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.AlignCalcManagerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.AlignmentViewPanel;
29 import jalview.api.FeaturesDisplayedI;
30 import jalview.api.ViewStyleI;
31 import jalview.commands.CommandI;
32 import jalview.datamodel.AlignedCodonFrame;
33 import jalview.datamodel.AlignmentAnnotation;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.AlignmentView;
36 import jalview.datamodel.Annotation;
37 import jalview.datamodel.ColumnSelection;
38 import jalview.datamodel.HiddenColumns;
39 import jalview.datamodel.HiddenSequences;
40 import jalview.datamodel.ProfilesI;
41 import jalview.datamodel.SearchResultsI;
42 import jalview.datamodel.Sequence;
43 import jalview.datamodel.SequenceCollectionI;
44 import jalview.datamodel.SequenceGroup;
45 import jalview.datamodel.SequenceI;
46 import jalview.renderer.ResidueShader;
47 import jalview.renderer.ResidueShaderI;
48 import jalview.schemes.ColourSchemeI;
49 import jalview.structure.CommandListener;
50 import jalview.structure.StructureSelectionManager;
51 import jalview.structure.VamsasSource;
52 import jalview.util.Comparison;
53 import jalview.util.MapList;
54 import jalview.util.MappingUtils;
55 import jalview.util.MessageManager;
56 import jalview.viewmodel.styles.ViewStyle;
57 import jalview.workers.AlignCalcManager;
58 import jalview.workers.ComplementConsensusThread;
59 import jalview.workers.ConsensusThread;
60 import jalview.workers.StrucConsensusThread;
62 import java.awt.Color;
63 import java.beans.PropertyChangeSupport;
64 import java.util.ArrayDeque;
65 import java.util.ArrayList;
66 import java.util.BitSet;
67 import java.util.Deque;
68 import java.util.HashMap;
69 import java.util.Hashtable;
70 import java.util.List;
74 * base class holding visualization and analysis attributes and common logic for
75 * an active alignment view displayed in the GUI
80 public abstract class AlignmentViewport
81 implements AlignViewportI, CommandListener, VamsasSource
83 protected ViewportRanges ranges;
85 protected ViewStyleI viewStyle = new ViewStyle();
88 * A viewport that hosts the cDna view of this (protein), or vice versa (if
91 AlignViewportI codingComplement = null;
93 FeaturesDisplayedI featuresDisplayed = null;
95 protected Deque<CommandI> historyList = new ArrayDeque<>();
97 protected Deque<CommandI> redoList = new ArrayDeque<>();
100 * alignment displayed in the viewport. Please use get/setter
102 protected AlignmentI alignment;
104 public AlignmentViewport(AlignmentI al)
107 ranges = new ViewportRanges(al);
112 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
115 public void setFontName(String name)
117 viewStyle.setFontName(name);
122 * @see jalview.api.ViewStyleI#setFontStyle(int)
125 public void setFontStyle(int style)
127 viewStyle.setFontStyle(style);
132 * @see jalview.api.ViewStyleI#setFontSize(int)
135 public void setFontSize(int size)
137 viewStyle.setFontSize(size);
142 * @see jalview.api.ViewStyleI#getFontStyle()
145 public int getFontStyle()
147 return viewStyle.getFontStyle();
152 * @see jalview.api.ViewStyleI#getFontName()
155 public String getFontName()
157 return viewStyle.getFontName();
162 * @see jalview.api.ViewStyleI#getFontSize()
165 public int getFontSize()
167 return viewStyle.getFontSize();
171 * @param upperCasebold
172 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
175 public void setUpperCasebold(boolean upperCasebold)
177 viewStyle.setUpperCasebold(upperCasebold);
182 * @see jalview.api.ViewStyleI#isUpperCasebold()
185 public boolean isUpperCasebold()
187 return viewStyle.isUpperCasebold();
192 * @see jalview.api.ViewStyleI#isSeqNameItalics()
195 public boolean isSeqNameItalics()
197 return viewStyle.isSeqNameItalics();
201 * @param colourByReferenceSeq
202 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
205 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
207 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
212 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
215 public void setColourAppliesToAllGroups(boolean b)
217 viewStyle.setColourAppliesToAllGroups(b);
222 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
225 public boolean getColourAppliesToAllGroups()
227 return viewStyle.getColourAppliesToAllGroups();
232 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
235 public boolean getAbovePIDThreshold()
237 return viewStyle.getAbovePIDThreshold();
242 * @see jalview.api.ViewStyleI#setIncrement(int)
245 public void setIncrement(int inc)
247 viewStyle.setIncrement(inc);
252 * @see jalview.api.ViewStyleI#getIncrement()
255 public int getIncrement()
257 return viewStyle.getIncrement();
262 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
265 public void setConservationSelected(boolean b)
267 viewStyle.setConservationSelected(b);
272 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
275 public void setShowHiddenMarkers(boolean show)
277 viewStyle.setShowHiddenMarkers(show);
282 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
285 public boolean getShowHiddenMarkers()
287 return viewStyle.getShowHiddenMarkers();
292 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
295 public void setScaleRightWrapped(boolean b)
297 viewStyle.setScaleRightWrapped(b);
302 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
305 public void setScaleLeftWrapped(boolean b)
307 viewStyle.setScaleLeftWrapped(b);
312 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
315 public void setScaleAboveWrapped(boolean b)
317 viewStyle.setScaleAboveWrapped(b);
322 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
325 public boolean getScaleLeftWrapped()
327 return viewStyle.getScaleLeftWrapped();
332 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
335 public boolean getScaleAboveWrapped()
337 return viewStyle.getScaleAboveWrapped();
342 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
345 public boolean getScaleRightWrapped()
347 return viewStyle.getScaleRightWrapped();
352 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
355 public void setAbovePIDThreshold(boolean b)
357 viewStyle.setAbovePIDThreshold(b);
362 * @see jalview.api.ViewStyleI#setThreshold(int)
365 public void setThreshold(int thresh)
367 viewStyle.setThreshold(thresh);
372 * @see jalview.api.ViewStyleI#getThreshold()
375 public int getThreshold()
377 return viewStyle.getThreshold();
382 * @see jalview.api.ViewStyleI#getShowJVSuffix()
385 public boolean getShowJVSuffix()
387 return viewStyle.getShowJVSuffix();
392 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
395 public void setShowJVSuffix(boolean b)
397 viewStyle.setShowJVSuffix(b);
402 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
405 public void setWrapAlignment(boolean state)
407 viewStyle.setWrapAlignment(state);
408 ranges.setWrappedMode(state);
413 * @see jalview.api.ViewStyleI#setShowText(boolean)
416 public void setShowText(boolean state)
418 viewStyle.setShowText(state);
423 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
426 public void setRenderGaps(boolean state)
428 viewStyle.setRenderGaps(state);
433 * @see jalview.api.ViewStyleI#getColourText()
436 public boolean getColourText()
438 return viewStyle.getColourText();
443 * @see jalview.api.ViewStyleI#setColourText(boolean)
446 public void setColourText(boolean state)
448 viewStyle.setColourText(state);
453 * @see jalview.api.ViewStyleI#getWrapAlignment()
456 public boolean getWrapAlignment()
458 return viewStyle.getWrapAlignment();
463 * @see jalview.api.ViewStyleI#getShowText()
466 public boolean getShowText()
468 return viewStyle.getShowText();
473 * @see jalview.api.ViewStyleI#getWrappedWidth()
476 public int getWrappedWidth()
478 return viewStyle.getWrappedWidth();
483 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
486 public void setWrappedWidth(int w)
488 viewStyle.setWrappedWidth(w);
493 * @see jalview.api.ViewStyleI#getCharHeight()
496 public int getCharHeight()
498 return viewStyle.getCharHeight();
503 * @see jalview.api.ViewStyleI#setCharHeight(int)
506 public void setCharHeight(int h)
508 viewStyle.setCharHeight(h);
513 * @see jalview.api.ViewStyleI#getCharWidth()
516 public int getCharWidth()
518 return viewStyle.getCharWidth();
523 * @see jalview.api.ViewStyleI#setCharWidth(int)
526 public void setCharWidth(int w)
528 viewStyle.setCharWidth(w);
533 * @see jalview.api.ViewStyleI#getShowBoxes()
536 public boolean getShowBoxes()
538 return viewStyle.getShowBoxes();
543 * @see jalview.api.ViewStyleI#getShowUnconserved()
546 public boolean getShowUnconserved()
548 return viewStyle.getShowUnconserved();
552 * @param showunconserved
553 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
556 public void setShowUnconserved(boolean showunconserved)
558 viewStyle.setShowUnconserved(showunconserved);
563 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
566 public void setSeqNameItalics(boolean default1)
568 viewStyle.setSeqNameItalics(default1);
572 public AlignmentI getAlignment()
578 public char getGapCharacter()
580 return alignment.getGapCharacter();
583 protected String sequenceSetID;
586 * probably unused indicator that view is of a dataset rather than an
589 protected boolean isDataset = false;
591 public void setDataset(boolean b)
596 public boolean isDataset()
601 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
603 protected ColumnSelection colSel = new ColumnSelection();
605 public boolean autoCalculateConsensus = true;
607 protected boolean autoCalculateStrucConsensus = true;
609 protected boolean ignoreGapsInConsensusCalculation = false;
611 protected ResidueShaderI residueShading = new ResidueShader();
614 public void setGlobalColourScheme(ColourSchemeI cs)
616 // TODO: logic refactored from AlignFrame changeColour -
617 // TODO: autorecalc stuff should be changed to rely on the worker system
618 // check to see if we should implement a changeColour(cs) method rather than
619 // put the logic in here
620 // - means that caller decides if they want to just modify state and defer
621 // calculation till later or to do all calculations in thread.
625 * only instantiate alignment colouring once, thereafter update it;
626 * this means that any conservation or PID threshold settings
627 * persist when the alignment colour scheme is changed
629 if (residueShading == null)
631 residueShading = new ResidueShader(viewStyle);
633 residueShading.setColourScheme(cs);
635 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
636 // ...problem: groups need these, but do not currently have a ViewStyle
640 if (getConservationSelected())
642 residueShading.setConservation(hconservation);
645 * reset conservation flag in case just set to false if
646 * Conservation was null (calculation still in progress)
648 residueShading.setConservationApplied(getConservationSelected());
649 residueShading.alignmentChanged(alignment, hiddenRepSequences);
653 * if 'apply colour to all groups' is selected... do so
654 * (but don't transfer any colour threshold settings to groups)
656 if (getColourAppliesToAllGroups())
658 for (SequenceGroup sg : getAlignment().getGroups())
661 * retain any colour thresholds per group while
662 * changing choice of colour scheme (JAL-2386)
664 sg.setColourScheme(cs);
667 sg.getGroupColourScheme().alignmentChanged(sg,
675 public ColourSchemeI getGlobalColourScheme()
677 return residueShading == null ? null : residueShading.getColourScheme();
681 public ResidueShaderI getResidueShading()
683 return residueShading;
686 protected AlignmentAnnotation consensus;
688 protected AlignmentAnnotation complementConsensus;
690 protected AlignmentAnnotation gapcounts;
692 protected AlignmentAnnotation strucConsensus;
694 protected AlignmentAnnotation conservation;
696 protected AlignmentAnnotation quality;
698 protected AlignmentAnnotation[] groupConsensus;
700 protected AlignmentAnnotation[] groupConservation;
703 * results of alignment consensus analysis for visible portion of view
705 protected ProfilesI hconsensus = null;
708 * results of cDNA complement consensus visible portion of view
710 protected Hashtable[] hcomplementConsensus = null;
713 * results of secondary structure base pair consensus for visible portion of
716 protected Hashtable[] hStrucConsensus = null;
718 protected Conservation hconservation = null;
721 public void setConservation(Conservation cons)
723 hconservation = cons;
727 * percentage gaps allowed in a column before all amino acid properties should
728 * be considered unconserved
730 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
733 public int getConsPercGaps()
739 public void setSequenceConsensusHash(ProfilesI hconsensus)
741 this.hconsensus = hconsensus;
745 public void setComplementConsensusHash(Hashtable[] hconsensus)
747 this.hcomplementConsensus = hconsensus;
751 public ProfilesI getSequenceConsensusHash()
757 public Hashtable[] getComplementConsensusHash()
759 return hcomplementConsensus;
763 public Hashtable[] getRnaStructureConsensusHash()
765 return hStrucConsensus;
769 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
771 this.hStrucConsensus = hStrucConsensus;
776 public AlignmentAnnotation getAlignmentQualityAnnot()
782 public AlignmentAnnotation getAlignmentConservationAnnotation()
788 public AlignmentAnnotation getAlignmentConsensusAnnotation()
794 public AlignmentAnnotation getAlignmentGapAnnotation()
800 public AlignmentAnnotation getComplementConsensusAnnotation()
802 return complementConsensus;
806 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
808 return strucConsensus;
811 protected AlignCalcManagerI calculator = new AlignCalcManager();
814 * trigger update of conservation annotation
816 public void updateConservation(final AlignmentViewPanel ap)
818 // see note in mantis : issue number 8585
819 if (alignment.isNucleotide()
820 || (conservation == null && quality == null)
821 || !autoCalculateConsensus)
825 if (calculator.getRegisteredWorkersOfClass(
826 jalview.workers.ConservationThread.class) == null)
828 calculator.registerWorker(
829 new jalview.workers.ConservationThread(this, ap));
834 * trigger update of consensus annotation
836 public void updateConsensus(final AlignmentViewPanel ap)
838 // see note in mantis : issue number 8585
839 if (consensus == null || !autoCalculateConsensus)
844 .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
846 calculator.registerWorker(new ConsensusThread(this, ap));
850 * A separate thread to compute cDNA consensus for a protein alignment
851 * which has mapping to cDNA
853 final AlignmentI al = this.getAlignment();
854 if (!al.isNucleotide() && al.getCodonFrames() != null
855 && !al.getCodonFrames().isEmpty())
858 * fudge - check first for protein-to-nucleotide mappings
859 * (we don't want to do this for protein-to-protein)
861 boolean doConsensus = false;
862 for (AlignedCodonFrame mapping : al.getCodonFrames())
864 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
865 MapList[] mapLists = mapping.getdnaToProt();
866 // mapLists can be empty if project load has not finished resolving seqs
867 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
875 if (calculator.getRegisteredWorkersOfClass(
876 ComplementConsensusThread.class) == null)
879 .registerWorker(new ComplementConsensusThread(this, ap));
885 // --------START Structure Conservation
886 public void updateStrucConsensus(final AlignmentViewPanel ap)
888 if (autoCalculateStrucConsensus && strucConsensus == null
889 && alignment.isNucleotide() && alignment.hasRNAStructure())
891 // secondary structure has been added - so init the consensus line
895 // see note in mantis : issue number 8585
896 if (strucConsensus == null || !autoCalculateStrucConsensus)
900 if (calculator.getRegisteredWorkersOfClass(
901 StrucConsensusThread.class) == null)
903 calculator.registerWorker(new StrucConsensusThread(this, ap));
907 public boolean isCalcInProgress()
909 return calculator.isWorking();
913 public boolean isCalculationInProgress(
914 AlignmentAnnotation alignmentAnnotation)
916 if (!alignmentAnnotation.autoCalculated)
920 if (calculator.workingInvolvedWith(alignmentAnnotation))
922 // System.err.println("grey out ("+alignmentAnnotation.label+")");
928 public void setAlignment(AlignmentI align)
930 this.alignment = align;
934 * Clean up references when this viewport is closed
937 public void dispose()
940 * defensively null out references to large objects in case
941 * this object is not garbage collected (as if!)
944 complementConsensus = null;
945 strucConsensus = null;
948 groupConsensus = null;
949 groupConservation = null;
951 hconservation = null;
952 hcomplementConsensus = null;
955 residueShading = null; // may hold a reference to Consensus
956 changeSupport = null;
959 selectionGroup = null;
964 public boolean isClosed()
966 // TODO: check that this isClosed is only true after panel is closed, not
967 // before it is fully constructed.
968 return alignment == null;
972 public AlignCalcManagerI getCalcManager()
978 * should conservation rows be shown for groups
980 protected boolean showGroupConservation = false;
983 * should consensus rows be shown for groups
985 protected boolean showGroupConsensus = false;
988 * should consensus profile be rendered by default
990 protected boolean showSequenceLogo = false;
993 * should consensus profile be rendered normalised to row height
995 protected boolean normaliseSequenceLogo = false;
998 * should consensus histograms be rendered by default
1000 protected boolean showConsensusHistogram = true;
1003 * @return the showConsensusProfile
1006 public boolean isShowSequenceLogo()
1008 return showSequenceLogo;
1012 * @param showSequenceLogo
1015 public void setShowSequenceLogo(boolean showSequenceLogo)
1017 if (showSequenceLogo != this.showSequenceLogo)
1019 // TODO: decouple settings setting from calculation when refactoring
1020 // annotation update method from alignframe to viewport
1021 this.showSequenceLogo = showSequenceLogo;
1022 calculator.updateAnnotationFor(ConsensusThread.class);
1023 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1024 calculator.updateAnnotationFor(StrucConsensusThread.class);
1026 this.showSequenceLogo = showSequenceLogo;
1030 * @param showConsensusHistogram
1031 * the showConsensusHistogram to set
1033 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1035 this.showConsensusHistogram = showConsensusHistogram;
1039 * @return the showGroupConservation
1041 public boolean isShowGroupConservation()
1043 return showGroupConservation;
1047 * @param showGroupConservation
1048 * the showGroupConservation to set
1050 public void setShowGroupConservation(boolean showGroupConservation)
1052 this.showGroupConservation = showGroupConservation;
1056 * @return the showGroupConsensus
1058 public boolean isShowGroupConsensus()
1060 return showGroupConsensus;
1064 * @param showGroupConsensus
1065 * the showGroupConsensus to set
1067 public void setShowGroupConsensus(boolean showGroupConsensus)
1069 this.showGroupConsensus = showGroupConsensus;
1074 * @return flag to indicate if the consensus histogram should be rendered by
1078 public boolean isShowConsensusHistogram()
1080 return this.showConsensusHistogram;
1084 * when set, updateAlignment will always ensure sequences are of equal length
1086 private boolean padGaps = false;
1089 * when set, alignment should be reordered according to a newly opened tree
1091 public boolean sortByTree = false;
1096 * @return null or the currently selected sequence region
1099 public SequenceGroup getSelectionGroup()
1101 return selectionGroup;
1105 * Set the selection group for this window. Also sets the current alignment as
1106 * the context for the group, if it does not already have one.
1109 * - group holding references to sequences in this alignment view
1113 public void setSelectionGroup(SequenceGroup sg)
1115 selectionGroup = sg;
1116 if (sg != null && sg.getContext() == null)
1118 sg.setContext(alignment);
1122 public void setHiddenColumns(HiddenColumns hidden)
1124 this.alignment.setHiddenColumns(hidden);
1128 public ColumnSelection getColumnSelection()
1134 public void setColumnSelection(ColumnSelection colSel)
1136 this.colSel = colSel;
1139 updateHiddenColumns();
1141 isColSelChanged(true);
1149 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1151 return hiddenRepSequences;
1155 public void setHiddenRepSequences(
1156 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1158 this.hiddenRepSequences = hiddenRepSequences;
1162 public boolean hasSelectedColumns()
1164 ColumnSelection columnSelection = getColumnSelection();
1165 return columnSelection != null && columnSelection.hasSelectedColumns();
1169 public boolean hasHiddenColumns()
1171 return alignment.getHiddenColumns() != null
1172 && alignment.getHiddenColumns().hasHiddenColumns();
1175 public void updateHiddenColumns()
1177 // this method doesn't really do anything now. But - it could, since a
1178 // column Selection could be in the process of modification
1179 // hasHiddenColumns = colSel.hasHiddenColumns();
1183 public boolean hasHiddenRows()
1185 return alignment.getHiddenSequences().getSize() > 0;
1188 protected SequenceGroup selectionGroup;
1190 public void setSequenceSetId(String newid)
1192 if (sequenceSetID != null)
1195 "Warning - overwriting a sequenceSetId for a viewport!");
1197 sequenceSetID = new String(newid);
1201 public String getSequenceSetId()
1203 if (sequenceSetID == null)
1205 sequenceSetID = alignment.hashCode() + "";
1208 return sequenceSetID;
1212 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1215 protected String viewId = null;
1218 public String getViewId()
1222 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1227 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1229 ignoreGapsInConsensusCalculation = b;
1232 updateConsensus(ap);
1233 if (residueShading != null)
1235 residueShading.setThreshold(residueShading.getThreshold(),
1236 ignoreGapsInConsensusCalculation);
1242 private long sgrouphash = -1, colselhash = -1;
1245 * checks current SelectionGroup against record of last hash value, and
1249 * update the record of last hash value
1251 * @return true if SelectionGroup changed since last call (when b is true)
1253 public boolean isSelectionGroupChanged(boolean b)
1255 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1256 : selectionGroup.hashCode();
1257 if (hc != -1 && hc != sgrouphash)
1269 * checks current colsel against record of last hash value, and optionally
1273 * update the record of last hash value
1274 * @return true if colsel changed since last call (when b is true)
1276 public boolean isColSelChanged(boolean b)
1278 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1279 if (hc != -1 && hc != colselhash)
1291 public boolean isIgnoreGapsConsensus()
1293 return ignoreGapsInConsensusCalculation;
1296 // property change stuff
1297 // JBPNote Prolly only need this in the applet version.
1298 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1301 protected boolean showConservation = true;
1303 protected boolean showQuality = true;
1305 protected boolean showConsensus = true;
1307 protected boolean showOccupancy = true;
1309 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1311 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1313 protected boolean showAutocalculatedAbove;
1316 * when set, view will scroll to show the highlighted position
1318 private boolean followHighlight = true;
1321 * Property change listener for changes in alignment
1326 public void addPropertyChangeListener(
1327 java.beans.PropertyChangeListener listener)
1329 changeSupport.addPropertyChangeListener(listener);
1338 public void removePropertyChangeListener(
1339 java.beans.PropertyChangeListener listener)
1341 changeSupport.removePropertyChangeListener(listener);
1345 * Property change listener for changes in alignment
1354 public void firePropertyChange(String prop, Object oldvalue,
1357 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1360 // common hide/show column stuff
1362 public void hideSelectedColumns()
1364 if (colSel.isEmpty())
1369 colSel.hideSelectedColumns(alignment);
1370 setSelectionGroup(null);
1371 isColSelChanged(true);
1374 public void hideColumns(int start, int end)
1378 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1382 alignment.getHiddenColumns().hideColumns(start, end);
1384 isColSelChanged(true);
1387 public void showColumn(int col)
1389 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1390 isColSelChanged(true);
1393 public void showAllHiddenColumns()
1395 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1396 isColSelChanged(true);
1399 // common hide/show seq stuff
1400 public void showAllHiddenSeqs()
1402 int startSeq = ranges.getStartSeq();
1403 int endSeq = ranges.getEndSeq();
1405 if (alignment.getHiddenSequences().getSize() > 0)
1407 if (selectionGroup == null)
1409 selectionGroup = new SequenceGroup();
1410 selectionGroup.setEndRes(alignment.getWidth() - 1);
1412 List<SequenceI> tmp = alignment.getHiddenSequences()
1413 .showAll(hiddenRepSequences);
1414 for (SequenceI seq : tmp)
1416 selectionGroup.addSequence(seq, false);
1417 setSequenceAnnotationsVisible(seq, true);
1420 hiddenRepSequences = null;
1422 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1424 firePropertyChange("alignment", null, alignment.getSequences());
1425 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1431 public void showSequence(int index)
1433 int startSeq = ranges.getStartSeq();
1434 int endSeq = ranges.getEndSeq();
1436 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
1437 hiddenRepSequences);
1440 if (selectionGroup == null)
1442 selectionGroup = new SequenceGroup();
1443 selectionGroup.setEndRes(alignment.getWidth() - 1);
1446 for (SequenceI seq : tmp)
1448 selectionGroup.addSequence(seq, false);
1449 setSequenceAnnotationsVisible(seq, true);
1452 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1454 firePropertyChange("alignment", null, alignment.getSequences());
1459 public void hideAllSelectedSeqs()
1461 if (selectionGroup == null || selectionGroup.getSize() < 1)
1466 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1470 setSelectionGroup(null);
1473 public void hideSequence(SequenceI[] seq)
1476 * cache offset to first visible sequence
1478 int startSeq = ranges.getStartSeq();
1482 for (int i = 0; i < seq.length; i++)
1484 alignment.getHiddenSequences().hideSequence(seq[i]);
1485 setSequenceAnnotationsVisible(seq[i], false);
1487 ranges.setStartSeq(startSeq);
1488 firePropertyChange("alignment", null, alignment.getSequences());
1493 * Hides the specified sequence, or the sequences it represents
1496 * the sequence to hide, or keep as representative
1497 * @param representGroup
1498 * if true, hide the current selection group except for the
1499 * representative sequence
1501 public void hideSequences(SequenceI sequence, boolean representGroup)
1503 if (selectionGroup == null || selectionGroup.getSize() < 1)
1505 hideSequence(new SequenceI[] { sequence });
1511 hideRepSequences(sequence, selectionGroup);
1512 setSelectionGroup(null);
1516 int gsize = selectionGroup.getSize();
1517 SequenceI[] hseqs = selectionGroup.getSequences()
1518 .toArray(new SequenceI[gsize]);
1520 hideSequence(hseqs);
1521 setSelectionGroup(null);
1526 * Set visibility for any annotations for the given sequence.
1530 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1533 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1536 for (AlignmentAnnotation ann : anns)
1538 if (ann.sequenceRef == sequenceI)
1540 ann.visible = visible;
1546 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1548 int sSize = sg.getSize();
1554 if (hiddenRepSequences == null)
1556 hiddenRepSequences = new Hashtable<>();
1559 hiddenRepSequences.put(repSequence, sg);
1561 // Hide all sequences except the repSequence
1562 SequenceI[] seqs = new SequenceI[sSize - 1];
1564 for (int i = 0; i < sSize; i++)
1566 if (sg.getSequenceAt(i) != repSequence)
1568 if (index == sSize - 1)
1573 seqs[index++] = sg.getSequenceAt(i);
1576 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1577 sg.setHidereps(true); // note: not done in 2.7applet
1584 * @return null or the current reference sequence
1586 public SequenceI getReferenceSeq()
1588 return alignment.getSeqrep();
1593 * @return true iff seq is the reference for the alignment
1595 public boolean isReferenceSeq(SequenceI seq)
1597 return alignment.getSeqrep() == seq;
1603 * @return true if there are sequences represented by this sequence that are
1606 public boolean isHiddenRepSequence(SequenceI seq)
1608 return (hiddenRepSequences != null
1609 && hiddenRepSequences.containsKey(seq));
1615 * @return null or a sequence group containing the sequences that seq
1618 public SequenceGroup getRepresentedSequences(SequenceI seq)
1620 return (SequenceGroup) (hiddenRepSequences == null ? null
1621 : hiddenRepSequences.get(seq));
1625 public int adjustForHiddenSeqs(int alignmentIndex)
1627 return alignment.getHiddenSequences()
1628 .adjustForHiddenSeqs(alignmentIndex);
1632 public void invertColumnSelection()
1634 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1638 public SequenceI[] getSelectionAsNewSequence()
1640 SequenceI[] sequences;
1641 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1642 // this was the only caller in the applet for this method
1643 // JBPNote: in applet, this method returned references to the alignment
1644 // sequences, and it did not honour the presence/absence of annotation
1645 // attached to the alignment (probably!)
1646 if (selectionGroup == null || selectionGroup.getSize() == 0)
1648 sequences = alignment.getSequencesArray();
1649 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1650 for (int i = 0; i < sequences.length; i++)
1652 // construct new sequence with subset of visible annotation
1653 sequences[i] = new Sequence(sequences[i], annots);
1658 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1665 public SequenceI[] getSequenceSelection()
1667 SequenceI[] sequences = null;
1668 if (selectionGroup != null)
1670 sequences = selectionGroup.getSequencesInOrder(alignment);
1672 if (sequences == null)
1674 sequences = alignment.getSequencesArray();
1680 public jalview.datamodel.AlignmentView getAlignmentView(
1681 boolean selectedOnly)
1683 return getAlignmentView(selectedOnly, false);
1687 public jalview.datamodel.AlignmentView getAlignmentView(
1688 boolean selectedOnly, boolean markGroups)
1690 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1692 alignment.getHiddenColumns() != null
1693 && alignment.getHiddenColumns().hasHiddenColumns(),
1694 selectedOnly, markGroups);
1698 public String[] getViewAsString(boolean selectedRegionOnly)
1700 return getViewAsString(selectedRegionOnly, true);
1704 public String[] getViewAsString(boolean selectedRegionOnly,
1705 boolean exportHiddenSeqs)
1707 String[] selection = null;
1708 SequenceI[] seqs = null;
1710 int start = 0, end = 0;
1711 if (selectedRegionOnly && selectionGroup != null)
1713 iSize = selectionGroup.getSize();
1714 seqs = selectionGroup.getSequencesInOrder(alignment);
1715 start = selectionGroup.getStartRes();
1716 end = selectionGroup.getEndRes() + 1;
1720 if (hasHiddenRows() && exportHiddenSeqs)
1722 AlignmentI fullAlignment = alignment.getHiddenSequences()
1723 .getFullAlignment();
1724 iSize = fullAlignment.getHeight();
1725 seqs = fullAlignment.getSequencesArray();
1726 end = fullAlignment.getWidth();
1730 iSize = alignment.getHeight();
1731 seqs = alignment.getSequencesArray();
1732 end = alignment.getWidth();
1736 selection = new String[iSize];
1737 if (alignment.getHiddenColumns() != null
1738 && alignment.getHiddenColumns().hasHiddenColumns())
1740 selection = alignment.getHiddenColumns()
1741 .getVisibleSequenceStrings(start, end, seqs);
1745 for (i = 0; i < iSize; i++)
1747 selection[i] = seqs[i].getSequenceAsString(start, end);
1755 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1757 ArrayList<int[]> regions = new ArrayList<>();
1763 HiddenColumns hidden = alignment.getHiddenColumns();
1764 if (hidden != null && hidden.hasHiddenColumns())
1768 start = hidden.adjustForHiddenColumns(start);
1771 end = hidden.getHiddenBoundaryRight(start);
1782 regions.add(new int[] { start, end });
1784 if (hidden != null && hidden.hasHiddenColumns())
1786 start = hidden.adjustForHiddenColumns(end);
1787 start = hidden.getHiddenBoundaryLeft(start) + 1;
1789 } while (end < max);
1791 int[][] startEnd = new int[regions.size()][2];
1797 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1798 boolean selectedOnly)
1800 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1801 AlignmentAnnotation[] aa;
1802 if ((aa = alignment.getAlignmentAnnotation()) != null)
1804 for (AlignmentAnnotation annot : aa)
1806 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1807 if (selectedOnly && selectionGroup != null)
1809 alignment.getHiddenColumns().makeVisibleAnnotation(
1810 selectionGroup.getStartRes(), selectionGroup.getEndRes(),
1815 alignment.getHiddenColumns().makeVisibleAnnotation(clone);
1824 public boolean isPadGaps()
1830 public void setPadGaps(boolean padGaps)
1832 this.padGaps = padGaps;
1836 * apply any post-edit constraints and trigger any calculations needed after
1837 * an edit has been performed on the alignment
1842 public void alignmentChanged(AlignmentViewPanel ap)
1846 alignment.padGaps();
1848 if (autoCalculateConsensus)
1850 updateConsensus(ap);
1852 if (hconsensus != null && autoCalculateConsensus)
1854 updateConservation(ap);
1856 if (autoCalculateStrucConsensus)
1858 updateStrucConsensus(ap);
1861 // Reset endRes of groups if beyond alignment width
1862 int alWidth = alignment.getWidth();
1863 List<SequenceGroup> groups = alignment.getGroups();
1866 for (SequenceGroup sg : groups)
1868 if (sg.getEndRes() > alWidth)
1870 sg.setEndRes(alWidth - 1);
1875 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1877 selectionGroup.setEndRes(alWidth - 1);
1880 updateAllColourSchemes();
1881 calculator.restartWorkers();
1882 // alignment.adjustSequenceAnnotations();
1886 * reset scope and do calculations for all applied colourschemes on alignment
1888 void updateAllColourSchemes()
1890 ResidueShaderI rs = residueShading;
1893 rs.alignmentChanged(alignment, hiddenRepSequences);
1895 rs.setConsensus(hconsensus);
1896 if (rs.conservationApplied())
1898 rs.setConservation(Conservation.calculateConservation("All",
1899 alignment.getSequences(), 0, alignment.getWidth(), false,
1900 getConsPercGaps(), false));
1904 for (SequenceGroup sg : alignment.getGroups())
1908 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1910 sg.recalcConservation();
1914 protected void initAutoAnnotation()
1916 // TODO: add menu option action that nulls or creates consensus object
1917 // depending on if the user wants to see the annotation or not in a
1918 // specific alignment
1920 if (hconsensus == null && !isDataset)
1922 if (!alignment.isNucleotide())
1931 consensus = new AlignmentAnnotation("Consensus",
1932 MessageManager.getString("label.consensus_descr"),
1933 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1934 initConsensus(consensus);
1937 initComplementConsensus();
1942 * If this is a protein alignment and there are mappings to cDNA, adds the
1943 * cDNA consensus annotation and returns true, else returns false.
1945 public boolean initComplementConsensus()
1947 if (!alignment.isNucleotide())
1949 final List<AlignedCodonFrame> codonMappings = alignment
1951 if (codonMappings != null && !codonMappings.isEmpty())
1953 boolean doConsensus = false;
1954 for (AlignedCodonFrame mapping : codonMappings)
1956 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1957 MapList[] mapLists = mapping.getdnaToProt();
1958 // mapLists can be empty if project load has not finished resolving
1960 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1968 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1970 .getString("label.complement_consensus_descr"),
1971 new Annotation[1], 0f, 100f,
1972 AlignmentAnnotation.BAR_GRAPH);
1973 initConsensus(complementConsensus);
1981 private void initConsensus(AlignmentAnnotation aa)
1984 aa.autoCalculated = true;
1988 alignment.addAnnotation(aa);
1992 // these should be extracted from the view model - style and settings for
1993 // derived annotation
1994 private void initGapCounts()
1998 gapcounts = new AlignmentAnnotation("Occupancy",
1999 MessageManager.getString("label.occupancy_descr"),
2000 new Annotation[1], 0f, alignment.getHeight(),
2001 AlignmentAnnotation.BAR_GRAPH);
2002 gapcounts.hasText = true;
2003 gapcounts.autoCalculated = true;
2004 gapcounts.scaleColLabel = true;
2005 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
2007 alignment.addAnnotation(gapcounts);
2011 private void initConservation()
2013 if (showConservation)
2015 if (conservation == null)
2017 conservation = new AlignmentAnnotation("Conservation",
2018 MessageManager.formatMessage("label.conservation_descr",
2020 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2021 conservation.hasText = true;
2022 conservation.autoCalculated = true;
2023 alignment.addAnnotation(conservation);
2028 private void initQuality()
2032 if (quality == null)
2034 quality = new AlignmentAnnotation("Quality",
2035 MessageManager.getString("label.quality_descr"),
2036 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2037 quality.hasText = true;
2038 quality.autoCalculated = true;
2039 alignment.addAnnotation(quality);
2044 private void initRNAStructure()
2046 if (alignment.hasRNAStructure() && strucConsensus == null)
2048 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2049 MessageManager.getString("label.strucconsensus_descr"),
2050 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2051 strucConsensus.hasText = true;
2052 strucConsensus.autoCalculated = true;
2056 alignment.addAnnotation(strucConsensus);
2064 * @see jalview.api.AlignViewportI#calcPanelHeight()
2067 public int calcPanelHeight()
2069 // setHeight of panels
2070 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2072 int charHeight = getCharHeight();
2075 BitSet graphgrp = new BitSet();
2076 for (AlignmentAnnotation aa : anns)
2080 System.err.println("Null annotation row: ignoring.");
2087 if (aa.graphGroup > -1)
2089 if (graphgrp.get(aa.graphGroup))
2095 graphgrp.set(aa.graphGroup);
2102 aa.height += charHeight;
2112 aa.height += aa.graphHeight;
2120 height += aa.height;
2132 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2133 boolean preserveNewGroupSettings)
2135 boolean updateCalcs = false;
2136 boolean conv = isShowGroupConservation();
2137 boolean cons = isShowGroupConsensus();
2138 boolean showprf = isShowSequenceLogo();
2139 boolean showConsHist = isShowConsensusHistogram();
2140 boolean normLogo = isNormaliseSequenceLogo();
2143 * TODO reorder the annotation rows according to group/sequence ordering on
2146 boolean sortg = true;
2148 // remove old automatic annotation
2149 // add any new annotation
2151 // intersect alignment annotation with alignment groups
2153 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2154 List<SequenceGroup> oldrfs = new ArrayList<>();
2157 for (int an = 0; an < aan.length; an++)
2159 if (aan[an].autoCalculated && aan[an].groupRef != null)
2161 oldrfs.add(aan[an].groupRef);
2162 alignment.deleteAnnotation(aan[an], false);
2166 if (alignment.getGroups() != null)
2168 for (SequenceGroup sg : alignment.getGroups())
2170 updateCalcs = false;
2171 if (applyGlobalSettings
2172 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2174 // set defaults for this group's conservation/consensus
2175 sg.setshowSequenceLogo(showprf);
2176 sg.setShowConsensusHistogram(showConsHist);
2177 sg.setNormaliseSequenceLogo(normLogo);
2182 alignment.addAnnotation(sg.getConservationRow(), 0);
2187 alignment.addAnnotation(sg.getConsensus(), 0);
2189 // refresh the annotation rows
2192 sg.recalcConservation();
2200 public boolean isDisplayReferenceSeq()
2202 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2206 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2208 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2212 public boolean isColourByReferenceSeq()
2214 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2218 public Color getSequenceColour(SequenceI seq)
2220 Color sqc = sequenceColours.get(seq);
2221 return (sqc == null ? Color.white : sqc);
2225 public void setSequenceColour(SequenceI seq, Color col)
2229 sequenceColours.remove(seq);
2233 sequenceColours.put(seq, col);
2238 public void updateSequenceIdColours()
2240 for (SequenceGroup sg : alignment.getGroups())
2242 if (sg.idColour != null)
2244 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2246 sequenceColours.put(s, sg.idColour);
2253 public void clearSequenceColours()
2255 sequenceColours.clear();
2259 public AlignViewportI getCodingComplement()
2261 return this.codingComplement;
2265 * Set this as the (cDna/protein) complement of the given viewport. Also
2266 * ensures the reverse relationship is set on the given viewport.
2269 public void setCodingComplement(AlignViewportI av)
2273 System.err.println("Ignoring recursive setCodingComplement request");
2277 this.codingComplement = av;
2278 // avoid infinite recursion!
2279 if (av.getCodingComplement() != this)
2281 av.setCodingComplement(this);
2287 public boolean isNucleotide()
2289 return getAlignment() == null ? false : getAlignment().isNucleotide();
2293 public FeaturesDisplayedI getFeaturesDisplayed()
2295 return featuresDisplayed;
2299 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2301 featuresDisplayed = featuresDisplayedI;
2305 public boolean areFeaturesDisplayed()
2307 return featuresDisplayed != null
2308 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2315 * features are displayed if true
2318 public void setShowSequenceFeatures(boolean b)
2320 viewStyle.setShowSequenceFeatures(b);
2324 public boolean isShowSequenceFeatures()
2326 return viewStyle.isShowSequenceFeatures();
2330 public void setShowSequenceFeaturesHeight(boolean selected)
2332 viewStyle.setShowSequenceFeaturesHeight(selected);
2336 public boolean isShowSequenceFeaturesHeight()
2338 return viewStyle.isShowSequenceFeaturesHeight();
2342 public void setShowAnnotation(boolean b)
2344 viewStyle.setShowAnnotation(b);
2348 public boolean isShowAnnotation()
2350 return viewStyle.isShowAnnotation();
2354 public boolean isRightAlignIds()
2356 return viewStyle.isRightAlignIds();
2360 public void setRightAlignIds(boolean rightAlignIds)
2362 viewStyle.setRightAlignIds(rightAlignIds);
2366 public boolean getConservationSelected()
2368 return viewStyle.getConservationSelected();
2372 public void setShowBoxes(boolean state)
2374 viewStyle.setShowBoxes(state);
2379 * @see jalview.api.ViewStyleI#getTextColour()
2382 public Color getTextColour()
2384 return viewStyle.getTextColour();
2389 * @see jalview.api.ViewStyleI#getTextColour2()
2392 public Color getTextColour2()
2394 return viewStyle.getTextColour2();
2399 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2402 public int getThresholdTextColour()
2404 return viewStyle.getThresholdTextColour();
2409 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2412 public boolean isConservationColourSelected()
2414 return viewStyle.isConservationColourSelected();
2419 * @see jalview.api.ViewStyleI#isRenderGaps()
2422 public boolean isRenderGaps()
2424 return viewStyle.isRenderGaps();
2429 * @see jalview.api.ViewStyleI#isShowColourText()
2432 public boolean isShowColourText()
2434 return viewStyle.isShowColourText();
2438 * @param conservationColourSelected
2439 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2442 public void setConservationColourSelected(
2443 boolean conservationColourSelected)
2445 viewStyle.setConservationColourSelected(conservationColourSelected);
2449 * @param showColourText
2450 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2453 public void setShowColourText(boolean showColourText)
2455 viewStyle.setShowColourText(showColourText);
2460 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2463 public void setTextColour(Color textColour)
2465 viewStyle.setTextColour(textColour);
2469 * @param thresholdTextColour
2470 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2473 public void setThresholdTextColour(int thresholdTextColour)
2475 viewStyle.setThresholdTextColour(thresholdTextColour);
2479 * @param textColour2
2480 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2483 public void setTextColour2(Color textColour2)
2485 viewStyle.setTextColour2(textColour2);
2489 public ViewStyleI getViewStyle()
2491 return new ViewStyle(viewStyle);
2495 public void setViewStyle(ViewStyleI settingsForView)
2497 viewStyle = new ViewStyle(settingsForView);
2498 if (residueShading != null)
2500 residueShading.setConservationApplied(
2501 settingsForView.isConservationColourSelected());
2506 public boolean sameStyle(ViewStyleI them)
2508 return viewStyle.sameStyle(them);
2513 * @see jalview.api.ViewStyleI#getIdWidth()
2516 public int getIdWidth()
2518 return viewStyle.getIdWidth();
2523 * @see jalview.api.ViewStyleI#setIdWidth(int)
2526 public void setIdWidth(int i)
2528 viewStyle.setIdWidth(i);
2533 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2536 public boolean isCentreColumnLabels()
2538 return viewStyle.isCentreColumnLabels();
2542 * @param centreColumnLabels
2543 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2546 public void setCentreColumnLabels(boolean centreColumnLabels)
2548 viewStyle.setCentreColumnLabels(centreColumnLabels);
2553 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2556 public void setShowDBRefs(boolean showdbrefs)
2558 viewStyle.setShowDBRefs(showdbrefs);
2563 * @see jalview.api.ViewStyleI#isShowDBRefs()
2566 public boolean isShowDBRefs()
2568 return viewStyle.isShowDBRefs();
2573 * @see jalview.api.ViewStyleI#isShowNPFeats()
2576 public boolean isShowNPFeats()
2578 return viewStyle.isShowNPFeats();
2582 * @param shownpfeats
2583 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2586 public void setShowNPFeats(boolean shownpfeats)
2588 viewStyle.setShowNPFeats(shownpfeats);
2591 public abstract StructureSelectionManager getStructureSelectionManager();
2594 * Add one command to the command history list.
2598 public void addToHistoryList(CommandI command)
2600 if (this.historyList != null)
2602 this.historyList.push(command);
2603 broadcastCommand(command, false);
2607 protected void broadcastCommand(CommandI command, boolean undo)
2609 getStructureSelectionManager().commandPerformed(command, undo,
2614 * Add one command to the command redo list.
2618 public void addToRedoList(CommandI command)
2620 if (this.redoList != null)
2622 this.redoList.push(command);
2624 broadcastCommand(command, true);
2628 * Clear the command redo list.
2630 public void clearRedoList()
2632 if (this.redoList != null)
2634 this.redoList.clear();
2638 public void setHistoryList(Deque<CommandI> list)
2640 this.historyList = list;
2643 public Deque<CommandI> getHistoryList()
2645 return this.historyList;
2648 public void setRedoList(Deque<CommandI> list)
2650 this.redoList = list;
2653 public Deque<CommandI> getRedoList()
2655 return this.redoList;
2659 public VamsasSource getVamsasSource()
2664 public SequenceAnnotationOrder getSortAnnotationsBy()
2666 return sortAnnotationsBy;
2669 public void setSortAnnotationsBy(
2670 SequenceAnnotationOrder sortAnnotationsBy)
2672 this.sortAnnotationsBy = sortAnnotationsBy;
2675 public boolean isShowAutocalculatedAbove()
2677 return showAutocalculatedAbove;
2680 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2682 this.showAutocalculatedAbove = showAutocalculatedAbove;
2686 public boolean isScaleProteinAsCdna()
2688 return viewStyle.isScaleProteinAsCdna();
2692 public void setScaleProteinAsCdna(boolean b)
2694 viewStyle.setScaleProteinAsCdna(b);
2698 public boolean isProteinFontAsCdna()
2700 return viewStyle.isProteinFontAsCdna();
2704 public void setProteinFontAsCdna(boolean b)
2706 viewStyle.setProteinFontAsCdna(b);
2710 * @return true if view should scroll to show the highlighted region of a
2715 public final boolean isFollowHighlight()
2717 return followHighlight;
2721 public final void setFollowHighlight(boolean b)
2723 this.followHighlight = b;
2727 public ViewportRanges getRanges()
2733 * Helper method to populate the SearchResults with the location in the
2734 * complementary alignment to scroll to, in order to match this one.
2737 * the SearchResults to add to
2738 * @return the offset (below top of visible region) of the matched sequence
2740 protected int findComplementScrollTarget(SearchResultsI sr)
2742 final AlignViewportI complement = getCodingComplement();
2743 if (complement == null || !complement.isFollowHighlight())
2747 boolean iAmProtein = !getAlignment().isNucleotide();
2748 AlignmentI proteinAlignment = iAmProtein ? getAlignment()
2749 : complement.getAlignment();
2750 if (proteinAlignment == null)
2754 final List<AlignedCodonFrame> mappings = proteinAlignment
2758 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2759 * residue in the middle column of the visible region. Scroll the
2760 * complementary alignment to line up the corresponding residue.
2763 SequenceI sequence = null;
2766 * locate 'middle' column (true middle if an odd number visible, left of
2767 * middle if an even number visible)
2769 int middleColumn = ranges.getStartRes()
2770 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2771 final HiddenSequences hiddenSequences = getAlignment()
2772 .getHiddenSequences();
2775 * searching to the bottom of the alignment gives smoother scrolling across
2776 * all gapped visible regions
2778 int lastSeq = alignment.getHeight() - 1;
2779 List<AlignedCodonFrame> seqMappings = null;
2780 for (int seqNo = ranges
2781 .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
2783 sequence = getAlignment().getSequenceAt(seqNo);
2784 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2788 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2792 seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
2794 getCodingComplement().getAlignment().getSequences());
2795 if (!seqMappings.isEmpty())
2801 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2804 * No ungapped mapped sequence in middle column - do nothing
2808 MappingUtils.addSearchResults(sr, sequence,
2809 sequence.findPosition(middleColumn), seqMappings);
2814 * synthesize a column selection if none exists so it covers the given
2815 * selection group. if wholewidth is false, no column selection is made if the
2816 * selection group covers the whole alignment width.
2821 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2824 if (sg != null && (sgs = sg.getStartRes()) >= 0
2825 && sg.getStartRes() <= (sge = sg.getEndRes())
2826 && !this.hasSelectedColumns())
2828 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2835 colSel = new ColumnSelection();
2837 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2839 colSel.addElement(cspos);
2845 * hold status of current selection group - defined on alignment or not.
2847 private boolean selectionIsDefinedGroup = false;
2850 public boolean isSelectionDefinedGroup()
2852 if (selectionGroup == null)
2856 if (isSelectionGroupChanged(true))
2858 selectionIsDefinedGroup = false;
2859 List<SequenceGroup> gps = alignment.getGroups();
2860 if (gps == null || gps.size() == 0)
2862 selectionIsDefinedGroup = false;
2866 selectionIsDefinedGroup = gps.contains(selectionGroup);
2869 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2873 * null, or currently highlighted results on this view
2875 private SearchResultsI searchResults = null;
2877 protected TreeModel currentTree = null;
2880 public boolean hasSearchResults()
2882 return searchResults != null;
2886 public void setSearchResults(SearchResultsI results)
2888 searchResults = results;
2892 public SearchResultsI getSearchResults()
2894 return searchResults;
2898 * get the consensus sequence as displayed under the PID consensus annotation
2901 * @return consensus sequence as a new sequence object
2903 public SequenceI getConsensusSeq()
2905 if (consensus == null)
2907 updateConsensus(null);
2909 if (consensus == null)
2913 StringBuffer seqs = new StringBuffer();
2914 for (int i = 0; i < consensus.annotations.length; i++)
2916 Annotation annotation = consensus.annotations[i];
2917 if (annotation != null)
2919 String description = annotation.description;
2920 if (description != null && description.startsWith("["))
2922 // consensus is a tie - just pick the first one
2923 seqs.append(description.charAt(1));
2927 seqs.append(annotation.displayCharacter);
2932 SequenceI sq = new Sequence("Consensus", seqs.toString());
2933 sq.setDescription("Percentage Identity Consensus "
2934 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
2939 public void setCurrentTree(TreeModel tree)
2945 public TreeModel getCurrentTree()