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.FeaturesFile;
37 import jalview.util.MessageManager;
39 import java.awt.Color;
40 import java.util.BitSet;
41 import java.util.List;
43 public class AlignViewController implements AlignViewControllerI
45 AlignViewportI viewport = null;
47 AlignmentViewPanel alignPanel = null;
50 * the GUI container that is handling interactions with the user
52 private AlignViewControllerGuiI avcg;
55 protected void finalize() throws Throwable
62 public AlignViewController(AlignViewControllerGuiI alignFrame,
63 AlignViewportI viewport, AlignmentViewPanel alignPanel)
65 this.avcg = alignFrame;
66 this.viewport = viewport;
67 this.alignPanel = alignPanel;
71 public void setViewportAndAlignmentPanel(AlignViewportI viewport,
72 AlignmentViewPanel alignPanel)
74 this.alignPanel = alignPanel;
75 this.viewport = viewport;
80 public boolean makeGroupsFromSelection()
82 SequenceGroup sg = viewport.getSelectionGroup();
83 ColumnSelection cs = viewport.getColumnSelection();
84 SequenceGroup[] gps = null;
85 if (sg != null && (cs == null || cs.isEmpty()))
87 gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
88 .getSequenceSelection(), viewport.getAlignmentView(true)
89 .getSequenceStrings(viewport.getGapCharacter()), viewport
90 .getAlignment().getGroups());
96 gps = jalview.analysis.Grouping.makeGroupsFromCols(
97 (sg == null) ? viewport.getAlignment().getSequencesArray()
98 : sg.getSequences().toArray(new SequenceI[0]), cs,
99 viewport.getAlignment().getGroups());
104 viewport.getAlignment().deleteAllGroups();
105 viewport.clearSequenceColours();
106 viewport.setSelectionGroup(null);
107 // set view properties for each group
108 for (int g = 0; g < gps.length; g++)
110 // gps[g].setShowunconserved(viewport.getShowUnconserved());
111 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
112 viewport.getAlignment().addGroup(gps[g]);
113 Color col = new Color((int) (Math.random() * 255),
114 (int) (Math.random() * 255), (int) (Math.random() * 255));
115 col = col.brighter();
116 for (SequenceI sq : gps[g].getSequences(null))
118 viewport.setSequenceColour(sq, col);
127 public boolean createGroup()
130 SequenceGroup sg = viewport.getSelectionGroup();
133 viewport.getAlignment().addGroup(sg);
140 public boolean unGroup()
142 SequenceGroup sg = viewport.getSelectionGroup();
145 viewport.getAlignment().deleteGroup(sg);
152 public boolean deleteGroups()
154 if (viewport.getAlignment().getGroups() != null
155 && viewport.getAlignment().getGroups().size() > 0)
157 viewport.getAlignment().deleteAllGroups();
158 viewport.clearSequenceColours();
159 viewport.setSelectionGroup(null);
166 public boolean markColumnsContainingFeatures(boolean invert,
167 boolean extendCurrent, boolean toggle, String featureType)
169 // JBPNote this routine could also mark rows, not just columns.
170 // need a decent query structure to allow all types of feature searches
171 BitSet bs = new BitSet();
172 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
173 .getAlignment() : viewport.getSelectionGroup();
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(true);
191 int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
194 avcg.setStatus(MessageManager.formatMessage(
195 "label.view_controller_toggled_marked",
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 avcg.setStatus(MessageManager.formatMessage(
210 "label.no_feature_of_type_found",
211 new String[] { featureType }));
215 alignPanel.paintAlignment(true);
222 * Sets a bit in the BitSet for each column (base 0) in the sequence
223 * collection which includes the specified feature type. Returns the number of
224 * sequences which have the feature in the selected range.
231 static int findColumnsWithFeature(String featureType,
232 SequenceCollectionI sqcol, BitSet bs)
234 final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
235 final int endPosition = sqcol.getEndRes() + 1;
236 List<SequenceI> seqs = sqcol.getSequences();
238 for (SequenceI sq : seqs)
240 boolean sequenceHasFeature = false;
243 SequenceFeature[] sfs = sq.getSequenceFeatures();
247 * check whether the feature start/end (base 1)
248 * overlaps the selection start/end
250 int ist = sq.findIndex(sq.getStart());
251 int iend = sq.findIndex(sq.getEnd());
252 if (iend < startPosition || ist > endPosition)
254 // sequence not in region
257 for (SequenceFeature sf : sfs)
259 // future functionality - featureType == null means mark columns
260 // containing all displayed features
261 if (sf != null && (featureType.equals(sf.getType())))
263 // optimisation - could consider 'spos,apos' like cursor argument
264 // - findIndex wastes time by starting from first character and
267 int i = sq.findIndex(sf.getBegin());
268 int j = sq.findIndex(sf.getEnd());
269 if (j < startPosition || i > endPosition)
271 // feature is outside selected region
274 sequenceHasFeature = true;
275 if (i < startPosition)
289 bs.set(i - 1); // convert to base 0
295 if (sequenceHasFeature)
305 public void sortAlignmentByFeatureDensity(List<String> typ)
307 sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
310 protected void sortBy(List<String> typ, String methodText,
313 FeatureRenderer fr = alignPanel.getFeatureRenderer();
314 if (typ == null && fr != null)
316 typ = fr.getDisplayedFeatureTypes();
318 List<String> gps = null;
321 gps = fr.getDisplayedFeatureGroups();
323 AlignmentI al = viewport.getAlignment();
326 SequenceGroup sg = viewport.getSelectionGroup();
329 start = sg.getStartRes();
330 stop = sg.getEndRes();
335 stop = al.getWidth();
337 SequenceI[] oldOrder = al.getSequencesArray();
338 AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
339 avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
341 alignPanel.paintAlignment(true);
346 public void sortAlignmentByFeatureScore(List<String> typ)
348 sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
352 public boolean parseFeaturesFile(String file, String protocol,
353 boolean relaxedIdMatching)
355 boolean featuresFile = false;
358 featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
359 .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
360 .getFeatureColours(), false, relaxedIdMatching);
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 || extendCurrent) ? viewport
397 .getAlignment() : viewport.getSelectionGroup();
399 // this could be a lambda... - the remains of the method is boilerplate,
400 // except for the different messages for reporting selection.
401 int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
403 ColumnSelection cs = viewport.getColumnSelection();
406 cs = new ColumnSelection();
409 if (bs.cardinality() > 0 || invert)
411 boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
412 sqcol.getEndRes(), invert, extendCurrent, toggle);
415 viewport.setColumnSelection(cs);
416 alignPanel.paintAlignment(true);
417 int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
420 avcg.setStatus(MessageManager.formatMessage(
421 "label.view_controller_toggled_marked",
423 toggle ? MessageManager.getString("label.toggled")
424 : MessageManager.getString("label.marked"),
425 String.valueOf(columnCount),
426 invert ? MessageManager
427 .getString("label.not_containing")
428 : MessageManager.getString("label.containing"),
429 "Highlight", Integer.valueOf(nseq).toString() }));
435 avcg.setStatus(MessageManager
436 .formatMessage("No highlighted regions marked"));
440 alignPanel.paintAlignment(true);