModel = modelNames.getSelectedItem().toString(); |
| 325 | ||
| 326 | 0 | if (selectedModel.equals(secondaryStructureModelName)) |
| 327 | { | |
| 328 | 0 | ssSourceDropdown.setVisible(true); |
| 329 | } | |
| 330 | else | |
| 331 | { | |
| 332 | 0 | ssSourceDropdown.setVisible(false); |
| 333 | } | |
| 334 | } | |
| 335 | }); | |
| 336 | ||
| 337 | 0 | JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER)); |
| 338 | 0 | scoreModelPanel.setOpaque(false); |
| 339 | 0 | scoreModelPanel.add(modelNames); |
| 340 | 0 | scoreModelPanel.add(ssSourceDropdown); |
| 341 | ||
| 342 | /* | |
| 343 | * score model parameters | |
| 344 | */ | |
| 345 | 0 | JPanel paramsPanel = new JPanel(new GridLayout(5, 1)); |
| 346 | 0 | paramsPanel.setOpaque(false); |
| 347 | 0 | includeGaps = new JCheckBox("Include gaps"); |
| 348 | 0 | matchGaps = new JCheckBox("Match gaps"); |
| 349 | 0 | includeGappedColumns = new JCheckBox("Include gapped columns"); |
| 350 | 0 | shorterSequence = new JCheckBox("Match on shorter sequence"); |
| 351 | 0 | paramsPanel.add(new JLabel("Pairwise sequence scoring options")); |
| 352 | 0 | paramsPanel.add(includeGaps); |
| 353 | 0 | paramsPanel.add(matchGaps); |
| 354 | 0 | paramsPanel.add(includeGappedColumns); |
| 355 | 0 | paramsPanel.add(shorterSequence); |
| 356 | ||
| 357 | /* | |
| 358 | * OK / Cancel buttons | |
| 359 | */ | |
| 360 | 0 | calculate = new JButton(MessageManager.getString("action.calculate")); |
| 361 | 0 | calculate.setFont(VERDANA_11PT); |
| 362 | 0 | calculate.addActionListener(new java.awt.event.ActionListener() |
| 363 | { | |
| 364 | 0 | @Override |
| 365 | public void actionPerformed(ActionEvent e) | |
| 366 | { | |
| 367 | 0 | calculate_actionPerformed(); |
| 368 | } | |
| 369 | }); | |
| 370 | 0 | JButton close = new JButton(MessageManager.getString("action.close")); |
| 371 | 0 | close.setFont(VERDANA_11PT); |
| 372 | 0 | close.addActionListener(new java.awt.event.ActionListener() |
| 373 | { | |
| 374 | 0 | @Override |
| 375 | public void actionPerformed(ActionEvent e) | |
| 376 | { | |
| 377 | 0 | close_actionPerformed(); |
| 378 | } | |
| 379 | }); | |
| 380 | 0 | JPanel actionPanel = new JPanel(); |
| 381 | 0 | actionPanel.setOpaque(false); |
| 382 | 0 | actionPanel.add(calculate); |
| 383 | 0 | actionPanel.add(close); |
| 384 | ||
| 385 | 0 | boolean includeParams = false; |
| 386 | 0 | this.add(calcChoicePanel, BorderLayout.CENTER); |
| 387 | 0 | calcChoicePanel.add(scoreModelPanel); |
| 388 | 0 | if (includeParams) |
| 389 | { | |
| 390 | 0 | scoreModelPanel.add(paramsPanel); |
| 391 | } | |
| 392 | 0 | this.add(actionPanel, BorderLayout.SOUTH); |
| 393 | ||
| 394 | 0 | int width = 365; |
| 395 | 0 | int height = includeParams ? 420 : 240; |
| 396 | ||
| 397 | 0 | setMinimumSize(new Dimension(325, height - 10)); |
| 398 | 0 | String title = MessageManager.getString("label.choose_calculation"); |
| 399 | 0 | if (af.getViewport().getViewName() != null) |
| 400 | { | |
| 401 | 0 | title = title + " (" + af.getViewport().getViewName() + ")"; |
| 402 | } | |
| 403 | ||
| 404 | 0 | Desktop.addInternalFrame(frame, title, width, height, false); |
| 405 | 0 | calcChoicePanel.doLayout(); |
| 406 | 0 | revalidate(); |
| 407 | /* | |
| 408 | * null the AlignmentPanel's reference to the dialog when it is closed | |
| 409 | */ | |
| 410 | 0 | frame.addInternalFrameListener(new InternalFrameAdapter() |
| 411 | { | |
| 412 | 0 | @Override |
| 413 | public void internalFrameClosed(InternalFrameEvent evt) | |
| 414 | { | |
| 415 | 0 | af.alignPanel.setCalculationDialog(null); |
| 416 | }; | |
| 417 | }); | |
| 418 | ||
| 419 | 0 | validateCalcTypes(); |
| 420 | 0 | frame.setLayer(JLayeredPane.PALETTE_LAYER); |
| 421 | } | |
| 422 | ||
| 423 | /** | |
| 424 | * enable calculations applicable for the current alignment or selection. | |
| 425 | */ | |
| 426 | 0 | protected void validateCalcTypes() |
| 427 | { | |
| 428 | 0 | int size = af.getViewport().getAlignment().getHeight(); |
| 429 | 0 | if (af.getViewport().getSelectionGroup() != null) |
| 430 | { | |
| 431 | 0 | size = af.getViewport().getSelectionGroup().getSize(); |
| 432 | } | |
| 433 | ||
| 434 | /* | |
| 435 | * disable calc options for which there is insufficient input data | |
| 436 | * return value of true means enabled and selected | |
| 437 | */ | |
| 438 | 0 | boolean checkPca = checkEnabled(pca, size, MIN_PCA_SELECTION); |
| 439 | 0 | boolean checkPasimap = checkEnabled(pasimap, size, |
| 440 | MIN_PASIMAP_SELECTION); // check if pasimap is enabled and min_size | |
| 441 | // is fulfilled | |
| 442 | 0 | boolean checkNeighbourJoining = checkEnabled(neighbourJoining, size, |
| 443 | MIN_TREE_SELECTION); | |
| 444 | 0 | boolean checkAverageDistance = checkEnabled(averageDistance, size, |
| 445 | MIN_TREE_SELECTION); | |
| 446 | 0 | boolean checkPairwise = checkEnabled(pairwise, size, |
| 447 | MIN_PAIRWISE_SELECTION); | |
| 448 | ||
| 449 | 0 | if (checkPca || checkPasimap || checkPca || checkNeighbourJoining |
| 450 | || checkAverageDistance || checkPairwise) | |
| 451 | { | |
| 452 | 0 | calculate.setToolTipText(null); |
| 453 | 0 | calculate.setEnabled(true); |
| 454 | } | |
| 455 | else | |
| 456 | { | |
| 457 | 0 | calculate.setEnabled(false); |
| 458 | } | |
| 459 | 0 | updateScoreModels(modelNames, tips); |
| 460 | } | |
| 461 | ||
| 462 | /** | |
| 463 | * Check the input and disable a calculation's radio button if necessary. A | |
| 464 | * tooltip is shown for disabled calculations. | |
| 465 | * | |
| 466 | * @param calc | |
| 467 | * - radio button for the calculation being validated | |
| 468 | * @param size | |
| 469 | * - size of input to calculation | |
| 470 | * @param minsize | |
| 471 | * - minimum size for calculation | |
| 472 | * @return true if size >= minsize and calc.isSelected | |
| 473 | */ | |
| 474 | 0 | private boolean checkEnabled(JRadioButton calc, int size, int minsize) |
| 475 | { | |
| 476 | 0 | String ttip = MessageManager |
| 477 | .formatMessage("label.you_need_at_least_n_sequences", minsize); | |
| 478 | ||
| 479 | 0 | calc.setEnabled(size >= minsize); |
| 480 | 0 | if (!calc.isEnabled()) |
| 481 | { | |
| 482 | 0 | calc.setToolTipText(ttip); |
| 483 | } | |
| 484 | else | |
| 485 | { | |
| 486 | 0 | calc.setToolTipText(null); |
| 487 | } | |
| 488 | 0 | if (calc.isSelected()) |
| 489 | { | |
| 490 | 0 | modelNames.setEnabled(calc.isEnabled()); |
| 491 | 0 | if (calc.isEnabled()) |
| 492 | { | |
| 493 | 0 | return true; |
| 494 | } | |
| 495 | else | |
| 496 | { | |
| 497 | 0 | calculate.setToolTipText(ttip); |
| 498 | } | |
| 499 | } | |
| 500 | 0 | return false; |
| 501 | } | |
| 502 | ||
| 503 | /** | |
| 504 | * A rather elaborate helper method (blame Swing, not me) that builds a | |
| 505 | * drop-down list of score models (by name) with descriptions as tooltips. | |
| 506 | * There is also a tooltip shown for the currently selected item when hovering | |
| 507 | * over it (without opening the list). | |
| 508 | */ | |
| 509 | 0 | protected JComboBox<String> buildModelOptionsList() |
| 510 | { | |
| 511 | 0 | final JComboBox<String> scoreModelsCombo = new JComboBox<>(); |
| 512 | 0 | scoreModelsCombo.setRenderer(renderer); |
| 513 | ||
| 514 | /* | |
| 515 | * show tooltip on mouse over the combobox | |
| 516 | * note the listener has to be on the components that make up | |
| 517 | * the combobox, doesn't work if just on the combobox | |
| 518 | */ | |
| 519 | 0 | final MouseAdapter mouseListener = new MouseAdapter() |
| 520 | { | |
| 521 | 0 | @Override |
| 522 | public void mouseEntered(MouseEvent e) | |
| 523 | { | |
| 524 | 0 | scoreModelsCombo.setToolTipText( |
| 525 | tips.get(scoreModelsCombo.getSelectedIndex())); | |
| 526 | } | |
| 527 | ||
| 528 | 0 | @Override |
| 529 | public void mouseExited(MouseEvent e) | |
| 530 | { | |
| 531 | 0 | scoreModelsCombo.setToolTipText(null); |
| 532 | } | |
| 533 | }; | |
| 534 | 0 | for (Component c : scoreModelsCombo.getComponents()) |
| 535 | { | |
| 536 | 0 | c.addMouseListener(mouseListener); |
| 537 | } | |
| 538 | ||
| 539 | 0 | updateScoreModels(scoreModelsCombo, tips); |
| 540 | ||
| 541 | /* | |
| 542 | * set the list of tooltips on the combobox's renderer | |
| 543 | */ | |
| 544 | 0 | renderer.setTooltips(tips); |
| 545 | ||
| 546 | 0 | return scoreModelsCombo; |
| 547 | } | |
| 548 | ||
| 549 | 0 | private JComboBox<String> buildSSSourcesOptionsList() |
| 550 | { | |
| 551 | 0 | final JComboBox<String> comboBox = new JComboBox<>(); |
| 552 | 0 | Object curSel = comboBox.getSelectedItem(); |
| 553 | 0 | DefaultComboBoxModel<String> sourcesModel = new DefaultComboBoxModel<>(); |
| 554 | ||
| 555 | 0 | List<String> ssSources = getApplicableSecondaryStructureSources(); |
| 556 | ||
| 557 | 0 | boolean selectedIsPresent = false; |
| 558 | 0 | for (String source : ssSources) |
| 559 | { | |
| 560 | 0 | if (curSel != null && source.equals(curSel)) |
| 561 | { | |
| 562 | 0 | selectedIsPresent = true; |
| 563 | 0 | curSel = source; |
| 564 | } | |
| 565 | 0 | sourcesModel.addElement(source); |
| 566 | ||
| 567 | } | |
| 568 | ||
| 569 | 0 | if (selectedIsPresent) |
| 570 | { | |
| 571 | 0 | sourcesModel.setSelectedItem(curSel); |
| 572 | } | |
| 573 | 0 | comboBox.setModel(sourcesModel); |
| 574 | ||
| 575 | 0 | return comboBox; |
| 576 | } | |
| 577 | ||
| 578 | 0 | private void updateScoreModels(JComboBox<String> comboBox, |
| 579 | List<String> toolTips) | |
| 580 | { | |
| 581 | 0 | Object curSel = comboBox.getSelectedItem(); |
| 582 | 0 | toolTips.clear(); |
| 583 | 0 | DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>(); |
| 584 | ||
| 585 | /* | |
| 586 | * select the score models applicable to the alignment type | |
| 587 | */ | |
| 588 | 0 | boolean nucleotide = af.getViewport().getAlignment().isNucleotide(); |
| 589 | 0 | AlignmentAnnotation[] alignmentAnnotations = af.getViewport() |
| 590 | .getAlignment().getAlignmentAnnotation(); | |
| 591 | ||
| 592 | 0 | boolean ssPresent = AlignmentUtils |
| 593 | .isSecondaryStructurePresent(alignmentAnnotations); | |
| 594 | ||
| 595 | 0 | List<ScoreModelI> models = getApplicableScoreModels(nucleotide, |
| 596 | pca.isSelected(), ssPresent, (pasimap.isSelected() || pairwise.isSelected())); | |
| 597 | ||
| 598 | /* | |
| 599 | * now we can actually add entries to the combobox, | |
| 600 | * remembering their descriptions for tooltips | |
| 601 | */ | |
| 602 | 0 | boolean selectedIsPresent = false; |
| 603 | 0 | for (ScoreModelI sm : models) |
| 604 | { | |
| 605 | 0 | if (curSel != null && sm.getName().equals(curSel)) |
| 606 | { | |
| 607 | 0 | selectedIsPresent = true; |
| 608 | 0 | curSel = sm.getName(); |
| 609 | } | |
| 610 | 0 | model.addElement(sm.getName()); |
| 611 | ||
| 612 | /* | |
| 613 | * tooltip is description if provided, else text lookup with | |
| 614 | * fallback on the model name | |
| 615 | */ | |
| 616 | 0 | String tooltip = sm.getDescription(); |
| 617 | 0 | if (tooltip == null) |
| 618 | { | |
| 619 | 0 | tooltip = MessageManager.getStringOrReturn("label.score_model_", |
| 620 | sm.getName()); | |
| 621 | } | |
| 622 | 0 | toolTips.add(tooltip); |
| 623 | } | |
| 624 | ||
| 625 | 0 | if (selectedIsPresent) |
| 626 | { | |
| 627 | 0 | model.setSelectedItem(curSel); |
| 628 | } | |
| 629 | // finally, update the model | |
| 630 | 0 | comboBox.setModel(model); |
| 631 | 0 | comboBox.setEnabled(model.getSize() > 0); |
| 632 | ||
| 633 | } | |
| 634 | ||
| 635 | /** | |
| 636 | * Builds a list of score models which are applicable for the alignment and | |
| 637 | * calculation type (peptide or generic models for protein, nucleotide or | |
| 638 | * generic models for nucleotide). | |
| 639 | * <p> | |
| 640 | * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA. | |
| 641 | * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62 | |
| 642 | * was the only score matrix supported. This is included if property | |
| 643 | * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file. | |
| 644 | * | |
| 645 | * @param nucleotide | |
| 646 | * @param forPca | |
| 647 | * @param ssPresent | |
| 648 | * - include secondary structure similarity model | |
| 649 | * @param forPasimap | |
| 650 | * - limit to ScoreMatrix based models - allows use of AlignSeq | |
| 651 | * @return | |
| 652 | */ | |
| 653 | 16 | protected static List<ScoreModelI> getApplicableScoreModels( |
| 654 | boolean nucleotide, boolean forPca, boolean ssPresent, | |
| 655 | boolean forPasimap) | |
| 656 | { | |
| 657 | 16 | List<ScoreModelI> filtered = new ArrayList<>(); |
| 658 | ||
| 659 | 16 | ScoreModels scoreModels = ScoreModels.getInstance(); |
| 660 | 16 | for (ScoreModelI sm : scoreModels.getModels()) |
| 661 | { | |
| 662 | 96 | if ((!forPasimap || sm instanceof ScoreMatrix) |
| 663 | && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() | |
| 664 | || sm.isSecondaryStructure() && ssPresent)) | |
| 665 | ||
| 666 | { | |
| 667 | 38 | filtered.add(sm); |
| 668 | } | |
| 669 | } | |
| 670 | ||
| 671 | /* | |
| 672 | * special case: add BLOSUM62 as last option for nucleotide PCA, | |
| 673 | * for backwards compatibility with Jalview < 2.8 (JAL-2962) | |
| 674 | */ | |
| 675 | 16 | if (!forPasimap && nucleotide && forPca |
| 676 | && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false)) | |
| 677 | { | |
| 678 | 1 | filtered.add(scoreModels.getBlosum62()); |
| 679 | } | |
| 680 | ||
| 681 | 16 | return filtered; |
| 682 | } | |
| 683 | ||
| 684 | 0 | protected List<String> getApplicableSecondaryStructureSources() |
| 685 | { | |
| 686 | 0 | AlignmentAnnotation[] annotations = af.getViewport().getAlignment() |
| 687 | .getAlignmentAnnotation(); | |
| 688 | ||
| 689 | 0 | List<String> ssSources = AlignmentUtils |
| 690 | .getSecondaryStructureSources(annotations); | |
| 691 | // List<String> ssSources = | |
| 692 | // AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations); | |
| 693 | ||
| 694 | 0 | return ssSources; |
| 695 | } | |
| 696 | ||
| 697 | /** | |
| 698 | * Open and calculate the selected tree or PCA on 'OK' | |
| 699 | */ | |
| 700 | 0 | protected void calculate_actionPerformed() |
| 701 | { | |
| 702 | 0 | boolean doPCA = pca.isSelected(); |
| 703 | 0 | boolean doPaSiMap = pasimap.isSelected(); |
| 704 | 0 | boolean doPairwise = pairwise.isSelected(); |
| 705 | 0 | String modelName = modelNames.getSelectedItem() == null ? "" |
| 706 | : modelNames.getSelectedItem().toString(); | |
| 707 | 0 | String ssSource = ""; |
| 708 | 0 | Object selectedItem = ssSourceDropdown.getSelectedItem(); |
| 709 | 0 | if (selectedItem != null) |
| 710 | { | |
| 711 | 0 | ssSource = selectedItem.toString(); |
| 712 | } | |
| 713 | 0 | SimilarityParams params = getSimilarityParameters(doPCA); |
| 714 | 0 | if (ssSource.length() > 0) |
| 715 | { | |
| 716 | 0 | params.setSecondaryStructureSource(ssSource); |
| 717 | } | |
| 718 | ||
| 719 | 0 | if (doPCA) |
| 720 | { | |
| 721 | 0 | openPcaPanel(modelName, params); |
| 722 | } | |
| 723 | 0 | else if (doPaSiMap) |
| 724 | { | |
| 725 | 0 | openPasimapPanel(modelName, params); |
| 726 | } | |
| 727 | 0 | else if (doPairwise) |
| 728 | { | |
| 729 | 0 | openPairwisePanel(modelName, params); |
| 730 | } | |
| 731 | else | |
| 732 | { | |
| 733 | 0 | openTreePanel(modelName, params); |
| 734 | } | |
| 735 | ||
| 736 | 0 | closeFrame(); |
| 737 | } | |
| 738 | ||
| 739 | 0 | private void openPairwisePanel(String modelName, SimilarityParamsI params) |
| 740 | { | |
| 741 | 0 | ScoreModelI sm = ScoreModels.getInstance().getScoreModel(modelName, |
| 742 | af.alignPanel); | |
| 743 | 0 | if (sm == null || !(sm instanceof ScoreMatrix)) |
| 744 | { | |
| 745 | 0 | return; |
| 746 | } | |
| 747 | 0 | new Thread(new Runnable() |
| 748 | { | |
| 749 | 0 | @Override |
| 750 | public void run() | |
| 751 | { | |
| 752 | 0 | String pairwise_alignment_title = af.formCalculationTitle( |
| 753 | MessageManager.getString("action.pairwise_alignment") | |
| 754 | + " with " + sm.getName(), | |
| 755 | af.getViewport().getSelectionGroup() != null, | |
| 756 | af.getTitle()); | |
| 757 | 0 | JInternalFrame frame = new JInternalFrame(); |
| 758 | 0 | frame.setFrameIcon(null); |
| 759 | 0 | frame.setContentPane( |
| 760 | new PairwiseAlignPanel(af.getViewport(), (ScoreMatrix) sm)); | |
| 761 | 0 | Desktop.addInternalFrame(frame, pairwise_alignment_title, 600, 500); |
| 762 | } | |
| 763 | }).start(); | |
| 764 | } | |
| 765 | ||
| 766 | /** | |
| 767 | * Open a new Tree panel on the desktop | |
| 768 | * | |
| 769 | * @param modelName | |
| 770 | * @param params | |
| 771 | */ | |
| 772 | 0 | protected void openTreePanel(String modelName, SimilarityParamsI params) |
| 773 | { | |
| 774 | /* | |
| 775 | * gui validation shouldn't allow insufficient sequences here, but leave | |
| 776 | * this check in in case this method gets exposed programmatically in future | |
| 777 | */ | |
| 778 | 0 | AlignViewport viewport = af.getViewport(); |
| 779 | 0 | SequenceGroup sg = viewport.getSelectionGroup(); |
| 780 | 0 | if (sg != null && sg.getSize() < MIN_TREE_SELECTION) |
| 781 | { | |
| 782 | 0 | JvOptionPane.showMessageDialog(Desktop.desktop, |
| 783 | MessageManager.formatMessage( | |
| 784 | "label.you_need_at_least_n_sequences", | |
| 785 | MIN_TREE_SELECTION), | |
| 786 | MessageManager.getString("label.not_enough_sequences"), | |
| 787 | JvOptionPane.WARNING_MESSAGE); | |
| 788 | 0 | return; |
| 789 | } | |
| 790 | ||
| 791 | 0 | String treeType = neighbourJoining.isSelected() |
| 792 | ? TreeBuilder.NEIGHBOUR_JOINING | |
| 793 | : TreeBuilder.AVERAGE_DISTANCE; | |
| 794 | 0 | af.newTreePanel(treeType, modelName, params); |
| 795 | } | |
| 796 | ||
| 797 | /** | |
| 798 | * Open a new PCA panel on the desktop | |
| 799 | * | |
| 800 | * @param modelName | |
| 801 | * @param params | |
| 802 | */ | |
| 803 | 0 | protected void openPcaPanel(String modelName, SimilarityParamsI params) |
| 804 | { | |
| 805 | 0 | AlignViewport viewport = af.getViewport(); |
| 806 | ||
| 807 | /* | |
| 808 | * gui validation shouldn't allow insufficient sequences here, but leave | |
| 809 | * this check in in case this method gets exposed programmatically in future | |
| 810 | */ | |
| 811 | 0 | if (((viewport.getSelectionGroup() != null) |
| 812 | && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) | |
| 813 | && (viewport.getSelectionGroup().getSize() > 0)) | |
| 814 | || (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION)) | |
| 815 | { | |
| 816 | 0 | JvOptionPane.showInternalMessageDialog(this, |
| 817 | MessageManager.formatMessage( | |
| 818 | "label.you_need_at_least_n_sequences", | |
| 819 | MIN_PCA_SELECTION), | |
| 820 | MessageManager | |
| 821 | .getString("label.sequence_selection_insufficient"), | |
| 822 | JvOptionPane.WARNING_MESSAGE); | |
| 823 | 0 | return; |
| 824 | } | |
| 825 | ||
| 826 | /* | |
| 827 | * construct the panel and kick off its calculation thread | |
| 828 | */ | |
| 829 | 0 | pcaPanel = new PCAPanel(af.alignPanel, modelName, params); |
| 830 | 0 | new Thread(pcaPanel).start(); |
| 831 | ||
| 832 | } | |
| 833 | ||
| 834 | /** | |
| 835 | * Open a new PaSiMap panel on the desktop | |
| 836 | * | |
| 837 | * @param modelName | |
| 838 | * @param params | |
| 839 | */ | |
| 840 | 0 | protected void openPasimapPanel(String modelName, |
| 841 | SimilarityParamsI params) | |
| 842 | { | |
| 843 | 0 | AlignViewport viewport = af.getViewport(); |
| 844 | ||
| 845 | /* | |
| 846 | * gui validation shouldn't allow insufficient sequences here, but leave | |
| 847 | * this check in in case this method gets exposed programmatically in future | |
| 848 | */ | |
| 849 | 0 | if (((viewport.getSelectionGroup() != null) |
| 850 | && (viewport.getSelectionGroup() | |
| 851 | .getSize() < MIN_PASIMAP_SELECTION) | |
| 852 | && (viewport.getSelectionGroup().getSize() > 0)) | |
| 853 | || (viewport.getAlignment() | |
| 854 | .getHeight() < MIN_PASIMAP_SELECTION)) | |
| 855 | { | |
| 856 | 0 | JvOptionPane.showInternalMessageDialog(this, |
| 857 | MessageManager.formatMessage( | |
| 858 | "label.you_need_at_least_n_sequences", | |
| 859 | MIN_PASIMAP_SELECTION), | |
| 860 | MessageManager | |
| 861 | .getString("label.sequence_selection_insufficient"), | |
| 862 | JvOptionPane.WARNING_MESSAGE); | |
| 863 | 0 | return; |
| 864 | } | |
| 865 | ||
| 866 | /* | |
| 867 | * construct the panel and kick off its calculation thread | |
| 868 | */ | |
| 869 | 0 | pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName); |
| 870 | 0 | new Thread(pasimapPanel).start(); |
| 871 | ||
| 872 | } | |
| 873 | ||
| 874 | /** | |
| 875 | * | |
| 876 | */ | |
| 877 | 0 | protected void closeFrame() |
| 878 | { | |
| 879 | 0 | try |
| 880 | { | |
| 881 | 0 | frame.setClosed(true); |
| 882 | } catch (PropertyVetoException ex) | |
| 883 | { | |
| 884 | } | |
| 885 | } | |
| 886 | ||
| 887 | /** | |
| 888 | * Returns a data bean holding parameters for similarity (or distance) model | |
| 889 | * calculation | |
| 890 | * | |
| 891 | * @param doPCA | |
| 892 | * @return | |
| 893 | */ | |
| 894 | 0 | protected SimilarityParams getSimilarityParameters(boolean doPCA) |
| 895 | { | |
| 896 | // commented out: parameter choices read from gui widgets | |
| 897 | // SimilarityParamsI params = new SimilarityParams( | |
| 898 | // includeGappedColumns.isSelected(), matchGaps.isSelected(), | |
| 899 | // includeGaps.isSelected(), shorterSequence.isSelected()); | |
| 900 | ||
| 901 | 0 | boolean includeGapGap = true; |
| 902 | 0 | boolean includeGapResidue = true; |
| 903 | 0 | boolean matchOnShortestLength = false; |
| 904 | ||
| 905 | /* | |
| 906 | * 'matchGaps' flag is only used in the PID calculation | |
| 907 | * - set to false for PCA so that PCA using PID reproduces SeqSpace PCA | |
| 908 | * - set to true for Tree to reproduce Jalview 2.10.1 calculation | |
| 909 | * - set to false for Tree for a more correct calculation (JAL-374) | |
| 910 | */ | |
| 911 | 0 | boolean matchGap = doPCA ? false : treeMatchGaps; |
| 912 | ||
| 913 | 0 | return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, |
| 914 | matchOnShortestLength); | |
| 915 | } | |
| 916 | ||
| 917 | /** | |
| 918 | * Closes dialog on Close button press | |
| 919 | */ | |
| 920 | 0 | protected void close_actionPerformed() |
| 921 | { | |
| 922 | 0 | try |
| 923 | { | |
| 924 | 0 | frame.setClosed(true); |
| 925 | } catch (Exception ex) | |
| 926 | { | |
| 927 | } | |
| 928 | } | |
| 929 | ||
| 930 | 0 | public PCAPanel getPcaPanel() |
| 931 | { | |
| 932 | 0 | return pcaPanel; |
| 933 | } | |
| 934 | } |