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.viewmodel;
23 import java.awt.Color;
24 import java.util.ArrayDeque;
25 import java.util.ArrayList;
26 import java.util.BitSet;
27 import java.util.Deque;
28 import java.util.HashMap;
29 import java.util.Hashtable;
30 import java.util.List;
34 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
35 import jalview.analysis.Conservation;
36 import jalview.api.AlignCalcManagerI;
37 import jalview.api.AlignViewportI;
38 import jalview.api.AlignmentViewPanel;
39 import jalview.api.FeaturesDisplayedI;
40 import jalview.api.ViewStyleI;
41 import jalview.commands.CommandI;
42 import jalview.datamodel.AlignedCodonFrame;
43 import jalview.datamodel.AlignmentAnnotation;
44 import jalview.datamodel.AlignmentI;
45 import jalview.datamodel.AlignmentView;
46 import jalview.datamodel.Annotation;
47 import jalview.datamodel.CigarArray;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.Sequence;
50 import jalview.datamodel.SequenceCollectionI;
51 import jalview.datamodel.SequenceGroup;
52 import jalview.datamodel.SequenceI;
53 import jalview.schemes.Blosum62ColourScheme;
54 import jalview.schemes.ColourSchemeI;
55 import jalview.schemes.PIDColourScheme;
56 import jalview.schemes.ResidueProperties;
57 import jalview.structure.CommandListener;
58 import jalview.structure.StructureSelectionManager;
59 import jalview.structure.VamsasSource;
60 import jalview.viewmodel.styles.ViewStyle;
61 import jalview.workers.AlignCalcManager;
62 import jalview.workers.ComplementConsensusThread;
63 import jalview.workers.ConsensusThread;
64 import jalview.workers.StrucConsensusThread;
67 * base class holding visualization and analysis attributes and common logic for
68 * an active alignment view displayed in the GUI
73 public abstract class AlignmentViewport implements AlignViewportI,
74 ViewStyleI, CommandListener, VamsasSource
76 protected ViewStyleI viewStyle = new ViewStyle();
79 * A viewport that hosts the cDna view of this (protein), or vice versa (if
82 AlignViewportI codingComplement = null;
84 FeaturesDisplayedI featuresDisplayed = null;
86 protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
88 protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
92 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
94 public void setFontName(String name)
96 viewStyle.setFontName(name);
101 * @see jalview.api.ViewStyleI#setFontStyle(int)
103 public void setFontStyle(int style)
105 viewStyle.setFontStyle(style);
110 * @see jalview.api.ViewStyleI#setFontSize(int)
112 public void setFontSize(int size)
114 viewStyle.setFontSize(size);
119 * @see jalview.api.ViewStyleI#getFontStyle()
121 public int getFontStyle()
123 return viewStyle.getFontStyle();
128 * @see jalview.api.ViewStyleI#getFontName()
130 public String getFontName()
132 return viewStyle.getFontName();
137 * @see jalview.api.ViewStyleI#getFontSize()
139 public int getFontSize()
141 return viewStyle.getFontSize();
145 * @param upperCasebold
146 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
148 public void setUpperCasebold(boolean upperCasebold)
150 viewStyle.setUpperCasebold(upperCasebold);
155 * @see jalview.api.ViewStyleI#isUpperCasebold()
157 public boolean isUpperCasebold()
159 return viewStyle.isUpperCasebold();
164 * @see jalview.api.ViewStyleI#isSeqNameItalics()
166 public boolean isSeqNameItalics()
168 return viewStyle.isSeqNameItalics();
172 * @param colourByReferenceSeq
173 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
175 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
177 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
182 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
184 public void setColourAppliesToAllGroups(boolean b)
186 viewStyle.setColourAppliesToAllGroups(b);
191 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
193 public boolean getColourAppliesToAllGroups()
195 return viewStyle.getColourAppliesToAllGroups();
200 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
202 public boolean getAbovePIDThreshold()
204 return viewStyle.getAbovePIDThreshold();
209 * @see jalview.api.ViewStyleI#setIncrement(int)
211 public void setIncrement(int inc)
213 viewStyle.setIncrement(inc);
218 * @see jalview.api.ViewStyleI#getIncrement()
220 public int getIncrement()
222 return viewStyle.getIncrement();
227 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
229 public void setConservationSelected(boolean b)
231 viewStyle.setConservationSelected(b);
236 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
238 public void setShowHiddenMarkers(boolean show)
240 viewStyle.setShowHiddenMarkers(show);
245 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
247 public boolean getShowHiddenMarkers()
249 return viewStyle.getShowHiddenMarkers();
254 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
256 public void setScaleRightWrapped(boolean b)
258 viewStyle.setScaleRightWrapped(b);
263 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
265 public void setScaleLeftWrapped(boolean b)
267 viewStyle.setScaleLeftWrapped(b);
272 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
274 public void setScaleAboveWrapped(boolean b)
276 viewStyle.setScaleAboveWrapped(b);
281 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
283 public boolean getScaleLeftWrapped()
285 return viewStyle.getScaleLeftWrapped();
290 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
292 public boolean getScaleAboveWrapped()
294 return viewStyle.getScaleAboveWrapped();
299 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
301 public boolean getScaleRightWrapped()
303 return viewStyle.getScaleRightWrapped();
308 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
310 public void setAbovePIDThreshold(boolean b)
312 viewStyle.setAbovePIDThreshold(b);
317 * @see jalview.api.ViewStyleI#setThreshold(int)
319 public void setThreshold(int thresh)
321 viewStyle.setThreshold(thresh);
326 * @see jalview.api.ViewStyleI#getThreshold()
328 public int getThreshold()
330 return viewStyle.getThreshold();
335 * @see jalview.api.ViewStyleI#getShowJVSuffix()
337 public boolean getShowJVSuffix()
339 return viewStyle.getShowJVSuffix();
344 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
346 public void setShowJVSuffix(boolean b)
348 viewStyle.setShowJVSuffix(b);
353 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
355 public void setWrapAlignment(boolean state)
357 viewStyle.setWrapAlignment(state);
362 * @see jalview.api.ViewStyleI#setShowText(boolean)
364 public void setShowText(boolean state)
366 viewStyle.setShowText(state);
371 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
373 public void setRenderGaps(boolean state)
375 viewStyle.setRenderGaps(state);
380 * @see jalview.api.ViewStyleI#getColourText()
382 public boolean getColourText()
384 return viewStyle.getColourText();
389 * @see jalview.api.ViewStyleI#setColourText(boolean)
391 public void setColourText(boolean state)
393 viewStyle.setColourText(state);
398 * @see jalview.api.ViewStyleI#getWrapAlignment()
400 public boolean getWrapAlignment()
402 return viewStyle.getWrapAlignment();
407 * @see jalview.api.ViewStyleI#getShowText()
409 public boolean getShowText()
411 return viewStyle.getShowText();
416 * @see jalview.api.ViewStyleI#getWrappedWidth()
418 public int getWrappedWidth()
420 return viewStyle.getWrappedWidth();
425 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
427 public void setWrappedWidth(int w)
429 viewStyle.setWrappedWidth(w);
434 * @see jalview.api.ViewStyleI#getCharHeight()
436 public int getCharHeight()
438 return viewStyle.getCharHeight();
443 * @see jalview.api.ViewStyleI#setCharHeight(int)
445 public void setCharHeight(int h)
447 viewStyle.setCharHeight(h);
452 * @see jalview.api.ViewStyleI#getCharWidth()
454 public int getCharWidth()
456 return viewStyle.getCharWidth();
461 * @see jalview.api.ViewStyleI#setCharWidth(int)
463 public void setCharWidth(int w)
465 viewStyle.setCharWidth(w);
470 * @see jalview.api.ViewStyleI#getShowBoxes()
472 public boolean getShowBoxes()
474 return viewStyle.getShowBoxes();
479 * @see jalview.api.ViewStyleI#getShowUnconserved()
481 public boolean getShowUnconserved()
483 return viewStyle.getShowUnconserved();
487 * @param showunconserved
488 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
490 public void setShowUnconserved(boolean showunconserved)
492 viewStyle.setShowUnconserved(showunconserved);
497 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
499 public void setSeqNameItalics(boolean default1)
501 viewStyle.setSeqNameItalics(default1);
506 * @see jalview.api.ViewStyleI#setShowSeqFeaturesHeight(boolean)
508 public void setShowSeqFeaturesHeight(boolean selected)
510 viewStyle.setShowSeqFeaturesHeight(selected);
514 * alignment displayed in the viewport. Please use get/setter
516 protected AlignmentI alignment;
519 public AlignmentI getAlignment()
525 public char getGapCharacter()
527 return alignment.getGapCharacter();
530 protected String sequenceSetID;
533 * probably unused indicator that view is of a dataset rather than an
536 protected boolean isDataset = false;
538 public void setDataset(boolean b)
543 public boolean isDataset()
549 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
551 protected ColumnSelection colSel = new ColumnSelection();
553 public boolean autoCalculateConsensus = true;
555 protected boolean autoCalculateStrucConsensus = true;
557 protected boolean ignoreGapsInConsensusCalculation = false;
559 protected ColourSchemeI globalColourScheme = null;
563 public void setGlobalColourScheme(ColourSchemeI cs)
565 // TODO: logic refactored from AlignFrame changeColour -
566 // autorecalc stuff should be changed to rely on the worker system
567 // check to see if we should implement a changeColour(cs) method rather than
568 // put th logic in here
569 // - means that caller decides if they want to just modify state and defer
570 // calculation till later or to do all calculations in thread.
572 globalColourScheme = cs;
573 boolean recalc = false;
576 cs.setConservationApplied(recalc = getConservationSelected());
577 if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
578 || cs instanceof Blosum62ColourScheme)
581 cs.setThreshold(viewStyle.getThreshold(),
582 ignoreGapsInConsensusCalculation);
586 cs.setThreshold(0, ignoreGapsInConsensusCalculation);
590 cs.setConsensus(hconsensus);
591 cs.setConservation(hconservation);
593 cs.alignmentChanged(alignment, hiddenRepSequences);
595 if (getColourAppliesToAllGroups())
597 for (SequenceGroup sg : getAlignment().getGroups())
604 sg.cs = cs.applyTo(sg, getHiddenRepSequences());
605 sg.setConsPercGaps(ConsPercGaps);
606 if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
607 || cs instanceof Blosum62ColourScheme)
609 sg.cs.setThreshold(viewStyle.getThreshold(),
610 isIgnoreGapsConsensus());
615 sg.cs.setThreshold(0, isIgnoreGapsConsensus());
618 if (getConservationSelected())
620 sg.cs.setConservationApplied(true);
625 sg.cs.setConservation(null);
626 // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
630 sg.recalcConservation();
634 sg.cs.alignmentChanged(sg, hiddenRepSequences);
642 public ColourSchemeI getGlobalColourScheme()
644 return globalColourScheme;
647 protected AlignmentAnnotation consensus;
649 protected AlignmentAnnotation complementConsensus;
651 protected AlignmentAnnotation strucConsensus;
653 protected AlignmentAnnotation conservation;
655 protected AlignmentAnnotation quality;
657 protected AlignmentAnnotation[] groupConsensus;
659 protected AlignmentAnnotation[] groupConservation;
662 * results of alignment consensus analysis for visible portion of view
664 protected Hashtable[] hconsensus = null;
667 * results of cDNA complement consensus visible portion of view
669 protected Hashtable[] hcomplementConsensus = null;
672 * results of secondary structure base pair consensus for visible portion of
675 protected Hashtable[] hStrucConsensus = null;
677 protected Conservation hconservation = null;
680 public void setConservation(Conservation cons)
682 hconservation = cons;
686 * percentage gaps allowed in a column before all amino acid properties should
687 * be considered unconserved
689 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
692 public int getConsPercGaps()
698 public void setSequenceConsensusHash(Hashtable[] hconsensus)
700 this.hconsensus = hconsensus;
704 public void setComplementConsensusHash(Hashtable[] hconsensus)
706 this.hcomplementConsensus = hconsensus;
710 public Hashtable[] getSequenceConsensusHash()
716 public Hashtable[] getComplementConsensusHash()
718 return hcomplementConsensus;
722 public Hashtable[] getRnaStructureConsensusHash()
724 return hStrucConsensus;
728 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
730 this.hStrucConsensus = hStrucConsensus;
735 public AlignmentAnnotation getAlignmentQualityAnnot()
741 public AlignmentAnnotation getAlignmentConservationAnnotation()
747 public AlignmentAnnotation getAlignmentConsensusAnnotation()
753 public AlignmentAnnotation getComplementConsensusAnnotation()
755 return complementConsensus;
759 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
761 return strucConsensus;
764 protected AlignCalcManagerI calculator = new AlignCalcManager();
767 * trigger update of conservation annotation
769 public void updateConservation(final AlignmentViewPanel ap)
771 // see note in mantis : issue number 8585
772 if (alignment.isNucleotide() || conservation == null
773 || !autoCalculateConsensus)
778 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
780 calculator.registerWorker(new jalview.workers.ConservationThread(
786 * trigger update of consensus annotation
788 public void updateConsensus(final AlignmentViewPanel ap)
790 // see note in mantis : issue number 8585
791 if (consensus == null || !autoCalculateConsensus)
795 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
797 calculator.registerWorker(new ConsensusThread(this, ap));
801 * A separate thread to compute cDNA consensus for a protein alignment
803 final AlignmentI al = this.getAlignment();
804 if (!al.isNucleotide() && al.getCodonFrames() != null
805 && !al.getCodonFrames().isEmpty())
808 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
810 calculator.registerWorker(new ComplementConsensusThread(this, ap));
815 // --------START Structure Conservation
816 public void updateStrucConsensus(final AlignmentViewPanel ap)
818 if (autoCalculateStrucConsensus && strucConsensus == null
819 && alignment.isNucleotide() && alignment.hasRNAStructure())
821 // secondary structure has been added - so init the consensus line
825 // see note in mantis : issue number 8585
826 if (strucConsensus == null || !autoCalculateStrucConsensus)
830 if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
832 calculator.registerWorker(new StrucConsensusThread(this, ap));
836 public boolean isCalcInProgress()
838 return calculator.isWorking();
842 public boolean isCalculationInProgress(
843 AlignmentAnnotation alignmentAnnotation)
845 if (!alignmentAnnotation.autoCalculated)
849 if (calculator.workingInvolvedWith(alignmentAnnotation))
851 // System.err.println("grey out ("+alignmentAnnotation.label+")");
858 public boolean isClosed()
860 // TODO: check that this isClosed is only true after panel is closed, not
861 // before it is fully constructed.
862 return alignment == null;
866 public AlignCalcManagerI getCalcManager()
872 * should conservation rows be shown for groups
874 protected boolean showGroupConservation = false;
877 * should consensus rows be shown for groups
879 protected boolean showGroupConsensus = false;
882 * should consensus profile be rendered by default
884 protected boolean showSequenceLogo = false;
887 * should consensus profile be rendered normalised to row height
889 protected boolean normaliseSequenceLogo = false;
892 * should consensus histograms be rendered by default
894 protected boolean showConsensusHistogram = true;
897 * @return the showConsensusProfile
900 public boolean isShowSequenceLogo()
902 return showSequenceLogo;
906 * @param showSequenceLogo
909 public void setShowSequenceLogo(boolean showSequenceLogo)
911 if (showSequenceLogo != this.showSequenceLogo)
913 // TODO: decouple settings setting from calculation when refactoring
914 // annotation update method from alignframe to viewport
915 this.showSequenceLogo = showSequenceLogo;
916 calculator.updateAnnotationFor(ConsensusThread.class);
917 calculator.updateAnnotationFor(ComplementConsensusThread.class);
918 calculator.updateAnnotationFor(StrucConsensusThread.class);
920 this.showSequenceLogo = showSequenceLogo;
924 * @param showConsensusHistogram
925 * the showConsensusHistogram to set
927 public void setShowConsensusHistogram(boolean showConsensusHistogram)
929 this.showConsensusHistogram = showConsensusHistogram;
933 * @return the showGroupConservation
935 public boolean isShowGroupConservation()
937 return showGroupConservation;
941 * @param showGroupConservation
942 * the showGroupConservation to set
944 public void setShowGroupConservation(boolean showGroupConservation)
946 this.showGroupConservation = showGroupConservation;
950 * @return the showGroupConsensus
952 public boolean isShowGroupConsensus()
954 return showGroupConsensus;
958 * @param showGroupConsensus
959 * the showGroupConsensus to set
961 public void setShowGroupConsensus(boolean showGroupConsensus)
963 this.showGroupConsensus = showGroupConsensus;
968 * @return flag to indicate if the consensus histogram should be rendered by
972 public boolean isShowConsensusHistogram()
974 return this.showConsensusHistogram;
978 * when set, updateAlignment will always ensure sequences are of equal length
980 private boolean padGaps = false;
983 * when set, alignment should be reordered according to a newly opened tree
985 public boolean sortByTree = false;
991 * @return null or the currently selected sequence region
994 public SequenceGroup getSelectionGroup()
996 return selectionGroup;
1000 * Set the selection group for this window.
1003 * - group holding references to sequences in this alignment view
1007 public void setSelectionGroup(SequenceGroup sg)
1009 selectionGroup = sg;
1012 public void setHiddenColumns(ColumnSelection colsel)
1014 this.colSel = colsel;
1018 public ColumnSelection getColumnSelection()
1024 public void setColumnSelection(ColumnSelection colSel)
1026 this.colSel = colSel;
1029 updateHiddenColumns();
1038 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1040 return hiddenRepSequences;
1044 public void setHiddenRepSequences(
1045 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1047 this.hiddenRepSequences = hiddenRepSequences;
1051 public boolean hasHiddenColumns()
1053 return colSel != null && colSel.hasHiddenColumns();
1056 public void updateHiddenColumns()
1058 // this method doesn't really do anything now. But - it could, since a
1059 // column Selection could be in the process of modification
1060 // hasHiddenColumns = colSel.hasHiddenColumns();
1063 protected boolean hasHiddenRows = false;
1066 public boolean hasHiddenRows()
1068 return hasHiddenRows;
1071 protected SequenceGroup selectionGroup;
1073 public void setSequenceSetId(String newid)
1075 if (sequenceSetID != null)
1078 .println("Warning - overwriting a sequenceSetId for a viewport!");
1080 sequenceSetID = new String(newid);
1084 public String getSequenceSetId()
1086 if (sequenceSetID == null)
1088 sequenceSetID = alignment.hashCode() + "";
1091 return sequenceSetID;
1095 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1098 protected String viewId = null;
1101 public String getViewId()
1105 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1110 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1112 ignoreGapsInConsensusCalculation = b;
1115 updateConsensus(ap);
1116 if (globalColourScheme != null)
1118 globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
1119 ignoreGapsInConsensusCalculation);
1125 private long sgrouphash = -1, colselhash = -1;
1128 * checks current SelectionGroup against record of last hash value, and
1132 * update the record of last hash value
1134 * @return true if SelectionGroup changed since last call (when b is true)
1136 public boolean isSelectionGroupChanged(boolean b)
1138 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1139 : selectionGroup.hashCode();
1140 if (hc != -1 && hc != sgrouphash)
1152 * checks current colsel against record of last hash value, and optionally
1156 * update the record of last hash value
1157 * @return true if colsel changed since last call (when b is true)
1159 public boolean isColSelChanged(boolean b)
1161 int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
1163 if (hc != -1 && hc != colselhash)
1175 public boolean isIgnoreGapsConsensus()
1177 return ignoreGapsInConsensusCalculation;
1180 // / property change stuff
1182 // JBPNote Prolly only need this in the applet version.
1183 private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
1186 protected boolean showConservation = true;
1188 protected boolean showQuality = true;
1190 protected boolean showConsensus = true;
1192 private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
1194 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1196 protected boolean showAutocalculatedAbove;
1199 * Property change listener for changes in alignment
1204 public void addPropertyChangeListener(
1205 java.beans.PropertyChangeListener listener)
1207 changeSupport.addPropertyChangeListener(listener);
1216 public void removePropertyChangeListener(
1217 java.beans.PropertyChangeListener listener)
1219 changeSupport.removePropertyChangeListener(listener);
1223 * Property change listener for changes in alignment
1232 public void firePropertyChange(String prop, Object oldvalue,
1235 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1238 // common hide/show column stuff
1240 public void hideSelectedColumns()
1242 if (colSel.size() < 1)
1247 colSel.hideSelectedColumns();
1248 setSelectionGroup(null);
1252 public void hideColumns(int start, int end)
1256 colSel.hideColumns(start);
1260 colSel.hideColumns(start, end);
1264 public void showColumn(int col)
1266 colSel.revealHiddenColumns(col);
1270 public void showAllHiddenColumns()
1272 colSel.revealAllHiddenColumns();
1275 // common hide/show seq stuff
1276 public void showAllHiddenSeqs()
1278 if (alignment.getHiddenSequences().getSize() > 0)
1280 if (selectionGroup == null)
1282 selectionGroup = new SequenceGroup();
1283 selectionGroup.setEndRes(alignment.getWidth() - 1);
1285 List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
1286 hiddenRepSequences);
1287 for (SequenceI seq : tmp)
1289 selectionGroup.addSequence(seq, false);
1290 setSequenceAnnotationsVisible(seq, true);
1293 hasHiddenRows = false;
1294 hiddenRepSequences = null;
1296 firePropertyChange("alignment", null, alignment.getSequences());
1297 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1303 public void showSequence(int index)
1305 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1307 hiddenRepSequences);
1310 if (selectionGroup == null)
1312 selectionGroup = new SequenceGroup();
1313 selectionGroup.setEndRes(alignment.getWidth() - 1);
1316 for (SequenceI seq : tmp)
1318 selectionGroup.addSequence(seq, false);
1319 setSequenceAnnotationsVisible(seq, true);
1321 // JBPNote: refactor: only update flag if we modified visiblity (used to
1322 // do this regardless)
1323 if (alignment.getHiddenSequences().getSize() < 1)
1325 hasHiddenRows = false;
1327 firePropertyChange("alignment", null, alignment.getSequences());
1332 public void hideAllSelectedSeqs()
1334 if (selectionGroup == null || selectionGroup.getSize() < 1)
1339 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1343 setSelectionGroup(null);
1346 public void hideSequence(SequenceI[] seq)
1350 for (int i = 0; i < seq.length; i++)
1352 alignment.getHiddenSequences().hideSequence(seq[i]);
1353 setSequenceAnnotationsVisible(seq[i], false);
1355 hasHiddenRows = true;
1356 firePropertyChange("alignment", null, alignment.getSequences());
1361 * Set visibility for any annotations for the given sequence.
1365 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1368 for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
1370 if (ann.sequenceRef == sequenceI)
1372 ann.visible = visible;
1377 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1379 int sSize = sg.getSize();
1385 if (hiddenRepSequences == null)
1387 hiddenRepSequences = new Hashtable();
1390 hiddenRepSequences.put(repSequence, sg);
1392 // Hide all sequences except the repSequence
1393 SequenceI[] seqs = new SequenceI[sSize - 1];
1395 for (int i = 0; i < sSize; i++)
1397 if (sg.getSequenceAt(i) != repSequence)
1399 if (index == sSize - 1)
1404 seqs[index++] = sg.getSequenceAt(i);
1407 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1408 sg.setHidereps(true); // note: not done in 2.7applet
1413 public boolean isHiddenRepSequence(SequenceI seq)
1415 return alignment.getSeqrep()==seq || (hiddenRepSequences != null
1416 && hiddenRepSequences.containsKey(seq));
1419 public SequenceGroup getRepresentedSequences(SequenceI seq)
1421 return (SequenceGroup) (hiddenRepSequences == null ? null
1422 : hiddenRepSequences.get(seq));
1426 public int adjustForHiddenSeqs(int alignmentIndex)
1428 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1433 public void invertColumnSelection()
1435 colSel.invertColumnSelection(0, alignment.getWidth());
1440 public SequenceI[] getSelectionAsNewSequence()
1442 SequenceI[] sequences;
1443 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1444 // this was the only caller in the applet for this method
1445 // JBPNote: in applet, this method returned references to the alignment
1446 // sequences, and it did not honour the presence/absence of annotation
1447 // attached to the alignment (probably!)
1448 if (selectionGroup == null || selectionGroup.getSize() == 0)
1450 sequences = alignment.getSequencesArray();
1451 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1452 for (int i = 0; i < sequences.length; i++)
1454 // construct new sequence with subset of visible annotation
1455 sequences[i] = new Sequence(sequences[i], annots);
1460 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1468 public SequenceI[] getSequenceSelection()
1470 SequenceI[] sequences = null;
1471 if (selectionGroup != null)
1473 sequences = selectionGroup.getSequencesInOrder(alignment);
1475 if (sequences == null)
1477 sequences = alignment.getSequencesArray();
1484 public CigarArray getViewAsCigars(
1485 boolean selectedRegionOnly)
1487 return new CigarArray(alignment, colSel,
1488 (selectedRegionOnly ? selectionGroup : null));
1493 public jalview.datamodel.AlignmentView getAlignmentView(
1494 boolean selectedOnly)
1496 return getAlignmentView(selectedOnly, false);
1501 public jalview.datamodel.AlignmentView getAlignmentView(
1502 boolean selectedOnly, boolean markGroups)
1504 return new AlignmentView(alignment, colSel, selectionGroup,
1505 colSel != null && colSel.hasHiddenColumns(), selectedOnly,
1511 public String[] getViewAsString(boolean selectedRegionOnly)
1513 String[] selection = null;
1514 SequenceI[] seqs = null;
1516 int start = 0, end = 0;
1517 if (selectedRegionOnly && selectionGroup != null)
1519 iSize = selectionGroup.getSize();
1520 seqs = selectionGroup.getSequencesInOrder(alignment);
1521 start = selectionGroup.getStartRes();
1522 end = selectionGroup.getEndRes() + 1;
1526 iSize = alignment.getHeight();
1527 seqs = alignment.getSequencesArray();
1528 end = alignment.getWidth();
1531 selection = new String[iSize];
1532 if (colSel != null && colSel.hasHiddenColumns())
1534 selection = colSel.getVisibleSequenceStrings(start, end, seqs);
1538 for (i = 0; i < iSize; i++)
1540 selection[i] = seqs[i].getSequenceAsString(start, end);
1549 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1551 ArrayList<int[]> regions = new ArrayList<int[]>();
1557 if (colSel != null && colSel.hasHiddenColumns())
1561 start = colSel.adjustForHiddenColumns(start);
1564 end = colSel.getHiddenBoundaryRight(start);
1575 regions.add(new int[]
1578 if (colSel != null && colSel.hasHiddenColumns())
1580 start = colSel.adjustForHiddenColumns(end);
1581 start = colSel.getHiddenBoundaryLeft(start) + 1;
1583 } while (end < max);
1585 int[][] startEnd = new int[regions.size()][2];
1591 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
1593 ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
1594 AlignmentAnnotation[] aa;
1595 if ((aa=alignment.getAlignmentAnnotation())!=null)
1597 for (AlignmentAnnotation annot:aa)
1599 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1600 if (selectedOnly && selectionGroup!=null)
1602 colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
1604 colSel.makeVisibleAnnotation(clone);
1614 public boolean isPadGaps()
1621 public void setPadGaps(boolean padGaps)
1623 this.padGaps = padGaps;
1627 * apply any post-edit constraints and trigger any calculations needed after
1628 * an edit has been performed on the alignment
1633 public void alignmentChanged(AlignmentViewPanel ap)
1637 alignment.padGaps();
1639 if (autoCalculateConsensus)
1641 updateConsensus(ap);
1643 if (hconsensus != null && autoCalculateConsensus)
1645 updateConservation(ap);
1647 if (autoCalculateStrucConsensus)
1649 updateStrucConsensus(ap);
1652 // Reset endRes of groups if beyond alignment width
1653 int alWidth = alignment.getWidth();
1654 List<SequenceGroup> groups = alignment.getGroups();
1657 for (SequenceGroup sg : groups)
1659 if (sg.getEndRes() > alWidth)
1661 sg.setEndRes(alWidth - 1);
1666 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1668 selectionGroup.setEndRes(alWidth - 1);
1671 resetAllColourSchemes();
1672 calculator.restartWorkers();
1673 // alignment.adjustSequenceAnnotations();
1677 * reset scope and do calculations for all applied colourschemes on alignment
1679 void resetAllColourSchemes()
1681 ColourSchemeI cs = globalColourScheme;
1684 cs.alignmentChanged(alignment, hiddenRepSequences);
1686 cs.setConsensus(hconsensus);
1687 if (cs.conservationApplied())
1689 cs.setConservation(Conservation.calculateConservation("All",
1690 ResidueProperties.propHash, 3, alignment.getSequences(), 0,
1691 alignment.getWidth(), false, getConsPercGaps(), false));
1695 for (SequenceGroup sg : alignment.getGroups())
1699 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1701 sg.recalcConservation();
1705 protected void initAutoAnnotation()
1707 // TODO: add menu option action that nulls or creates consensus object
1708 // depending on if the user wants to see the annotation or not in a
1709 // specific alignment
1711 if (hconsensus == null && !isDataset)
1713 if (!alignment.isNucleotide())
1722 consensus = new AlignmentAnnotation("Consensus", "PID",
1723 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1724 initConsensus(consensus);
1726 initComplementConsensus();
1731 * If this is a protein alignment and there are mappings to cDNA, add the cDNA
1732 * consensus annotation.
1734 public void initComplementConsensus()
1736 if (!alignment.isNucleotide())
1738 final Set<AlignedCodonFrame> codonMappings = alignment
1740 if (codonMappings != null && !codonMappings.isEmpty())
1742 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1743 "PID for cDNA", new Annotation[1], 0f, 100f,
1744 AlignmentAnnotation.BAR_GRAPH);
1745 initConsensus(complementConsensus);
1750 private void initConsensus(AlignmentAnnotation aa)
1753 aa.autoCalculated = true;
1757 alignment.addAnnotation(aa);
1761 private void initConservation()
1763 if (showConservation)
1765 if (conservation == null)
1767 conservation = new AlignmentAnnotation("Conservation",
1768 "Conservation of total alignment less than "
1769 + getConsPercGaps() + "% gaps", new Annotation[1],
1770 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1771 conservation.hasText = true;
1772 conservation.autoCalculated = true;
1773 alignment.addAnnotation(conservation);
1778 private void initQuality()
1782 if (quality == null)
1784 quality = new AlignmentAnnotation("Quality",
1785 "Alignment Quality based on Blosum62 scores",
1786 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1787 quality.hasText = true;
1788 quality.autoCalculated = true;
1789 alignment.addAnnotation(quality);
1794 private void initRNAStructure()
1796 if (alignment.hasRNAStructure() && strucConsensus == null)
1798 strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
1799 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1800 strucConsensus.hasText = true;
1801 strucConsensus.autoCalculated = true;
1805 alignment.addAnnotation(strucConsensus);
1813 * @see jalview.api.AlignViewportI#calcPanelHeight()
1816 public int calcPanelHeight()
1818 // setHeight of panels
1819 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
1821 int charHeight = getCharHeight();
1824 BitSet graphgrp = new BitSet();
1825 for (AlignmentAnnotation aa : anns)
1829 System.err.println("Null annotation row: ignoring.");
1836 if (aa.graphGroup > -1)
1838 if (graphgrp.get(aa.graphGroup))
1844 graphgrp.set(aa.graphGroup);
1851 aa.height += charHeight;
1861 aa.height += aa.graphHeight;
1869 height += aa.height;
1881 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
1882 boolean preserveNewGroupSettings)
1884 boolean updateCalcs = false;
1885 boolean conv = isShowGroupConservation();
1886 boolean cons = isShowGroupConsensus();
1887 boolean showprf = isShowSequenceLogo();
1888 boolean showConsHist = isShowConsensusHistogram();
1889 boolean normLogo = isNormaliseSequenceLogo();
1892 * TODO reorder the annotation rows according to group/sequence ordering on
1895 boolean sortg = true;
1897 // remove old automatic annotation
1898 // add any new annotation
1900 // intersect alignment annotation with alignment groups
1902 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
1903 List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
1906 for (int an = 0; an < aan.length; an++)
1908 if (aan[an].autoCalculated && aan[an].groupRef != null)
1910 oldrfs.add(aan[an].groupRef);
1911 alignment.deleteAnnotation(aan[an], false);
1915 if (alignment.getGroups() != null)
1917 for (SequenceGroup sg : alignment.getGroups())
1919 updateCalcs = false;
1920 if (applyGlobalSettings
1921 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
1923 // set defaults for this group's conservation/consensus
1924 sg.setshowSequenceLogo(showprf);
1925 sg.setShowConsensusHistogram(showConsHist);
1926 sg.setNormaliseSequenceLogo(normLogo);
1931 alignment.addAnnotation(sg.getConservationRow(), 0);
1936 alignment.addAnnotation(sg.getConsensus(), 0);
1938 // refresh the annotation rows
1941 sg.recalcConservation();
1948 public boolean isDisplayReferenceSeq()
1950 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
1954 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
1956 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
1960 public boolean isColourByReferenceSeq()
1962 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
1966 public Color getSequenceColour(SequenceI seq)
1968 Color sqc = sequenceColours.get(seq);
1969 return (sqc == null ? Color.white : sqc);
1973 public void setSequenceColour(SequenceI seq, Color col)
1977 sequenceColours.remove(seq);
1981 sequenceColours.put(seq, col);
1986 public void updateSequenceIdColours()
1988 for (SequenceGroup sg : alignment.getGroups())
1990 if (sg.idColour != null)
1992 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
1994 sequenceColours.put(s, sg.idColour);
2001 public void clearSequenceColours()
2003 sequenceColours.clear();
2007 public AlignViewportI getCodingComplement()
2009 return this.codingComplement;
2013 * Set this as the (cDna/protein) complement of the given viewport. Also
2014 * ensures the reverse relationship is set on the given viewport.
2017 public void setCodingComplement(AlignViewportI av)
2021 System.err.println("Ignoring recursive setCodingComplement request");
2025 this.codingComplement = av;
2026 // avoid infinite recursion!
2027 if (av.getCodingComplement() != this)
2029 av.setCodingComplement(this);
2035 public boolean isNucleotide()
2037 return getAlignment() == null ? false : getAlignment().isNucleotide();
2041 public FeaturesDisplayedI getFeaturesDisplayed()
2043 return featuresDisplayed;
2047 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2049 featuresDisplayed = featuresDisplayedI;
2053 public boolean areFeaturesDisplayed()
2055 return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
2062 * features are displayed if true
2065 public void setShowSequenceFeatures(boolean b)
2067 viewStyle.setShowSequenceFeatures(b);
2070 public boolean isShowSequenceFeatures()
2072 return viewStyle.isShowSequenceFeatures();
2076 public void setShowSequenceFeaturesHeight(boolean selected)
2078 viewStyle.setShowSeqFeaturesHeight(selected);
2082 public boolean isShowSequenceFeaturesHeight()
2084 return viewStyle.isShowSequenceFeaturesHeight();
2090 public void setShowAnnotation(boolean b)
2092 viewStyle.setShowAnnotation(b);
2096 public boolean isShowAnnotation()
2098 return viewStyle.isShowAnnotation();
2102 public boolean isRightAlignIds()
2104 return viewStyle.isRightAlignIds();
2108 public void setRightAlignIds(boolean rightAlignIds)
2110 viewStyle.setRightAlignIds(rightAlignIds);
2114 public boolean getConservationSelected()
2116 return viewStyle.getConservationSelected();
2120 public void setShowBoxes(boolean state)
2122 viewStyle.setShowBoxes(state);
2127 * @see jalview.api.ViewStyleI#getTextColour()
2129 public Color getTextColour()
2131 return viewStyle.getTextColour();
2136 * @see jalview.api.ViewStyleI#getTextColour2()
2138 public Color getTextColour2()
2140 return viewStyle.getTextColour2();
2145 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2147 public int getThresholdTextColour()
2149 return viewStyle.getThresholdTextColour();
2154 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2156 public boolean isConservationColourSelected()
2158 return viewStyle.isConservationColourSelected();
2163 * @see jalview.api.ViewStyleI#isRenderGaps()
2165 public boolean isRenderGaps()
2167 return viewStyle.isRenderGaps();
2172 * @see jalview.api.ViewStyleI#isShowColourText()
2174 public boolean isShowColourText()
2176 return viewStyle.isShowColourText();
2180 * @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()
2182 public boolean isShowSeqFeaturesHeight()
2184 return viewStyle.isShowSeqFeaturesHeight();
2188 * @param conservationColourSelected
2189 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2191 public void setConservationColourSelected(
2192 boolean conservationColourSelected)
2194 viewStyle.setConservationColourSelected(conservationColourSelected);
2198 * @param showColourText
2199 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2201 public void setShowColourText(boolean showColourText)
2203 viewStyle.setShowColourText(showColourText);
2208 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2210 public void setTextColour(Color textColour)
2212 viewStyle.setTextColour(textColour);
2216 * @param thresholdTextColour
2217 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2219 public void setThresholdTextColour(int thresholdTextColour)
2221 viewStyle.setThresholdTextColour(thresholdTextColour);
2225 * @param textColour2
2226 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2228 public void setTextColour2(Color textColour2)
2230 viewStyle.setTextColour2(textColour2);
2234 public ViewStyleI getViewStyle()
2236 return new ViewStyle(viewStyle);
2240 public void setViewStyle(ViewStyleI settingsForView)
2242 viewStyle = new ViewStyle(settingsForView);
2246 public boolean sameStyle(ViewStyleI them)
2248 return viewStyle.sameStyle(them);
2253 * @see jalview.api.ViewStyleI#getIdWidth()
2255 public int getIdWidth()
2257 return viewStyle.getIdWidth();
2262 * @see jalview.api.ViewStyleI#setIdWidth(int)
2264 public void setIdWidth(int i)
2266 viewStyle.setIdWidth(i);
2271 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2273 public boolean isCentreColumnLabels()
2275 return viewStyle.isCentreColumnLabels();
2279 * @param centreColumnLabels
2280 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2282 public void setCentreColumnLabels(boolean centreColumnLabels)
2284 viewStyle.setCentreColumnLabels(centreColumnLabels);
2289 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2291 public void setShowDBRefs(boolean showdbrefs)
2293 viewStyle.setShowDBRefs(showdbrefs);
2298 * @see jalview.api.ViewStyleI#isShowDBRefs()
2300 public boolean isShowDBRefs()
2302 return viewStyle.isShowDBRefs();
2307 * @see jalview.api.ViewStyleI#isShowNPFeats()
2309 public boolean isShowNPFeats()
2311 return viewStyle.isShowNPFeats();
2315 * @param shownpfeats
2316 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2318 public void setShowNPFeats(boolean shownpfeats)
2320 viewStyle.setShowNPFeats(shownpfeats);
2323 public abstract StructureSelectionManager getStructureSelectionManager();
2326 * Add one command to the command history list.
2330 public void addToHistoryList(CommandI command)
2332 if (this.historyList != null)
2334 this.historyList.push(command);
2335 broadcastCommand(command, false);
2339 protected void broadcastCommand(CommandI command, boolean undo)
2341 getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
2345 * Add one command to the command redo list.
2349 public void addToRedoList(CommandI command)
2351 if (this.redoList != null)
2353 this.redoList.push(command);
2355 broadcastCommand(command, true);
2359 * Clear the command redo list.
2361 public void clearRedoList()
2363 if (this.redoList != null)
2365 this.redoList.clear();
2369 public void setHistoryList(Deque<CommandI> list)
2371 this.historyList = list;
2374 public Deque<CommandI> getHistoryList()
2376 return this.historyList;
2379 public void setRedoList(Deque<CommandI> list)
2381 this.redoList = list;
2384 public Deque<CommandI> getRedoList()
2386 return this.redoList;
2390 public VamsasSource getVamsasSource()
2395 public SequenceAnnotationOrder getSortAnnotationsBy()
2397 return sortAnnotationsBy;
2400 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2402 this.sortAnnotationsBy = sortAnnotationsBy;
2405 public boolean isShowAutocalculatedAbove()
2407 return showAutocalculatedAbove;
2410 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2412 this.showAutocalculatedAbove = showAutocalculatedAbove;
2416 public boolean isScaleProteinAsCdna()
2418 return viewStyle.isScaleProteinAsCdna();
2422 public void setScaleProteinAsCdna(boolean b)
2424 viewStyle.setScaleProteinAsCdna(b);