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.appletgui;
23 import jalview.analysis.NJTree;
24 import jalview.api.AlignViewportI;
25 import jalview.bin.JalviewLite;
26 import jalview.commands.CommandI;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.SearchResults;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceGroup;
32 import jalview.datamodel.SequenceI;
33 import jalview.schemes.ColourSchemeProperty;
34 import jalview.schemes.UserColourScheme;
35 import jalview.structure.CommandListener;
36 import jalview.structure.SelectionSource;
37 import jalview.structure.StructureSelectionManager;
38 import jalview.structure.VamsasSource;
39 import jalview.viewmodel.AlignmentViewport;
43 public class AlignViewport extends AlignmentViewport implements
44 SelectionSource, VamsasSource, CommandListener
46 boolean cursorMode = false;
48 Font font = new Font("SansSerif", Font.PLAIN, 10);
50 boolean validCharWidth = true;
52 NJTree currentTree = null;
54 public jalview.bin.JalviewLite applet;
58 private AnnotationColumnChooser annotationColumnSelectionState;
60 public void finalize()
68 public AlignViewport(AlignmentI al, JalviewLite applet)
71 calculator = new jalview.workers.AlignCalcManager();
75 this.setPadGaps(true);
77 this.endRes = al.getWidth() - 1;
79 this.endSeq = al.getHeight() - 1;
82 // get the width and height scaling factors if they were specified
83 String param = applet.getParameter("widthScale");
88 widthScale = new Float(param).floatValue();
92 if (widthScale <= 1.0)
95 .println("Invalid alignment character width scaling factor ("
96 + widthScale + "). Ignoring.");
99 if (JalviewLite.debug)
102 .println("Alignment character width scaling factor is now "
106 param = applet.getParameter("heightScale");
111 heightScale = new Float(param).floatValue();
112 } catch (Exception e)
115 if (heightScale <= 1.0)
118 .println("Invalid alignment character height scaling factor ("
119 + heightScale + "). Ignoring.");
122 if (JalviewLite.debug)
125 .println("Alignment character height scaling factor is now "
132 MAC = new jalview.util.Platform().isAMac();
136 setShowJVSuffix(applet.getDefaultParameter("showFullId",
139 setShowAnnotation(applet.getDefaultParameter("showAnnotation",
140 isShowAnnotation()));
142 showConservation = applet.getDefaultParameter("showConservation",
145 showQuality = applet.getDefaultParameter("showQuality", showQuality);
147 showConsensus = applet.getDefaultParameter("showConsensus",
150 setShowUnconserved(applet.getDefaultParameter("showUnconserved",
151 getShowUnconserved()));
153 setScaleProteinAsCdna(applet.getDefaultParameter(
154 "scaleProteinAsCdna", isScaleProteinAsCdna()));
156 String param = applet.getParameter("upperCase");
159 if (param.equalsIgnoreCase("bold"))
161 setUpperCasebold(true);
164 sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
166 setFollowHighlight(applet.getDefaultParameter("automaticScrolling",
167 isFollowHighlight()));
168 followSelection = isFollowHighlight();
170 showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
173 normaliseSequenceLogo = applet.getDefaultParameter(
174 "normaliseSequenceLogo", applet.getDefaultParameter(
175 "normaliseLogo", normaliseSequenceLogo));
177 showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
180 showGroupConservation = applet.getDefaultParameter(
181 "showGroupConservation", showGroupConservation);
183 showConsensusHistogram = applet.getDefaultParameter(
184 "showConsensusHistogram", showConsensusHistogram);
190 String colour = al.isNucleotide() ? applet
191 .getParameter("defaultColourNuc") : applet
192 .getParameter("defaultColourProt");
195 colour = applet.getParameter("defaultColour");
199 colour = applet.getParameter("userDefinedColour");
202 colour = "User Defined";
208 globalColourScheme = ColourSchemeProperty.getColour(alignment,
210 if (globalColourScheme != null)
212 globalColourScheme.setConsensus(hconsensus);
216 if (applet.getParameter("userDefinedColour") != null)
218 ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
219 .getParameter("userDefinedColour"));
222 initAutoAnnotation();
227 * get the consensus sequence as displayed under the PID consensus annotation
230 * @return consensus sequence as a new sequence object
232 public SequenceI getConsensusSeq()
234 if (consensus == null)
236 updateConsensus(null);
238 if (consensus == null)
242 StringBuilder seqs = new StringBuilder(consensus.annotations.length);
243 for (int i = 0; i < consensus.annotations.length; i++)
245 if (consensus.annotations[i] != null)
247 if (consensus.annotations[i].description.charAt(0) == '[')
249 seqs.append(consensus.annotations[i].description.charAt(1));
253 seqs.append(consensus.annotations[i].displayCharacter);
257 SequenceI sq = new Sequence("Consensus", seqs.toString());
258 sq.setDescription("Percentage Identity Consensus "
259 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
263 java.awt.Frame nullFrame;
265 protected FeatureSettings featureSettings = null;
267 private float heightScale = 1, widthScale = 1;
269 public void setFont(Font f)
272 if (nullFrame == null)
274 nullFrame = new java.awt.Frame();
275 nullFrame.addNotify();
278 java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
279 setCharHeight((int) (heightScale * fm.getHeight()));
280 setCharWidth((int) (widthScale * fm.charWidth('M')));
282 if (isUpperCasebold())
284 Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
285 fm = nullFrame.getGraphics().getFontMetrics(f2);
286 setCharWidth((int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10)));
290 public Font getFont()
295 public void resetSeqLimits(int height)
297 setEndSeq(height / getCharHeight());
300 public void setCurrentTree(NJTree tree)
305 public NJTree getCurrentTree()
310 boolean centreColumnLabels;
312 public boolean getCentreColumnLabels()
314 return centreColumnLabels;
317 public boolean followSelection = true;
320 * @return true if view selection should always follow the selections
321 * broadcast by other selection sources
323 public boolean getFollowSelection()
325 return followSelection;
328 public void sendSelection()
330 getStructureSelectionManager().sendSelection(
331 new SequenceGroup(getSelectionGroup()),
332 new ColumnSelection(getColumnSelection()), this);
336 * Returns an instance of the StructureSelectionManager scoped to this applet
342 public StructureSelectionManager getStructureSelectionManager()
344 return jalview.structure.StructureSelectionManager
345 .getStructureSelectionManager(applet);
349 * synthesize a column selection if none exists so it covers the given
350 * selection group. if wholewidth is false, no column selection is made if the
351 * selection group covers the whole alignment width.
356 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
360 && (sgs = sg.getStartRes()) >= 0
361 && sg.getStartRes() <= (sge = sg.getEndRes())
362 && (colSel == null || colSel.getSelected() == null || colSel
363 .getSelected().size() == 0))
365 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
372 colSel = new ColumnSelection();
374 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
376 colSel.addElement(cspos);
381 public boolean isNormaliseSequenceLogo()
383 return normaliseSequenceLogo;
386 public void setNormaliseSequenceLogo(boolean state)
388 normaliseSequenceLogo = state;
393 * @return true if alignment characters should be displayed
395 public boolean isValidCharWidth()
397 return validCharWidth;
400 public AnnotationColumnChooser getAnnotationColumnSelectionState()
402 return annotationColumnSelectionState;
405 public void setAnnotationColumnSelectionState(
406 AnnotationColumnChooser annotationColumnSelectionState)
408 this.annotationColumnSelectionState = annotationColumnSelectionState;
412 public void mirrorCommand(CommandI command, boolean undo,
413 StructureSelectionManager ssm, VamsasSource source)
415 // TODO refactor so this can be pulled up to superclass or controller
417 * Do nothing unless we are a 'complement' of the source. May replace this
418 * with direct calls not via SSM.
420 if (source instanceof AlignViewportI
421 && ((AlignViewportI) source).getCodingComplement() == this)
430 CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
432 if (mappedCommand != null)
434 mappedCommand.doCommand(null);
435 firePropertyChange("alignment", null, getAlignment().getSequences());
437 // ap.scalePanelHolder.repaint();
443 public VamsasSource getVamsasSource()
449 * If this viewport has a (Protein/cDNA) complement, then scroll the
450 * complementary alignment to match this one.
452 public void scrollComplementaryAlignment(AlignmentPanel complementPanel)
454 if (complementPanel == null)
460 * Populate a SearchResults object with the mapped location to scroll to. If
461 * there is no complement, or it is not following highlights, or no mapping
462 * is found, the result will be empty.
464 SearchResults sr = new SearchResults();
465 int seqOffset = findComplementScrollTarget(sr);
468 complementPanel.setFollowingComplementScroll(true);
469 complementPanel.scrollToCentre(sr, seqOffset);