2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.controller;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.api.AlignViewControllerGuiI;
25 import jalview.api.AlignViewControllerI;
26 import jalview.api.AlignViewportI;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.api.FeatureRenderer;
29 import jalview.commands.OrderCommand;
30 import jalview.datamodel.AlignmentI;
31 import jalview.datamodel.ColumnSelection;
32 import jalview.datamodel.SequenceCollectionI;
33 import jalview.datamodel.SequenceFeature;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.io.DataSourceType;
37 import jalview.io.FeaturesFile;
38 import jalview.schemes.ColourSchemeI;
39 import jalview.util.MessageManager;
41 import java.awt.Color;
42 import java.util.BitSet;
43 import java.util.List;
45 public class AlignViewController implements AlignViewControllerI
47 AlignViewportI viewport = null;
49 AlignmentViewPanel alignPanel = null;
52 * the GUI container that is handling interactions with the user
54 private AlignViewControllerGuiI avcg;
56 public AlignViewController(AlignViewControllerGuiI alignFrame,
57 AlignViewportI vp, AlignmentViewPanel ap)
59 this.avcg = alignFrame;
65 public void setViewportAndAlignmentPanel(AlignViewportI vp,
66 AlignmentViewPanel ap)
73 public boolean makeGroupsFromSelection()
75 SequenceGroup sg = viewport.getSelectionGroup();
76 ColumnSelection cs = viewport.getColumnSelection();
77 SequenceGroup[] gps = null;
78 if (sg != null && (cs == null || cs.isEmpty()))
80 gps = jalview.analysis.Grouping.makeGroupsFrom(
81 viewport.getSequenceSelection(),
82 viewport.getAlignmentView(true)
83 .getSequenceStrings(viewport.getGapCharacter()),
84 viewport.getAlignment().getGroups());
90 gps = jalview.analysis.Grouping.makeGroupsFromCols(
91 (sg == null) ? viewport.getAlignment().getSequencesArray()
92 : sg.getSequences().toArray(new SequenceI[0]),
93 cs, viewport.getAlignment().getGroups(),
94 viewport.getAlignment().getHiddenColumns());
99 viewport.getAlignment().deleteAllGroups();
100 viewport.clearSequenceColours();
101 viewport.setSelectionGroup(null);
102 ColourSchemeI colours = viewport.getGlobalColourScheme();
103 // set view properties for each group
104 for (int g = 0; g < gps.length; g++)
106 // gps[g].setShowunconserved(viewport.getShowUnconserved());
107 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
108 viewport.getAlignment().addGroup(gps[g]);
111 gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
113 Color col = new Color((int) (Math.random() * 255),
114 (int) (Math.random() * 255), (int) (Math.random() * 255));
115 gps[g].idColour = col;
116 viewport.setUpdateStructures(true);
117 viewport.addSequenceGroup(gps[g]);
125 public boolean createGroup()
128 SequenceGroup sg = viewport.getSelectionGroup();
131 viewport.getAlignment().addGroup(sg);
138 public boolean unGroup()
140 SequenceGroup sg = viewport.getSelectionGroup();
143 viewport.getAlignment().deleteGroup(sg);
150 public boolean deleteGroups()
152 if (viewport.getAlignment().getGroups() != null
153 && viewport.getAlignment().getGroups().size() > 0)
155 viewport.getAlignment().deleteAllGroups();
156 viewport.clearSequenceColours();
157 viewport.setSelectionGroup(null);
164 public boolean markColumnsContainingFeatures(boolean invert,
165 boolean extendCurrent, boolean toggle, String featureType)
167 // JBPNote this routine could also mark rows, not just columns.
168 // need a decent query structure to allow all types of feature searches
169 BitSet bs = new BitSet();
170 boolean searchSelection = viewport.getSelectionGroup() != null
172 SequenceCollectionI sqcol = searchSelection ? viewport
173 .getSelectionGroup() : viewport.getAlignment();
175 int nseq = findColumnsWithFeature(featureType, sqcol, bs);
177 ColumnSelection cs = viewport.getColumnSelection();
180 cs = new ColumnSelection();
183 if (bs.cardinality() > 0 || invert)
185 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
186 sqcol.getEndRes(), invert, extendCurrent, toggle);
189 viewport.setColumnSelection(cs);
190 alignPanel.paintAlignment(false, false);
191 int columnCount = invert
192 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
195 avcg.setStatus(MessageManager.formatMessage(
196 "label.view_controller_toggled_marked", new String[]
197 { toggle ? MessageManager.getString("label.toggled")
198 : MessageManager.getString("label.marked"),
199 String.valueOf(columnCount),
200 invert ? MessageManager
201 .getString("label.not_containing")
202 : MessageManager.getString("label.containing"),
203 featureType, Integer.valueOf(nseq).toString() }));
209 String key = searchSelection ? "label.no_feature_found_selection"
210 : "label.no_feature_of_type_found";
211 avcg.setStatus(MessageManager.formatMessage(key,
212 new String[] { featureType }));
216 alignPanel.paintAlignment(false, false);
223 * Sets a bit in the BitSet for each column (base 0) in the sequence
224 * collection which includes a visible feature of the specified feature type.
225 * Returns the number of sequences which have the feature visible in the
233 int findColumnsWithFeature(String featureType,
234 SequenceCollectionI sqcol, BitSet bs)
236 FeatureRenderer fr = alignPanel == null ? null : alignPanel
237 .getFeatureRenderer();
239 final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
240 final int endColumn = sqcol.getEndRes() + 1;
241 List<SequenceI> seqs = sqcol.getSequences();
243 for (SequenceI sq : seqs)
247 // int ist = sq.findPosition(sqcol.getStartRes());
248 List<SequenceFeature> sfs = sq.findFeatures(startColumn,
249 endColumn, featureType);
251 boolean found = false;
252 for (SequenceFeature sf : sfs)
254 if (fr.getColour(sf) == null)
264 int sfStartCol = sq.findIndex(sf.getBegin());
265 int sfEndCol = sq.findIndex(sf.getEnd());
267 if (sf.isContactFeature())
270 * 'contact' feature - check for 'start' or 'end'
271 * position within the selected region
273 if (sfStartCol >= startColumn && sfStartCol <= endColumn)
275 bs.set(sfStartCol - 1);
277 if (sfEndCol >= startColumn && sfEndCol <= endColumn)
279 bs.set(sfEndCol - 1);
285 * contiguous feature - select feature positions (if any)
286 * within the selected region
288 if (sfStartCol < startColumn)
290 sfStartCol = startColumn;
292 // not sure what the point of this is
293 // if (sfStartCol < ist)
297 if (sfEndCol > endColumn)
299 sfEndCol = endColumn;
301 for (; sfStartCol <= sfEndCol; sfStartCol++)
303 bs.set(sfStartCol - 1); // convert to base 0
312 public void sortAlignmentByFeatureDensity(List<String> typ)
314 String methodText = MessageManager.getString("label.sort_by_density");
315 sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
319 * Sorts the alignment (or current selection) by either average score or density
320 * of the specified feature types, and adds to the command history. If
321 * {@code types} is null, all visible feature types are used for the sort. If no
322 * feature types apply, does nothing.
326 * - text shown in Undo/Redo command
329 * jalview.analysis.AlignmentSorter.sortByFeatures()
331 protected void sortByFeatures(List<String> types, String methodText,
334 FeatureRenderer fr = alignPanel.getFeatureRenderer();
335 if (types == null && fr != null)
337 types = fr.getDisplayedFeatureTypes();
341 return; // nothing to do
343 List<String> gps = null;
346 gps = fr.getDisplayedFeatureGroups();
348 AlignmentI al = viewport.getAlignment();
351 SequenceGroup sg = viewport.getSelectionGroup();
354 start = sg.getStartRes();
355 stop = sg.getEndRes();
360 stop = al.getWidth();
362 SequenceI[] oldOrder = al.getSequencesArray();
363 AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
364 avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
365 viewport.getAlignment()));
366 alignPanel.paintAlignment(true, false);
371 public void sortAlignmentByFeatureScore(List<String> typ)
373 String methodText = MessageManager.getString("label.sort_by_score");
374 sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
378 public boolean parseFeaturesFile(String file, DataSourceType protocol,
379 boolean relaxedIdMatching)
381 boolean featuresAdded = false;
382 FeatureRenderer fr = alignPanel.getFeatureRenderer();
385 featuresAdded = new FeaturesFile(false, file, protocol).parse(
386 viewport.getAlignment().getDataset(), fr.getFeatureColours(),
387 fr.getFeatureFilters(), false, relaxedIdMatching);
388 } catch (Exception ex)
390 ex.printStackTrace();
395 avcg.refreshFeatureUI(true);
398 // update the min/max ranges where necessary
399 fr.findAllFeatures(true);
401 if (avcg.getFeatureSettingsUI() != null)
403 avcg.getFeatureSettingsUI().discoverAllFeatureData();
405 alignPanel.paintAlignment(true, true);
408 return featuresAdded;
413 public boolean markHighlightedColumns(boolean invert,
414 boolean extendCurrent, boolean toggle)
416 if (!viewport.hasSearchResults())
418 // do nothing if no selection exists
421 // JBPNote this routine could also mark rows, not just columns.
422 BitSet bs = new BitSet();
423 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
424 || extendCurrent) ? viewport.getAlignment()
425 : viewport.getSelectionGroup();
427 // this could be a lambda... - the remains of the method is boilerplate,
428 // except for the different messages for reporting selection.
429 int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
431 ColumnSelection cs = viewport.getColumnSelection();
434 cs = new ColumnSelection();
437 if (bs.cardinality() > 0 || invert)
439 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
440 sqcol.getEndRes(), invert, extendCurrent, toggle);
443 viewport.setColumnSelection(cs);
444 alignPanel.paintAlignment(false, false);
445 int columnCount = invert
446 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
449 avcg.setStatus(MessageManager.formatMessage(
450 "label.view_controller_toggled_marked", new String[]
451 { toggle ? MessageManager.getString("label.toggled")
452 : MessageManager.getString("label.marked"),
453 String.valueOf(columnCount),
454 invert ? MessageManager
455 .getString("label.not_containing")
456 : MessageManager.getString("label.containing"),
457 "Highlight", Integer.valueOf(nseq).toString() }));
463 avcg.setStatus(MessageManager
464 .formatMessage("No highlighted regions marked"));
468 alignPanel.paintAlignment(false, false);