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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.analysis.Conservation;
25 import jalview.analysis.TreeModel;
26 import jalview.api.AlignCalcManagerI2;
27 import jalview.api.AlignCalcWorkerI;
28 import jalview.api.AlignExportSettingsI;
29 import jalview.api.AlignViewportI;
30 import jalview.api.AlignmentViewPanel;
31 import jalview.api.FeaturesDisplayedI;
32 import jalview.api.ViewStyleI;
33 import jalview.commands.CommandI;
34 import jalview.datamodel.AlignedCodonFrame;
35 import jalview.datamodel.AlignmentAnnotation;
36 import jalview.datamodel.AlignmentExportData;
37 import jalview.datamodel.AlignmentI;
38 import jalview.datamodel.AlignmentView;
39 import jalview.datamodel.Annotation;
40 import jalview.datamodel.ColumnSelection;
41 import jalview.datamodel.HiddenColumns;
42 import jalview.datamodel.HiddenSequences;
43 import jalview.datamodel.ProfilesI;
44 import jalview.datamodel.SearchResultsI;
45 import jalview.datamodel.Sequence;
46 import jalview.datamodel.SequenceCollectionI;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.renderer.ResidueShader;
50 import jalview.renderer.ResidueShaderI;
51 import jalview.schemes.ColourSchemeI;
52 import jalview.structure.CommandListener;
53 import jalview.structure.StructureSelectionManager;
54 import jalview.structure.VamsasSource;
55 import jalview.util.Comparison;
56 import jalview.util.MapList;
57 import jalview.util.MappingUtils;
58 import jalview.util.MessageManager;
59 import jalview.viewmodel.styles.ViewStyle;
60 import jalview.workers.AlignCalcManager2;
61 import jalview.workers.ComplementConsensusThread;
62 import jalview.workers.ConsensusThread;
63 import jalview.workers.InformationThread;
64 import jalview.workers.StrucConsensusThread;
66 import java.awt.Color;
67 import java.beans.PropertyChangeSupport;
68 import java.util.ArrayDeque;
69 import java.util.ArrayList;
70 import java.util.BitSet;
71 import java.util.Deque;
72 import java.util.HashMap;
73 import java.util.Hashtable;
74 import java.util.Iterator;
75 import java.util.List;
79 * base class holding visualization and analysis attributes and common logic for
80 * an active alignment view displayed in the GUI
85 public abstract class AlignmentViewport
86 implements AlignViewportI, CommandListener, VamsasSource
88 public static final String PROPERTY_ALIGNMENT = "alignment";
89 public static final String PROPERTY_SEQUENCE = "sequence";
90 protected ViewportRanges ranges;
92 protected ViewStyleI viewStyle = new ViewStyle();
95 * A viewport that hosts the cDna view of this (protein), or vice versa (if
98 AlignViewportI codingComplement = null;
100 FeaturesDisplayedI featuresDisplayed = null;
102 protected Deque<CommandI> historyList = new ArrayDeque<>();
104 protected Deque<CommandI> redoList = new ArrayDeque<>();
107 * alignment displayed in the viewport. Please use get/setter
109 protected AlignmentI alignment;
112 * probably unused indicator that view is of a dataset rather than an
116 protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
118 protected boolean infoLetterHeight = false;
120 protected AlignmentAnnotation occupancy;
123 * results of alignment consensus analysis for visible portion of view
125 protected ProfilesI consensusProfiles;
128 * HMM profile for the alignment
130 protected ProfilesI hmmProfiles;
132 public AlignmentViewport(AlignmentI al)
135 ranges = new ViewportRanges(al);
140 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
143 public void setFontName(String name)
145 viewStyle.setFontName(name);
150 * @see jalview.api.ViewStyleI#setFontStyle(int)
153 public void setFontStyle(int style)
155 viewStyle.setFontStyle(style);
160 * @see jalview.api.ViewStyleI#setFontSize(int)
163 public void setFontSize(int size)
165 viewStyle.setFontSize(size);
170 * @see jalview.api.ViewStyleI#getFontStyle()
173 public int getFontStyle()
175 return viewStyle.getFontStyle();
180 * @see jalview.api.ViewStyleI#getFontName()
183 public String getFontName()
185 return viewStyle.getFontName();
190 * @see jalview.api.ViewStyleI#getFontSize()
193 public int getFontSize()
195 return viewStyle.getFontSize();
199 * @param upperCasebold
200 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
203 public void setUpperCasebold(boolean upperCasebold)
205 viewStyle.setUpperCasebold(upperCasebold);
210 * @see jalview.api.ViewStyleI#isUpperCasebold()
213 public boolean isUpperCasebold()
215 return viewStyle.isUpperCasebold();
220 * @see jalview.api.ViewStyleI#isSeqNameItalics()
223 public boolean isSeqNameItalics()
225 return viewStyle.isSeqNameItalics();
229 * @param colourByReferenceSeq
230 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
233 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
235 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
240 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
243 public void setColourAppliesToAllGroups(boolean b)
245 viewStyle.setColourAppliesToAllGroups(b);
250 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
253 public boolean getColourAppliesToAllGroups()
255 return viewStyle.getColourAppliesToAllGroups();
260 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
263 public boolean getAbovePIDThreshold()
265 return viewStyle.getAbovePIDThreshold();
270 * @see jalview.api.ViewStyleI#setIncrement(int)
273 public void setIncrement(int inc)
275 viewStyle.setIncrement(inc);
280 * @see jalview.api.ViewStyleI#getIncrement()
283 public int getIncrement()
285 return viewStyle.getIncrement();
290 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
293 public void setConservationSelected(boolean b)
295 viewStyle.setConservationSelected(b);
300 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
303 public void setShowHiddenMarkers(boolean show)
305 viewStyle.setShowHiddenMarkers(show);
310 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
313 public boolean getShowHiddenMarkers()
315 return viewStyle.getShowHiddenMarkers();
320 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
323 public void setScaleRightWrapped(boolean b)
325 viewStyle.setScaleRightWrapped(b);
330 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
333 public void setScaleLeftWrapped(boolean b)
335 viewStyle.setScaleLeftWrapped(b);
340 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
343 public void setScaleAboveWrapped(boolean b)
345 viewStyle.setScaleAboveWrapped(b);
350 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
353 public boolean getScaleLeftWrapped()
355 return viewStyle.getScaleLeftWrapped();
360 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
363 public boolean getScaleAboveWrapped()
365 return viewStyle.getScaleAboveWrapped();
370 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
373 public boolean getScaleRightWrapped()
375 return viewStyle.getScaleRightWrapped();
380 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
383 public void setAbovePIDThreshold(boolean b)
385 viewStyle.setAbovePIDThreshold(b);
390 * @see jalview.api.ViewStyleI#setThreshold(int)
393 public void setThreshold(int thresh)
395 viewStyle.setThreshold(thresh);
400 * @see jalview.api.ViewStyleI#getThreshold()
403 public int getThreshold()
405 return viewStyle.getThreshold();
410 * @see jalview.api.ViewStyleI#getShowJVSuffix()
413 public boolean getShowJVSuffix()
415 return viewStyle.getShowJVSuffix();
420 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
423 public void setShowJVSuffix(boolean b)
425 viewStyle.setShowJVSuffix(b);
430 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
433 public void setWrapAlignment(boolean state)
435 viewStyle.setWrapAlignment(state);
436 ranges.setWrappedMode(state);
441 * @see jalview.api.ViewStyleI#setShowText(boolean)
444 public void setShowText(boolean state)
446 viewStyle.setShowText(state);
451 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
454 public void setRenderGaps(boolean state)
456 viewStyle.setRenderGaps(state);
461 * @see jalview.api.ViewStyleI#getColourText()
464 public boolean getColourText()
466 return viewStyle.getColourText();
471 * @see jalview.api.ViewStyleI#setColourText(boolean)
474 public void setColourText(boolean state)
476 viewStyle.setColourText(state);
481 * @see jalview.api.ViewStyleI#getWrapAlignment()
484 public boolean getWrapAlignment()
486 return viewStyle.getWrapAlignment();
491 * @see jalview.api.ViewStyleI#getShowText()
494 public boolean getShowText()
496 return viewStyle.getShowText();
501 * @see jalview.api.ViewStyleI#getWrappedWidth()
504 public int getWrappedWidth()
506 return viewStyle.getWrappedWidth();
511 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
514 public void setWrappedWidth(int w)
516 viewStyle.setWrappedWidth(w);
521 * @see jalview.api.ViewStyleI#getCharHeight()
524 public int getCharHeight()
526 return viewStyle.getCharHeight();
531 * @see jalview.api.ViewStyleI#setCharHeight(int)
534 public void setCharHeight(int h)
536 viewStyle.setCharHeight(h);
541 * @see jalview.api.ViewStyleI#getCharWidth()
544 public int getCharWidth()
546 return viewStyle.getCharWidth();
551 * @see jalview.api.ViewStyleI#setCharWidth(int)
554 public void setCharWidth(int w)
556 viewStyle.setCharWidth(w);
561 * @see jalview.api.ViewStyleI#getShowBoxes()
564 public boolean getShowBoxes()
566 return viewStyle.getShowBoxes();
571 * @see jalview.api.ViewStyleI#getShowUnconserved()
574 public boolean getShowUnconserved()
576 return viewStyle.getShowUnconserved();
580 * @param showunconserved
581 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
584 public void setShowUnconserved(boolean showunconserved)
586 viewStyle.setShowUnconserved(showunconserved);
591 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
594 public void setSeqNameItalics(boolean default1)
596 viewStyle.setSeqNameItalics(default1);
600 public AlignmentI getAlignment()
606 public char getGapCharacter()
608 return alignment.getGapCharacter();
611 protected String sequenceSetID;
614 * probably unused indicator that view is of a dataset rather than an
617 protected boolean isDataset = false;
620 public void setDataset(boolean b)
625 public boolean isDataset()
630 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
632 protected ColumnSelection colSel = new ColumnSelection();
634 protected boolean autoCalculateConsensusAndConservation = true;
636 public boolean getAutoCalculateConsensusAndConservation()
638 return autoCalculateConsensusAndConservation;
641 public void setAutoCalculateConsensusAndConservation(boolean b)
643 autoCalculateConsensusAndConservation = b;
646 protected boolean autoCalculateStrucConsensus = true;
648 public boolean getAutoCalculateStrucConsensus()
650 return autoCalculateStrucConsensus;
653 public void setAutoCalculateStrucConsensus(boolean b)
655 autoCalculateStrucConsensus = b;
657 protected boolean ignoreGapsInConsensusCalculation = false;
659 protected ResidueShaderI residueShading = new ResidueShader();
663 public void setGlobalColourScheme(ColourSchemeI cs)
665 // TODO: logic refactored from AlignFrame changeColour -
666 // TODO: autorecalc stuff should be changed to rely on the worker system
667 // check to see if we should implement a changeColour(cs) method rather than
668 // put the logic in here
669 // - means that caller decides if they want to just modify state and defer
670 // calculation till later or to do all calculations in thread.
674 * only instantiate alignment colouring once, thereafter update it;
675 * this means that any conservation or PID threshold settings
676 * persist when the alignment colour scheme is changed
678 if (residueShading == null)
680 residueShading = new ResidueShader(viewStyle);
682 residueShading.setColourScheme(cs);
684 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
685 // ...problem: groups need these, but do not currently have a ViewStyle
689 if (getConservationSelected())
691 residueShading.setConservation(hconservation);
694 * reset conservation flag in case just set to false if
695 * Conservation was null (calculation still in progress)
697 residueShading.setConservationApplied(getConservationSelected());
698 residueShading.alignmentChanged(alignment, hiddenRepSequences);
702 * if 'apply colour to all groups' is selected... do so
703 * (but don't transfer any colour threshold settings to groups)
705 if (getColourAppliesToAllGroups())
707 for (SequenceGroup sg : getAlignment().getGroups())
710 * retain any colour thresholds per group while
711 * changing choice of colour scheme (JAL-2386)
714 cs == null ? null : cs.getInstance(this, sg));
717 sg.getGroupColourScheme().alignmentChanged(sg,
725 public ColourSchemeI getGlobalColourScheme()
727 return residueShading == null ? null : residueShading.getColourScheme();
731 public ResidueShaderI getResidueShading()
733 return residueShading;
737 protected AlignmentAnnotation consensus;
739 protected AlignmentAnnotation complementConsensus;
741 protected AlignmentAnnotation gapcounts;
743 protected AlignmentAnnotation strucConsensus;
745 protected AlignmentAnnotation conservation;
747 protected AlignmentAnnotation quality;
749 protected AlignmentAnnotation[] groupConsensus;
751 protected AlignmentAnnotation[] groupConservation;
754 * results of alignment consensus analysis for visible portion of view
756 protected ProfilesI hconsensus = null;
759 * results of cDNA complement consensus visible portion of view
761 protected Hashtable<String, Object>[] hcomplementConsensus = null;
764 * results of secondary structure base pair consensus for visible portion of
767 protected Hashtable<String, Object>[] hStrucConsensus = null;
769 protected Conservation hconservation = null;
773 public void setConservation(Conservation cons)
775 hconservation = cons;
779 * percentage gaps allowed in a column before all amino acid properties should
780 * be considered unconserved
782 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
785 public int getConsPercGaps()
791 public void setSequenceConsensusHash(ProfilesI hconsensus)
793 this.hconsensus = hconsensus;
797 public void setComplementConsensusHash(
798 Hashtable<String, Object>[] hconsensus)
800 this.hcomplementConsensus = hconsensus;
804 public ProfilesI getSequenceConsensusHash()
810 public void setHmmProfiles(ProfilesI info)
816 public ProfilesI getHmmProfiles()
822 public Hashtable<String, Object>[] getComplementConsensusHash()
824 return hcomplementConsensus;
828 public Hashtable<String, Object>[] getRnaStructureConsensusHash()
830 return hStrucConsensus;
834 public void setRnaStructureConsensusHash(
835 Hashtable<String, Object>[] hStrucConsensus)
837 this.hStrucConsensus = hStrucConsensus;
842 public AlignmentAnnotation getAlignmentQualityAnnot()
848 public AlignmentAnnotation getAlignmentConservationAnnotation()
854 public AlignmentAnnotation getAlignmentConsensusAnnotation()
860 public AlignmentAnnotation getAlignmentGapAnnotation()
866 public AlignmentAnnotation getComplementConsensusAnnotation()
868 return complementConsensus;
872 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
874 return strucConsensus;
877 protected AlignCalcManagerI2 calculator = new AlignCalcManager2();
880 * trigger update of conservation annotation
882 public void updateConservation(final AlignmentViewPanel ap)
884 // see note in mantis : issue number 8585
885 if (alignment.isNucleotide()
886 || (conservation == null && quality == null)
887 || !autoCalculateConsensusAndConservation)
891 if (calculator.getWorkersOfClass(
892 jalview.workers.ConservationThread.class).isEmpty())
894 calculator.registerWorker(
895 new jalview.workers.ConservationThread(this, ap));
900 * trigger update of consensus annotation
902 public void updateConsensus(final AlignmentViewPanel ap)
904 // see note in mantis : issue number 8585
905 if (consensus == null || !autoCalculateConsensusAndConservation)
909 if (calculator.getWorkersOfClass(ConsensusThread.class).isEmpty())
911 calculator.registerWorker(new ConsensusThread(this, ap));
915 * A separate thread to compute cDNA consensus for a protein alignment
916 * which has mapping to cDNA
918 final AlignmentI al = this.getAlignment();
919 if (!al.isNucleotide() && al.getCodonFrames() != null
920 && !al.getCodonFrames().isEmpty())
923 * fudge - check first for protein-to-nucleotide mappings
924 * (we don't want to do this for protein-to-protein)
926 boolean doConsensus = false;
927 for (AlignedCodonFrame mapping : al.getCodonFrames())
929 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
930 MapList[] mapLists = mapping.getdnaToProt();
931 // mapLists can be empty if project load has not finished resolving seqs
932 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
940 if (calculator.getWorkersOfClass(ComplementConsensusThread.class).isEmpty())
942 calculator.registerWorker(new ComplementConsensusThread(this, ap));
949 public void initInformationWorker(final AlignmentViewPanel ap)
951 if (calculator.getWorkersOfClass(InformationThread.class).isEmpty())
953 calculator.registerWorker(new InformationThread(this, ap));
956 // --------START Structure Conservation
957 public void updateStrucConsensus(final AlignmentViewPanel ap)
959 if (autoCalculateStrucConsensus && strucConsensus == null
960 && alignment.isNucleotide() && alignment.hasRNAStructure())
962 // secondary structure has been added - so init the consensus line
966 // see note in mantis : issue number 8585
967 if (strucConsensus == null || !autoCalculateStrucConsensus)
971 if (calculator.getWorkersOfClass(StrucConsensusThread.class).isEmpty())
973 calculator.registerWorker(new StrucConsensusThread(this, ap));
977 public boolean isCalcInProgress()
979 return calculator.isWorking();
983 public boolean isCalculationInProgress(
984 AlignmentAnnotation alignmentAnnotation)
986 if (!alignmentAnnotation.autoCalculated)
990 if (calculator.isWorkingWithAnnotation(alignmentAnnotation))
992 // System.err.println("grey out ("+alignmentAnnotation.label+")");
998 public void setAlignment(AlignmentI align)
1000 this.alignment = align;
1004 * Clean up references when this viewport is closed
1007 public void dispose()
1010 * defensively null out references to large objects in case
1011 * this object is not garbage collected (as if!)
1014 complementConsensus = null;
1015 strucConsensus = null;
1016 conservation = null;
1018 consensusProfiles = null;
1019 groupConsensus = null;
1020 groupConservation = null;
1022 hconservation = null;
1023 hcomplementConsensus = null;
1025 calculator.shutdown();
1027 residueShading = null; // may hold a reference to Consensus
1028 changeSupport = null;
1031 selectionGroup = null;
1037 public boolean isClosed()
1039 // TODO: check that this isClosed is only true after panel is closed, not
1040 // before it is fully constructed.
1041 return alignment == null;
1045 public AlignCalcManagerI2 getCalcManager()
1051 * should conservation rows be shown for groups
1053 protected boolean showGroupConservation = false;
1056 * should consensus rows be shown for groups
1058 protected boolean showGroupConsensus = false;
1061 * should consensus profile be rendered by default
1063 protected boolean showSequenceLogo = false;
1066 * should consensus profile be rendered normalised to row height
1068 protected boolean normaliseSequenceLogo = false;
1071 * should consensus histograms be rendered by default
1073 protected boolean showConsensusHistogram = true;
1076 * should hmm profile be rendered by default
1078 protected boolean hmmShowSequenceLogo = false;
1081 * should hmm profile be rendered normalised to row height
1083 protected boolean hmmNormaliseSequenceLogo = false;
1086 * should information histograms be rendered by default
1088 protected boolean hmmShowHistogram = true;
1091 * @return the showConsensusProfile
1094 public boolean isShowSequenceLogo()
1096 return showSequenceLogo;
1100 * @return the showInformationProfile
1103 public boolean isShowHMMSequenceLogo()
1105 return hmmShowSequenceLogo;
1109 * @param showSequenceLogo
1112 public void setShowSequenceLogo(boolean showSequenceLogo)
1114 if (showSequenceLogo != this.showSequenceLogo)
1116 // TODO: decouple settings setting from calculation when refactoring
1117 // annotation update method from alignframe to viewport
1118 this.showSequenceLogo = showSequenceLogo;
1119 for (AlignCalcWorkerI worker : calculator.getWorkers())
1121 if (worker.getClass().equals(ConsensusThread.class) ||
1122 worker.getClass().equals(ComplementConsensusThread.class) ||
1123 worker.getClass().equals(StrucConsensusThread.class))
1125 worker.updateAnnotation();
1129 this.showSequenceLogo = showSequenceLogo;
1132 public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
1134 if (showHMMSequenceLogo != this.hmmShowSequenceLogo)
1136 this.hmmShowSequenceLogo = showHMMSequenceLogo;
1137 // TODO: updateAnnotation if description (tooltip) will show
1138 // profile in place of information content?
1139 // calculator.updateAnnotationFor(InformationThread.class);
1141 this.hmmShowSequenceLogo = showHMMSequenceLogo;
1144 * @param showConsensusHistogram
1145 * the showConsensusHistogram to set
1147 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1149 this.showConsensusHistogram = showConsensusHistogram;
1153 * @param showInformationHistogram
1155 public void setShowInformationHistogram(boolean showInformationHistogram)
1157 this.hmmShowHistogram = showInformationHistogram;
1161 * @return the showGroupConservation
1163 public boolean isShowGroupConservation()
1165 return showGroupConservation;
1169 * @param showGroupConservation
1170 * the showGroupConservation to set
1172 public void setShowGroupConservation(boolean showGroupConservation)
1174 this.showGroupConservation = showGroupConservation;
1178 * @return the showGroupConsensus
1180 public boolean isShowGroupConsensus()
1182 return showGroupConsensus;
1186 * @param showGroupConsensus
1187 * the showGroupConsensus to set
1189 public void setShowGroupConsensus(boolean showGroupConsensus)
1191 this.showGroupConsensus = showGroupConsensus;
1196 * @return flag to indicate if the consensus histogram should be rendered by
1200 public boolean isShowConsensusHistogram()
1202 return this.showConsensusHistogram;
1207 * @return flag to indicate if the information content histogram should be
1208 * rendered by default
1211 public boolean isShowInformationHistogram()
1213 return this.hmmShowHistogram;
1217 * when set, updateAlignment will always ensure sequences are of equal length
1219 private boolean padGaps = false;
1222 * when set, alignment should be reordered according to a newly opened tree
1224 public boolean sortByTree = false;
1229 * @return null or the currently selected sequence region
1232 public SequenceGroup getSelectionGroup()
1234 return selectionGroup;
1238 * Set the selection group for this window. Also sets the current alignment as
1239 * the context for the group, if it does not already have one.
1242 * - group holding references to sequences in this alignment view
1246 public void setSelectionGroup(SequenceGroup sg)
1248 selectionGroup = sg;
1249 if (sg != null && sg.getContext() == null)
1251 sg.setContext(alignment);
1255 public void setHiddenColumns(HiddenColumns hidden)
1257 this.alignment.setHiddenColumns(hidden);
1261 public ColumnSelection getColumnSelection()
1267 public void setColumnSelection(ColumnSelection colSel)
1269 this.colSel = colSel;
1272 updateHiddenColumns();
1274 isColSelChanged(true);
1282 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1284 return hiddenRepSequences;
1288 public void setHiddenRepSequences(
1289 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1291 this.hiddenRepSequences = hiddenRepSequences;
1295 public boolean hasSelectedColumns()
1297 ColumnSelection columnSelection = getColumnSelection();
1298 return columnSelection != null && columnSelection.hasSelectedColumns();
1302 public boolean hasHiddenColumns()
1304 return alignment.getHiddenColumns() != null
1305 && alignment.getHiddenColumns().hasHiddenColumns();
1308 public void updateHiddenColumns()
1310 // this method doesn't really do anything now. But - it could, since a
1311 // column Selection could be in the process of modification
1312 // hasHiddenColumns = colSel.hasHiddenColumns();
1316 public boolean hasHiddenRows()
1318 return alignment.getHiddenSequences().getSize() > 0;
1321 protected SequenceGroup selectionGroup;
1323 public void setSequenceSetId(String newid)
1325 if (sequenceSetID != null)
1328 "Warning - overwriting a sequenceSetId for a viewport!");
1330 sequenceSetID = new String(newid);
1334 public String getSequenceSetId()
1336 if (sequenceSetID == null)
1338 sequenceSetID = alignment.hashCode() + "";
1341 return sequenceSetID;
1345 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1348 protected String viewId = null;
1351 public String getViewId()
1355 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1360 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1362 ignoreGapsInConsensusCalculation = b;
1365 updateConsensus(ap);
1366 if (residueShading != null)
1368 residueShading.setThreshold(residueShading.getThreshold(),
1369 ignoreGapsInConsensusCalculation);
1374 public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
1376 ignoreBelowBackGroundFrequencyCalculation = b;
1379 public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
1381 infoLetterHeight = b;
1384 private long sgrouphash = -1, colselhash = -1;
1387 * checks current SelectionGroup against record of last hash value, and
1391 * update the record of last hash value
1393 * @return true if SelectionGroup changed since last call (when b is true)
1395 public boolean isSelectionGroupChanged(boolean b)
1397 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1398 : selectionGroup.hashCode();
1399 if (hc != -1 && hc != sgrouphash)
1411 * checks current colsel against record of last hash value, and optionally
1415 * update the record of last hash value
1416 * @return true if colsel changed since last call (when b is true)
1418 public boolean isColSelChanged(boolean updateHash)
1420 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1421 if (hc != -1 && hc != colselhash)
1434 public boolean isIgnoreGapsConsensus()
1436 return ignoreGapsInConsensusCalculation;
1440 public boolean isIgnoreBelowBackground()
1442 return ignoreBelowBackGroundFrequencyCalculation;
1446 public boolean isInfoLetterHeight()
1448 return infoLetterHeight;
1450 // property change stuff
1451 // JBPNote Prolly only need this in the applet version.
1452 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1455 protected boolean showConservation = true;
1457 protected boolean showQuality = true;
1459 protected boolean showConsensus = true;
1461 protected boolean showOccupancy = true;
1463 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1465 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1467 protected boolean showAutocalculatedAbove;
1470 * when set, view will scroll to show the highlighted position
1472 private boolean followHighlight = true;
1475 * Property change listener for changes in alignment
1480 public void addPropertyChangeListener(
1481 java.beans.PropertyChangeListener listener)
1483 changeSupport.addPropertyChangeListener(listener);
1492 public void removePropertyChangeListener(
1493 java.beans.PropertyChangeListener listener)
1495 if (changeSupport != null)
1497 changeSupport.removePropertyChangeListener(listener);
1502 // common hide/show column stuff
1504 public void hideSelectedColumns()
1506 if (colSel.isEmpty())
1511 colSel.hideSelectedColumns(alignment);
1512 setSelectionGroup(null);
1513 isColSelChanged(true);
1516 public void hideColumns(int start, int end)
1520 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1524 alignment.getHiddenColumns().hideColumns(start, end);
1526 isColSelChanged(true);
1529 public void showColumn(int col)
1531 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1532 isColSelChanged(true);
1535 public void showAllHiddenColumns()
1537 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1538 isColSelChanged(true);
1541 // common hide/show seq stuff
1542 public void showAllHiddenSeqs()
1544 int startSeq = ranges.getStartSeq();
1545 int endSeq = ranges.getEndSeq();
1547 if (alignment.getHiddenSequences().getSize() > 0)
1549 if (selectionGroup == null)
1551 selectionGroup = new SequenceGroup();
1552 selectionGroup.setEndRes(alignment.getWidth() - 1);
1554 List<SequenceI> tmp = alignment.getHiddenSequences()
1555 .showAll(hiddenRepSequences);
1556 for (SequenceI seq : tmp)
1558 selectionGroup.addSequence(seq, false);
1559 setSequenceAnnotationsVisible(seq, true);
1562 hiddenRepSequences = null;
1564 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1566 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1573 public void showSequence(int index)
1575 int startSeq = ranges.getStartSeq();
1576 int endSeq = ranges.getEndSeq();
1578 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
1579 hiddenRepSequences);
1582 if (selectionGroup == null)
1584 selectionGroup = new SequenceGroup();
1585 selectionGroup.setEndRes(alignment.getWidth() - 1);
1588 for (SequenceI seq : tmp)
1590 selectionGroup.addSequence(seq, false);
1591 setSequenceAnnotationsVisible(seq, true);
1594 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1601 public void hideAllSelectedSeqs()
1603 if (selectionGroup == null || selectionGroup.getSize() < 1)
1608 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1612 setSelectionGroup(null);
1615 public void hideSequence(SequenceI[] seq)
1618 * cache offset to first visible sequence
1620 int startSeq = ranges.getStartSeq();
1624 for (int i = 0; i < seq.length; i++)
1626 alignment.getHiddenSequences().hideSequence(seq[i]);
1627 setSequenceAnnotationsVisible(seq[i], false);
1629 ranges.setStartSeq(startSeq);
1635 * Hides the specified sequence, or the sequences it represents
1638 * the sequence to hide, or keep as representative
1639 * @param representGroup
1640 * if true, hide the current selection group except for the
1641 * representative sequence
1643 public void hideSequences(SequenceI sequence, boolean representGroup)
1645 if (selectionGroup == null || selectionGroup.getSize() < 1)
1647 hideSequence(new SequenceI[] { sequence });
1653 hideRepSequences(sequence, selectionGroup);
1654 setSelectionGroup(null);
1658 int gsize = selectionGroup.getSize();
1659 SequenceI[] hseqs = selectionGroup.getSequences()
1660 .toArray(new SequenceI[gsize]);
1662 hideSequence(hseqs);
1663 setSelectionGroup(null);
1668 * Set visibility for any annotations for the given sequence.
1672 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1675 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1678 for (AlignmentAnnotation ann : anns)
1680 if (ann.sequenceRef == sequenceI)
1682 ann.visible = visible;
1688 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1690 int sSize = sg.getSize();
1696 if (hiddenRepSequences == null)
1698 hiddenRepSequences = new Hashtable<>();
1701 hiddenRepSequences.put(repSequence, sg);
1703 // Hide all sequences except the repSequence
1704 SequenceI[] seqs = new SequenceI[sSize - 1];
1706 for (int i = 0; i < sSize; i++)
1708 if (sg.getSequenceAt(i) != repSequence)
1710 if (index == sSize - 1)
1715 seqs[index++] = sg.getSequenceAt(i);
1718 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1719 sg.setHidereps(true); // note: not done in 2.7applet
1726 * @return null or the current reference sequence
1728 public SequenceI getReferenceSeq()
1730 return alignment.getSeqrep();
1735 * @return true iff seq is the reference for the alignment
1737 public boolean isReferenceSeq(SequenceI seq)
1739 return alignment.getSeqrep() == seq;
1745 * @return true if there are sequences represented by this sequence that are
1748 public boolean isHiddenRepSequence(SequenceI seq)
1750 return (hiddenRepSequences != null
1751 && hiddenRepSequences.containsKey(seq));
1757 * @return null or a sequence group containing the sequences that seq
1760 public SequenceGroup getRepresentedSequences(SequenceI seq)
1762 return (SequenceGroup) (hiddenRepSequences == null ? null
1763 : hiddenRepSequences.get(seq));
1767 public int adjustForHiddenSeqs(int alignmentIndex)
1769 return alignment.getHiddenSequences()
1770 .adjustForHiddenSeqs(alignmentIndex);
1774 public void invertColumnSelection()
1776 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1777 isColSelChanged(true);
1781 public SequenceI[] getSelectionAsNewSequence()
1783 SequenceI[] sequences;
1784 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1785 // this was the only caller in the applet for this method
1786 // JBPNote: in applet, this method returned references to the alignment
1787 // sequences, and it did not honour the presence/absence of annotation
1788 // attached to the alignment (probably!)
1789 if (selectionGroup == null || selectionGroup.getSize() == 0)
1791 sequences = alignment.getSequencesArray();
1792 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1793 for (int i = 0; i < sequences.length; i++)
1795 // construct new sequence with subset of visible annotation
1796 sequences[i] = new Sequence(sequences[i], annots);
1801 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1808 public SequenceI[] getSequenceSelection()
1810 SequenceI[] sequences = null;
1811 if (selectionGroup != null)
1813 sequences = selectionGroup.getSequencesInOrder(alignment);
1815 if (sequences == null)
1817 sequences = alignment.getSequencesArray();
1823 public jalview.datamodel.AlignmentView getAlignmentView(
1824 boolean selectedOnly)
1826 return getAlignmentView(selectedOnly, false);
1830 public jalview.datamodel.AlignmentView getAlignmentView(
1831 boolean selectedOnly, boolean markGroups)
1833 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1835 alignment.getHiddenColumns() != null
1836 && alignment.getHiddenColumns().hasHiddenColumns(),
1837 selectedOnly, markGroups);
1841 public String[] getViewAsString(boolean selectedRegionOnly)
1843 return getViewAsString(selectedRegionOnly, true);
1847 public String[] getViewAsString(boolean selectedRegionOnly,
1848 boolean exportHiddenSeqs)
1850 String[] selection = null;
1851 SequenceI[] seqs = null;
1853 int start = 0, end = 0;
1854 if (selectedRegionOnly && selectionGroup != null)
1856 iSize = selectionGroup.getSize();
1857 seqs = selectionGroup.getSequencesInOrder(alignment);
1858 start = selectionGroup.getStartRes();
1859 end = selectionGroup.getEndRes() + 1;
1863 if (hasHiddenRows() && exportHiddenSeqs)
1865 AlignmentI fullAlignment = alignment.getHiddenSequences()
1866 .getFullAlignment();
1867 iSize = fullAlignment.getHeight();
1868 seqs = fullAlignment.getSequencesArray();
1869 end = fullAlignment.getWidth();
1873 iSize = alignment.getHeight();
1874 seqs = alignment.getSequencesArray();
1875 end = alignment.getWidth();
1879 selection = new String[iSize];
1880 if (alignment.getHiddenColumns() != null
1881 && alignment.getHiddenColumns().hasHiddenColumns())
1883 for (i = 0; i < iSize; i++)
1885 Iterator<int[]> blocks = alignment.getHiddenColumns()
1886 .getVisContigsIterator(start, end + 1, false);
1887 selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
1892 for (i = 0; i < iSize; i++)
1894 selection[i] = seqs[i].getSequenceAsString(start, end);
1902 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1904 ArrayList<int[]> regions = new ArrayList<>();
1910 HiddenColumns hidden = alignment.getHiddenColumns();
1911 if (hidden != null && hidden.hasHiddenColumns())
1915 start = hidden.visibleToAbsoluteColumn(start);
1918 end = hidden.getNextHiddenBoundary(false, start);
1929 regions.add(new int[] { start, end });
1931 if (hidden != null && hidden.hasHiddenColumns())
1933 start = hidden.visibleToAbsoluteColumn(end);
1934 start = hidden.getNextHiddenBoundary(true, start) + 1;
1936 } while (end < max);
1938 // int[][] startEnd = new int[regions.size()][2];
1944 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1945 boolean selectedOnly)
1947 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1948 AlignmentAnnotation[] aa;
1949 if ((aa = alignment.getAlignmentAnnotation()) != null)
1951 for (AlignmentAnnotation annot : aa)
1953 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1954 if (selectedOnly && selectionGroup != null)
1956 clone.makeVisibleAnnotation(
1957 selectionGroup.getStartRes(), selectionGroup.getEndRes(),
1958 alignment.getHiddenColumns());
1962 clone.makeVisibleAnnotation(alignment.getHiddenColumns());
1971 public boolean isPadGaps()
1977 public void setPadGaps(boolean padGaps)
1979 this.padGaps = padGaps;
1983 * apply any post-edit constraints and trigger any calculations needed after
1984 * an edit has been performed on the alignment
1989 public void alignmentChanged(AlignmentViewPanel ap)
1993 alignment.padGaps();
1995 if (autoCalculateConsensusAndConservation)
1997 updateConsensus(ap);
1999 if (hconsensus != null && autoCalculateConsensusAndConservation)
2001 updateConservation(ap);
2003 if (autoCalculateStrucConsensus)
2005 updateStrucConsensus(ap);
2008 // Reset endRes of groups if beyond alignment width
2009 int alWidth = alignment.getWidth();
2010 List<SequenceGroup> groups = alignment.getGroups();
2013 for (SequenceGroup sg : groups)
2015 if (sg.getEndRes() > alWidth)
2017 sg.setEndRes(alWidth - 1);
2022 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
2024 selectionGroup.setEndRes(alWidth - 1);
2027 updateAllColourSchemes();
2028 calculator.restartWorkers();
2032 * reset scope and do calculations for all applied colourschemes on alignment
2034 void updateAllColourSchemes()
2036 ResidueShaderI rs = residueShading;
2039 rs.alignmentChanged(alignment, hiddenRepSequences);
2041 rs.setConsensus(hconsensus);
2042 if (rs.conservationApplied())
2044 rs.setConservation(Conservation.calculateConservation("All",
2045 alignment.getSequences(), 0, alignment.getWidth(), false,
2046 getConsPercGaps(), false));
2050 for (SequenceGroup sg : alignment.getGroups())
2054 sg.cs.alignmentChanged(sg, hiddenRepSequences);
2056 sg.recalcConservation();
2060 protected void initAutoAnnotation()
2062 // TODO: add menu option action that nulls or creates consensus object
2063 // depending on if the user wants to see the annotation or not in a
2064 // specific alignment
2066 if (hconsensus == null && !isDataset)
2068 if (!alignment.isNucleotide())
2077 consensus = new AlignmentAnnotation("Consensus",
2078 MessageManager.getString("label.consensus_descr"),
2079 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2080 initConsensus(consensus);
2083 initComplementConsensus();
2088 * If this is a protein alignment and there are mappings to cDNA, adds the
2089 * cDNA consensus annotation and returns true, else returns false.
2091 public boolean initComplementConsensus()
2093 if (!alignment.isNucleotide())
2095 final List<AlignedCodonFrame> codonMappings = alignment
2097 if (codonMappings != null && !codonMappings.isEmpty())
2099 boolean doConsensus = false;
2100 for (AlignedCodonFrame mapping : codonMappings)
2102 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
2103 MapList[] mapLists = mapping.getdnaToProt();
2104 // mapLists can be empty if project load has not finished resolving
2106 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
2114 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
2116 .getString("label.complement_consensus_descr"),
2117 new Annotation[1], 0f, 100f,
2118 AlignmentAnnotation.BAR_GRAPH);
2119 initConsensus(complementConsensus);
2127 private void initConsensus(AlignmentAnnotation aa)
2130 aa.autoCalculated = true;
2134 alignment.addAnnotation(aa);
2138 // these should be extracted from the view model - style and settings for
2139 // derived annotation
2140 private void initGapCounts()
2144 gapcounts = new AlignmentAnnotation("Occupancy",
2145 MessageManager.getString("label.occupancy_descr"),
2146 new Annotation[1], 0f, alignment.getHeight(),
2147 AlignmentAnnotation.BAR_GRAPH);
2148 gapcounts.hasText = true;
2149 gapcounts.autoCalculated = true;
2150 gapcounts.scaleColLabel = true;
2151 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
2153 alignment.addAnnotation(gapcounts);
2157 private void initConservation()
2159 if (showConservation)
2161 if (conservation == null)
2163 conservation = new AlignmentAnnotation("Conservation",
2164 MessageManager.formatMessage("label.conservation_descr",
2166 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2167 conservation.hasText = true;
2168 conservation.autoCalculated = true;
2169 alignment.addAnnotation(conservation);
2174 private void initQuality()
2178 if (quality == null)
2180 quality = new AlignmentAnnotation("Quality",
2181 MessageManager.getString("label.quality_descr"),
2182 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2183 quality.hasText = true;
2184 quality.autoCalculated = true;
2185 alignment.addAnnotation(quality);
2190 private void initRNAStructure()
2192 if (alignment.hasRNAStructure() && strucConsensus == null)
2194 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2195 MessageManager.getString("label.strucconsensus_descr"),
2196 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2197 strucConsensus.hasText = true;
2198 strucConsensus.autoCalculated = true;
2202 alignment.addAnnotation(strucConsensus);
2210 * @see jalview.api.AlignViewportI#calcPanelHeight()
2213 public int calcPanelHeight()
2215 // setHeight of panels
2216 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2218 int charHeight = getCharHeight();
2221 BitSet graphgrp = new BitSet();
2222 for (AlignmentAnnotation aa : anns)
2226 System.err.println("Null annotation row: ignoring.");
2233 if (aa.graphGroup > -1)
2235 if (graphgrp.get(aa.graphGroup))
2241 graphgrp.set(aa.graphGroup);
2248 aa.height += charHeight;
2258 aa.height += aa.graphHeight;
2266 height += aa.height;
2278 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2279 boolean preserveNewGroupSettings)
2281 boolean updateCalcs = false;
2282 boolean conv = isShowGroupConservation();
2283 boolean cons = isShowGroupConsensus();
2284 boolean showprf = isShowSequenceLogo();
2285 boolean showConsHist = isShowConsensusHistogram();
2286 boolean normLogo = isNormaliseSequenceLogo();
2287 boolean showHMMPrf = isShowHMMSequenceLogo();
2288 boolean showInfoHist = isShowInformationHistogram();
2289 boolean normHMMLogo = isNormaliseHMMSequenceLogo();
2292 * TODO reorder the annotation rows according to group/sequence ordering on
2295 // boolean sortg = true;
2297 // remove old automatic annotation
2298 // add any new annotation
2300 // intersect alignment annotation with alignment groups
2302 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2303 List<SequenceGroup> oldrfs = new ArrayList<>();
2306 for (int an = 0; an < aan.length; an++)
2308 if (aan[an].autoCalculated && aan[an].groupRef != null)
2310 oldrfs.add(aan[an].groupRef);
2311 alignment.deleteAnnotation(aan[an], false);
2315 if (alignment.getGroups() != null)
2317 for (SequenceGroup sg : alignment.getGroups())
2319 updateCalcs = false;
2320 if (applyGlobalSettings
2321 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2323 // set defaults for this group's conservation/consensus
2324 sg.setshowSequenceLogo(showprf);
2325 sg.setShowConsensusHistogram(showConsHist);
2326 sg.setNormaliseSequenceLogo(normLogo);
2327 sg.setShowHMMSequenceLogo(showHMMPrf);
2328 sg.setShowInformationHistogram(showInfoHist);
2329 sg.setNormaliseHMMSequenceLogo(normHMMLogo);
2334 alignment.addAnnotation(sg.getConservationRow(), 0);
2339 alignment.addAnnotation(sg.getConsensus(), 0);
2341 // refresh the annotation rows
2344 sg.recalcConservation();
2352 public boolean isDisplayReferenceSeq()
2354 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2358 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2360 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2364 public boolean isColourByReferenceSeq()
2366 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2370 public Color getSequenceColour(SequenceI seq)
2372 Color sqc = sequenceColours.get(seq);
2373 return (sqc == null ? Color.white : sqc);
2377 public void setSequenceColour(SequenceI seq, Color col)
2381 sequenceColours.remove(seq);
2385 sequenceColours.put(seq, col);
2390 public void updateSequenceIdColours()
2392 for (SequenceGroup sg : alignment.getGroups())
2394 if (sg.idColour != null)
2396 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2398 sequenceColours.put(s, sg.idColour);
2405 public void clearSequenceColours()
2407 sequenceColours.clear();
2411 public AlignViewportI getCodingComplement()
2413 return this.codingComplement;
2417 * Set this as the (cDna/protein) complement of the given viewport. Also
2418 * ensures the reverse relationship is set on the given viewport.
2421 public void setCodingComplement(AlignViewportI av)
2425 System.err.println("Ignoring recursive setCodingComplement request");
2429 this.codingComplement = av;
2430 // avoid infinite recursion!
2431 if (av.getCodingComplement() != this)
2433 av.setCodingComplement(this);
2439 public boolean isNucleotide()
2441 return getAlignment() == null ? false : getAlignment().isNucleotide();
2445 public FeaturesDisplayedI getFeaturesDisplayed()
2447 return featuresDisplayed;
2451 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2453 featuresDisplayed = featuresDisplayedI;
2457 public boolean areFeaturesDisplayed()
2459 return featuresDisplayed != null
2460 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2467 * features are displayed if true
2470 public void setShowSequenceFeatures(boolean b)
2472 viewStyle.setShowSequenceFeatures(b);
2476 public boolean isShowSequenceFeatures()
2478 return viewStyle.isShowSequenceFeatures();
2482 public void setShowSequenceFeaturesHeight(boolean selected)
2484 viewStyle.setShowSequenceFeaturesHeight(selected);
2488 public boolean isShowSequenceFeaturesHeight()
2490 return viewStyle.isShowSequenceFeaturesHeight();
2494 public void setShowAnnotation(boolean b)
2496 viewStyle.setShowAnnotation(b);
2500 public boolean isShowAnnotation()
2502 return viewStyle.isShowAnnotation();
2506 public boolean isRightAlignIds()
2508 return viewStyle.isRightAlignIds();
2512 public void setRightAlignIds(boolean rightAlignIds)
2514 viewStyle.setRightAlignIds(rightAlignIds);
2518 public boolean getConservationSelected()
2520 return viewStyle.getConservationSelected();
2524 public void setShowBoxes(boolean state)
2526 viewStyle.setShowBoxes(state);
2531 * @see jalview.api.ViewStyleI#getTextColour()
2534 public Color getTextColour()
2536 return viewStyle.getTextColour();
2541 * @see jalview.api.ViewStyleI#getTextColour2()
2544 public Color getTextColour2()
2546 return viewStyle.getTextColour2();
2551 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2554 public int getThresholdTextColour()
2556 return viewStyle.getThresholdTextColour();
2561 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2564 public boolean isConservationColourSelected()
2566 return viewStyle.isConservationColourSelected();
2571 * @see jalview.api.ViewStyleI#isRenderGaps()
2574 public boolean isRenderGaps()
2576 return viewStyle.isRenderGaps();
2581 * @see jalview.api.ViewStyleI#isShowColourText()
2584 public boolean isShowColourText()
2586 return viewStyle.isShowColourText();
2590 * @param conservationColourSelected
2591 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2594 public void setConservationColourSelected(
2595 boolean conservationColourSelected)
2597 viewStyle.setConservationColourSelected(conservationColourSelected);
2601 * @param showColourText
2602 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2605 public void setShowColourText(boolean showColourText)
2607 viewStyle.setShowColourText(showColourText);
2612 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2615 public void setTextColour(Color textColour)
2617 viewStyle.setTextColour(textColour);
2621 * @param thresholdTextColour
2622 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2625 public void setThresholdTextColour(int thresholdTextColour)
2627 viewStyle.setThresholdTextColour(thresholdTextColour);
2631 * @param textColour2
2632 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2635 public void setTextColour2(Color textColour2)
2637 viewStyle.setTextColour2(textColour2);
2641 public ViewStyleI getViewStyle()
2643 return new ViewStyle(viewStyle);
2647 public void setViewStyle(ViewStyleI settingsForView)
2649 viewStyle = new ViewStyle(settingsForView);
2650 if (residueShading != null)
2652 residueShading.setConservationApplied(
2653 settingsForView.isConservationColourSelected());
2658 public boolean sameStyle(ViewStyleI them)
2660 return viewStyle.sameStyle(them);
2665 * @see jalview.api.ViewStyleI#getIdWidth()
2668 public int getIdWidth()
2670 return viewStyle.getIdWidth();
2675 * @see jalview.api.ViewStyleI#setIdWidth(int)
2678 public void setIdWidth(int i)
2680 viewStyle.setIdWidth(i);
2685 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2688 public boolean isCentreColumnLabels()
2690 return viewStyle.isCentreColumnLabels();
2694 * @param centreColumnLabels
2695 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2698 public void setCentreColumnLabels(boolean centreColumnLabels)
2700 viewStyle.setCentreColumnLabels(centreColumnLabels);
2705 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2708 public void setShowDBRefs(boolean showdbrefs)
2710 viewStyle.setShowDBRefs(showdbrefs);
2715 * @see jalview.api.ViewStyleI#isShowDBRefs()
2718 public boolean isShowDBRefs()
2720 return viewStyle.isShowDBRefs();
2725 * @see jalview.api.ViewStyleI#isShowNPFeats()
2728 public boolean isShowNPFeats()
2730 return viewStyle.isShowNPFeats();
2734 * @param shownpfeats
2735 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2738 public void setShowNPFeats(boolean shownpfeats)
2740 viewStyle.setShowNPFeats(shownpfeats);
2743 public abstract StructureSelectionManager getStructureSelectionManager();
2746 * Add one command to the command history list.
2750 public void addToHistoryList(CommandI command)
2752 if (this.historyList != null)
2754 this.historyList.push(command);
2755 broadcastCommand(command, false);
2759 protected void broadcastCommand(CommandI command, boolean undo)
2761 getStructureSelectionManager().commandPerformed(command, undo,
2766 * Add one command to the command redo list.
2770 public void addToRedoList(CommandI command)
2772 if (this.redoList != null)
2774 this.redoList.push(command);
2776 broadcastCommand(command, true);
2780 * Clear the command redo list.
2782 public void clearRedoList()
2784 if (this.redoList != null)
2786 this.redoList.clear();
2790 public void setHistoryList(Deque<CommandI> list)
2792 this.historyList = list;
2795 public Deque<CommandI> getHistoryList()
2797 return this.historyList;
2800 public void setRedoList(Deque<CommandI> list)
2802 this.redoList = list;
2805 public Deque<CommandI> getRedoList()
2807 return this.redoList;
2811 public VamsasSource getVamsasSource()
2816 public SequenceAnnotationOrder getSortAnnotationsBy()
2818 return sortAnnotationsBy;
2821 public void setSortAnnotationsBy(
2822 SequenceAnnotationOrder sortAnnotationsBy)
2824 this.sortAnnotationsBy = sortAnnotationsBy;
2827 public boolean isShowAutocalculatedAbove()
2829 return showAutocalculatedAbove;
2832 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2834 this.showAutocalculatedAbove = showAutocalculatedAbove;
2838 public boolean isScaleProteinAsCdna()
2840 return viewStyle.isScaleProteinAsCdna();
2844 public void setScaleProteinAsCdna(boolean b)
2846 viewStyle.setScaleProteinAsCdna(b);
2850 public boolean isProteinFontAsCdna()
2852 return viewStyle.isProteinFontAsCdna();
2856 public void setProteinFontAsCdna(boolean b)
2858 viewStyle.setProteinFontAsCdna(b);
2862 public void setShowComplementFeatures(boolean b)
2864 viewStyle.setShowComplementFeatures(b);
2868 public boolean isShowComplementFeatures()
2870 return viewStyle.isShowComplementFeatures();
2874 public void setShowComplementFeaturesOnTop(boolean b)
2876 viewStyle.setShowComplementFeaturesOnTop(b);
2880 public boolean isShowComplementFeaturesOnTop()
2882 return viewStyle.isShowComplementFeaturesOnTop();
2886 * @return true if view should scroll to show the highlighted region of a
2891 public final boolean isFollowHighlight()
2893 return followHighlight;
2897 public final void setFollowHighlight(boolean b)
2899 this.followHighlight = b;
2903 public ViewportRanges getRanges()
2909 * Helper method to populate the SearchResults with the location in the
2910 * complementary alignment to scroll to, in order to match this one.
2913 * the SearchResults to add to
2914 * @return the offset (below top of visible region) of the matched sequence
2916 protected int findComplementScrollTarget(SearchResultsI sr)
2918 final AlignViewportI complement = getCodingComplement();
2919 if (complement == null || !complement.isFollowHighlight())
2923 boolean iAmProtein = !getAlignment().isNucleotide();
2924 AlignmentI proteinAlignment = iAmProtein ? getAlignment()
2925 : complement.getAlignment();
2926 if (proteinAlignment == null)
2930 final List<AlignedCodonFrame> mappings = proteinAlignment
2934 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2935 * residue in the middle column of the visible region. Scroll the
2936 * complementary alignment to line up the corresponding residue.
2939 SequenceI sequence = null;
2942 * locate 'middle' column (true middle if an odd number visible, left of
2943 * middle if an even number visible)
2945 int middleColumn = ranges.getStartRes()
2946 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2947 final HiddenSequences hiddenSequences = getAlignment()
2948 .getHiddenSequences();
2951 * searching to the bottom of the alignment gives smoother scrolling across
2952 * all gapped visible regions
2954 int lastSeq = alignment.getHeight() - 1;
2955 List<AlignedCodonFrame> seqMappings = null;
2956 for (int seqNo = ranges
2957 .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
2959 sequence = getAlignment().getSequenceAt(seqNo);
2960 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2964 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2968 seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
2970 getCodingComplement().getAlignment().getSequences());
2971 if (!seqMappings.isEmpty())
2977 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2980 * No ungapped mapped sequence in middle column - do nothing
2984 MappingUtils.addSearchResults(sr, sequence,
2985 sequence.findPosition(middleColumn), seqMappings);
2990 * synthesize a column selection if none exists so it covers the given
2991 * selection group. if wholewidth is false, no column selection is made if the
2992 * selection group covers the whole alignment width.
2997 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
3000 if (sg != null && (sgs = sg.getStartRes()) >= 0
3001 && sg.getStartRes() <= (sge = sg.getEndRes())
3002 && !this.hasSelectedColumns())
3004 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
3011 colSel = new ColumnSelection();
3013 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
3015 colSel.addElement(cspos);
3021 * hold status of current selection group - defined on alignment or not.
3023 private boolean selectionIsDefinedGroup = false;
3026 public boolean isSelectionDefinedGroup()
3028 if (selectionGroup == null)
3032 if (isSelectionGroupChanged(true))
3034 selectionIsDefinedGroup = false;
3035 List<SequenceGroup> gps = alignment.getGroups();
3036 if (gps == null || gps.size() == 0)
3038 selectionIsDefinedGroup = false;
3042 selectionIsDefinedGroup = gps.contains(selectionGroup);
3045 return selectionGroup.isDefined() || selectionIsDefinedGroup;
3049 * null, or currently highlighted results on this view
3051 private SearchResultsI searchResults = null;
3053 protected TreeModel currentTree = null;
3056 public boolean hasSearchResults()
3058 return searchResults != null;
3062 public void setSearchResults(SearchResultsI results)
3064 searchResults = results;
3068 public SearchResultsI getSearchResults()
3070 return searchResults;
3074 * get the consensus sequence as displayed under the PID consensus annotation
3077 * @return consensus sequence as a new sequence object
3079 public SequenceI getConsensusSeq()
3081 if (consensus == null)
3083 updateConsensus(null);
3085 if (consensus == null)
3089 StringBuffer seqs = new StringBuffer();
3090 for (int i = 0; i < consensus.annotations.length; i++)
3092 Annotation annotation = consensus.annotations[i];
3093 if (annotation != null)
3095 String description = annotation.description;
3096 if (description != null && description.startsWith("["))
3098 // consensus is a tie - just pick the first one
3099 seqs.append(description.charAt(1));
3103 seqs.append(annotation.displayCharacter);
3108 SequenceI sq = new Sequence("Consensus", seqs.toString());
3109 sq.setDescription("Percentage Identity Consensus "
3110 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
3114 public boolean hasReferenceAnnotation()
3116 AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation();
3117 for (AlignmentAnnotation annot : annots)
3119 if ("RF".equals(annot.label) || annot.label.contains("Reference"))
3127 public void setCurrentTree(TreeModel tree)
3133 public TreeModel getCurrentTree()
3139 public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
3141 AlignmentI alignmentToExport = null;
3142 String[] omitHidden = null;
3143 alignmentToExport = null;
3145 if (hasHiddenColumns() && !options.isExportHiddenColumns())
3147 omitHidden = getViewAsString(false,
3148 options.isExportHiddenSequences());
3151 int[] alignmentStartEnd = new int[2];
3152 if (hasHiddenRows() && options.isExportHiddenSequences())
3154 alignmentToExport = getAlignment().getHiddenSequences()
3155 .getFullAlignment();
3159 alignmentToExport = getAlignment();
3161 alignmentStartEnd = getAlignment().getHiddenColumns()
3162 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
3163 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
3164 omitHidden, alignmentStartEnd);
3169 public boolean isNormaliseSequenceLogo()
3171 return normaliseSequenceLogo;
3174 public void setNormaliseSequenceLogo(boolean state)
3176 normaliseSequenceLogo = state;
3180 public boolean isNormaliseHMMSequenceLogo()
3182 return hmmNormaliseSequenceLogo;
3185 public void setNormaliseHMMSequenceLogo(boolean state)
3187 hmmNormaliseSequenceLogo = state;
3190 * flag set to indicate if structure views might be out of sync with sequences
3194 private boolean needToUpdateStructureViews = false;
3197 public boolean isUpdateStructures()
3199 return needToUpdateStructureViews;
3203 public void setUpdateStructures(boolean update)
3205 needToUpdateStructureViews = update;
3209 public boolean needToUpdateStructureViews()
3211 boolean update = needToUpdateStructureViews;
3212 needToUpdateStructureViews = false;
3217 public void addSequenceGroup(SequenceGroup sequenceGroup)
3219 alignment.addGroup(sequenceGroup);
3221 Color col = sequenceGroup.idColour;
3224 col = col.brighter();
3226 for (SequenceI sq : sequenceGroup.getSequences())
3228 setSequenceColour(sq, col);
3232 if (codingComplement != null)
3234 SequenceGroup mappedGroup = MappingUtils
3235 .mapSequenceGroup(sequenceGroup, this, codingComplement);
3236 if (mappedGroup.getSequences().size() > 0)
3238 codingComplement.getAlignment().addGroup(mappedGroup);
3242 for (SequenceI seq : mappedGroup.getSequences())
3244 codingComplement.setSequenceColour(seq, col);
3248 // propagate the structure view update flag according to our own setting
3249 codingComplement.setUpdateStructures(needToUpdateStructureViews);
3254 public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
3258 if (selectedRegionOnly && selectionGroup != null)
3260 start = selectionGroup.getStartRes();
3261 end = selectionGroup.getEndRes() + 1;
3265 end = alignment.getWidth();
3267 return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
3271 * Filters out sequences with an eValue higher than the specified value. The
3272 * filtered sequences are hidden or deleted. Sequences with no eValues are also
3278 public void filterByEvalue(double eValue)
3280 for (SequenceI seq : alignment.getSequencesArray())
3282 if ((seq.getAnnotation("Search Scores") == null
3283 || seq.getAnnotation("Search Scores")[0].getEValue() > eValue)
3284 && seq.getHMM() == null)
3286 hideSequence(new SequenceI[] { seq });
3292 * Filters out sequences with an score lower than the specified value. The
3293 * filtered sequences are hidden or deleted.
3298 public void filterByScore(double score)
3300 for (SequenceI seq : alignment.getSequencesArray())
3302 if ((seq.getAnnotation("Search Scores") == null
3303 || seq.getAnnotation("Search Scores")[0]
3304 .getBitScore() < score)
3305 && seq.getHMM() == null)
3307 hideSequence(new SequenceI[] { seq });
3313 * Notify TreePanel and AlignmentPanel of some sort of alignment change.
3315 public void notifyAlignment()
3317 changeSupport.firePropertyChange(PROPERTY_ALIGNMENT, null, alignment.getSequences());
3321 * Notify AlignmentPanel of a sequence column selection or visibility changes.
3323 public void notifySequence()
3325 changeSupport.firePropertyChange(PROPERTY_SEQUENCE, null, null);