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.Iterator;
71 import java.util.List;
75 * base class holding visualization and analysis attributes and common logic for
76 * an active alignment view displayed in the GUI
81 public abstract class AlignmentViewport
82 implements AlignViewportI, CommandListener, VamsasSource
84 protected ViewportRanges ranges;
86 protected ViewStyleI viewStyle = new ViewStyle();
89 * A viewport that hosts the cDna view of this (protein), or vice versa (if
92 AlignViewportI codingComplement = null;
94 FeaturesDisplayedI featuresDisplayed = null;
96 protected Deque<CommandI> historyList = new ArrayDeque<>();
98 protected Deque<CommandI> redoList = new ArrayDeque<>();
101 * alignment displayed in the viewport. Please use get/setter
103 protected AlignmentI alignment;
105 public AlignmentViewport(AlignmentI al)
108 ranges = new ViewportRanges(al);
113 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
116 public void setFontName(String name)
118 viewStyle.setFontName(name);
123 * @see jalview.api.ViewStyleI#setFontStyle(int)
126 public void setFontStyle(int style)
128 viewStyle.setFontStyle(style);
133 * @see jalview.api.ViewStyleI#setFontSize(int)
136 public void setFontSize(int size)
138 viewStyle.setFontSize(size);
143 * @see jalview.api.ViewStyleI#getFontStyle()
146 public int getFontStyle()
148 return viewStyle.getFontStyle();
153 * @see jalview.api.ViewStyleI#getFontName()
156 public String getFontName()
158 return viewStyle.getFontName();
163 * @see jalview.api.ViewStyleI#getFontSize()
166 public int getFontSize()
168 return viewStyle.getFontSize();
172 * @param upperCasebold
173 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
176 public void setUpperCasebold(boolean upperCasebold)
178 viewStyle.setUpperCasebold(upperCasebold);
183 * @see jalview.api.ViewStyleI#isUpperCasebold()
186 public boolean isUpperCasebold()
188 return viewStyle.isUpperCasebold();
193 * @see jalview.api.ViewStyleI#isSeqNameItalics()
196 public boolean isSeqNameItalics()
198 return viewStyle.isSeqNameItalics();
202 * @param colourByReferenceSeq
203 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
206 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
208 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
213 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
216 public void setColourAppliesToAllGroups(boolean b)
218 viewStyle.setColourAppliesToAllGroups(b);
223 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
226 public boolean getColourAppliesToAllGroups()
228 return viewStyle.getColourAppliesToAllGroups();
233 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
236 public boolean getAbovePIDThreshold()
238 return viewStyle.getAbovePIDThreshold();
243 * @see jalview.api.ViewStyleI#setIncrement(int)
246 public void setIncrement(int inc)
248 viewStyle.setIncrement(inc);
253 * @see jalview.api.ViewStyleI#getIncrement()
256 public int getIncrement()
258 return viewStyle.getIncrement();
263 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
266 public void setConservationSelected(boolean b)
268 viewStyle.setConservationSelected(b);
273 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
276 public void setShowHiddenMarkers(boolean show)
278 viewStyle.setShowHiddenMarkers(show);
283 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
286 public boolean getShowHiddenMarkers()
288 return viewStyle.getShowHiddenMarkers();
293 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
296 public void setScaleRightWrapped(boolean b)
298 viewStyle.setScaleRightWrapped(b);
303 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
306 public void setScaleLeftWrapped(boolean b)
308 viewStyle.setScaleLeftWrapped(b);
313 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
316 public void setScaleAboveWrapped(boolean b)
318 viewStyle.setScaleAboveWrapped(b);
323 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
326 public boolean getScaleLeftWrapped()
328 return viewStyle.getScaleLeftWrapped();
333 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
336 public boolean getScaleAboveWrapped()
338 return viewStyle.getScaleAboveWrapped();
343 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
346 public boolean getScaleRightWrapped()
348 return viewStyle.getScaleRightWrapped();
353 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
356 public void setAbovePIDThreshold(boolean b)
358 viewStyle.setAbovePIDThreshold(b);
363 * @see jalview.api.ViewStyleI#setThreshold(int)
366 public void setThreshold(int thresh)
368 viewStyle.setThreshold(thresh);
373 * @see jalview.api.ViewStyleI#getThreshold()
376 public int getThreshold()
378 return viewStyle.getThreshold();
383 * @see jalview.api.ViewStyleI#getShowJVSuffix()
386 public boolean getShowJVSuffix()
388 return viewStyle.getShowJVSuffix();
393 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
396 public void setShowJVSuffix(boolean b)
398 viewStyle.setShowJVSuffix(b);
403 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
406 public void setWrapAlignment(boolean state)
408 viewStyle.setWrapAlignment(state);
409 ranges.setWrappedMode(state);
414 * @see jalview.api.ViewStyleI#setShowText(boolean)
417 public void setShowText(boolean state)
419 viewStyle.setShowText(state);
424 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
427 public void setRenderGaps(boolean state)
429 viewStyle.setRenderGaps(state);
434 * @see jalview.api.ViewStyleI#getColourText()
437 public boolean getColourText()
439 return viewStyle.getColourText();
444 * @see jalview.api.ViewStyleI#setColourText(boolean)
447 public void setColourText(boolean state)
449 viewStyle.setColourText(state);
454 * @see jalview.api.ViewStyleI#getWrapAlignment()
457 public boolean getWrapAlignment()
459 return viewStyle.getWrapAlignment();
464 * @see jalview.api.ViewStyleI#getShowText()
467 public boolean getShowText()
469 return viewStyle.getShowText();
474 * @see jalview.api.ViewStyleI#getWrappedWidth()
477 public int getWrappedWidth()
479 return viewStyle.getWrappedWidth();
484 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
487 public void setWrappedWidth(int w)
489 viewStyle.setWrappedWidth(w);
494 * @see jalview.api.ViewStyleI#getCharHeight()
497 public int getCharHeight()
499 return viewStyle.getCharHeight();
504 * @see jalview.api.ViewStyleI#setCharHeight(int)
507 public void setCharHeight(int h)
509 viewStyle.setCharHeight(h);
514 * @see jalview.api.ViewStyleI#getCharWidth()
517 public int getCharWidth()
519 return viewStyle.getCharWidth();
524 * @see jalview.api.ViewStyleI#setCharWidth(int)
527 public void setCharWidth(int w)
529 viewStyle.setCharWidth(w);
534 * @see jalview.api.ViewStyleI#getShowBoxes()
537 public boolean getShowBoxes()
539 return viewStyle.getShowBoxes();
544 * @see jalview.api.ViewStyleI#getShowUnconserved()
547 public boolean getShowUnconserved()
549 return viewStyle.getShowUnconserved();
553 * @param showunconserved
554 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
557 public void setShowUnconserved(boolean showunconserved)
559 viewStyle.setShowUnconserved(showunconserved);
564 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
567 public void setSeqNameItalics(boolean default1)
569 viewStyle.setSeqNameItalics(default1);
573 public AlignmentI getAlignment()
579 public char getGapCharacter()
581 return alignment.getGapCharacter();
584 protected String sequenceSetID;
587 * probably unused indicator that view is of a dataset rather than an
590 protected boolean isDataset = false;
592 public void setDataset(boolean b)
597 public boolean isDataset()
602 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
604 protected ColumnSelection colSel = new ColumnSelection();
606 public boolean autoCalculateConsensus = true;
608 protected boolean autoCalculateStrucConsensus = true;
610 protected boolean ignoreGapsInConsensusCalculation = false;
612 protected ResidueShaderI residueShading = new ResidueShader();
615 public void setGlobalColourScheme(ColourSchemeI cs)
617 // TODO: logic refactored from AlignFrame changeColour -
618 // TODO: autorecalc stuff should be changed to rely on the worker system
619 // check to see if we should implement a changeColour(cs) method rather than
620 // put the logic in here
621 // - means that caller decides if they want to just modify state and defer
622 // calculation till later or to do all calculations in thread.
626 * only instantiate alignment colouring once, thereafter update it;
627 * this means that any conservation or PID threshold settings
628 * persist when the alignment colour scheme is changed
630 if (residueShading == null)
632 residueShading = new ResidueShader(viewStyle);
634 residueShading.setColourScheme(cs);
636 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
637 // ...problem: groups need these, but do not currently have a ViewStyle
641 if (getConservationSelected())
643 residueShading.setConservation(hconservation);
646 * reset conservation flag in case just set to false if
647 * Conservation was null (calculation still in progress)
649 residueShading.setConservationApplied(getConservationSelected());
650 residueShading.alignmentChanged(alignment, hiddenRepSequences);
654 * if 'apply colour to all groups' is selected... do so
655 * (but don't transfer any colour threshold settings to groups)
657 if (getColourAppliesToAllGroups())
659 for (SequenceGroup sg : getAlignment().getGroups())
662 * retain any colour thresholds per group while
663 * changing choice of colour scheme (JAL-2386)
665 sg.setColourScheme(cs);
668 sg.getGroupColourScheme().alignmentChanged(sg,
676 public ColourSchemeI getGlobalColourScheme()
678 return residueShading == null ? null : residueShading.getColourScheme();
682 public ResidueShaderI getResidueShading()
684 return residueShading;
687 protected AlignmentAnnotation consensus;
689 protected AlignmentAnnotation complementConsensus;
691 protected AlignmentAnnotation gapcounts;
693 protected AlignmentAnnotation strucConsensus;
695 protected AlignmentAnnotation conservation;
697 protected AlignmentAnnotation quality;
699 protected AlignmentAnnotation[] groupConsensus;
701 protected AlignmentAnnotation[] groupConservation;
704 * results of alignment consensus analysis for visible portion of view
706 protected ProfilesI hconsensus = null;
709 * results of cDNA complement consensus visible portion of view
711 protected Hashtable[] hcomplementConsensus = null;
714 * results of secondary structure base pair consensus for visible portion of
717 protected Hashtable[] hStrucConsensus = null;
719 protected Conservation hconservation = null;
722 public void setConservation(Conservation cons)
724 hconservation = cons;
728 * percentage gaps allowed in a column before all amino acid properties should
729 * be considered unconserved
731 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
734 public int getConsPercGaps()
740 public void setSequenceConsensusHash(ProfilesI hconsensus)
742 this.hconsensus = hconsensus;
746 public void setComplementConsensusHash(Hashtable[] hconsensus)
748 this.hcomplementConsensus = hconsensus;
752 public ProfilesI getSequenceConsensusHash()
758 public Hashtable[] getComplementConsensusHash()
760 return hcomplementConsensus;
764 public Hashtable[] getRnaStructureConsensusHash()
766 return hStrucConsensus;
770 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
772 this.hStrucConsensus = hStrucConsensus;
777 public AlignmentAnnotation getAlignmentQualityAnnot()
783 public AlignmentAnnotation getAlignmentConservationAnnotation()
789 public AlignmentAnnotation getAlignmentConsensusAnnotation()
795 public AlignmentAnnotation getAlignmentGapAnnotation()
801 public AlignmentAnnotation getComplementConsensusAnnotation()
803 return complementConsensus;
807 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
809 return strucConsensus;
812 protected AlignCalcManagerI calculator = new AlignCalcManager();
815 * trigger update of conservation annotation
817 public void updateConservation(final AlignmentViewPanel ap)
819 // see note in mantis : issue number 8585
820 if (alignment.isNucleotide()
821 || (conservation == null && quality == null)
822 || !autoCalculateConsensus)
826 if (calculator.getRegisteredWorkersOfClass(
827 jalview.workers.ConservationThread.class) == null)
829 calculator.registerWorker(
830 new jalview.workers.ConservationThread(this, ap));
835 * trigger update of consensus annotation
837 public void updateConsensus(final AlignmentViewPanel ap)
839 // see note in mantis : issue number 8585
840 if (consensus == null || !autoCalculateConsensus)
845 .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
847 calculator.registerWorker(new ConsensusThread(this, ap));
851 * A separate thread to compute cDNA consensus for a protein alignment
852 * which has mapping to cDNA
854 final AlignmentI al = this.getAlignment();
855 if (!al.isNucleotide() && al.getCodonFrames() != null
856 && !al.getCodonFrames().isEmpty())
859 * fudge - check first for protein-to-nucleotide mappings
860 * (we don't want to do this for protein-to-protein)
862 boolean doConsensus = false;
863 for (AlignedCodonFrame mapping : al.getCodonFrames())
865 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
866 MapList[] mapLists = mapping.getdnaToProt();
867 // mapLists can be empty if project load has not finished resolving seqs
868 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
876 if (calculator.getRegisteredWorkersOfClass(
877 ComplementConsensusThread.class) == null)
880 .registerWorker(new ComplementConsensusThread(this, ap));
886 // --------START Structure Conservation
887 public void updateStrucConsensus(final AlignmentViewPanel ap)
889 if (autoCalculateStrucConsensus && strucConsensus == null
890 && alignment.isNucleotide() && alignment.hasRNAStructure())
892 // secondary structure has been added - so init the consensus line
896 // see note in mantis : issue number 8585
897 if (strucConsensus == null || !autoCalculateStrucConsensus)
901 if (calculator.getRegisteredWorkersOfClass(
902 StrucConsensusThread.class) == null)
904 calculator.registerWorker(new StrucConsensusThread(this, ap));
908 public boolean isCalcInProgress()
910 return calculator.isWorking();
914 public boolean isCalculationInProgress(
915 AlignmentAnnotation alignmentAnnotation)
917 if (!alignmentAnnotation.autoCalculated)
921 if (calculator.workingInvolvedWith(alignmentAnnotation))
923 // System.err.println("grey out ("+alignmentAnnotation.label+")");
929 public void setAlignment(AlignmentI align)
931 this.alignment = align;
935 * Clean up references when this viewport is closed
938 public void dispose()
941 * defensively null out references to large objects in case
942 * this object is not garbage collected (as if!)
945 complementConsensus = null;
946 strucConsensus = null;
949 groupConsensus = null;
950 groupConservation = null;
952 hconservation = null;
953 hcomplementConsensus = null;
956 residueShading = null; // may hold a reference to Consensus
957 changeSupport = null;
960 selectionGroup = null;
965 public boolean isClosed()
967 // TODO: check that this isClosed is only true after panel is closed, not
968 // before it is fully constructed.
969 return alignment == null;
973 public AlignCalcManagerI getCalcManager()
979 * should conservation rows be shown for groups
981 protected boolean showGroupConservation = false;
984 * should consensus rows be shown for groups
986 protected boolean showGroupConsensus = false;
989 * should consensus profile be rendered by default
991 protected boolean showSequenceLogo = false;
994 * should consensus profile be rendered normalised to row height
996 protected boolean normaliseSequenceLogo = false;
999 * should consensus histograms be rendered by default
1001 protected boolean showConsensusHistogram = true;
1004 * @return the showConsensusProfile
1007 public boolean isShowSequenceLogo()
1009 return showSequenceLogo;
1013 * @param showSequenceLogo
1016 public void setShowSequenceLogo(boolean showSequenceLogo)
1018 if (showSequenceLogo != this.showSequenceLogo)
1020 // TODO: decouple settings setting from calculation when refactoring
1021 // annotation update method from alignframe to viewport
1022 this.showSequenceLogo = showSequenceLogo;
1023 calculator.updateAnnotationFor(ConsensusThread.class);
1024 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1025 calculator.updateAnnotationFor(StrucConsensusThread.class);
1027 this.showSequenceLogo = showSequenceLogo;
1031 * @param showConsensusHistogram
1032 * the showConsensusHistogram to set
1034 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1036 this.showConsensusHistogram = showConsensusHistogram;
1040 * @return the showGroupConservation
1042 public boolean isShowGroupConservation()
1044 return showGroupConservation;
1048 * @param showGroupConservation
1049 * the showGroupConservation to set
1051 public void setShowGroupConservation(boolean showGroupConservation)
1053 this.showGroupConservation = showGroupConservation;
1057 * @return the showGroupConsensus
1059 public boolean isShowGroupConsensus()
1061 return showGroupConsensus;
1065 * @param showGroupConsensus
1066 * the showGroupConsensus to set
1068 public void setShowGroupConsensus(boolean showGroupConsensus)
1070 this.showGroupConsensus = showGroupConsensus;
1075 * @return flag to indicate if the consensus histogram should be rendered by
1079 public boolean isShowConsensusHistogram()
1081 return this.showConsensusHistogram;
1085 * when set, updateAlignment will always ensure sequences are of equal length
1087 private boolean padGaps = false;
1090 * when set, alignment should be reordered according to a newly opened tree
1092 public boolean sortByTree = false;
1097 * @return null or the currently selected sequence region
1100 public SequenceGroup getSelectionGroup()
1102 return selectionGroup;
1106 * Set the selection group for this window. Also sets the current alignment as
1107 * the context for the group, if it does not already have one.
1110 * - group holding references to sequences in this alignment view
1114 public void setSelectionGroup(SequenceGroup sg)
1116 selectionGroup = sg;
1117 if (sg != null && sg.getContext() == null)
1119 sg.setContext(alignment);
1123 public void setHiddenColumns(HiddenColumns hidden)
1125 this.alignment.setHiddenColumns(hidden);
1129 public ColumnSelection getColumnSelection()
1135 public void setColumnSelection(ColumnSelection colSel)
1137 this.colSel = colSel;
1140 updateHiddenColumns();
1142 isColSelChanged(true);
1150 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1152 return hiddenRepSequences;
1156 public void setHiddenRepSequences(
1157 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1159 this.hiddenRepSequences = hiddenRepSequences;
1163 public boolean hasSelectedColumns()
1165 ColumnSelection columnSelection = getColumnSelection();
1166 return columnSelection != null && columnSelection.hasSelectedColumns();
1170 public boolean hasHiddenColumns()
1172 return alignment.getHiddenColumns() != null
1173 && alignment.getHiddenColumns().hasHiddenColumns();
1176 public void updateHiddenColumns()
1178 // this method doesn't really do anything now. But - it could, since a
1179 // column Selection could be in the process of modification
1180 // hasHiddenColumns = colSel.hasHiddenColumns();
1184 public boolean hasHiddenRows()
1186 return alignment.getHiddenSequences().getSize() > 0;
1189 protected SequenceGroup selectionGroup;
1191 public void setSequenceSetId(String newid)
1193 if (sequenceSetID != null)
1196 "Warning - overwriting a sequenceSetId for a viewport!");
1198 sequenceSetID = new String(newid);
1202 public String getSequenceSetId()
1204 if (sequenceSetID == null)
1206 sequenceSetID = alignment.hashCode() + "";
1209 return sequenceSetID;
1213 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1216 protected String viewId = null;
1219 public String getViewId()
1223 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1228 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1230 ignoreGapsInConsensusCalculation = b;
1233 updateConsensus(ap);
1234 if (residueShading != null)
1236 residueShading.setThreshold(residueShading.getThreshold(),
1237 ignoreGapsInConsensusCalculation);
1243 private long sgrouphash = -1, colselhash = -1;
1246 * checks current SelectionGroup against record of last hash value, and
1250 * update the record of last hash value
1252 * @return true if SelectionGroup changed since last call (when b is true)
1254 public boolean isSelectionGroupChanged(boolean b)
1256 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1257 : selectionGroup.hashCode();
1258 if (hc != -1 && hc != sgrouphash)
1270 * checks current colsel against record of last hash value, and optionally
1274 * update the record of last hash value
1275 * @return true if colsel changed since last call (when b is true)
1277 public boolean isColSelChanged(boolean b)
1279 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1280 if (hc != -1 && hc != colselhash)
1292 public boolean isIgnoreGapsConsensus()
1294 return ignoreGapsInConsensusCalculation;
1297 // property change stuff
1298 // JBPNote Prolly only need this in the applet version.
1299 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1302 protected boolean showConservation = true;
1304 protected boolean showQuality = true;
1306 protected boolean showConsensus = true;
1308 protected boolean showOccupancy = true;
1310 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1312 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1314 protected boolean showAutocalculatedAbove;
1317 * when set, view will scroll to show the highlighted position
1319 private boolean followHighlight = true;
1322 * Property change listener for changes in alignment
1327 public void addPropertyChangeListener(
1328 java.beans.PropertyChangeListener listener)
1330 changeSupport.addPropertyChangeListener(listener);
1339 public void removePropertyChangeListener(
1340 java.beans.PropertyChangeListener listener)
1342 if (changeSupport != null)
1344 changeSupport.removePropertyChangeListener(listener);
1349 * Property change listener for changes in alignment
1358 public void firePropertyChange(String prop, Object oldvalue,
1361 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1364 // common hide/show column stuff
1366 public void hideSelectedColumns()
1368 if (colSel.isEmpty())
1373 colSel.hideSelectedColumns(alignment);
1374 setSelectionGroup(null);
1375 isColSelChanged(true);
1378 public void hideColumns(int start, int end)
1382 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1386 alignment.getHiddenColumns().hideColumns(start, end);
1388 isColSelChanged(true);
1391 public void showColumn(int col)
1393 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1394 isColSelChanged(true);
1397 public void showAllHiddenColumns()
1399 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1400 isColSelChanged(true);
1403 // common hide/show seq stuff
1404 public void showAllHiddenSeqs()
1406 int startSeq = ranges.getStartSeq();
1407 int endSeq = ranges.getEndSeq();
1409 if (alignment.getHiddenSequences().getSize() > 0)
1411 if (selectionGroup == null)
1413 selectionGroup = new SequenceGroup();
1414 selectionGroup.setEndRes(alignment.getWidth() - 1);
1416 List<SequenceI> tmp = alignment.getHiddenSequences()
1417 .showAll(hiddenRepSequences);
1418 for (SequenceI seq : tmp)
1420 selectionGroup.addSequence(seq, false);
1421 setSequenceAnnotationsVisible(seq, true);
1424 hiddenRepSequences = null;
1426 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1428 firePropertyChange("alignment", null, alignment.getSequences());
1429 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1435 public void showSequence(int index)
1437 int startSeq = ranges.getStartSeq();
1438 int endSeq = ranges.getEndSeq();
1440 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
1441 hiddenRepSequences);
1444 if (selectionGroup == null)
1446 selectionGroup = new SequenceGroup();
1447 selectionGroup.setEndRes(alignment.getWidth() - 1);
1450 for (SequenceI seq : tmp)
1452 selectionGroup.addSequence(seq, false);
1453 setSequenceAnnotationsVisible(seq, true);
1456 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1458 firePropertyChange("alignment", null, alignment.getSequences());
1463 public void hideAllSelectedSeqs()
1465 if (selectionGroup == null || selectionGroup.getSize() < 1)
1470 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1474 setSelectionGroup(null);
1477 public void hideSequence(SequenceI[] seq)
1480 * cache offset to first visible sequence
1482 int startSeq = ranges.getStartSeq();
1486 for (int i = 0; i < seq.length; i++)
1488 alignment.getHiddenSequences().hideSequence(seq[i]);
1489 setSequenceAnnotationsVisible(seq[i], false);
1491 ranges.setStartSeq(startSeq);
1492 firePropertyChange("alignment", null, alignment.getSequences());
1497 * Hides the specified sequence, or the sequences it represents
1500 * the sequence to hide, or keep as representative
1501 * @param representGroup
1502 * if true, hide the current selection group except for the
1503 * representative sequence
1505 public void hideSequences(SequenceI sequence, boolean representGroup)
1507 if (selectionGroup == null || selectionGroup.getSize() < 1)
1509 hideSequence(new SequenceI[] { sequence });
1515 hideRepSequences(sequence, selectionGroup);
1516 setSelectionGroup(null);
1520 int gsize = selectionGroup.getSize();
1521 SequenceI[] hseqs = selectionGroup.getSequences()
1522 .toArray(new SequenceI[gsize]);
1524 hideSequence(hseqs);
1525 setSelectionGroup(null);
1530 * Set visibility for any annotations for the given sequence.
1534 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1537 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1540 for (AlignmentAnnotation ann : anns)
1542 if (ann.sequenceRef == sequenceI)
1544 ann.visible = visible;
1550 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1552 int sSize = sg.getSize();
1558 if (hiddenRepSequences == null)
1560 hiddenRepSequences = new Hashtable<>();
1563 hiddenRepSequences.put(repSequence, sg);
1565 // Hide all sequences except the repSequence
1566 SequenceI[] seqs = new SequenceI[sSize - 1];
1568 for (int i = 0; i < sSize; i++)
1570 if (sg.getSequenceAt(i) != repSequence)
1572 if (index == sSize - 1)
1577 seqs[index++] = sg.getSequenceAt(i);
1580 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1581 sg.setHidereps(true); // note: not done in 2.7applet
1588 * @return null or the current reference sequence
1590 public SequenceI getReferenceSeq()
1592 return alignment.getSeqrep();
1597 * @return true iff seq is the reference for the alignment
1599 public boolean isReferenceSeq(SequenceI seq)
1601 return alignment.getSeqrep() == seq;
1607 * @return true if there are sequences represented by this sequence that are
1610 public boolean isHiddenRepSequence(SequenceI seq)
1612 return (hiddenRepSequences != null
1613 && hiddenRepSequences.containsKey(seq));
1619 * @return null or a sequence group containing the sequences that seq
1622 public SequenceGroup getRepresentedSequences(SequenceI seq)
1624 return (SequenceGroup) (hiddenRepSequences == null ? null
1625 : hiddenRepSequences.get(seq));
1629 public int adjustForHiddenSeqs(int alignmentIndex)
1631 return alignment.getHiddenSequences()
1632 .adjustForHiddenSeqs(alignmentIndex);
1636 public void invertColumnSelection()
1638 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1642 public SequenceI[] getSelectionAsNewSequence()
1644 SequenceI[] sequences;
1645 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1646 // this was the only caller in the applet for this method
1647 // JBPNote: in applet, this method returned references to the alignment
1648 // sequences, and it did not honour the presence/absence of annotation
1649 // attached to the alignment (probably!)
1650 if (selectionGroup == null || selectionGroup.getSize() == 0)
1652 sequences = alignment.getSequencesArray();
1653 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1654 for (int i = 0; i < sequences.length; i++)
1656 // construct new sequence with subset of visible annotation
1657 sequences[i] = new Sequence(sequences[i], annots);
1662 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1669 public SequenceI[] getSequenceSelection()
1671 SequenceI[] sequences = null;
1672 if (selectionGroup != null)
1674 sequences = selectionGroup.getSequencesInOrder(alignment);
1676 if (sequences == null)
1678 sequences = alignment.getSequencesArray();
1684 public jalview.datamodel.AlignmentView getAlignmentView(
1685 boolean selectedOnly)
1687 return getAlignmentView(selectedOnly, false);
1691 public jalview.datamodel.AlignmentView getAlignmentView(
1692 boolean selectedOnly, boolean markGroups)
1694 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1696 alignment.getHiddenColumns() != null
1697 && alignment.getHiddenColumns().hasHiddenColumns(),
1698 selectedOnly, markGroups);
1702 public String[] getViewAsString(boolean selectedRegionOnly)
1704 return getViewAsString(selectedRegionOnly, true);
1708 public String[] getViewAsString(boolean selectedRegionOnly,
1709 boolean exportHiddenSeqs)
1711 String[] selection = null;
1712 SequenceI[] seqs = null;
1714 int start = 0, end = 0;
1715 if (selectedRegionOnly && selectionGroup != null)
1717 iSize = selectionGroup.getSize();
1718 seqs = selectionGroup.getSequencesInOrder(alignment);
1719 start = selectionGroup.getStartRes();
1720 end = selectionGroup.getEndRes() + 1;
1724 if (hasHiddenRows() && exportHiddenSeqs)
1726 AlignmentI fullAlignment = alignment.getHiddenSequences()
1727 .getFullAlignment();
1728 iSize = fullAlignment.getHeight();
1729 seqs = fullAlignment.getSequencesArray();
1730 end = fullAlignment.getWidth();
1734 iSize = alignment.getHeight();
1735 seqs = alignment.getSequencesArray();
1736 end = alignment.getWidth();
1740 selection = new String[iSize];
1741 if (alignment.getHiddenColumns() != null
1742 && alignment.getHiddenColumns().hasHiddenColumns())
1744 for (i = 0; i < iSize; i++)
1746 Iterator<int[]> blocks = alignment.getHiddenColumns()
1747 .getVisContigsIterator(start, end + 1, false);
1748 selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
1753 for (i = 0; i < iSize; i++)
1755 selection[i] = seqs[i].getSequenceAsString(start, end);
1763 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1765 ArrayList<int[]> regions = new ArrayList<>();
1771 HiddenColumns hidden = alignment.getHiddenColumns();
1772 if (hidden != null && hidden.hasHiddenColumns())
1776 start = hidden.visibleToAbsoluteColumn(start);
1779 end = hidden.getNextHiddenBoundary(false, start);
1790 regions.add(new int[] { start, end });
1792 if (hidden != null && hidden.hasHiddenColumns())
1794 start = hidden.visibleToAbsoluteColumn(end);
1795 start = hidden.getNextHiddenBoundary(true, start) + 1;
1797 } while (end < max);
1799 int[][] startEnd = new int[regions.size()][2];
1805 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1806 boolean selectedOnly)
1808 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1809 AlignmentAnnotation[] aa;
1810 if ((aa = alignment.getAlignmentAnnotation()) != null)
1812 for (AlignmentAnnotation annot : aa)
1814 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1815 if (selectedOnly && selectionGroup != null)
1817 clone.makeVisibleAnnotation(
1818 selectionGroup.getStartRes(), selectionGroup.getEndRes(),
1819 alignment.getHiddenColumns());
1823 clone.makeVisibleAnnotation(alignment.getHiddenColumns());
1832 public boolean isPadGaps()
1838 public void setPadGaps(boolean padGaps)
1840 this.padGaps = padGaps;
1844 * apply any post-edit constraints and trigger any calculations needed after
1845 * an edit has been performed on the alignment
1850 public void alignmentChanged(AlignmentViewPanel ap)
1854 alignment.padGaps();
1856 if (autoCalculateConsensus)
1858 updateConsensus(ap);
1860 if (hconsensus != null && autoCalculateConsensus)
1862 updateConservation(ap);
1864 if (autoCalculateStrucConsensus)
1866 updateStrucConsensus(ap);
1869 // Reset endRes of groups if beyond alignment width
1870 int alWidth = alignment.getWidth();
1871 List<SequenceGroup> groups = alignment.getGroups();
1874 for (SequenceGroup sg : groups)
1876 if (sg.getEndRes() > alWidth)
1878 sg.setEndRes(alWidth - 1);
1883 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1885 selectionGroup.setEndRes(alWidth - 1);
1888 updateAllColourSchemes();
1889 calculator.restartWorkers();
1890 // alignment.adjustSequenceAnnotations();
1894 * reset scope and do calculations for all applied colourschemes on alignment
1896 void updateAllColourSchemes()
1898 ResidueShaderI rs = residueShading;
1901 rs.alignmentChanged(alignment, hiddenRepSequences);
1903 rs.setConsensus(hconsensus);
1904 if (rs.conservationApplied())
1906 rs.setConservation(Conservation.calculateConservation("All",
1907 alignment.getSequences(), 0, alignment.getWidth(), false,
1908 getConsPercGaps(), false));
1912 for (SequenceGroup sg : alignment.getGroups())
1916 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1918 sg.recalcConservation();
1922 protected void initAutoAnnotation()
1924 // TODO: add menu option action that nulls or creates consensus object
1925 // depending on if the user wants to see the annotation or not in a
1926 // specific alignment
1928 if (hconsensus == null && !isDataset)
1930 if (!alignment.isNucleotide())
1939 consensus = new AlignmentAnnotation("Consensus",
1940 MessageManager.getString("label.consensus_descr"),
1941 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1942 initConsensus(consensus);
1945 initComplementConsensus();
1950 * If this is a protein alignment and there are mappings to cDNA, adds the
1951 * cDNA consensus annotation and returns true, else returns false.
1953 public boolean initComplementConsensus()
1955 if (!alignment.isNucleotide())
1957 final List<AlignedCodonFrame> codonMappings = alignment
1959 if (codonMappings != null && !codonMappings.isEmpty())
1961 boolean doConsensus = false;
1962 for (AlignedCodonFrame mapping : codonMappings)
1964 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1965 MapList[] mapLists = mapping.getdnaToProt();
1966 // mapLists can be empty if project load has not finished resolving
1968 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1976 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1978 .getString("label.complement_consensus_descr"),
1979 new Annotation[1], 0f, 100f,
1980 AlignmentAnnotation.BAR_GRAPH);
1981 initConsensus(complementConsensus);
1989 private void initConsensus(AlignmentAnnotation aa)
1992 aa.autoCalculated = true;
1996 alignment.addAnnotation(aa);
2000 // these should be extracted from the view model - style and settings for
2001 // derived annotation
2002 private void initGapCounts()
2006 gapcounts = new AlignmentAnnotation("Occupancy",
2007 MessageManager.getString("label.occupancy_descr"),
2008 new Annotation[1], 0f, alignment.getHeight(),
2009 AlignmentAnnotation.BAR_GRAPH);
2010 gapcounts.hasText = true;
2011 gapcounts.autoCalculated = true;
2012 gapcounts.scaleColLabel = true;
2013 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
2015 alignment.addAnnotation(gapcounts);
2019 private void initConservation()
2021 if (showConservation)
2023 if (conservation == null)
2025 conservation = new AlignmentAnnotation("Conservation",
2026 MessageManager.formatMessage("label.conservation_descr",
2028 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2029 conservation.hasText = true;
2030 conservation.autoCalculated = true;
2031 alignment.addAnnotation(conservation);
2036 private void initQuality()
2040 if (quality == null)
2042 quality = new AlignmentAnnotation("Quality",
2043 MessageManager.getString("label.quality_descr"),
2044 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2045 quality.hasText = true;
2046 quality.autoCalculated = true;
2047 alignment.addAnnotation(quality);
2052 private void initRNAStructure()
2054 if (alignment.hasRNAStructure() && strucConsensus == null)
2056 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2057 MessageManager.getString("label.strucconsensus_descr"),
2058 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2059 strucConsensus.hasText = true;
2060 strucConsensus.autoCalculated = true;
2064 alignment.addAnnotation(strucConsensus);
2072 * @see jalview.api.AlignViewportI#calcPanelHeight()
2075 public int calcPanelHeight()
2077 // setHeight of panels
2078 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2080 int charHeight = getCharHeight();
2083 BitSet graphgrp = new BitSet();
2084 for (AlignmentAnnotation aa : anns)
2088 System.err.println("Null annotation row: ignoring.");
2095 if (aa.graphGroup > -1)
2097 if (graphgrp.get(aa.graphGroup))
2103 graphgrp.set(aa.graphGroup);
2110 aa.height += charHeight;
2120 aa.height += aa.graphHeight;
2128 height += aa.height;
2140 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2141 boolean preserveNewGroupSettings)
2143 boolean updateCalcs = false;
2144 boolean conv = isShowGroupConservation();
2145 boolean cons = isShowGroupConsensus();
2146 boolean showprf = isShowSequenceLogo();
2147 boolean showConsHist = isShowConsensusHistogram();
2148 boolean normLogo = isNormaliseSequenceLogo();
2151 * TODO reorder the annotation rows according to group/sequence ordering on
2154 boolean sortg = true;
2156 // remove old automatic annotation
2157 // add any new annotation
2159 // intersect alignment annotation with alignment groups
2161 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2162 List<SequenceGroup> oldrfs = new ArrayList<>();
2165 for (int an = 0; an < aan.length; an++)
2167 if (aan[an].autoCalculated && aan[an].groupRef != null)
2169 oldrfs.add(aan[an].groupRef);
2170 alignment.deleteAnnotation(aan[an], false);
2174 if (alignment.getGroups() != null)
2176 for (SequenceGroup sg : alignment.getGroups())
2178 updateCalcs = false;
2179 if (applyGlobalSettings
2180 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2182 // set defaults for this group's conservation/consensus
2183 sg.setshowSequenceLogo(showprf);
2184 sg.setShowConsensusHistogram(showConsHist);
2185 sg.setNormaliseSequenceLogo(normLogo);
2190 alignment.addAnnotation(sg.getConservationRow(), 0);
2195 alignment.addAnnotation(sg.getConsensus(), 0);
2197 // refresh the annotation rows
2200 sg.recalcConservation();
2208 public boolean isDisplayReferenceSeq()
2210 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2214 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2216 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2220 public boolean isColourByReferenceSeq()
2222 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2226 public Color getSequenceColour(SequenceI seq)
2228 Color sqc = sequenceColours.get(seq);
2229 return (sqc == null ? Color.white : sqc);
2233 public void setSequenceColour(SequenceI seq, Color col)
2237 sequenceColours.remove(seq);
2241 sequenceColours.put(seq, col);
2246 public void updateSequenceIdColours()
2248 for (SequenceGroup sg : alignment.getGroups())
2250 if (sg.idColour != null)
2252 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2254 sequenceColours.put(s, sg.idColour);
2261 public void clearSequenceColours()
2263 sequenceColours.clear();
2267 public AlignViewportI getCodingComplement()
2269 return this.codingComplement;
2273 * Set this as the (cDna/protein) complement of the given viewport. Also
2274 * ensures the reverse relationship is set on the given viewport.
2277 public void setCodingComplement(AlignViewportI av)
2281 System.err.println("Ignoring recursive setCodingComplement request");
2285 this.codingComplement = av;
2286 // avoid infinite recursion!
2287 if (av.getCodingComplement() != this)
2289 av.setCodingComplement(this);
2295 public boolean isNucleotide()
2297 return getAlignment() == null ? false : getAlignment().isNucleotide();
2301 public FeaturesDisplayedI getFeaturesDisplayed()
2303 return featuresDisplayed;
2307 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2309 featuresDisplayed = featuresDisplayedI;
2313 public boolean areFeaturesDisplayed()
2315 return featuresDisplayed != null
2316 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2323 * features are displayed if true
2326 public void setShowSequenceFeatures(boolean b)
2328 viewStyle.setShowSequenceFeatures(b);
2332 public boolean isShowSequenceFeatures()
2334 return viewStyle.isShowSequenceFeatures();
2338 public void setShowSequenceFeaturesHeight(boolean selected)
2340 viewStyle.setShowSequenceFeaturesHeight(selected);
2344 public boolean isShowSequenceFeaturesHeight()
2346 return viewStyle.isShowSequenceFeaturesHeight();
2350 public void setShowAnnotation(boolean b)
2352 viewStyle.setShowAnnotation(b);
2356 public boolean isShowAnnotation()
2358 return viewStyle.isShowAnnotation();
2362 public boolean isRightAlignIds()
2364 return viewStyle.isRightAlignIds();
2368 public void setRightAlignIds(boolean rightAlignIds)
2370 viewStyle.setRightAlignIds(rightAlignIds);
2374 public boolean getConservationSelected()
2376 return viewStyle.getConservationSelected();
2380 public void setShowBoxes(boolean state)
2382 viewStyle.setShowBoxes(state);
2387 * @see jalview.api.ViewStyleI#getTextColour()
2390 public Color getTextColour()
2392 return viewStyle.getTextColour();
2397 * @see jalview.api.ViewStyleI#getTextColour2()
2400 public Color getTextColour2()
2402 return viewStyle.getTextColour2();
2407 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2410 public int getThresholdTextColour()
2412 return viewStyle.getThresholdTextColour();
2417 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2420 public boolean isConservationColourSelected()
2422 return viewStyle.isConservationColourSelected();
2427 * @see jalview.api.ViewStyleI#isRenderGaps()
2430 public boolean isRenderGaps()
2432 return viewStyle.isRenderGaps();
2437 * @see jalview.api.ViewStyleI#isShowColourText()
2440 public boolean isShowColourText()
2442 return viewStyle.isShowColourText();
2446 * @param conservationColourSelected
2447 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2450 public void setConservationColourSelected(
2451 boolean conservationColourSelected)
2453 viewStyle.setConservationColourSelected(conservationColourSelected);
2457 * @param showColourText
2458 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2461 public void setShowColourText(boolean showColourText)
2463 viewStyle.setShowColourText(showColourText);
2468 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2471 public void setTextColour(Color textColour)
2473 viewStyle.setTextColour(textColour);
2477 * @param thresholdTextColour
2478 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2481 public void setThresholdTextColour(int thresholdTextColour)
2483 viewStyle.setThresholdTextColour(thresholdTextColour);
2487 * @param textColour2
2488 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2491 public void setTextColour2(Color textColour2)
2493 viewStyle.setTextColour2(textColour2);
2497 public ViewStyleI getViewStyle()
2499 return new ViewStyle(viewStyle);
2503 public void setViewStyle(ViewStyleI settingsForView)
2505 viewStyle = new ViewStyle(settingsForView);
2506 if (residueShading != null)
2508 residueShading.setConservationApplied(
2509 settingsForView.isConservationColourSelected());
2514 public boolean sameStyle(ViewStyleI them)
2516 return viewStyle.sameStyle(them);
2521 * @see jalview.api.ViewStyleI#getIdWidth()
2524 public int getIdWidth()
2526 return viewStyle.getIdWidth();
2531 * @see jalview.api.ViewStyleI#setIdWidth(int)
2534 public void setIdWidth(int i)
2536 viewStyle.setIdWidth(i);
2541 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2544 public boolean isCentreColumnLabels()
2546 return viewStyle.isCentreColumnLabels();
2550 * @param centreColumnLabels
2551 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2554 public void setCentreColumnLabels(boolean centreColumnLabels)
2556 viewStyle.setCentreColumnLabels(centreColumnLabels);
2561 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2564 public void setShowDBRefs(boolean showdbrefs)
2566 viewStyle.setShowDBRefs(showdbrefs);
2571 * @see jalview.api.ViewStyleI#isShowDBRefs()
2574 public boolean isShowDBRefs()
2576 return viewStyle.isShowDBRefs();
2581 * @see jalview.api.ViewStyleI#isShowNPFeats()
2584 public boolean isShowNPFeats()
2586 return viewStyle.isShowNPFeats();
2590 * @param shownpfeats
2591 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2594 public void setShowNPFeats(boolean shownpfeats)
2596 viewStyle.setShowNPFeats(shownpfeats);
2599 public abstract StructureSelectionManager getStructureSelectionManager();
2602 * Add one command to the command history list.
2606 public void addToHistoryList(CommandI command)
2608 if (this.historyList != null)
2610 this.historyList.push(command);
2611 broadcastCommand(command, false);
2615 protected void broadcastCommand(CommandI command, boolean undo)
2617 getStructureSelectionManager().commandPerformed(command, undo,
2622 * Add one command to the command redo list.
2626 public void addToRedoList(CommandI command)
2628 if (this.redoList != null)
2630 this.redoList.push(command);
2632 broadcastCommand(command, true);
2636 * Clear the command redo list.
2638 public void clearRedoList()
2640 if (this.redoList != null)
2642 this.redoList.clear();
2646 public void setHistoryList(Deque<CommandI> list)
2648 this.historyList = list;
2651 public Deque<CommandI> getHistoryList()
2653 return this.historyList;
2656 public void setRedoList(Deque<CommandI> list)
2658 this.redoList = list;
2661 public Deque<CommandI> getRedoList()
2663 return this.redoList;
2667 public VamsasSource getVamsasSource()
2672 public SequenceAnnotationOrder getSortAnnotationsBy()
2674 return sortAnnotationsBy;
2677 public void setSortAnnotationsBy(
2678 SequenceAnnotationOrder sortAnnotationsBy)
2680 this.sortAnnotationsBy = sortAnnotationsBy;
2683 public boolean isShowAutocalculatedAbove()
2685 return showAutocalculatedAbove;
2688 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2690 this.showAutocalculatedAbove = showAutocalculatedAbove;
2694 public boolean isScaleProteinAsCdna()
2696 return viewStyle.isScaleProteinAsCdna();
2700 public void setScaleProteinAsCdna(boolean b)
2702 viewStyle.setScaleProteinAsCdna(b);
2706 public boolean isProteinFontAsCdna()
2708 return viewStyle.isProteinFontAsCdna();
2712 public void setProteinFontAsCdna(boolean b)
2714 viewStyle.setProteinFontAsCdna(b);
2718 * @return true if view should scroll to show the highlighted region of a
2723 public final boolean isFollowHighlight()
2725 return followHighlight;
2729 public final void setFollowHighlight(boolean b)
2731 this.followHighlight = b;
2735 public ViewportRanges getRanges()
2741 * Helper method to populate the SearchResults with the location in the
2742 * complementary alignment to scroll to, in order to match this one.
2745 * the SearchResults to add to
2746 * @return the offset (below top of visible region) of the matched sequence
2748 protected int findComplementScrollTarget(SearchResultsI sr)
2750 final AlignViewportI complement = getCodingComplement();
2751 if (complement == null || !complement.isFollowHighlight())
2755 boolean iAmProtein = !getAlignment().isNucleotide();
2756 AlignmentI proteinAlignment = iAmProtein ? getAlignment()
2757 : complement.getAlignment();
2758 if (proteinAlignment == null)
2762 final List<AlignedCodonFrame> mappings = proteinAlignment
2766 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2767 * residue in the middle column of the visible region. Scroll the
2768 * complementary alignment to line up the corresponding residue.
2771 SequenceI sequence = null;
2774 * locate 'middle' column (true middle if an odd number visible, left of
2775 * middle if an even number visible)
2777 int middleColumn = ranges.getStartRes()
2778 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2779 final HiddenSequences hiddenSequences = getAlignment()
2780 .getHiddenSequences();
2783 * searching to the bottom of the alignment gives smoother scrolling across
2784 * all gapped visible regions
2786 int lastSeq = alignment.getHeight() - 1;
2787 List<AlignedCodonFrame> seqMappings = null;
2788 for (int seqNo = ranges
2789 .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
2791 sequence = getAlignment().getSequenceAt(seqNo);
2792 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2796 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2800 seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
2802 getCodingComplement().getAlignment().getSequences());
2803 if (!seqMappings.isEmpty())
2809 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2812 * No ungapped mapped sequence in middle column - do nothing
2816 MappingUtils.addSearchResults(sr, sequence,
2817 sequence.findPosition(middleColumn), seqMappings);
2822 * synthesize a column selection if none exists so it covers the given
2823 * selection group. if wholewidth is false, no column selection is made if the
2824 * selection group covers the whole alignment width.
2829 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2832 if (sg != null && (sgs = sg.getStartRes()) >= 0
2833 && sg.getStartRes() <= (sge = sg.getEndRes())
2834 && !this.hasSelectedColumns())
2836 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2843 colSel = new ColumnSelection();
2845 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2847 colSel.addElement(cspos);
2853 * hold status of current selection group - defined on alignment or not.
2855 private boolean selectionIsDefinedGroup = false;
2858 public boolean isSelectionDefinedGroup()
2860 if (selectionGroup == null)
2864 if (isSelectionGroupChanged(true))
2866 selectionIsDefinedGroup = false;
2867 List<SequenceGroup> gps = alignment.getGroups();
2868 if (gps == null || gps.size() == 0)
2870 selectionIsDefinedGroup = false;
2874 selectionIsDefinedGroup = gps.contains(selectionGroup);
2877 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2881 * null, or currently highlighted results on this view
2883 private SearchResultsI searchResults = null;
2885 protected TreeModel currentTree = null;
2888 public boolean hasSearchResults()
2890 return searchResults != null;
2894 public void setSearchResults(SearchResultsI results)
2896 searchResults = results;
2900 public SearchResultsI getSearchResults()
2902 return searchResults;
2906 * get the consensus sequence as displayed under the PID consensus annotation
2909 * @return consensus sequence as a new sequence object
2911 public SequenceI getConsensusSeq()
2913 if (consensus == null)
2915 updateConsensus(null);
2917 if (consensus == null)
2921 StringBuffer seqs = new StringBuffer();
2922 for (int i = 0; i < consensus.annotations.length; i++)
2924 Annotation annotation = consensus.annotations[i];
2925 if (annotation != null)
2927 String description = annotation.description;
2928 if (description != null && description.startsWith("["))
2930 // consensus is a tie - just pick the first one
2931 seqs.append(description.charAt(1));
2935 seqs.append(annotation.displayCharacter);
2940 SequenceI sq = new Sequence("Consensus", seqs.toString());
2941 sq.setDescription("Percentage Identity Consensus "
2942 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
2947 public void setCurrentTree(TreeModel tree)
2953 public TreeModel getCurrentTree()
2958 List<SequenceI> highlightedSeqs = null;
2961 * Highlight the IDs for the given sequences call alignPanel.repaint() to
2962 * update view after setting.
2968 public void setHighlightedSeqs(List<SequenceI> list)
2970 highlightedSeqs = list;
2974 public List<SequenceI> getHighlightedSeqs()
2976 return highlightedSeqs;