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.ArrayList;
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(viewport
89 .getSequenceSelection(), viewport.getAlignmentView(true)
90 .getSequenceStrings(viewport.getGapCharacter()), viewport
91 .getAlignment().getGroups());
97 gps = jalview.analysis.Grouping.makeGroupsFromCols(
98 (sg == null) ? viewport.getAlignment().getSequencesArray()
99 : sg.getSequences().toArray(new SequenceI[0]), cs,
100 viewport.getAlignment().getGroups());
105 viewport.getAlignment().deleteAllGroups();
106 viewport.clearSequenceColours();
107 viewport.setSelectionGroup(null);
108 // set view properties for each group
109 for (int g = 0; g < gps.length; g++)
111 // gps[g].setShowunconserved(viewport.getShowUnconserved());
112 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
113 viewport.getAlignment().addGroup(gps[g]);
114 Color col = new Color((int) (Math.random() * 255),
115 (int) (Math.random() * 255), (int) (Math.random() * 255));
116 col = col.brighter();
117 for (SequenceI sq : gps[g].getSequences(null))
119 viewport.setSequenceColour(sq, col);
128 public boolean createGroup()
131 SequenceGroup sg = viewport.getSelectionGroup();
134 viewport.getAlignment().addGroup(sg);
141 public boolean unGroup()
143 SequenceGroup sg = viewport.getSelectionGroup();
146 viewport.getAlignment().deleteGroup(sg);
153 public boolean deleteGroups()
155 if (viewport.getAlignment().getGroups() != null
156 && viewport.getAlignment().getGroups().size() > 0)
158 viewport.getAlignment().deleteAllGroups();
159 viewport.clearSequenceColours();
160 viewport.setSelectionGroup(null);
167 public boolean markColumnsContainingFeatures(boolean invert,
168 boolean extendCurrent, boolean toggle, String featureType)
170 // JBPNote this routine could also mark rows, not just columns.
171 // need a decent query structure to allow all types of feature searches
172 BitSet bs = new BitSet();
174 SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
175 .getAlignment() : viewport.getSelectionGroup());
176 alStart = sqcol.getStartRes();
177 alw = sqcol.getEndRes() + 1;
178 List<SequenceI> seqs = sqcol.getSequences();
180 for (SequenceI sq : seqs)
185 SequenceFeature[] sf = sq.getSequenceFeatures();
188 int ist = sq.findIndex(sq.getStart());
189 int iend = sq.findIndex(sq.getEnd());
190 if (iend < alStart || ist > alw)
192 // sequence not in region
195 for (SequenceFeature sfpos : sf)
197 // future functionalty - featureType == null means mark columns
198 // containing all displayed features
199 if (sfpos != null && (featureType.equals(sfpos.getType())))
202 // optimisation - could consider 'spos,apos' like cursor argument
203 // - findIndex wastes time by starting from first character and
206 int i = sq.findIndex(sfpos.getBegin());
207 int j = sq.findIndex(sfpos.getEnd());
208 if (j < alStart || i > alw)
210 // feature is outside selected region
239 ColumnSelection cs = viewport.getColumnSelection();
240 if (bs.cardinality() > 0 || invert)
244 cs = new ColumnSelection();
255 // invert only in the currently selected sequence region
256 for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
259 if (ibs < 0 || i < ibs)
261 if (toggle && cs.contains(i))
263 cs.removeElement(i++);
272 i = bs.nextClearBit(ibs);
273 ibs = bs.nextSetBit(i);
279 for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
282 if (toggle && cs.contains(i))
292 viewport.setColumnSelection(cs);
293 alignPanel.paintAlignment(true);
294 avcg.setStatus(MessageManager.formatMessage(
295 "label.view_controller_toggled_marked",
297 (toggle ? MessageManager.getString("label.toggled")
298 : MessageManager.getString("label.marked")),
299 (invert ? (Integer.valueOf((alw - alStart)
300 - bs.cardinality()).toString()) : (Integer
301 .valueOf(bs.cardinality()).toString())),
302 featureType, Integer.valueOf(nseq).toString() }));
307 avcg.setStatus(MessageManager.formatMessage(
308 "label.no_feature_of_type_found",
309 new String[] { featureType }));
310 if (!extendCurrent && cs != null)
313 alignPanel.paintAlignment(true);
320 public void sortAlignmentByFeatureDensity(String[] typ)
322 sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
325 protected void sortBy(String[] typ, String methodText, final String method)
327 FeatureRenderer fr = alignPanel.getFeatureRenderer();
330 typ = fr == null ? null : fr.getDisplayedFeatureTypes();
333 gps = fr == null ? null : fr.getDisplayedFeatureGroups();
336 List<String> types = new ArrayList<String>();
337 for (String displayed : typ)
339 if (displayed != null)
341 types.add(displayed);
344 typ = new String[types.size()];
349 List<String> grps = new ArrayList<String>();
351 for (int i = 0; i < gps.length; i++)
358 gps = new String[grps.size()];
361 AlignmentI al = viewport.getAlignment();
364 SequenceGroup sg = viewport.getSelectionGroup();
367 start = sg.getStartRes();
368 stop = sg.getEndRes();
373 stop = al.getWidth();
375 SequenceI[] oldOrder = al.getSequencesArray();
376 AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
377 avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
379 alignPanel.paintAlignment(true);
384 public void sortAlignmentByFeatureScore(String[] typ)
386 sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
390 public boolean parseFeaturesFile(String file, String protocol,
391 boolean relaxedIdMatching)
393 boolean featuresFile = false;
396 featuresFile = new FeaturesFile(file, protocol).parse(viewport
397 .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
398 .getFeatureColours(), false, relaxedIdMatching);
399 } catch (Exception ex)
401 ex.printStackTrace();
406 avcg.refreshFeatureUI(true);
407 if (alignPanel.getFeatureRenderer() != null)
409 // update the min/max ranges where necessary
410 alignPanel.getFeatureRenderer().findAllFeatures(true);
412 if (avcg.getFeatureSettingsUI() != null)
414 avcg.getFeatureSettingsUI().discoverAllFeatureData();
416 alignPanel.paintAlignment(true);