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 startColumn = sqcol.getStartRes() + 1; // converted to base 1
238 final int endColumn = sqcol.getEndRes() + 1;
239 List<SequenceI> seqs = sqcol.getSequences();
241 for (SequenceI sq : seqs)
245 // int ist = sq.findPosition(sqcol.getStartRes());
246 List<SequenceFeature> sfs = sq.findFeatures(startColumn,
247 endColumn, featureType);
254 for (SequenceFeature sf : sfs)
256 int sfStartCol = sq.findIndex(sf.getBegin());
257 int sfEndCol = sq.findIndex(sf.getEnd());
259 if (sf.isContactFeature())
262 * 'contact' feature - check for 'start' or 'end'
263 * position within the selected region
265 if (sfStartCol >= startColumn && sfStartCol <= endColumn)
267 bs.set(sfStartCol - 1);
269 if (sfEndCol >= startColumn && sfEndCol <= endColumn)
271 bs.set(sfEndCol - 1);
277 * contiguous feature - select feature positions (if any)
278 * within the selected region
280 if (sfStartCol < startColumn)
282 sfStartCol = startColumn;
284 // not sure what the point of this is
285 // if (sfStartCol < ist)
289 if (sfEndCol > endColumn)
291 sfEndCol = endColumn;
293 for (; sfStartCol <= sfEndCol; sfStartCol++)
295 bs.set(sfStartCol - 1); // convert to base 0
304 public void sortAlignmentByFeatureDensity(List<String> typ)
306 sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
309 protected void sortBy(List<String> typ, String methodText,
312 FeatureRenderer fr = alignPanel.getFeatureRenderer();
313 if (typ == null && fr != null)
315 typ = fr.getDisplayedFeatureTypes();
317 List<String> gps = null;
320 gps = fr.getDisplayedFeatureGroups();
322 AlignmentI al = viewport.getAlignment();
325 SequenceGroup sg = viewport.getSelectionGroup();
328 start = sg.getStartRes();
329 stop = sg.getEndRes();
334 stop = al.getWidth();
336 SequenceI[] oldOrder = al.getSequencesArray();
337 AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
338 avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
339 viewport.getAlignment()));
340 alignPanel.paintAlignment(true);
345 public void sortAlignmentByFeatureScore(List<String> typ)
347 sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
351 public boolean parseFeaturesFile(String file, DataSourceType protocol,
352 boolean relaxedIdMatching)
354 boolean featuresFile = false;
357 featuresFile = new FeaturesFile(false, file, protocol).parse(
358 viewport.getAlignment().getDataset(),
359 alignPanel.getFeatureRenderer().getFeatureColours(), false,
361 } catch (Exception ex)
363 ex.printStackTrace();
368 avcg.refreshFeatureUI(true);
369 if (alignPanel.getFeatureRenderer() != null)
371 // update the min/max ranges where necessary
372 alignPanel.getFeatureRenderer().findAllFeatures(true);
374 if (avcg.getFeatureSettingsUI() != null)
376 avcg.getFeatureSettingsUI().discoverAllFeatureData();
378 alignPanel.paintAlignment(true);
386 public boolean markHighlightedColumns(boolean invert,
387 boolean extendCurrent, boolean toggle)
389 if (!viewport.hasSearchResults())
391 // do nothing if no selection exists
394 // JBPNote this routine could also mark rows, not just columns.
395 BitSet bs = new BitSet();
396 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
397 || extendCurrent) ? viewport.getAlignment()
398 : viewport.getSelectionGroup();
400 // this could be a lambda... - the remains of the method is boilerplate,
401 // except for the different messages for reporting selection.
402 int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
404 ColumnSelection cs = viewport.getColumnSelection();
407 cs = new ColumnSelection();
410 if (bs.cardinality() > 0 || invert)
412 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
413 sqcol.getEndRes(), invert, extendCurrent, toggle);
416 viewport.setColumnSelection(cs);
417 alignPanel.paintAlignment(true);
418 int columnCount = invert
419 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
422 avcg.setStatus(MessageManager.formatMessage(
423 "label.view_controller_toggled_marked", new String[]
424 { toggle ? MessageManager.getString("label.toggled")
425 : MessageManager.getString("label.marked"),
426 String.valueOf(columnCount),
427 invert ? MessageManager
428 .getString("label.not_containing")
429 : MessageManager.getString("label.containing"),
430 "Highlight", Integer.valueOf(nseq).toString() }));
436 avcg.setStatus(MessageManager
437 .formatMessage("No highlighted regions marked"));
441 alignPanel.paintAlignment(true);