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.Connectivity;
25 import jalview.analysis.Conservation;
26 import jalview.analysis.TreeModel;
27 import jalview.api.AlignCalcManagerI;
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.AlignCalcManager;
61 import jalview.workers.ComplementConsensusThread;
62 import jalview.workers.ConsensusThread;
63 import jalview.workers.StrucConsensusThread;
65 import java.awt.Color;
66 import java.beans.PropertyChangeSupport;
67 import java.util.ArrayDeque;
68 import java.util.ArrayList;
69 import java.util.BitSet;
70 import java.util.Deque;
71 import java.util.HashMap;
72 import java.util.Hashtable;
73 import java.util.Iterator;
74 import java.util.List;
78 * base class holding visualization and analysis attributes and common logic for
79 * an active alignment view displayed in the GUI
84 public abstract class AlignmentViewport
85 implements AlignViewportI, CommandListener, VamsasSource
87 protected ViewportRanges ranges;
89 protected ViewStyleI viewStyle = new ViewStyle();
92 * A viewport that hosts the cDna view of this (protein), or vice versa (if
95 AlignViewportI codingComplement = null;
97 FeaturesDisplayedI featuresDisplayed = null;
99 protected Deque<CommandI> historyList = new ArrayDeque<>();
101 protected Deque<CommandI> redoList = new ArrayDeque<>();
104 * alignment displayed in the viewport. Please use get/setter
106 protected AlignmentI alignment;
108 public AlignmentViewport(AlignmentI al)
111 ranges = new ViewportRanges(al);
116 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
119 public void setFontName(String name)
121 viewStyle.setFontName(name);
126 * @see jalview.api.ViewStyleI#setFontStyle(int)
129 public void setFontStyle(int style)
131 viewStyle.setFontStyle(style);
136 * @see jalview.api.ViewStyleI#setFontSize(int)
139 public void setFontSize(int size)
141 viewStyle.setFontSize(size);
146 * @see jalview.api.ViewStyleI#getFontStyle()
149 public int getFontStyle()
151 return viewStyle.getFontStyle();
156 * @see jalview.api.ViewStyleI#getFontName()
159 public String getFontName()
161 return viewStyle.getFontName();
166 * @see jalview.api.ViewStyleI#getFontSize()
169 public int getFontSize()
171 return viewStyle.getFontSize();
175 * @param upperCasebold
176 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
179 public void setUpperCasebold(boolean upperCasebold)
181 viewStyle.setUpperCasebold(upperCasebold);
186 * @see jalview.api.ViewStyleI#isUpperCasebold()
189 public boolean isUpperCasebold()
191 return viewStyle.isUpperCasebold();
196 * @see jalview.api.ViewStyleI#isSeqNameItalics()
199 public boolean isSeqNameItalics()
201 return viewStyle.isSeqNameItalics();
205 * @param colourByReferenceSeq
206 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
209 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
211 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
216 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
219 public void setColourAppliesToAllGroups(boolean b)
221 viewStyle.setColourAppliesToAllGroups(b);
226 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
229 public boolean getColourAppliesToAllGroups()
231 return viewStyle.getColourAppliesToAllGroups();
236 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
239 public boolean getAbovePIDThreshold()
241 return viewStyle.getAbovePIDThreshold();
246 * @see jalview.api.ViewStyleI#setIncrement(int)
249 public void setIncrement(int inc)
251 viewStyle.setIncrement(inc);
256 * @see jalview.api.ViewStyleI#getIncrement()
259 public int getIncrement()
261 return viewStyle.getIncrement();
266 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
269 public void setConservationSelected(boolean b)
271 viewStyle.setConservationSelected(b);
276 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
279 public void setShowHiddenMarkers(boolean show)
281 viewStyle.setShowHiddenMarkers(show);
286 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
289 public boolean getShowHiddenMarkers()
291 return viewStyle.getShowHiddenMarkers();
296 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
299 public void setScaleRightWrapped(boolean b)
301 viewStyle.setScaleRightWrapped(b);
306 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
309 public void setScaleLeftWrapped(boolean b)
311 viewStyle.setScaleLeftWrapped(b);
316 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
319 public void setScaleAboveWrapped(boolean b)
321 viewStyle.setScaleAboveWrapped(b);
326 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
329 public boolean getScaleLeftWrapped()
331 return viewStyle.getScaleLeftWrapped();
336 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
339 public boolean getScaleAboveWrapped()
341 return viewStyle.getScaleAboveWrapped();
346 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
349 public boolean getScaleRightWrapped()
351 return viewStyle.getScaleRightWrapped();
356 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
359 public void setAbovePIDThreshold(boolean b)
361 viewStyle.setAbovePIDThreshold(b);
366 * @see jalview.api.ViewStyleI#setThreshold(int)
369 public void setThreshold(int thresh)
371 viewStyle.setThreshold(thresh);
376 * @see jalview.api.ViewStyleI#getThreshold()
379 public int getThreshold()
381 return viewStyle.getThreshold();
386 * @see jalview.api.ViewStyleI#getShowJVSuffix()
389 public boolean getShowJVSuffix()
391 return viewStyle.getShowJVSuffix();
396 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
399 public void setShowJVSuffix(boolean b)
401 viewStyle.setShowJVSuffix(b);
406 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
409 public void setWrapAlignment(boolean state)
411 viewStyle.setWrapAlignment(state);
412 ranges.setWrappedMode(state);
417 * @see jalview.api.ViewStyleI#setShowText(boolean)
420 public void setShowText(boolean state)
422 viewStyle.setShowText(state);
427 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
430 public void setRenderGaps(boolean state)
432 viewStyle.setRenderGaps(state);
437 * @see jalview.api.ViewStyleI#getColourText()
440 public boolean getColourText()
442 return viewStyle.getColourText();
447 * @see jalview.api.ViewStyleI#setColourText(boolean)
450 public void setColourText(boolean state)
452 viewStyle.setColourText(state);
457 * @see jalview.api.ViewStyleI#getWrapAlignment()
460 public boolean getWrapAlignment()
462 return viewStyle.getWrapAlignment();
467 * @see jalview.api.ViewStyleI#getShowText()
470 public boolean getShowText()
472 return viewStyle.getShowText();
477 * @see jalview.api.ViewStyleI#getWrappedWidth()
480 public int getWrappedWidth()
482 return viewStyle.getWrappedWidth();
487 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
490 public void setWrappedWidth(int w)
492 viewStyle.setWrappedWidth(w);
497 * @see jalview.api.ViewStyleI#getCharHeight()
500 public int getCharHeight()
502 return viewStyle.getCharHeight();
507 * @see jalview.api.ViewStyleI#setCharHeight(int)
510 public void setCharHeight(int h)
512 viewStyle.setCharHeight(h);
517 * @see jalview.api.ViewStyleI#getCharWidth()
520 public int getCharWidth()
522 return viewStyle.getCharWidth();
527 * @see jalview.api.ViewStyleI#setCharWidth(int)
530 public void setCharWidth(int w)
532 viewStyle.setCharWidth(w);
537 * @see jalview.api.ViewStyleI#getShowBoxes()
540 public boolean getShowBoxes()
542 return viewStyle.getShowBoxes();
547 * @see jalview.api.ViewStyleI#getShowUnconserved()
550 public boolean getShowUnconserved()
552 return viewStyle.getShowUnconserved();
556 * @param showunconserved
557 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
560 public void setShowUnconserved(boolean showunconserved)
562 viewStyle.setShowUnconserved(showunconserved);
567 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
570 public void setSeqNameItalics(boolean default1)
572 viewStyle.setSeqNameItalics(default1);
576 public AlignmentI getAlignment()
582 public char getGapCharacter()
584 return alignment.getGapCharacter();
587 protected String sequenceSetID;
590 * probably unused indicator that view is of a dataset rather than an
593 protected boolean isDataset = false;
595 public void setDataset(boolean b)
600 public boolean isDataset()
605 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
607 protected ColumnSelection colSel = new ColumnSelection();
609 public boolean autoCalculateConsensus = true;
611 protected boolean autoCalculateStrucConsensus = true;
613 protected boolean ignoreGapsInConsensusCalculation = false;
615 protected ResidueShaderI residueShading = new ResidueShader();
618 public void setGlobalColourScheme(ColourSchemeI cs)
620 // TODO: logic refactored from AlignFrame changeColour -
621 // TODO: autorecalc stuff should be changed to rely on the worker system
622 // check to see if we should implement a changeColour(cs) method rather than
623 // put the logic in here
624 // - means that caller decides if they want to just modify state and defer
625 // calculation till later or to do all calculations in thread.
629 * only instantiate alignment colouring once, thereafter update it;
630 * this means that any conservation or PID threshold settings
631 * persist when the alignment colour scheme is changed
633 if (residueShading == null)
635 residueShading = new ResidueShader(viewStyle);
637 residueShading.setColourScheme(cs);
639 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
640 // ...problem: groups need these, but do not currently have a ViewStyle
644 if (getConservationSelected())
646 residueShading.setConservation(hconservation);
649 * reset conservation flag in case just set to false if
650 * Conservation was null (calculation still in progress)
652 residueShading.setConservationApplied(getConservationSelected());
653 residueShading.alignmentChanged(alignment, hiddenRepSequences);
657 * if 'apply colour to all groups' is selected... do so
658 * (but don't transfer any colour threshold settings to groups)
660 if (getColourAppliesToAllGroups())
662 for (SequenceGroup sg : getAlignment().getGroups())
665 * retain any colour thresholds per group while
666 * changing choice of colour scheme (JAL-2386)
668 sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg));
671 sg.getGroupColourScheme().alignmentChanged(sg,
679 public ColourSchemeI getGlobalColourScheme()
681 return residueShading == null ? null : residueShading.getColourScheme();
685 public ResidueShaderI getResidueShading()
687 return residueShading;
690 protected AlignmentAnnotation consensus;
692 protected AlignmentAnnotation complementConsensus;
694 protected AlignmentAnnotation gapcounts;
696 protected AlignmentAnnotation strucConsensus;
698 protected AlignmentAnnotation conservation;
700 protected AlignmentAnnotation quality;
702 protected AlignmentAnnotation[] groupConsensus;
704 protected AlignmentAnnotation[] groupConservation;
707 * results of alignment consensus analysis for visible portion of view
709 protected ProfilesI hconsensus = null;
712 * results of cDNA complement consensus visible portion of view
714 protected Hashtable<String, Object>[] hcomplementConsensus = null;
717 * results of secondary structure base pair consensus for visible portion of
720 protected Hashtable<String, Object>[] hStrucConsensus = null;
722 protected Conservation hconservation = null;
725 public void setConservation(Conservation cons)
727 hconservation = cons;
731 * percentage gaps allowed in a column before all amino acid properties should
732 * be considered unconserved
734 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
737 public int getConsPercGaps()
743 public void setSequenceConsensusHash(ProfilesI hconsensus)
745 this.hconsensus = hconsensus;
749 public void setComplementConsensusHash(
750 Hashtable<String, Object>[] hconsensus)
752 this.hcomplementConsensus = hconsensus;
756 public ProfilesI getSequenceConsensusHash()
762 public Hashtable<String, Object>[] getComplementConsensusHash()
764 return hcomplementConsensus;
768 public Hashtable<String, Object>[] getRnaStructureConsensusHash()
770 return hStrucConsensus;
774 public void setRnaStructureConsensusHash(
775 Hashtable<String, Object>[] hStrucConsensus)
777 this.hStrucConsensus = hStrucConsensus;
782 public AlignmentAnnotation getAlignmentQualityAnnot()
788 public AlignmentAnnotation getAlignmentConservationAnnotation()
794 public AlignmentAnnotation getAlignmentConsensusAnnotation()
800 public AlignmentAnnotation getAlignmentGapAnnotation()
806 public AlignmentAnnotation getComplementConsensusAnnotation()
808 return complementConsensus;
812 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
814 return strucConsensus;
817 protected AlignCalcManagerI calculator = new AlignCalcManager();
820 * trigger update of conservation annotation
822 public void updateConservation(final AlignmentViewPanel ap)
824 // see note in mantis : issue number 8585
825 if (alignment.isNucleotide()
826 || (conservation == null && quality == null)
827 || !autoCalculateConsensus)
831 if (calculator.getRegisteredWorkersOfClass(
832 jalview.workers.ConservationThread.class) == null)
834 calculator.registerWorker(
835 new jalview.workers.ConservationThread(this, ap));
840 * trigger update of consensus annotation
842 public void updateConsensus(final AlignmentViewPanel ap)
844 // see note in mantis : issue number 8585
845 if (consensus == null || !autoCalculateConsensus)
850 .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
852 calculator.registerWorker(new ConsensusThread(this, ap));
856 * A separate thread to compute cDNA consensus for a protein alignment
857 * which has mapping to cDNA
859 final AlignmentI al = this.getAlignment();
860 if (!al.isNucleotide() && al.getCodonFrames() != null
861 && !al.getCodonFrames().isEmpty())
864 * fudge - check first for protein-to-nucleotide mappings
865 * (we don't want to do this for protein-to-protein)
867 boolean doConsensus = false;
868 for (AlignedCodonFrame mapping : al.getCodonFrames())
870 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
871 MapList[] mapLists = mapping.getdnaToProt();
872 // mapLists can be empty if project load has not finished resolving seqs
873 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
881 if (calculator.getRegisteredWorkersOfClass(
882 ComplementConsensusThread.class) == null)
885 .registerWorker(new ComplementConsensusThread(this, ap));
891 // --------START Structure Conservation
892 public void updateStrucConsensus(final AlignmentViewPanel ap)
894 if (autoCalculateStrucConsensus && strucConsensus == null
895 && alignment.isNucleotide() && alignment.hasRNAStructure())
897 // secondary structure has been added - so init the consensus line
901 // see note in mantis : issue number 8585
902 if (strucConsensus == null || !autoCalculateStrucConsensus)
906 if (calculator.getRegisteredWorkersOfClass(
907 StrucConsensusThread.class) == null)
909 calculator.registerWorker(new StrucConsensusThread(this, ap));
913 public boolean isCalcInProgress()
915 return calculator.isWorking();
919 public boolean isCalculationInProgress(
920 AlignmentAnnotation alignmentAnnotation)
922 if (!alignmentAnnotation.autoCalculated)
926 if (calculator.workingInvolvedWith(alignmentAnnotation))
928 // System.err.println("grey out ("+alignmentAnnotation.label+")");
934 public void setAlignment(AlignmentI align)
936 this.alignment = align;
940 * Clean up references when this viewport is closed
943 public void dispose()
946 * defensively null out references to large objects in case
947 * this object is not garbage collected (as if!)
950 complementConsensus = null;
951 strucConsensus = null;
954 groupConsensus = null;
955 groupConservation = null;
957 hconservation = null;
958 hcomplementConsensus = null;
961 residueShading = null; // may hold a reference to Consensus
962 changeSupport = null;
965 selectionGroup = null;
971 public boolean isClosed()
973 // TODO: check that this isClosed is only true after panel is closed, not
974 // before it is fully constructed.
975 return alignment == null;
979 public AlignCalcManagerI getCalcManager()
985 * should conservation rows be shown for groups
987 protected boolean showGroupConservation = false;
990 * should consensus rows be shown for groups
992 protected boolean showGroupConsensus = false;
995 * should consensus profile be rendered by default
997 protected boolean showSequenceLogo = false;
1000 * should consensus profile be rendered normalised to row height
1002 protected boolean normaliseSequenceLogo = false;
1005 * should consensus histograms be rendered by default
1007 protected boolean showConsensusHistogram = true;
1010 * @return the showConsensusProfile
1013 public boolean isShowSequenceLogo()
1015 return showSequenceLogo;
1019 * @param showSequenceLogo
1022 public void setShowSequenceLogo(boolean showSequenceLogo)
1024 if (showSequenceLogo != this.showSequenceLogo)
1026 // TODO: decouple settings setting from calculation when refactoring
1027 // annotation update method from alignframe to viewport
1028 this.showSequenceLogo = showSequenceLogo;
1029 calculator.updateAnnotationFor(ConsensusThread.class);
1030 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1031 calculator.updateAnnotationFor(StrucConsensusThread.class);
1033 this.showSequenceLogo = showSequenceLogo;
1037 * @param showConsensusHistogram
1038 * the showConsensusHistogram to set
1040 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1042 this.showConsensusHistogram = showConsensusHistogram;
1046 * @return the showGroupConservation
1048 public boolean isShowGroupConservation()
1050 return showGroupConservation;
1054 * @param showGroupConservation
1055 * the showGroupConservation to set
1057 public void setShowGroupConservation(boolean showGroupConservation)
1059 this.showGroupConservation = showGroupConservation;
1063 * @return the showGroupConsensus
1065 public boolean isShowGroupConsensus()
1067 return showGroupConsensus;
1071 * @param showGroupConsensus
1072 * the showGroupConsensus to set
1074 public void setShowGroupConsensus(boolean showGroupConsensus)
1076 this.showGroupConsensus = showGroupConsensus;
1081 * @return flag to indicate if the consensus histogram should be rendered by
1085 public boolean isShowConsensusHistogram()
1087 return this.showConsensusHistogram;
1091 * when set, updateAlignment will always ensure sequences are of equal length
1093 private boolean padGaps = false;
1096 * when set, alignment should be reordered according to a newly opened tree
1098 public boolean sortByTree = false;
1103 * @return null or the currently selected sequence region
1106 public SequenceGroup getSelectionGroup()
1108 return selectionGroup;
1112 * Set the selection group for this window. Also sets the current alignment as
1113 * the context for the group, if it does not already have one.
1116 * - group holding references to sequences in this alignment view
1120 public void setSelectionGroup(SequenceGroup sg)
1122 selectionGroup = sg;
1123 if (sg != null && sg.getContext() == null)
1125 sg.setContext(alignment);
1129 public void setHiddenColumns(HiddenColumns hidden)
1131 this.alignment.setHiddenColumns(hidden);
1135 public ColumnSelection getColumnSelection()
1141 public void setColumnSelection(ColumnSelection colSel)
1143 this.colSel = colSel;
1146 updateHiddenColumns();
1148 isColSelChanged(true);
1156 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1158 return hiddenRepSequences;
1162 public void setHiddenRepSequences(
1163 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1165 this.hiddenRepSequences = hiddenRepSequences;
1169 public boolean hasSelectedColumns()
1171 ColumnSelection columnSelection = getColumnSelection();
1172 return columnSelection != null && columnSelection.hasSelectedColumns();
1176 public boolean hasHiddenColumns()
1178 return alignment.getHiddenColumns() != null
1179 && alignment.getHiddenColumns().hasHiddenColumns();
1182 public void updateHiddenColumns()
1184 // this method doesn't really do anything now. But - it could, since a
1185 // column Selection could be in the process of modification
1186 // hasHiddenColumns = colSel.hasHiddenColumns();
1190 public boolean hasHiddenRows()
1192 return alignment.getHiddenSequences().getSize() > 0;
1195 protected SequenceGroup selectionGroup;
1197 public void setSequenceSetId(String newid)
1199 if (sequenceSetID != null)
1202 "Warning - overwriting a sequenceSetId for a viewport!");
1204 sequenceSetID = new String(newid);
1208 public String getSequenceSetId()
1210 if (sequenceSetID == null)
1212 sequenceSetID = alignment.hashCode() + "";
1215 return sequenceSetID;
1219 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1222 protected String viewId = null;
1225 public String getViewId()
1229 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1234 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1236 ignoreGapsInConsensusCalculation = b;
1239 updateConsensus(ap);
1240 if (residueShading != null)
1242 residueShading.setThreshold(residueShading.getThreshold(),
1243 ignoreGapsInConsensusCalculation);
1249 private long sgrouphash = -1, colselhash = -1;
1252 * checks current SelectionGroup against record of last hash value, and
1256 * update the record of last hash value
1258 * @return true if SelectionGroup changed since last call (when b is true)
1260 public boolean isSelectionGroupChanged(boolean b)
1262 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1263 : selectionGroup.hashCode();
1264 if (hc != -1 && hc != sgrouphash)
1276 * checks current colsel against record of last hash value, and optionally
1280 * update the record of last hash value
1281 * @return true if colsel changed since last call (when b is true)
1283 public boolean isColSelChanged(boolean b)
1285 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1286 if (hc != -1 && hc != colselhash)
1298 public boolean isIgnoreGapsConsensus()
1300 return ignoreGapsInConsensusCalculation;
1303 // property change stuff
1304 // JBPNote Prolly only need this in the applet version.
1305 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1308 protected boolean showConservation = true;
1310 protected boolean showQuality = true;
1312 protected boolean showConsensus = true;
1314 protected boolean showOccupancy = true;
1316 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1318 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1320 protected boolean showAutocalculatedAbove;
1323 * when set, view will scroll to show the highlighted position
1325 private boolean followHighlight = true;
1328 * Property change listener for changes in alignment
1333 public void addPropertyChangeListener(
1334 java.beans.PropertyChangeListener listener)
1336 changeSupport.addPropertyChangeListener(listener);
1345 public void removePropertyChangeListener(
1346 java.beans.PropertyChangeListener listener)
1348 if (changeSupport != null)
1350 changeSupport.removePropertyChangeListener(listener);
1355 * Property change listener for changes in alignment
1364 public void firePropertyChange(String prop, Object oldvalue,
1367 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1370 // common hide/show column stuff
1372 public void hideSelectedColumns()
1374 if (colSel.isEmpty())
1379 colSel.hideSelectedColumns(alignment);
1380 setSelectionGroup(null);
1381 isColSelChanged(true);
1384 public void hideColumns(int start, int end)
1388 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1392 alignment.getHiddenColumns().hideColumns(start, end);
1394 isColSelChanged(true);
1397 public void showColumn(int col)
1399 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1400 isColSelChanged(true);
1403 public void showAllHiddenColumns()
1405 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1406 isColSelChanged(true);
1409 // common hide/show seq stuff
1410 public void showAllHiddenSeqs()
1412 int startSeq = ranges.getStartSeq();
1413 int endSeq = ranges.getEndSeq();
1415 if (alignment.getHiddenSequences().getSize() > 0)
1417 if (selectionGroup == null)
1419 selectionGroup = new SequenceGroup();
1420 selectionGroup.setEndRes(alignment.getWidth() - 1);
1422 List<SequenceI> tmp = alignment.getHiddenSequences()
1423 .showAll(hiddenRepSequences);
1424 for (SequenceI seq : tmp)
1426 selectionGroup.addSequence(seq, false);
1427 setSequenceAnnotationsVisible(seq, true);
1430 hiddenRepSequences = null;
1432 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1434 firePropertyChange("alignment", null, alignment.getSequences());
1435 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1441 public void showSequence(int index)
1443 int startSeq = ranges.getStartSeq();
1444 int endSeq = ranges.getEndSeq();
1446 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
1447 hiddenRepSequences);
1450 if (selectionGroup == null)
1452 selectionGroup = new SequenceGroup();
1453 selectionGroup.setEndRes(alignment.getWidth() - 1);
1456 for (SequenceI seq : tmp)
1458 selectionGroup.addSequence(seq, false);
1459 setSequenceAnnotationsVisible(seq, true);
1462 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1464 firePropertyChange("alignment", null, alignment.getSequences());
1469 public void hideAllSelectedSeqs()
1471 if (selectionGroup == null || selectionGroup.getSize() < 1)
1476 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1480 setSelectionGroup(null);
1483 public void hideSequence(SequenceI[] seq)
1486 * cache offset to first visible sequence
1488 int startSeq = ranges.getStartSeq();
1492 for (int i = 0; i < seq.length; i++)
1494 alignment.getHiddenSequences().hideSequence(seq[i]);
1495 setSequenceAnnotationsVisible(seq[i], false);
1497 ranges.setStartSeq(startSeq);
1498 firePropertyChange("alignment", null, alignment.getSequences());
1503 * Hides the specified sequence, or the sequences it represents
1506 * the sequence to hide, or keep as representative
1507 * @param representGroup
1508 * if true, hide the current selection group except for the
1509 * representative sequence
1511 public void hideSequences(SequenceI sequence, boolean representGroup)
1513 if (selectionGroup == null || selectionGroup.getSize() < 1)
1515 hideSequence(new SequenceI[] { sequence });
1521 hideRepSequences(sequence, selectionGroup);
1522 setSelectionGroup(null);
1526 int gsize = selectionGroup.getSize();
1527 SequenceI[] hseqs = selectionGroup.getSequences()
1528 .toArray(new SequenceI[gsize]);
1530 hideSequence(hseqs);
1531 setSelectionGroup(null);
1536 * Set visibility for any annotations for the given sequence.
1540 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1543 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1546 for (AlignmentAnnotation ann : anns)
1548 if (ann.sequenceRef == sequenceI)
1550 ann.visible = visible;
1556 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1558 int sSize = sg.getSize();
1564 if (hiddenRepSequences == null)
1566 hiddenRepSequences = new Hashtable<>();
1569 hiddenRepSequences.put(repSequence, sg);
1571 // Hide all sequences except the repSequence
1572 SequenceI[] seqs = new SequenceI[sSize - 1];
1574 for (int i = 0; i < sSize; i++)
1576 if (sg.getSequenceAt(i) != repSequence)
1578 if (index == sSize - 1)
1583 seqs[index++] = sg.getSequenceAt(i);
1586 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1587 sg.setHidereps(true); // note: not done in 2.7applet
1594 * @return null or the current reference sequence
1596 public SequenceI getReferenceSeq()
1598 return alignment.getSeqrep();
1603 * @return true iff seq is the reference for the alignment
1605 public boolean isReferenceSeq(SequenceI seq)
1607 return alignment.getSeqrep() == seq;
1613 * @return true if there are sequences represented by this sequence that are
1616 public boolean isHiddenRepSequence(SequenceI seq)
1618 return (hiddenRepSequences != null
1619 && hiddenRepSequences.containsKey(seq));
1625 * @return null or a sequence group containing the sequences that seq
1628 public SequenceGroup getRepresentedSequences(SequenceI seq)
1630 return (SequenceGroup) (hiddenRepSequences == null ? null
1631 : hiddenRepSequences.get(seq));
1635 public int adjustForHiddenSeqs(int alignmentIndex)
1637 return alignment.getHiddenSequences()
1638 .adjustForHiddenSeqs(alignmentIndex);
1642 public void invertColumnSelection()
1644 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1645 isColSelChanged(true);
1649 public SequenceI[] getSelectionAsNewSequence()
1651 SequenceI[] sequences;
1652 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1653 // this was the only caller in the applet for this method
1654 // JBPNote: in applet, this method returned references to the alignment
1655 // sequences, and it did not honour the presence/absence of annotation
1656 // attached to the alignment (probably!)
1657 if (selectionGroup == null || selectionGroup.getSize() == 0)
1659 sequences = alignment.getSequencesArray();
1660 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1661 for (int i = 0; i < sequences.length; i++)
1663 // construct new sequence with subset of visible annotation
1664 sequences[i] = new Sequence(sequences[i], annots);
1669 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1676 public SequenceI[] getSequenceSelection()
1678 SequenceI[] sequences = null;
1679 if (selectionGroup != null)
1681 sequences = selectionGroup.getSequencesInOrder(alignment);
1683 if (sequences == null)
1685 sequences = alignment.getSequencesArray();
1691 public jalview.datamodel.AlignmentView getAlignmentView(
1692 boolean selectedOnly)
1694 return getAlignmentView(selectedOnly, false);
1698 public jalview.datamodel.AlignmentView getAlignmentView(
1699 boolean selectedOnly, boolean markGroups)
1701 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1703 alignment.getHiddenColumns() != null
1704 && alignment.getHiddenColumns().hasHiddenColumns(),
1705 selectedOnly, markGroups);
1709 public String[] getViewAsString(boolean selectedRegionOnly)
1711 return getViewAsString(selectedRegionOnly, true);
1715 public String[] getViewAsString(boolean selectedRegionOnly,
1716 boolean exportHiddenSeqs)
1718 String[] selection = null;
1719 SequenceI[] seqs = null;
1721 int start = 0, end = 0;
1722 if (selectedRegionOnly && selectionGroup != null)
1724 iSize = selectionGroup.getSize();
1725 seqs = selectionGroup.getSequencesInOrder(alignment);
1726 start = selectionGroup.getStartRes();
1727 end = selectionGroup.getEndRes() + 1;
1731 if (hasHiddenRows() && exportHiddenSeqs)
1733 AlignmentI fullAlignment = alignment.getHiddenSequences()
1734 .getFullAlignment();
1735 iSize = fullAlignment.getHeight();
1736 seqs = fullAlignment.getSequencesArray();
1737 end = fullAlignment.getWidth();
1741 iSize = alignment.getHeight();
1742 seqs = alignment.getSequencesArray();
1743 end = alignment.getWidth();
1747 selection = new String[iSize];
1748 if (alignment.getHiddenColumns() != null
1749 && alignment.getHiddenColumns().hasHiddenColumns())
1751 for (i = 0; i < iSize; i++)
1753 Iterator<int[]> blocks = alignment.getHiddenColumns()
1754 .getVisContigsIterator(start, end + 1, false);
1755 selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
1760 for (i = 0; i < iSize; i++)
1762 selection[i] = seqs[i].getSequenceAsString(start, end);
1770 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1772 ArrayList<int[]> regions = new ArrayList<>();
1778 HiddenColumns hidden = alignment.getHiddenColumns();
1779 if (hidden != null && hidden.hasHiddenColumns())
1783 start = hidden.visibleToAbsoluteColumn(start);
1786 end = hidden.getNextHiddenBoundary(false, start);
1797 regions.add(new int[] { start, end });
1799 if (hidden != null && hidden.hasHiddenColumns())
1801 start = hidden.visibleToAbsoluteColumn(end);
1802 start = hidden.getNextHiddenBoundary(true, start) + 1;
1804 } while (end < max);
1806 // int[][] startEnd = new int[regions.size()][2];
1812 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1813 boolean selectedOnly)
1815 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1816 AlignmentAnnotation[] aa;
1817 if ((aa = alignment.getAlignmentAnnotation()) != null)
1819 for (AlignmentAnnotation annot : aa)
1821 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1822 if (selectedOnly && selectionGroup != null)
1824 clone.makeVisibleAnnotation(selectionGroup.getStartRes(),
1825 selectionGroup.getEndRes(), alignment.getHiddenColumns());
1829 clone.makeVisibleAnnotation(alignment.getHiddenColumns());
1838 public boolean isPadGaps()
1844 public void setPadGaps(boolean padGaps)
1846 this.padGaps = padGaps;
1850 * apply any post-edit constraints and trigger any calculations needed after
1851 * an edit has been performed on the alignment
1856 public void alignmentChanged(AlignmentViewPanel ap)
1860 alignment.padGaps();
1862 if (autoCalculateConsensus)
1864 updateConsensus(ap);
1866 if (hconsensus != null && autoCalculateConsensus)
1868 updateConservation(ap);
1870 if (autoCalculateStrucConsensus)
1872 updateStrucConsensus(ap);
1875 // Reset endRes of groups if beyond alignment width
1876 int alWidth = alignment.getWidth();
1877 List<SequenceGroup> groups = alignment.getGroups();
1880 for (SequenceGroup sg : groups)
1882 if (sg.getEndRes() > alWidth)
1884 sg.setEndRes(alWidth - 1);
1889 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1891 selectionGroup.setEndRes(alWidth - 1);
1894 updateAllColourSchemes();
1895 calculator.restartWorkers();
1896 // alignment.adjustSequenceAnnotations();
1900 * reset scope and do calculations for all applied colourschemes on alignment
1902 void updateAllColourSchemes()
1904 ResidueShaderI rs = residueShading;
1907 rs.alignmentChanged(alignment, hiddenRepSequences);
1909 rs.setConsensus(hconsensus);
1910 if (rs.conservationApplied())
1912 rs.setConservation(Conservation.calculateConservation("All",
1913 alignment.getSequences(), 0, alignment.getWidth(), false,
1914 getConsPercGaps(), false));
1918 for (SequenceGroup sg : alignment.getGroups())
1922 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1924 sg.recalcConservation();
1928 protected void initAutoAnnotation()
1930 // TODO: add menu option action that nulls or creates consensus object
1931 // depending on if the user wants to see the annotation or not in a
1932 // specific alignment
1934 if (hconsensus == null && !isDataset)
1936 if (!alignment.isNucleotide())
1945 consensus = new AlignmentAnnotation("Consensus",
1946 MessageManager.getString("label.consensus_descr"),
1947 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1948 initConsensus(consensus);
1951 initComplementConsensus();
1956 * If this is a protein alignment and there are mappings to cDNA, adds the
1957 * cDNA consensus annotation and returns true, else returns false.
1959 public boolean initComplementConsensus()
1961 if (!alignment.isNucleotide())
1963 final List<AlignedCodonFrame> codonMappings = alignment
1965 if (codonMappings != null && !codonMappings.isEmpty())
1967 boolean doConsensus = false;
1968 for (AlignedCodonFrame mapping : codonMappings)
1970 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1971 MapList[] mapLists = mapping.getdnaToProt();
1972 // mapLists can be empty if project load has not finished resolving
1974 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1982 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1984 .getString("label.complement_consensus_descr"),
1985 new Annotation[1], 0f, 100f,
1986 AlignmentAnnotation.BAR_GRAPH);
1987 initConsensus(complementConsensus);
1995 private void initConsensus(AlignmentAnnotation aa)
1998 aa.autoCalculated = true;
2002 alignment.addAnnotation(aa);
2006 // these should be extracted from the view model - style and settings for
2007 // derived annotation
2008 private void initGapCounts()
2012 gapcounts = new AlignmentAnnotation("Occupancy",
2013 MessageManager.getString("label.occupancy_descr"),
2014 new Annotation[1], 0f, alignment.getHeight(),
2015 AlignmentAnnotation.BAR_GRAPH);
2016 gapcounts.hasText = true;
2017 gapcounts.autoCalculated = true;
2018 gapcounts.scaleColLabel = true;
2019 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
2021 alignment.addAnnotation(gapcounts);
2025 private void initConservation()
2027 if (showConservation)
2029 if (conservation == null)
2031 conservation = new AlignmentAnnotation("Conservation",
2032 MessageManager.formatMessage("label.conservation_descr",
2034 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2035 conservation.hasText = true;
2036 conservation.autoCalculated = true;
2037 alignment.addAnnotation(conservation);
2042 private void initQuality()
2046 if (quality == null)
2048 quality = new AlignmentAnnotation("Quality",
2049 MessageManager.getString("label.quality_descr"),
2050 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2051 quality.hasText = true;
2052 quality.autoCalculated = true;
2053 alignment.addAnnotation(quality);
2058 private void initRNAStructure()
2060 if (alignment.hasRNAStructure() && strucConsensus == null)
2062 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2063 MessageManager.getString("label.strucconsensus_descr"),
2064 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2065 strucConsensus.hasText = true;
2066 strucConsensus.autoCalculated = true;
2070 alignment.addAnnotation(strucConsensus);
2078 * @see jalview.api.AlignViewportI#calcPanelHeight()
2081 public int calcPanelHeight()
2083 // setHeight of panels
2084 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2086 int charHeight = getCharHeight();
2089 BitSet graphgrp = new BitSet();
2090 for (AlignmentAnnotation aa : anns)
2094 System.err.println("Null annotation row: ignoring.");
2101 if (aa.graphGroup > -1)
2103 if (graphgrp.get(aa.graphGroup))
2109 graphgrp.set(aa.graphGroup);
2116 aa.height += charHeight;
2126 aa.height += aa.graphHeight;
2134 height += aa.height;
2146 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2147 boolean preserveNewGroupSettings)
2149 boolean updateCalcs = false;
2150 boolean conv = isShowGroupConservation();
2151 boolean cons = isShowGroupConsensus();
2152 boolean showprf = isShowSequenceLogo();
2153 boolean showConsHist = isShowConsensusHistogram();
2154 boolean normLogo = isNormaliseSequenceLogo();
2157 * TODO reorder the annotation rows according to group/sequence ordering on
2160 // boolean sortg = true;
2162 // remove old automatic annotation
2163 // add any new annotation
2165 // intersect alignment annotation with alignment groups
2167 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2168 List<SequenceGroup> oldrfs = new ArrayList<>();
2171 for (int an = 0; an < aan.length; an++)
2173 if (aan[an].autoCalculated && aan[an].groupRef != null)
2175 oldrfs.add(aan[an].groupRef);
2176 alignment.deleteAnnotation(aan[an], false);
2180 if (alignment.getGroups() != null)
2182 for (SequenceGroup sg : alignment.getGroups())
2184 updateCalcs = false;
2185 if (applyGlobalSettings
2186 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2188 // set defaults for this group's conservation/consensus
2189 sg.setshowSequenceLogo(showprf);
2190 sg.setShowConsensusHistogram(showConsHist);
2191 sg.setNormaliseSequenceLogo(normLogo);
2196 alignment.addAnnotation(sg.getConservationRow(), 0);
2201 alignment.addAnnotation(sg.getConsensus(), 0);
2203 // refresh the annotation rows
2206 sg.recalcConservation();
2214 public boolean isDisplayReferenceSeq()
2216 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2220 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2222 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2226 public boolean isColourByReferenceSeq()
2228 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2232 public Color getSequenceColour(SequenceI seq)
2234 Color sqc = sequenceColours.get(seq);
2235 return (sqc == null ? Color.white : sqc);
2239 public void setSequenceColour(SequenceI seq, Color col)
2243 sequenceColours.remove(seq);
2247 sequenceColours.put(seq, col);
2252 public void updateSequenceIdColours()
2254 for (SequenceGroup sg : alignment.getGroups())
2256 if (sg.idColour != null)
2258 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2260 sequenceColours.put(s, sg.idColour);
2267 public void clearSequenceColours()
2269 sequenceColours.clear();
2273 public AlignViewportI getCodingComplement()
2275 return this.codingComplement;
2279 * Set this as the (cDna/protein) complement of the given viewport. Also
2280 * ensures the reverse relationship is set on the given viewport.
2283 public void setCodingComplement(AlignViewportI av)
2287 System.err.println("Ignoring recursive setCodingComplement request");
2291 this.codingComplement = av;
2292 // avoid infinite recursion!
2293 if (av.getCodingComplement() != this)
2295 av.setCodingComplement(this);
2301 public boolean isNucleotide()
2303 return getAlignment() == null ? false : getAlignment().isNucleotide();
2307 public FeaturesDisplayedI getFeaturesDisplayed()
2309 return featuresDisplayed;
2313 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2315 featuresDisplayed = featuresDisplayedI;
2319 public boolean areFeaturesDisplayed()
2321 return featuresDisplayed != null
2322 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2329 * features are displayed if true
2332 public void setShowSequenceFeatures(boolean b)
2334 viewStyle.setShowSequenceFeatures(b);
2338 public boolean isShowSequenceFeatures()
2340 return viewStyle.isShowSequenceFeatures();
2344 public void setShowSequenceFeaturesHeight(boolean selected)
2346 viewStyle.setShowSequenceFeaturesHeight(selected);
2350 public boolean isShowSequenceFeaturesHeight()
2352 return viewStyle.isShowSequenceFeaturesHeight();
2356 public void setShowAnnotation(boolean b)
2358 viewStyle.setShowAnnotation(b);
2362 public boolean isShowAnnotation()
2364 return viewStyle.isShowAnnotation();
2368 public boolean isRightAlignIds()
2370 return viewStyle.isRightAlignIds();
2374 public void setRightAlignIds(boolean rightAlignIds)
2376 viewStyle.setRightAlignIds(rightAlignIds);
2380 public boolean getConservationSelected()
2382 return viewStyle.getConservationSelected();
2386 public void setShowBoxes(boolean state)
2388 viewStyle.setShowBoxes(state);
2393 * @see jalview.api.ViewStyleI#getTextColour()
2396 public Color getTextColour()
2398 return viewStyle.getTextColour();
2403 * @see jalview.api.ViewStyleI#getTextColour2()
2406 public Color getTextColour2()
2408 return viewStyle.getTextColour2();
2413 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2416 public int getThresholdTextColour()
2418 return viewStyle.getThresholdTextColour();
2423 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2426 public boolean isConservationColourSelected()
2428 return viewStyle.isConservationColourSelected();
2433 * @see jalview.api.ViewStyleI#isRenderGaps()
2436 public boolean isRenderGaps()
2438 return viewStyle.isRenderGaps();
2443 * @see jalview.api.ViewStyleI#isShowColourText()
2446 public boolean isShowColourText()
2448 return viewStyle.isShowColourText();
2452 * @param conservationColourSelected
2453 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2456 public void setConservationColourSelected(
2457 boolean conservationColourSelected)
2459 viewStyle.setConservationColourSelected(conservationColourSelected);
2463 * @param showColourText
2464 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2467 public void setShowColourText(boolean showColourText)
2469 viewStyle.setShowColourText(showColourText);
2474 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2477 public void setTextColour(Color textColour)
2479 viewStyle.setTextColour(textColour);
2483 * @param thresholdTextColour
2484 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2487 public void setThresholdTextColour(int thresholdTextColour)
2489 viewStyle.setThresholdTextColour(thresholdTextColour);
2493 * @param textColour2
2494 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2497 public void setTextColour2(Color textColour2)
2499 viewStyle.setTextColour2(textColour2);
2503 public ViewStyleI getViewStyle()
2505 return new ViewStyle(viewStyle);
2509 public void setViewStyle(ViewStyleI settingsForView)
2511 viewStyle = new ViewStyle(settingsForView);
2512 if (residueShading != null)
2514 residueShading.setConservationApplied(
2515 settingsForView.isConservationColourSelected());
2520 public boolean sameStyle(ViewStyleI them)
2522 return viewStyle.sameStyle(them);
2527 * @see jalview.api.ViewStyleI#getIdWidth()
2530 public int getIdWidth()
2532 return viewStyle.getIdWidth();
2537 * @see jalview.api.ViewStyleI#setIdWidth(int)
2540 public void setIdWidth(int i)
2542 viewStyle.setIdWidth(i);
2547 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2550 public boolean isCentreColumnLabels()
2552 return viewStyle.isCentreColumnLabels();
2556 * @param centreColumnLabels
2557 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2560 public void setCentreColumnLabels(boolean centreColumnLabels)
2562 viewStyle.setCentreColumnLabels(centreColumnLabels);
2567 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2570 public void setShowDBRefs(boolean showdbrefs)
2572 viewStyle.setShowDBRefs(showdbrefs);
2577 * @see jalview.api.ViewStyleI#isShowDBRefs()
2580 public boolean isShowDBRefs()
2582 return viewStyle.isShowDBRefs();
2587 * @see jalview.api.ViewStyleI#isShowNPFeats()
2590 public boolean isShowNPFeats()
2592 return viewStyle.isShowNPFeats();
2596 * @param shownpfeats
2597 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2600 public void setShowNPFeats(boolean shownpfeats)
2602 viewStyle.setShowNPFeats(shownpfeats);
2605 public abstract StructureSelectionManager getStructureSelectionManager();
2608 * Add one command to the command history list.
2612 public void addToHistoryList(CommandI command)
2614 if (this.historyList != null)
2616 this.historyList.push(command);
2617 broadcastCommand(command, false);
2621 protected void broadcastCommand(CommandI command, boolean undo)
2623 getStructureSelectionManager().commandPerformed(command, undo,
2628 * Add one command to the command redo list.
2632 public void addToRedoList(CommandI command)
2634 if (this.redoList != null)
2636 this.redoList.push(command);
2638 broadcastCommand(command, true);
2642 * Clear the command redo list.
2644 public void clearRedoList()
2646 if (this.redoList != null)
2648 this.redoList.clear();
2652 public void setHistoryList(Deque<CommandI> list)
2654 this.historyList = list;
2657 public Deque<CommandI> getHistoryList()
2659 return this.historyList;
2662 public void setRedoList(Deque<CommandI> list)
2664 this.redoList = list;
2667 public Deque<CommandI> getRedoList()
2669 return this.redoList;
2673 public VamsasSource getVamsasSource()
2678 public SequenceAnnotationOrder getSortAnnotationsBy()
2680 return sortAnnotationsBy;
2683 public void setSortAnnotationsBy(
2684 SequenceAnnotationOrder sortAnnotationsBy)
2686 this.sortAnnotationsBy = sortAnnotationsBy;
2689 public boolean isShowAutocalculatedAbove()
2691 return showAutocalculatedAbove;
2694 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2696 this.showAutocalculatedAbove = showAutocalculatedAbove;
2700 public boolean isScaleProteinAsCdna()
2702 return viewStyle.isScaleProteinAsCdna();
2706 public void setScaleProteinAsCdna(boolean b)
2708 viewStyle.setScaleProteinAsCdna(b);
2712 public boolean isProteinFontAsCdna()
2714 return viewStyle.isProteinFontAsCdna();
2718 public void setProteinFontAsCdna(boolean b)
2720 viewStyle.setProteinFontAsCdna(b);
2724 public void setShowComplementFeatures(boolean b)
2726 viewStyle.setShowComplementFeatures(b);
2730 public boolean isShowComplementFeatures()
2732 return viewStyle.isShowComplementFeatures();
2736 public void setShowComplementFeaturesOnTop(boolean b)
2738 viewStyle.setShowComplementFeaturesOnTop(b);
2742 public boolean isShowComplementFeaturesOnTop()
2744 return viewStyle.isShowComplementFeaturesOnTop();
2748 * @return true if view should scroll to show the highlighted region of a
2753 public final boolean isFollowHighlight()
2755 return followHighlight;
2759 public final void setFollowHighlight(boolean b)
2761 this.followHighlight = b;
2765 public ViewportRanges getRanges()
2771 * Helper method to populate the SearchResults with the location in the
2772 * complementary alignment to scroll to, in order to match this one.
2775 * the SearchResults to add to
2776 * @return the offset (below top of visible region) of the matched sequence
2778 protected int findComplementScrollTarget(SearchResultsI sr)
2780 final AlignViewportI complement = getCodingComplement();
2781 if (complement == null || !complement.isFollowHighlight())
2785 boolean iAmProtein = !getAlignment().isNucleotide();
2786 AlignmentI proteinAlignment = iAmProtein ? getAlignment()
2787 : complement.getAlignment();
2788 if (proteinAlignment == null)
2792 final List<AlignedCodonFrame> mappings = proteinAlignment
2796 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2797 * residue in the middle column of the visible region. Scroll the
2798 * complementary alignment to line up the corresponding residue.
2801 SequenceI sequence = null;
2804 * locate 'middle' column (true middle if an odd number visible, left of
2805 * middle if an even number visible)
2807 int middleColumn = ranges.getStartRes()
2808 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2809 final HiddenSequences hiddenSequences = getAlignment()
2810 .getHiddenSequences();
2813 * searching to the bottom of the alignment gives smoother scrolling across
2814 * all gapped visible regions
2816 int lastSeq = alignment.getHeight() - 1;
2817 List<AlignedCodonFrame> seqMappings = null;
2818 for (int seqNo = ranges
2819 .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
2821 sequence = getAlignment().getSequenceAt(seqNo);
2822 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2826 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2830 seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
2832 getCodingComplement().getAlignment().getSequences());
2833 if (!seqMappings.isEmpty())
2839 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2842 * No ungapped mapped sequence in middle column - do nothing
2846 MappingUtils.addSearchResults(sr, sequence,
2847 sequence.findPosition(middleColumn), seqMappings);
2852 * synthesize a column selection if none exists so it covers the given
2853 * selection group. if wholewidth is false, no column selection is made if the
2854 * selection group covers the whole alignment width.
2859 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2862 if (sg != null && (sgs = sg.getStartRes()) >= 0
2863 && sg.getStartRes() <= (sge = sg.getEndRes())
2864 && !this.hasSelectedColumns())
2866 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2873 colSel = new ColumnSelection();
2875 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2877 colSel.addElement(cspos);
2883 * hold status of current selection group - defined on alignment or not.
2885 private boolean selectionIsDefinedGroup = false;
2888 public boolean isSelectionDefinedGroup()
2890 if (selectionGroup == null)
2894 if (isSelectionGroupChanged(true))
2896 selectionIsDefinedGroup = false;
2897 List<SequenceGroup> gps = alignment.getGroups();
2898 if (gps == null || gps.size() == 0)
2900 selectionIsDefinedGroup = false;
2904 selectionIsDefinedGroup = gps.contains(selectionGroup);
2907 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2911 * null, or currently highlighted results on this view
2913 private SearchResultsI searchResults = null;
2915 protected TreeModel currentTree = null;
2918 public boolean hasSearchResults()
2920 return searchResults != null;
2924 public void setSearchResults(SearchResultsI results)
2926 searchResults = results;
2930 public SearchResultsI getSearchResults()
2932 return searchResults;
2936 * get the consensus sequence as displayed under the PID consensus annotation
2939 * @return consensus sequence as a new sequence object
2941 public SequenceI getConsensusSeq()
2943 if (consensus == null)
2945 updateConsensus(null);
2947 if (consensus == null)
2951 StringBuffer seqs = new StringBuffer();
2952 for (int i = 0; i < consensus.annotations.length; i++)
2954 Annotation annotation = consensus.annotations[i];
2955 if (annotation != null)
2957 String description = annotation.description;
2958 if (description != null && description.startsWith("["))
2960 // consensus is a tie - just pick the first one
2961 seqs.append(description.charAt(1));
2965 seqs.append(annotation.displayCharacter);
2970 SequenceI sq = new Sequence("Consensus", seqs.toString());
2971 sq.setDescription("Percentage Identity Consensus "
2972 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
2977 public void setCurrentTree(TreeModel tree)
2983 public TreeModel getCurrentTree()
2989 public AlignmentExportData getAlignExportData(
2990 AlignExportSettingsI options)
2992 AlignmentI alignmentToExport = null;
2993 String[] omitHidden = null;
2994 alignmentToExport = null;
2996 if (hasHiddenColumns() && !options.isExportHiddenColumns())
2998 omitHidden = getViewAsString(false,
2999 options.isExportHiddenSequences());
3002 int[] alignmentStartEnd = new int[2];
3003 if (hasHiddenRows() && options.isExportHiddenSequences())
3005 alignmentToExport = getAlignment().getHiddenSequences()
3006 .getFullAlignment();
3010 alignmentToExport = getAlignment();
3012 alignmentStartEnd = getAlignment().getHiddenColumns()
3013 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
3014 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
3015 omitHidden, alignmentStartEnd);
3020 * flag set to indicate if structure views might be out of sync with sequences
3024 private boolean needToUpdateStructureViews = false;
3027 public boolean isUpdateStructures()
3029 return needToUpdateStructureViews;
3033 public void setUpdateStructures(boolean update)
3035 needToUpdateStructureViews = update;
3039 public boolean needToUpdateStructureViews()
3041 boolean update = needToUpdateStructureViews;
3042 needToUpdateStructureViews = false;
3047 public void addSequenceGroup(SequenceGroup sequenceGroup)
3049 alignment.addGroup(sequenceGroup);
3051 Color col = sequenceGroup.idColour;
3054 col = col.brighter();
3056 for (SequenceI sq : sequenceGroup.getSequences())
3058 setSequenceColour(sq, col);
3062 if (codingComplement != null)
3064 SequenceGroup mappedGroup = MappingUtils
3065 .mapSequenceGroup(sequenceGroup, this, codingComplement);
3066 if (mappedGroup.getSequences().size() > 0)
3068 codingComplement.getAlignment().addGroup(mappedGroup);
3072 for (SequenceI seq : mappedGroup.getSequences())
3074 codingComplement.setSequenceColour(seq, col);
3078 // propagate the structure view update flag according to our own setting
3079 codingComplement.setUpdateStructures(needToUpdateStructureViews);
3084 public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
3088 if (selectedRegionOnly && selectionGroup != null)
3090 start = selectionGroup.getStartRes();
3091 end = selectionGroup.getEndRes() + 1;
3095 end = alignment.getWidth();
3097 return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
3101 public Hashtable<SequenceI, Integer> calculateConnectivity(float[][] scores, byte dim)
3103 return Connectivity.getConnectivity(this, scores, dim);