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.analysis.Grouping;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.AlignmentViewPanel;
29 import jalview.api.FeatureRenderer;
30 import jalview.commands.OrderCommand;
31 import jalview.datamodel.AlignmentI;
32 import jalview.datamodel.ColumnSelection;
33 import jalview.datamodel.SequenceCollectionI;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceGroup;
36 import jalview.datamodel.SequenceI;
37 import jalview.io.FeaturesFile;
38 import jalview.util.MessageManager;
40 import java.awt.Color;
41 import java.util.ArrayList;
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;
57 protected void finalize() throws Throwable
64 public AlignViewController(AlignViewControllerGuiI alignFrame,
65 AlignViewportI viewport, AlignmentViewPanel alignPanel)
67 this.avcg = alignFrame;
68 this.viewport = viewport;
69 this.alignPanel = alignPanel;
73 public void setViewportAndAlignmentPanel(AlignViewportI viewport,
74 AlignmentViewPanel alignPanel)
76 this.alignPanel = alignPanel;
77 this.viewport = viewport;
82 public boolean makeGroupsFromSelection()
84 SequenceGroup sg = viewport.getSelectionGroup();
85 ColumnSelection cs = viewport.getColumnSelection();
86 SequenceGroup[] gps = null;
88 && (cs == null || cs.getSelected() == null || cs.size() == 0))
90 gps = Grouping.makeGroupsFrom(
91 viewport.getSequenceSelection(),
92 viewport.getAlignmentView(true).getSequenceStrings(
93 viewport.getGapCharacter()), viewport.getAlignment()
97 gps = Grouping.makeGroupsFromCols(
98 (sg == null) ? viewport.getAlignment().getSequencesArray()
99 : sg.getSequences().toArray(new SequenceI[0]), cs,
100 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();
173 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
174 .getAlignment() : viewport.getSelectionGroup());
175 alStart = sqcol.getStartRes();
176 alw = sqcol.getEndRes() + 1;
177 List<SequenceI> seqs = sqcol.getSequences();
179 for (SequenceI sq : seqs)
184 SequenceFeature[] sf = sq.getSequenceFeatures();
187 int ist = sq.findIndex(sq.getStart());
188 int iend = sq.findIndex(sq.getEnd());
189 if (iend < alStart || ist > alw)
191 // sequence not in region
194 for (SequenceFeature sfpos : sf)
196 // future functionalty - featureType == null means mark columns
197 // containing all displayed features
198 if (sfpos != null && (featureType.equals(sfpos.getType())))
201 // optimisation - could consider 'spos,apos' like cursor argument
202 // - findIndex wastes time by starting from first character and
205 int i = sq.findIndex(sfpos.getBegin());
206 int j = sq.findIndex(sfpos.getEnd());
207 if (j < alStart || i > alw)
209 // feature is outside selected region
238 ColumnSelection cs = viewport.getColumnSelection();
239 if (bs.cardinality() > 0 || invert)
243 cs = new ColumnSelection();
254 // invert only in the currently selected sequence region
255 for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
258 if (ibs < 0 || i < ibs)
260 if (toggle && cs.contains(i))
262 cs.removeElement(i++);
271 i = bs.nextClearBit(ibs);
272 ibs = bs.nextSetBit(i);
278 for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
281 if (toggle && cs.contains(i))
291 viewport.setColumnSelection(cs);
292 alignPanel.paintAlignment(true);
293 avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
295 (toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
296 (invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
297 featureType, Integer.valueOf(nseq).toString()
303 avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
304 if (!extendCurrent && cs != null)
307 alignPanel.paintAlignment(true);
316 public void sortAlignmentByFeatureDensity(String[] typ)
318 sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
321 protected void sortBy(String[] typ, String methodText, final String method)
323 FeatureRenderer fr = alignPanel.getFeatureRenderer();
326 typ = fr==null ? null : fr.getDisplayedFeatureTypes();
329 gps = fr==null ? null : fr.getDisplayedFeatureGroups();
332 ArrayList types = new ArrayList();
333 for (int i = 0; i < typ.length; i++)
339 typ = new String[types.size()];
345 ArrayList grps = new ArrayList();
347 for (int i = 0; i < gps.length; i++)
354 gps = new String[grps.size()];
357 AlignmentI al = viewport.getAlignment();
360 SequenceGroup sg = viewport.getSelectionGroup();
363 start = sg.getStartRes();
364 stop = sg.getEndRes();
369 stop = al.getWidth();
371 SequenceI[] oldOrder = al.getSequencesArray();
372 AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
373 avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
375 alignPanel.paintAlignment(true);
380 public void sortAlignmentByFeatureScore(String[] typ)
382 sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
386 public boolean parseFeaturesFile(String file, String protocol,
387 boolean relaxedIdMatching)
389 boolean featuresFile = false;
392 featuresFile = new FeaturesFile(file, protocol).parse(viewport
393 .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
394 .getFeatureColours(), false, relaxedIdMatching);
395 } catch (Exception ex)
397 ex.printStackTrace();
402 avcg.refreshFeatureUI(true);
403 if (alignPanel.getFeatureRenderer() != null)
405 // update the min/max ranges where necessary
406 alignPanel.getFeatureRenderer().findAllFeatures(true);
408 if (avcg.getFeatureSettingsUI() != null)
410 avcg.getFeatureSettingsUI().discoverAllFeatureData();
412 alignPanel.paintAlignment(true);