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.api.AlignCalcManagerI;
26 import jalview.api.AlignViewportI;
27 import jalview.api.AlignmentViewPanel;
28 import jalview.api.FeaturesDisplayedI;
29 import jalview.api.ViewStyleI;
30 import jalview.commands.CommandI;
31 import jalview.datamodel.AlignedCodonFrame;
32 import jalview.datamodel.AlignmentAnnotation;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.AlignmentView;
35 import jalview.datamodel.Annotation;
36 import jalview.datamodel.CigarArray;
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 implements AlignViewportI,
81 CommandListener, VamsasSource
83 final 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);
574 public AlignmentI getAlignment()
580 public char getGapCharacter()
582 return alignment.getGapCharacter();
585 protected String sequenceSetID;
588 * probably unused indicator that view is of a dataset rather than an
591 protected boolean isDataset = false;
593 public void setDataset(boolean b)
598 public boolean isDataset()
603 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
605 protected ColumnSelection colSel = new ColumnSelection();
607 public boolean autoCalculateConsensus = true;
609 protected boolean autoCalculateStrucConsensus = true;
611 protected boolean ignoreGapsInConsensusCalculation = false;
613 protected ResidueShaderI residueShading = new ResidueShader();
616 public void setGlobalColourScheme(ColourSchemeI cs)
618 // TODO: logic refactored from AlignFrame changeColour -
619 // TODO: autorecalc stuff should be changed to rely on the worker system
620 // check to see if we should implement a changeColour(cs) method rather than
621 // put the logic in here
622 // - means that caller decides if they want to just modify state and defer
623 // calculation till later or to do all calculations in thread.
627 * only instantiate alignment colouring once, thereafter update it;
628 * this means that any conservation or PID threshold settings
629 * persist when the alignment colour scheme is changed
631 if (residueShading == null)
633 residueShading = new ResidueShader(viewStyle);
635 residueShading.setColourScheme(cs);
637 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
638 // ...problem: groups need these, but do not currently have a ViewStyle
642 if (getConservationSelected())
644 residueShading.setConservation(hconservation);
647 * reset conservation flag in case just set to false if
648 * Conservation was null (calculation still in progress)
650 residueShading.setConservationApplied(getConservationSelected());
651 residueShading.alignmentChanged(alignment, hiddenRepSequences);
655 * if 'apply colour to all groups' is selected... do so
656 * (but don't transfer any colour threshold settings to groups)
658 if (getColourAppliesToAllGroups())
660 for (SequenceGroup sg : getAlignment().getGroups())
663 * retain any colour thresholds per group while
664 * changing choice of colour scheme (JAL-2386)
666 sg.setColourScheme(cs);
669 sg.getGroupColourScheme()
670 .alignmentChanged(sg, hiddenRepSequences);
677 public ColourSchemeI getGlobalColourScheme()
679 return residueShading == null ? null : residueShading
684 public ResidueShaderI getResidueShading()
686 return residueShading;
689 protected AlignmentAnnotation consensus;
691 protected AlignmentAnnotation complementConsensus;
693 protected AlignmentAnnotation gapcounts;
695 protected AlignmentAnnotation strucConsensus;
697 protected AlignmentAnnotation conservation;
699 protected AlignmentAnnotation quality;
701 protected AlignmentAnnotation[] groupConsensus;
703 protected AlignmentAnnotation[] groupConservation;
706 * results of alignment consensus analysis for visible portion of view
708 protected ProfilesI hconsensus = null;
711 * results of cDNA complement consensus visible portion of view
713 protected Hashtable[] hcomplementConsensus = null;
716 * results of secondary structure base pair consensus for visible portion of
719 protected Hashtable[] hStrucConsensus = null;
721 protected Conservation hconservation = null;
724 public void setConservation(Conservation cons)
726 hconservation = cons;
730 * percentage gaps allowed in a column before all amino acid properties should
731 * be considered unconserved
733 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
736 public int getConsPercGaps()
742 public void setSequenceConsensusHash(ProfilesI hconsensus)
744 this.hconsensus = hconsensus;
748 public void setComplementConsensusHash(Hashtable[] hconsensus)
750 this.hcomplementConsensus = hconsensus;
754 public ProfilesI getSequenceConsensusHash()
760 public Hashtable[] getComplementConsensusHash()
762 return hcomplementConsensus;
766 public Hashtable[] getRnaStructureConsensusHash()
768 return hStrucConsensus;
772 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
774 this.hStrucConsensus = hStrucConsensus;
779 public AlignmentAnnotation getAlignmentQualityAnnot()
785 public AlignmentAnnotation getAlignmentConservationAnnotation()
791 public AlignmentAnnotation getAlignmentConsensusAnnotation()
797 public AlignmentAnnotation getAlignmentGapAnnotation()
803 public AlignmentAnnotation getComplementConsensusAnnotation()
805 return complementConsensus;
809 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
811 return strucConsensus;
814 protected AlignCalcManagerI calculator = new AlignCalcManager();
817 * trigger update of conservation annotation
819 public void updateConservation(final AlignmentViewPanel ap)
821 // see note in mantis : issue number 8585
822 if (alignment.isNucleotide()
823 || (conservation == null && quality == null)
824 || !autoCalculateConsensus)
829 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
831 calculator.registerWorker(new jalview.workers.ConservationThread(
837 * trigger update of consensus annotation
839 public void updateConsensus(final AlignmentViewPanel ap)
841 // see note in mantis : issue number 8585
842 if (consensus == null || !autoCalculateConsensus)
846 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
848 calculator.registerWorker(new ConsensusThread(this, ap));
852 * A separate thread to compute cDNA consensus for a protein alignment
853 * which has mapping to cDNA
855 final AlignmentI al = this.getAlignment();
856 if (!al.isNucleotide() && al.getCodonFrames() != null
857 && !al.getCodonFrames().isEmpty())
860 * fudge - check first for protein-to-nucleotide mappings
861 * (we don't want to do this for protein-to-protein)
863 boolean doConsensus = false;
864 for (AlignedCodonFrame mapping : al.getCodonFrames())
866 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
867 MapList[] mapLists = mapping.getdnaToProt();
868 // mapLists can be empty if project load has not finished resolving seqs
869 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
878 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
881 .registerWorker(new ComplementConsensusThread(this, ap));
887 // --------START Structure Conservation
888 public void updateStrucConsensus(final AlignmentViewPanel ap)
890 if (autoCalculateStrucConsensus && strucConsensus == null
891 && alignment.isNucleotide() && alignment.hasRNAStructure())
893 // secondary structure has been added - so init the consensus line
897 // see note in mantis : issue number 8585
898 if (strucConsensus == null || !autoCalculateStrucConsensus)
902 if (calculator.getRegisteredWorkersOfClass(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 hcomplementConsensus = null;
953 // colour scheme may hold reference to consensus
954 residueShading = null;
955 // TODO remove listeners from changeSupport?
956 changeSupport = null;
961 public boolean isClosed()
963 // TODO: check that this isClosed is only true after panel is closed, not
964 // before it is fully constructed.
965 return alignment == null;
969 public AlignCalcManagerI getCalcManager()
975 * should conservation rows be shown for groups
977 protected boolean showGroupConservation = false;
980 * should consensus rows be shown for groups
982 protected boolean showGroupConsensus = false;
985 * should consensus profile be rendered by default
987 protected boolean showSequenceLogo = false;
990 * should consensus profile be rendered normalised to row height
992 protected boolean normaliseSequenceLogo = false;
995 * should consensus histograms be rendered by default
997 protected boolean showConsensusHistogram = true;
1000 * @return the showConsensusProfile
1003 public boolean isShowSequenceLogo()
1005 return showSequenceLogo;
1009 * @param showSequenceLogo
1012 public void setShowSequenceLogo(boolean showSequenceLogo)
1014 if (showSequenceLogo != this.showSequenceLogo)
1016 // TODO: decouple settings setting from calculation when refactoring
1017 // annotation update method from alignframe to viewport
1018 this.showSequenceLogo = showSequenceLogo;
1019 calculator.updateAnnotationFor(ConsensusThread.class);
1020 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1021 calculator.updateAnnotationFor(StrucConsensusThread.class);
1023 this.showSequenceLogo = showSequenceLogo;
1027 * @param showConsensusHistogram
1028 * the showConsensusHistogram to set
1030 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1032 this.showConsensusHistogram = showConsensusHistogram;
1036 * @return the showGroupConservation
1038 public boolean isShowGroupConservation()
1040 return showGroupConservation;
1044 * @param showGroupConservation
1045 * the showGroupConservation to set
1047 public void setShowGroupConservation(boolean showGroupConservation)
1049 this.showGroupConservation = showGroupConservation;
1053 * @return the showGroupConsensus
1055 public boolean isShowGroupConsensus()
1057 return showGroupConsensus;
1061 * @param showGroupConsensus
1062 * the showGroupConsensus to set
1064 public void setShowGroupConsensus(boolean showGroupConsensus)
1066 this.showGroupConsensus = showGroupConsensus;
1071 * @return flag to indicate if the consensus histogram should be rendered by
1075 public boolean isShowConsensusHistogram()
1077 return this.showConsensusHistogram;
1081 * when set, updateAlignment will always ensure sequences are of equal length
1083 private boolean padGaps = false;
1086 * when set, alignment should be reordered according to a newly opened tree
1088 public boolean sortByTree = false;
1093 * @return null or the currently selected sequence region
1096 public SequenceGroup getSelectionGroup()
1098 return selectionGroup;
1102 * Set the selection group for this window. Also sets the current alignment as
1103 * the context for the group, if it does not already have one.
1106 * - group holding references to sequences in this alignment view
1110 public void setSelectionGroup(SequenceGroup sg)
1112 selectionGroup = sg;
1113 if (sg != null && sg.getContext() == null)
1115 sg.setContext(alignment);
1119 public void setHiddenColumns(HiddenColumns hidden)
1121 this.alignment.setHiddenColumns(hidden);
1125 public ColumnSelection getColumnSelection()
1131 public void setColumnSelection(ColumnSelection colSel)
1133 this.colSel = colSel;
1136 updateHiddenColumns();
1138 isColSelChanged(true);
1146 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1148 return hiddenRepSequences;
1152 public void setHiddenRepSequences(
1153 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1155 this.hiddenRepSequences = hiddenRepSequences;
1159 public boolean hasSelectedColumns()
1161 ColumnSelection columnSelection = getColumnSelection();
1162 return columnSelection != null && columnSelection.hasSelectedColumns();
1166 public boolean hasHiddenColumns()
1168 return alignment.getHiddenColumns() != null
1169 && alignment.getHiddenColumns().hasHiddenColumns();
1172 public void updateHiddenColumns()
1174 // this method doesn't really do anything now. But - it could, since a
1175 // column Selection could be in the process of modification
1176 // hasHiddenColumns = colSel.hasHiddenColumns();
1180 public boolean hasHiddenRows()
1182 return alignment.getHiddenSequences().getSize() > 0;
1185 protected SequenceGroup selectionGroup;
1187 public void setSequenceSetId(String newid)
1189 if (sequenceSetID != null)
1192 .println("Warning - overwriting a sequenceSetId for a viewport!");
1194 sequenceSetID = new String(newid);
1198 public String getSequenceSetId()
1200 if (sequenceSetID == null)
1202 sequenceSetID = alignment.hashCode() + "";
1205 return sequenceSetID;
1209 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1212 protected String viewId = null;
1215 public String getViewId()
1219 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1224 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1226 ignoreGapsInConsensusCalculation = b;
1229 updateConsensus(ap);
1230 if (residueShading != null)
1232 residueShading.setThreshold(residueShading.getThreshold(),
1233 ignoreGapsInConsensusCalculation);
1239 private long sgrouphash = -1, colselhash = -1;
1242 * checks current SelectionGroup against record of last hash value, and
1246 * update the record of last hash value
1248 * @return true if SelectionGroup changed since last call (when b is true)
1250 public boolean isSelectionGroupChanged(boolean b)
1252 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1253 : selectionGroup.hashCode();
1254 if (hc != -1 && hc != sgrouphash)
1266 * checks current colsel against record of last hash value, and optionally
1270 * update the record of last hash value
1271 * @return true if colsel changed since last call (when b is true)
1273 public boolean isColSelChanged(boolean b)
1275 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1276 if (hc != -1 && hc != colselhash)
1288 public boolean isIgnoreGapsConsensus()
1290 return ignoreGapsInConsensusCalculation;
1293 // property change stuff
1294 // JBPNote Prolly only need this in the applet version.
1295 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1298 protected boolean showConservation = true;
1300 protected boolean showQuality = true;
1302 protected boolean showConsensus = true;
1304 protected boolean showOccupancy = true;
1306 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1308 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1310 protected boolean showAutocalculatedAbove;
1313 * when set, view will scroll to show the highlighted position
1315 private boolean followHighlight = true;
1318 * Property change listener for changes in alignment
1323 public void addPropertyChangeListener(
1324 java.beans.PropertyChangeListener listener)
1326 changeSupport.addPropertyChangeListener(listener);
1335 public void removePropertyChangeListener(
1336 java.beans.PropertyChangeListener listener)
1338 changeSupport.removePropertyChangeListener(listener);
1342 * Property change listener for changes in alignment
1351 public void firePropertyChange(String prop, Object oldvalue,
1354 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1357 // common hide/show column stuff
1359 public void hideSelectedColumns()
1361 if (colSel.isEmpty())
1366 colSel.hideSelectedColumns(alignment);
1367 setSelectionGroup(null);
1368 isColSelChanged(true);
1371 public void hideColumns(int start, int end)
1375 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1379 alignment.getHiddenColumns().hideColumns(start, end);
1381 isColSelChanged(true);
1384 public void showColumn(int col)
1386 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1387 isColSelChanged(true);
1390 public void showAllHiddenColumns()
1392 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1393 isColSelChanged(true);
1396 // common hide/show seq stuff
1397 public void showAllHiddenSeqs()
1399 int startSeq = ranges.getStartSeq();
1400 int endSeq = ranges.getEndSeq();
1402 if (alignment.getHiddenSequences().getSize() > 0)
1404 if (selectionGroup == null)
1406 selectionGroup = new SequenceGroup();
1407 selectionGroup.setEndRes(alignment.getWidth() - 1);
1409 List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
1410 hiddenRepSequences);
1411 for (SequenceI seq : tmp)
1413 selectionGroup.addSequence(seq, false);
1414 setSequenceAnnotationsVisible(seq, true);
1417 hiddenRepSequences = null;
1419 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1421 firePropertyChange("alignment", null, alignment.getSequences());
1422 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1428 public void showSequence(int index)
1430 int startSeq = ranges.getStartSeq();
1431 int endSeq = ranges.getEndSeq();
1433 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1434 index, hiddenRepSequences);
1437 if (selectionGroup == null)
1439 selectionGroup = new SequenceGroup();
1440 selectionGroup.setEndRes(alignment.getWidth() - 1);
1443 for (SequenceI seq : tmp)
1445 selectionGroup.addSequence(seq, false);
1446 setSequenceAnnotationsVisible(seq, true);
1449 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1451 firePropertyChange("alignment", null, alignment.getSequences());
1456 public void hideAllSelectedSeqs()
1458 if (selectionGroup == null || selectionGroup.getSize() < 1)
1463 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1467 setSelectionGroup(null);
1470 public void hideSequence(SequenceI[] seq)
1473 * cache offset to first visible sequence
1475 int startSeq = ranges.getStartSeq();
1479 for (int i = 0; i < seq.length; i++)
1481 alignment.getHiddenSequences().hideSequence(seq[i]);
1482 setSequenceAnnotationsVisible(seq[i], false);
1484 ranges.setStartSeq(startSeq);
1485 firePropertyChange("alignment", null, alignment.getSequences());
1490 * Hides the specified sequence, or the sequences it represents
1493 * the sequence to hide, or keep as representative
1494 * @param representGroup
1495 * if true, hide the current selection group except for the
1496 * representative sequence
1498 public void hideSequences(SequenceI sequence, boolean representGroup)
1500 if (selectionGroup == null || selectionGroup.getSize() < 1)
1502 hideSequence(new SequenceI[] { sequence });
1508 hideRepSequences(sequence, selectionGroup);
1509 setSelectionGroup(null);
1513 int gsize = selectionGroup.getSize();
1514 SequenceI[] hseqs = selectionGroup.getSequences().toArray(
1515 new SequenceI[gsize]);
1517 hideSequence(hseqs);
1518 setSelectionGroup(null);
1523 * Set visibility for any annotations for the given sequence.
1527 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1530 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1533 for (AlignmentAnnotation ann : anns)
1535 if (ann.sequenceRef == sequenceI)
1537 ann.visible = visible;
1543 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1545 int sSize = sg.getSize();
1551 if (hiddenRepSequences == null)
1553 hiddenRepSequences = new Hashtable<>();
1556 hiddenRepSequences.put(repSequence, sg);
1558 // Hide all sequences except the repSequence
1559 SequenceI[] seqs = new SequenceI[sSize - 1];
1561 for (int i = 0; i < sSize; i++)
1563 if (sg.getSequenceAt(i) != repSequence)
1565 if (index == sSize - 1)
1570 seqs[index++] = sg.getSequenceAt(i);
1573 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1574 sg.setHidereps(true); // note: not done in 2.7applet
1581 * @return null or the current reference sequence
1583 public SequenceI getReferenceSeq()
1585 return alignment.getSeqrep();
1590 * @return true iff seq is the reference for the alignment
1592 public boolean isReferenceSeq(SequenceI seq)
1594 return alignment.getSeqrep() == seq;
1600 * @return true if there are sequences represented by this sequence that are
1603 public boolean isHiddenRepSequence(SequenceI seq)
1605 return (hiddenRepSequences != null && hiddenRepSequences
1612 * @return null or a sequence group containing the sequences that seq
1615 public SequenceGroup getRepresentedSequences(SequenceI seq)
1617 return (SequenceGroup) (hiddenRepSequences == null ? null
1618 : hiddenRepSequences.get(seq));
1622 public int adjustForHiddenSeqs(int alignmentIndex)
1624 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1629 public void invertColumnSelection()
1631 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1635 public SequenceI[] getSelectionAsNewSequence()
1637 SequenceI[] sequences;
1638 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1639 // this was the only caller in the applet for this method
1640 // JBPNote: in applet, this method returned references to the alignment
1641 // sequences, and it did not honour the presence/absence of annotation
1642 // attached to the alignment (probably!)
1643 if (selectionGroup == null || selectionGroup.getSize() == 0)
1645 sequences = alignment.getSequencesArray();
1646 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1647 for (int i = 0; i < sequences.length; i++)
1649 // construct new sequence with subset of visible annotation
1650 sequences[i] = new Sequence(sequences[i], annots);
1655 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1662 public SequenceI[] getSequenceSelection()
1664 SequenceI[] sequences = null;
1665 if (selectionGroup != null)
1667 sequences = selectionGroup.getSequencesInOrder(alignment);
1669 if (sequences == null)
1671 sequences = alignment.getSequencesArray();
1677 public CigarArray getViewAsCigars(boolean selectedRegionOnly)
1679 return new CigarArray(alignment, alignment.getHiddenColumns(),
1680 (selectedRegionOnly ? selectionGroup : null));
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(),
1695 selectionGroup, alignment.getHiddenColumns() != null
1696 && alignment.getHiddenColumns().hasHiddenColumns(),
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 selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
1749 for (i = 0; i < iSize; i++)
1751 selection[i] = seqs[i].getSequenceAsString(start, end);
1759 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1761 ArrayList<int[]> regions = new ArrayList<>();
1767 HiddenColumns hidden = alignment.getHiddenColumns();
1768 if (hidden != null && hidden.hasHiddenColumns())
1772 start = hidden.adjustForHiddenColumns(start);
1775 end = hidden.getHiddenBoundaryRight(start);
1786 regions.add(new int[] { start, end });
1788 if (hidden != null && hidden.hasHiddenColumns())
1790 start = hidden.adjustForHiddenColumns(end);
1791 start = hidden.getHiddenBoundaryLeft(start) + 1;
1793 } while (end < max);
1795 int[][] startEnd = new int[regions.size()][2];
1801 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1802 boolean selectedOnly)
1804 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1805 AlignmentAnnotation[] aa;
1806 if ((aa = alignment.getAlignmentAnnotation()) != null)
1808 for (AlignmentAnnotation annot : aa)
1810 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1811 if (selectedOnly && selectionGroup != null)
1813 alignment.getHiddenColumns().makeVisibleAnnotation(
1814 selectionGroup.getStartRes(),
1815 selectionGroup.getEndRes(), clone);
1819 alignment.getHiddenColumns().makeVisibleAnnotation(clone);
1828 public boolean isPadGaps()
1834 public void setPadGaps(boolean padGaps)
1836 this.padGaps = padGaps;
1840 * apply any post-edit constraints and trigger any calculations needed after
1841 * an edit has been performed on the alignment
1846 public void alignmentChanged(AlignmentViewPanel ap)
1850 alignment.padGaps();
1852 if (autoCalculateConsensus)
1854 updateConsensus(ap);
1856 if (hconsensus != null && autoCalculateConsensus)
1858 updateConservation(ap);
1860 if (autoCalculateStrucConsensus)
1862 updateStrucConsensus(ap);
1865 // Reset endRes of groups if beyond alignment width
1866 int alWidth = alignment.getWidth();
1867 List<SequenceGroup> groups = alignment.getGroups();
1870 for (SequenceGroup sg : groups)
1872 if (sg.getEndRes() > alWidth)
1874 sg.setEndRes(alWidth - 1);
1879 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1881 selectionGroup.setEndRes(alWidth - 1);
1884 updateAllColourSchemes();
1885 calculator.restartWorkers();
1886 // alignment.adjustSequenceAnnotations();
1890 * reset scope and do calculations for all applied colourschemes on alignment
1892 void updateAllColourSchemes()
1894 ResidueShaderI rs = residueShading;
1897 rs.alignmentChanged(alignment, hiddenRepSequences);
1899 rs.setConsensus(hconsensus);
1900 if (rs.conservationApplied())
1902 rs.setConservation(Conservation.calculateConservation("All",
1903 alignment.getSequences(), 0, alignment.getWidth(), false,
1904 getConsPercGaps(), false));
1908 for (SequenceGroup sg : alignment.getGroups())
1912 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1914 sg.recalcConservation();
1918 protected void initAutoAnnotation()
1920 // TODO: add menu option action that nulls or creates consensus object
1921 // depending on if the user wants to see the annotation or not in a
1922 // specific alignment
1924 if (hconsensus == null && !isDataset)
1926 if (!alignment.isNucleotide())
1935 consensus = new AlignmentAnnotation("Consensus",
1936 MessageManager.getString("label.consensus_descr"),
1937 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1938 initConsensus(consensus);
1941 initComplementConsensus();
1946 * If this is a protein alignment and there are mappings to cDNA, adds the
1947 * cDNA consensus annotation and returns true, else returns false.
1949 public boolean initComplementConsensus()
1951 if (!alignment.isNucleotide())
1953 final List<AlignedCodonFrame> codonMappings = alignment
1955 if (codonMappings != null && !codonMappings.isEmpty())
1957 boolean doConsensus = false;
1958 for (AlignedCodonFrame mapping : codonMappings)
1960 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1961 MapList[] mapLists = mapping.getdnaToProt();
1962 // mapLists can be empty if project load has not finished resolving
1964 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1972 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1974 .getString("label.complement_consensus_descr"),
1975 new Annotation[1], 0f, 100f,
1976 AlignmentAnnotation.BAR_GRAPH);
1977 initConsensus(complementConsensus);
1985 private void initConsensus(AlignmentAnnotation aa)
1988 aa.autoCalculated = true;
1992 alignment.addAnnotation(aa);
1996 // these should be extracted from the view model - style and settings for
1997 // derived annotation
1998 private void initGapCounts()
2002 gapcounts = new AlignmentAnnotation("Occupancy",
2003 MessageManager.getString("label.occupancy_descr"),
2004 new Annotation[1], 0f,
2005 alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
2006 gapcounts.hasText = true;
2007 gapcounts.autoCalculated = true;
2008 gapcounts.scaleColLabel = true;
2009 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
2011 alignment.addAnnotation(gapcounts);
2015 private void initConservation()
2017 if (showConservation)
2019 if (conservation == null)
2021 conservation = new AlignmentAnnotation("Conservation",
2022 MessageManager.formatMessage("label.conservation_descr",
2023 getConsPercGaps()), new Annotation[1],
2024 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2025 conservation.hasText = true;
2026 conservation.autoCalculated = true;
2027 alignment.addAnnotation(conservation);
2032 private void initQuality()
2036 if (quality == null)
2038 quality = new AlignmentAnnotation("Quality",
2039 MessageManager.getString("label.quality_descr"),
2040 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2041 quality.hasText = true;
2042 quality.autoCalculated = true;
2043 alignment.addAnnotation(quality);
2048 private void initRNAStructure()
2050 if (alignment.hasRNAStructure() && strucConsensus == null)
2052 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2053 MessageManager.getString("label.strucconsensus_descr"),
2054 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2055 strucConsensus.hasText = true;
2056 strucConsensus.autoCalculated = true;
2060 alignment.addAnnotation(strucConsensus);
2068 * @see jalview.api.AlignViewportI#calcPanelHeight()
2071 public int calcPanelHeight()
2073 // setHeight of panels
2074 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2076 int charHeight = getCharHeight();
2079 BitSet graphgrp = new BitSet();
2080 for (AlignmentAnnotation aa : anns)
2084 System.err.println("Null annotation row: ignoring.");
2091 if (aa.graphGroup > -1)
2093 if (graphgrp.get(aa.graphGroup))
2099 graphgrp.set(aa.graphGroup);
2106 aa.height += charHeight;
2116 aa.height += aa.graphHeight;
2124 height += aa.height;
2136 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2137 boolean preserveNewGroupSettings)
2139 boolean updateCalcs = false;
2140 boolean conv = isShowGroupConservation();
2141 boolean cons = isShowGroupConsensus();
2142 boolean showprf = isShowSequenceLogo();
2143 boolean showConsHist = isShowConsensusHistogram();
2144 boolean normLogo = isNormaliseSequenceLogo();
2147 * TODO reorder the annotation rows according to group/sequence ordering on
2150 boolean sortg = true;
2152 // remove old automatic annotation
2153 // add any new annotation
2155 // intersect alignment annotation with alignment groups
2157 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2158 List<SequenceGroup> oldrfs = new ArrayList<>();
2161 for (int an = 0; an < aan.length; an++)
2163 if (aan[an].autoCalculated && aan[an].groupRef != null)
2165 oldrfs.add(aan[an].groupRef);
2166 alignment.deleteAnnotation(aan[an], false);
2170 if (alignment.getGroups() != null)
2172 for (SequenceGroup sg : alignment.getGroups())
2174 updateCalcs = false;
2175 if (applyGlobalSettings
2176 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2178 // set defaults for this group's conservation/consensus
2179 sg.setshowSequenceLogo(showprf);
2180 sg.setShowConsensusHistogram(showConsHist);
2181 sg.setNormaliseSequenceLogo(normLogo);
2186 alignment.addAnnotation(sg.getConservationRow(), 0);
2191 alignment.addAnnotation(sg.getConsensus(), 0);
2193 // refresh the annotation rows
2196 sg.recalcConservation();
2204 public boolean isDisplayReferenceSeq()
2206 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2210 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2212 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2216 public boolean isColourByReferenceSeq()
2218 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2222 public Color getSequenceColour(SequenceI seq)
2224 Color sqc = sequenceColours.get(seq);
2225 return (sqc == null ? Color.white : sqc);
2229 public void setSequenceColour(SequenceI seq, Color col)
2233 sequenceColours.remove(seq);
2237 sequenceColours.put(seq, col);
2242 public void updateSequenceIdColours()
2244 for (SequenceGroup sg : alignment.getGroups())
2246 if (sg.idColour != null)
2248 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2250 sequenceColours.put(s, sg.idColour);
2257 public void clearSequenceColours()
2259 sequenceColours.clear();
2263 public AlignViewportI getCodingComplement()
2265 return this.codingComplement;
2269 * Set this as the (cDna/protein) complement of the given viewport. Also
2270 * ensures the reverse relationship is set on the given viewport.
2273 public void setCodingComplement(AlignViewportI av)
2277 System.err.println("Ignoring recursive setCodingComplement request");
2281 this.codingComplement = av;
2282 // avoid infinite recursion!
2283 if (av.getCodingComplement() != this)
2285 av.setCodingComplement(this);
2291 public boolean isNucleotide()
2293 return getAlignment() == null ? false : getAlignment().isNucleotide();
2297 public FeaturesDisplayedI getFeaturesDisplayed()
2299 return featuresDisplayed;
2303 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2305 featuresDisplayed = featuresDisplayedI;
2309 public boolean areFeaturesDisplayed()
2311 return featuresDisplayed != null
2312 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2319 * features are displayed if true
2322 public void setShowSequenceFeatures(boolean b)
2324 viewStyle.setShowSequenceFeatures(b);
2328 public boolean isShowSequenceFeatures()
2330 return viewStyle.isShowSequenceFeatures();
2334 public void setShowSequenceFeaturesHeight(boolean selected)
2336 viewStyle.setShowSequenceFeaturesHeight(selected);
2340 public boolean isShowSequenceFeaturesHeight()
2342 return viewStyle.isShowSequenceFeaturesHeight();
2346 public void setShowAnnotation(boolean b)
2348 viewStyle.setShowAnnotation(b);
2352 public boolean isShowAnnotation()
2354 return viewStyle.isShowAnnotation();
2358 public boolean isRightAlignIds()
2360 return viewStyle.isRightAlignIds();
2364 public void setRightAlignIds(boolean rightAlignIds)
2366 viewStyle.setRightAlignIds(rightAlignIds);
2370 public boolean getConservationSelected()
2372 return viewStyle.getConservationSelected();
2376 public void setShowBoxes(boolean state)
2378 viewStyle.setShowBoxes(state);
2383 * @see jalview.api.ViewStyleI#getTextColour()
2386 public Color getTextColour()
2388 return viewStyle.getTextColour();
2393 * @see jalview.api.ViewStyleI#getTextColour2()
2396 public Color getTextColour2()
2398 return viewStyle.getTextColour2();
2403 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2406 public int getThresholdTextColour()
2408 return viewStyle.getThresholdTextColour();
2413 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2416 public boolean isConservationColourSelected()
2418 return viewStyle.isConservationColourSelected();
2423 * @see jalview.api.ViewStyleI#isRenderGaps()
2426 public boolean isRenderGaps()
2428 return viewStyle.isRenderGaps();
2433 * @see jalview.api.ViewStyleI#isShowColourText()
2436 public boolean isShowColourText()
2438 return viewStyle.isShowColourText();
2442 * @param conservationColourSelected
2443 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2446 public void setConservationColourSelected(
2447 boolean conservationColourSelected)
2449 viewStyle.setConservationColourSelected(conservationColourSelected);
2453 * @param showColourText
2454 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2457 public void setShowColourText(boolean showColourText)
2459 viewStyle.setShowColourText(showColourText);
2464 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2467 public void setTextColour(Color textColour)
2469 viewStyle.setTextColour(textColour);
2473 * @param thresholdTextColour
2474 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2477 public void setThresholdTextColour(int thresholdTextColour)
2479 viewStyle.setThresholdTextColour(thresholdTextColour);
2483 * @param textColour2
2484 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2487 public void setTextColour2(Color textColour2)
2489 viewStyle.setTextColour2(textColour2);
2493 public ViewStyleI getViewStyle()
2495 return new ViewStyle(viewStyle);
2499 public void setViewStyle(ViewStyleI settingsForView)
2501 viewStyle = new ViewStyle(settingsForView);
2502 if (residueShading != null)
2504 residueShading.setConservationApplied(settingsForView
2505 .isConservationColourSelected());
2510 public boolean sameStyle(ViewStyleI them)
2512 return viewStyle.sameStyle(them);
2517 * @see jalview.api.ViewStyleI#getIdWidth()
2520 public int getIdWidth()
2522 return viewStyle.getIdWidth();
2527 * @see jalview.api.ViewStyleI#setIdWidth(int)
2530 public void setIdWidth(int i)
2532 viewStyle.setIdWidth(i);
2537 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2540 public boolean isCentreColumnLabels()
2542 return viewStyle.isCentreColumnLabels();
2546 * @param centreColumnLabels
2547 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2550 public void setCentreColumnLabels(boolean centreColumnLabels)
2552 viewStyle.setCentreColumnLabels(centreColumnLabels);
2557 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2560 public void setShowDBRefs(boolean showdbrefs)
2562 viewStyle.setShowDBRefs(showdbrefs);
2567 * @see jalview.api.ViewStyleI#isShowDBRefs()
2570 public boolean isShowDBRefs()
2572 return viewStyle.isShowDBRefs();
2577 * @see jalview.api.ViewStyleI#isShowNPFeats()
2580 public boolean isShowNPFeats()
2582 return viewStyle.isShowNPFeats();
2586 * @param shownpfeats
2587 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2590 public void setShowNPFeats(boolean shownpfeats)
2592 viewStyle.setShowNPFeats(shownpfeats);
2595 public abstract StructureSelectionManager getStructureSelectionManager();
2598 * Add one command to the command history list.
2602 public void addToHistoryList(CommandI command)
2604 if (this.historyList != null)
2606 this.historyList.push(command);
2607 broadcastCommand(command, false);
2611 protected void broadcastCommand(CommandI command, boolean undo)
2613 getStructureSelectionManager().commandPerformed(command, undo,
2618 * Add one command to the command redo list.
2622 public void addToRedoList(CommandI command)
2624 if (this.redoList != null)
2626 this.redoList.push(command);
2628 broadcastCommand(command, true);
2632 * Clear the command redo list.
2634 public void clearRedoList()
2636 if (this.redoList != null)
2638 this.redoList.clear();
2642 public void setHistoryList(Deque<CommandI> list)
2644 this.historyList = list;
2647 public Deque<CommandI> getHistoryList()
2649 return this.historyList;
2652 public void setRedoList(Deque<CommandI> list)
2654 this.redoList = list;
2657 public Deque<CommandI> getRedoList()
2659 return this.redoList;
2663 public VamsasSource getVamsasSource()
2668 public SequenceAnnotationOrder getSortAnnotationsBy()
2670 return sortAnnotationsBy;
2673 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2675 this.sortAnnotationsBy = sortAnnotationsBy;
2678 public boolean isShowAutocalculatedAbove()
2680 return showAutocalculatedAbove;
2683 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2685 this.showAutocalculatedAbove = showAutocalculatedAbove;
2689 public boolean isScaleProteinAsCdna()
2691 return viewStyle.isScaleProteinAsCdna();
2695 public void setScaleProteinAsCdna(boolean b)
2697 viewStyle.setScaleProteinAsCdna(b);
2701 public boolean isProteinFontAsCdna()
2703 return viewStyle.isProteinFontAsCdna();
2707 public void setProteinFontAsCdna(boolean b)
2709 viewStyle.setProteinFontAsCdna(b);
2713 * @return true if view should scroll to show the highlighted region of a
2718 public final boolean isFollowHighlight()
2720 return followHighlight;
2724 public final void setFollowHighlight(boolean b)
2726 this.followHighlight = b;
2730 public ViewportRanges getRanges()
2736 * Helper method to populate the SearchResults with the location in the
2737 * complementary alignment to scroll to, in order to match this one.
2740 * the SearchResults to add to
2741 * @return the offset (below top of visible region) of the matched sequence
2743 protected int findComplementScrollTarget(SearchResultsI sr)
2745 final AlignViewportI complement = getCodingComplement();
2746 if (complement == null || !complement.isFollowHighlight())
2750 boolean iAmProtein = !getAlignment().isNucleotide();
2751 AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
2753 if (proteinAlignment == null)
2757 final List<AlignedCodonFrame> mappings = proteinAlignment
2761 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2762 * residue in the middle column of the visible region. Scroll the
2763 * complementary alignment to line up the corresponding residue.
2766 SequenceI sequence = null;
2769 * locate 'middle' column (true middle if an odd number visible, left of
2770 * middle if an even number visible)
2772 int middleColumn = ranges.getStartRes()
2773 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2774 final HiddenSequences hiddenSequences = getAlignment()
2775 .getHiddenSequences();
2778 * searching to the bottom of the alignment gives smoother scrolling across
2779 * all gapped visible regions
2781 int lastSeq = alignment.getHeight() - 1;
2782 List<AlignedCodonFrame> seqMappings = null;
2783 for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
2785 sequence = getAlignment().getSequenceAt(seqNo);
2786 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2790 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2794 seqMappings = MappingUtils
2795 .findMappingsForSequenceAndOthers(sequence, mappings,
2796 getCodingComplement().getAlignment().getSequences());
2797 if (!seqMappings.isEmpty())
2803 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2806 * No ungapped mapped sequence in middle column - do nothing
2810 MappingUtils.addSearchResults(sr, sequence,
2811 sequence.findPosition(middleColumn), seqMappings);
2816 * synthesize a column selection if none exists so it covers the given
2817 * selection group. if wholewidth is false, no column selection is made if the
2818 * selection group covers the whole alignment width.
2823 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2826 if (sg != null && (sgs = sg.getStartRes()) >= 0
2827 && sg.getStartRes() <= (sge = sg.getEndRes())
2828 && !this.hasSelectedColumns())
2830 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2837 colSel = new ColumnSelection();
2839 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2841 colSel.addElement(cspos);
2847 * hold status of current selection group - defined on alignment or not.
2849 private boolean selectionIsDefinedGroup = false;
2852 public boolean isSelectionDefinedGroup()
2854 if (selectionGroup == null)
2858 if (isSelectionGroupChanged(true))
2860 selectionIsDefinedGroup = false;
2861 List<SequenceGroup> gps = alignment.getGroups();
2862 if (gps == null || gps.size() == 0)
2864 selectionIsDefinedGroup = false;
2868 selectionIsDefinedGroup = gps.contains(selectionGroup);
2871 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2875 * null, or currently highlighted results on this view
2877 private SearchResultsI searchResults = 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" : ""));