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;
55 public AlignViewController(AlignViewControllerGuiI alignFrame,
56 AlignViewportI viewport, AlignmentViewPanel alignPanel)
58 this.avcg = alignFrame;
59 this.viewport = viewport;
60 this.alignPanel = alignPanel;
64 public void setViewportAndAlignmentPanel(AlignViewportI viewport,
65 AlignmentViewPanel alignPanel)
67 this.alignPanel = alignPanel;
68 this.viewport = viewport;
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());
98 viewport.getAlignment().deleteAllGroups();
99 viewport.clearSequenceColours();
100 viewport.setSelectionGroup(null);
101 // set view properties for each group
102 for (int g = 0; g < gps.length; g++)
104 // gps[g].setShowunconserved(viewport.getShowUnconserved());
105 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
106 viewport.getAlignment().addGroup(gps[g]);
107 Color col = new Color((int) (Math.random() * 255),
108 (int) (Math.random() * 255), (int) (Math.random() * 255));
109 col = col.brighter();
110 for (SequenceI sq : gps[g].getSequences(null))
112 viewport.setSequenceColour(sq, col);
121 public boolean createGroup()
124 SequenceGroup sg = viewport.getSelectionGroup();
127 viewport.getAlignment().addGroup(sg);
134 public boolean unGroup()
136 SequenceGroup sg = viewport.getSelectionGroup();
139 viewport.getAlignment().deleteGroup(sg);
146 public boolean deleteGroups()
148 if (viewport.getAlignment().getGroups() != null
149 && viewport.getAlignment().getGroups().size() > 0)
151 viewport.getAlignment().deleteAllGroups();
152 viewport.clearSequenceColours();
153 viewport.setSelectionGroup(null);
160 public boolean markColumnsContainingFeatures(boolean invert,
161 boolean extendCurrent, boolean toggle, String featureType)
163 // JBPNote this routine could also mark rows, not just columns.
164 // need a decent query structure to allow all types of feature searches
165 BitSet bs = new BitSet();
166 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
167 || extendCurrent) ? viewport.getAlignment()
168 : viewport.getSelectionGroup();
170 int nseq = findColumnsWithFeature(featureType, sqcol, bs);
172 ColumnSelection cs = viewport.getColumnSelection();
175 cs = new ColumnSelection();
178 if (bs.cardinality() > 0 || invert)
180 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
181 sqcol.getEndRes(), invert, extendCurrent, toggle);
184 viewport.setColumnSelection(cs);
185 alignPanel.paintAlignment(false, false);
186 int columnCount = invert
187 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
190 avcg.setStatus(MessageManager.formatMessage(
191 "label.view_controller_toggled_marked", new String[]
192 { toggle ? MessageManager.getString("label.toggled")
193 : MessageManager.getString("label.marked"),
194 String.valueOf(columnCount),
195 invert ? MessageManager
196 .getString("label.not_containing")
197 : MessageManager.getString("label.containing"),
198 featureType, Integer.valueOf(nseq).toString() }));
204 avcg.setStatus(MessageManager
205 .formatMessage("label.no_feature_of_type_found", new String[]
210 alignPanel.paintAlignment(false, false);
217 * Sets a bit in the BitSet for each column (base 0) in the sequence
218 * collection which includes the specified feature type. Returns the number of
219 * sequences which have the feature in the selected range.
226 static int findColumnsWithFeature(String featureType,
227 SequenceCollectionI sqcol, BitSet bs)
229 final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
230 final int endColumn = sqcol.getEndRes() + 1;
231 List<SequenceI> seqs = sqcol.getSequences();
233 for (SequenceI sq : seqs)
237 // int ist = sq.findPosition(sqcol.getStartRes());
238 List<SequenceFeature> sfs = sq.findFeatures(startColumn,
239 endColumn, featureType);
246 for (SequenceFeature sf : sfs)
248 int sfStartCol = sq.findIndex(sf.getBegin());
249 int sfEndCol = sq.findIndex(sf.getEnd());
251 if (sf.isContactFeature())
254 * 'contact' feature - check for 'start' or 'end'
255 * position within the selected region
257 if (sfStartCol >= startColumn && sfStartCol <= endColumn)
259 bs.set(sfStartCol - 1);
261 if (sfEndCol >= startColumn && sfEndCol <= endColumn)
263 bs.set(sfEndCol - 1);
269 * contiguous feature - select feature positions (if any)
270 * within the selected region
272 if (sfStartCol < startColumn)
274 sfStartCol = startColumn;
276 // not sure what the point of this is
277 // if (sfStartCol < ist)
281 if (sfEndCol > endColumn)
283 sfEndCol = endColumn;
285 for (; sfStartCol <= sfEndCol; sfStartCol++)
287 bs.set(sfStartCol - 1); // convert to base 0
296 public void sortAlignmentByFeatureDensity(List<String> typ)
298 sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
301 protected void sortBy(List<String> typ, String methodText,
304 FeatureRenderer fr = alignPanel.getFeatureRenderer();
305 if (typ == null && fr != null)
307 typ = fr.getDisplayedFeatureTypes();
309 List<String> gps = null;
312 gps = fr.getDisplayedFeatureGroups();
314 AlignmentI al = viewport.getAlignment();
317 SequenceGroup sg = viewport.getSelectionGroup();
320 start = sg.getStartRes();
321 stop = sg.getEndRes();
326 stop = al.getWidth();
328 SequenceI[] oldOrder = al.getSequencesArray();
329 AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
330 avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
331 viewport.getAlignment()));
332 alignPanel.paintAlignment(true, false);
337 public void sortAlignmentByFeatureScore(List<String> typ)
339 sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
343 public boolean parseFeaturesFile(String file, DataSourceType protocol,
344 boolean relaxedIdMatching)
346 boolean featuresFile = false;
349 featuresFile = new FeaturesFile(false, file, protocol).parse(
350 viewport.getAlignment().getDataset(),
351 alignPanel.getFeatureRenderer().getFeatureColours(), false,
353 } catch (Exception ex)
355 ex.printStackTrace();
360 avcg.refreshFeatureUI(true);
361 if (alignPanel.getFeatureRenderer() != null)
363 // update the min/max ranges where necessary
364 alignPanel.getFeatureRenderer().findAllFeatures(true);
366 if (avcg.getFeatureSettingsUI() != null)
368 avcg.getFeatureSettingsUI().discoverAllFeatureData();
370 alignPanel.paintAlignment(true, true);
378 public boolean markHighlightedColumns(boolean invert,
379 boolean extendCurrent, boolean toggle)
381 if (!viewport.hasSearchResults())
383 // do nothing if no selection exists
386 // JBPNote this routine could also mark rows, not just columns.
387 BitSet bs = new BitSet();
388 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
389 || extendCurrent) ? viewport.getAlignment()
390 : viewport.getSelectionGroup();
392 // this could be a lambda... - the remains of the method is boilerplate,
393 // except for the different messages for reporting selection.
394 int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
396 ColumnSelection cs = viewport.getColumnSelection();
399 cs = new ColumnSelection();
402 if (bs.cardinality() > 0 || invert)
404 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
405 sqcol.getEndRes(), invert, extendCurrent, toggle);
408 viewport.setColumnSelection(cs);
409 alignPanel.paintAlignment(false, false);
410 int columnCount = invert
411 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
414 avcg.setStatus(MessageManager.formatMessage(
415 "label.view_controller_toggled_marked", new String[]
416 { toggle ? MessageManager.getString("label.toggled")
417 : MessageManager.getString("label.marked"),
418 String.valueOf(columnCount),
419 invert ? MessageManager
420 .getString("label.not_containing")
421 : MessageManager.getString("label.containing"),
422 "Highlight", Integer.valueOf(nseq).toString() }));
428 avcg.setStatus(MessageManager
429 .formatMessage("No highlighted regions marked"));
433 alignPanel.paintAlignment(false, false);