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.util.MessageManager;
40 import java.awt.Color;
41 import java.util.BitSet;
42 import java.util.List;
44 public class AlignViewController implements AlignViewControllerI
46 AlignViewportI viewport = null;
48 AlignmentViewPanel alignPanel = null;
51 * the GUI container that is handling interactions with the user
53 private AlignViewControllerGuiI avcg;
56 protected void finalize() throws Throwable
63 public AlignViewController(AlignViewControllerGuiI alignFrame,
64 AlignViewportI viewport, AlignmentViewPanel alignPanel)
66 this.avcg = alignFrame;
67 this.viewport = viewport;
68 this.alignPanel = alignPanel;
72 public void setViewportAndAlignmentPanel(AlignViewportI viewport,
73 AlignmentViewPanel alignPanel)
75 this.alignPanel = alignPanel;
76 this.viewport = viewport;
81 public boolean makeGroupsFromSelection()
83 SequenceGroup sg = viewport.getSelectionGroup();
84 ColumnSelection cs = viewport.getColumnSelection();
85 SequenceGroup[] gps = null;
86 if (sg != null && (cs == null || cs.isEmpty()))
88 gps = jalview.analysis.Grouping.makeGroupsFrom(
89 viewport.getSequenceSelection(),
90 viewport.getAlignmentView(true)
91 .getSequenceStrings(viewport.getGapCharacter()),
92 viewport.getAlignment().getGroups());
98 gps = jalview.analysis.Grouping.makeGroupsFromCols(
99 (sg == null) ? viewport.getAlignment().getSequencesArray()
100 : sg.getSequences().toArray(new SequenceI[0]),
101 cs, viewport.getAlignment().getGroups());
106 viewport.getAlignment().deleteAllGroups();
107 viewport.clearSequenceColours();
108 viewport.setSelectionGroup(null);
109 // set view properties for each group
110 for (int g = 0; g < gps.length; g++)
112 // gps[g].setShowunconserved(viewport.getShowUnconserved());
113 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
114 viewport.getAlignment().addGroup(gps[g]);
115 Color col = new Color((int) (Math.random() * 255),
116 (int) (Math.random() * 255), (int) (Math.random() * 255));
117 col = col.brighter();
118 for (SequenceI sq : gps[g].getSequences(null))
120 viewport.setSequenceColour(sq, col);
129 public boolean createGroup()
132 SequenceGroup sg = viewport.getSelectionGroup();
135 viewport.getAlignment().addGroup(sg);
142 public boolean unGroup()
144 SequenceGroup sg = viewport.getSelectionGroup();
147 viewport.getAlignment().deleteGroup(sg);
154 public boolean deleteGroups()
156 if (viewport.getAlignment().getGroups() != null
157 && viewport.getAlignment().getGroups().size() > 0)
159 viewport.getAlignment().deleteAllGroups();
160 viewport.clearSequenceColours();
161 viewport.setSelectionGroup(null);
168 public boolean markColumnsContainingFeatures(boolean invert,
169 boolean extendCurrent, boolean toggle, String featureType)
171 // JBPNote this routine could also mark rows, not just columns.
172 // need a decent query structure to allow all types of feature searches
173 BitSet bs = new BitSet();
174 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
175 || extendCurrent) ? viewport.getAlignment()
176 : viewport.getSelectionGroup();
178 int nseq = findColumnsWithFeature(featureType, sqcol, bs);
180 ColumnSelection cs = viewport.getColumnSelection();
183 cs = new ColumnSelection();
186 if (bs.cardinality() > 0 || invert)
188 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
189 sqcol.getEndRes(), invert, extendCurrent, toggle);
192 viewport.setColumnSelection(cs);
193 alignPanel.paintAlignment(true);
194 int columnCount = invert
195 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
198 avcg.setStatus(MessageManager.formatMessage(
199 "label.view_controller_toggled_marked", new String[]
200 { toggle ? MessageManager.getString("label.toggled")
201 : MessageManager.getString("label.marked"),
202 String.valueOf(columnCount),
203 invert ? MessageManager
204 .getString("label.not_containing")
205 : MessageManager.getString("label.containing"),
206 featureType, Integer.valueOf(nseq).toString() }));
212 avcg.setStatus(MessageManager
213 .formatMessage("label.no_feature_of_type_found", new String[]
218 alignPanel.paintAlignment(true);
225 * Sets a bit in the BitSet for each column (base 0) in the sequence
226 * collection which includes the specified feature type. Returns the number of
227 * sequences which have the feature in the selected range.
234 static int findColumnsWithFeature(String featureType,
235 SequenceCollectionI sqcol, BitSet bs)
237 final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
238 final int endPosition = sqcol.getEndRes() + 1;
239 List<SequenceI> seqs = sqcol.getSequences();
241 for (SequenceI sq : seqs)
243 boolean sequenceHasFeature = false;
246 SequenceFeature[] sfs = sq.getSequenceFeatures();
249 int ist = sq.findIndex(sq.getStart());
250 int iend = sq.findIndex(sq.getEnd());
251 if (iend < startPosition || ist > endPosition)
253 // sequence not in region
256 for (SequenceFeature sf : sfs)
258 // future functionality - featureType == null means mark columns
259 // containing all displayed features
260 if (sf != null && (featureType.equals(sf.getType())))
262 // optimisation - could consider 'spos,apos' like cursor argument
263 // - findIndex wastes time by starting from first character and
266 int sfStartCol = sq.findIndex(sf.getBegin());
267 int sfEndCol = sq.findIndex(sf.getEnd());
269 if (sf.isContactFeature())
272 * 'contact' feature - check for 'start' or 'end'
273 * position within the selected region
275 if (sfStartCol >= startPosition
276 && sfStartCol <= endPosition)
278 bs.set(sfStartCol - 1);
279 sequenceHasFeature = true;
281 if (sfEndCol >= startPosition && sfEndCol <= endPosition)
283 bs.set(sfEndCol - 1);
284 sequenceHasFeature = true;
290 * contiguous feature - select feature positions (if any)
291 * within the selected region
293 if (sfStartCol > endPosition || sfEndCol < startPosition)
295 // feature is outside selected region
298 sequenceHasFeature = true;
299 if (sfStartCol < startPosition)
301 sfStartCol = startPosition;
303 if (sfStartCol < ist)
307 if (sfEndCol > endPosition)
309 sfEndCol = endPosition;
311 for (; sfStartCol <= sfEndCol; sfStartCol++)
313 bs.set(sfStartCol - 1); // convert to base 0
319 if (sequenceHasFeature)
329 public void sortAlignmentByFeatureDensity(List<String> typ)
331 sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
334 protected void sortBy(List<String> typ, String methodText,
337 FeatureRenderer fr = alignPanel.getFeatureRenderer();
338 if (typ == null && fr != null)
340 typ = fr.getDisplayedFeatureTypes();
342 List<String> gps = null;
345 gps = fr.getDisplayedFeatureGroups();
347 AlignmentI al = viewport.getAlignment();
350 SequenceGroup sg = viewport.getSelectionGroup();
353 start = sg.getStartRes();
354 stop = sg.getEndRes();
359 stop = al.getWidth();
361 SequenceI[] oldOrder = al.getSequencesArray();
362 AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
363 avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
364 viewport.getAlignment()));
365 alignPanel.paintAlignment(true);
370 public void sortAlignmentByFeatureScore(List<String> typ)
372 sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
376 public boolean parseFeaturesFile(String file, DataSourceType protocol,
377 boolean relaxedIdMatching)
379 boolean featuresFile = false;
382 featuresFile = new FeaturesFile(false, file, protocol).parse(
383 viewport.getAlignment().getDataset(),
384 alignPanel.getFeatureRenderer().getFeatureColours(), false,
386 } catch (Exception ex)
388 ex.printStackTrace();
393 avcg.refreshFeatureUI(true);
394 if (alignPanel.getFeatureRenderer() != null)
396 // update the min/max ranges where necessary
397 alignPanel.getFeatureRenderer().findAllFeatures(true);
399 if (avcg.getFeatureSettingsUI() != null)
401 avcg.getFeatureSettingsUI().discoverAllFeatureData();
403 alignPanel.paintAlignment(true);
411 public boolean markHighlightedColumns(boolean invert,
412 boolean extendCurrent, boolean toggle)
414 if (!viewport.hasSearchResults())
416 // do nothing if no selection exists
419 // JBPNote this routine could also mark rows, not just columns.
420 BitSet bs = new BitSet();
421 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
422 || extendCurrent) ? viewport.getAlignment()
423 : viewport.getSelectionGroup();
425 // this could be a lambda... - the remains of the method is boilerplate,
426 // except for the different messages for reporting selection.
427 int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
429 ColumnSelection cs = viewport.getColumnSelection();
432 cs = new ColumnSelection();
435 if (bs.cardinality() > 0 || invert)
437 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
438 sqcol.getEndRes(), invert, extendCurrent, toggle);
441 viewport.setColumnSelection(cs);
442 alignPanel.paintAlignment(true);
443 int columnCount = invert
444 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
447 avcg.setStatus(MessageManager.formatMessage(
448 "label.view_controller_toggled_marked", new String[]
449 { toggle ? MessageManager.getString("label.toggled")
450 : MessageManager.getString("label.marked"),
451 String.valueOf(columnCount),
452 invert ? MessageManager
453 .getString("label.not_containing")
454 : MessageManager.getString("label.containing"),
455 "Highlight", Integer.valueOf(nseq).toString() }));
461 avcg.setStatus(MessageManager
462 .formatMessage("No highlighted regions marked"));
466 alignPanel.paintAlignment(true);