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);
646 residueShading.alignmentChanged(alignment, hiddenRepSequences);
650 * if 'apply colour to all groups' is selected... do so
651 * (but don't transfer any colour threshold settings to groups)
653 if (getColourAppliesToAllGroups())
655 for (SequenceGroup sg : getAlignment().getGroups())
658 * retain any colour thresholds per group while
659 * changing choice of colour scheme (JAL-2386)
661 sg.setColourScheme(cs);
664 sg.getGroupColourScheme()
665 .alignmentChanged(sg, hiddenRepSequences);
672 public ColourSchemeI getGlobalColourScheme()
674 return residueShading == null ? null : residueShading
679 public ResidueShaderI getResidueShading()
681 return residueShading;
684 protected AlignmentAnnotation consensus;
686 protected AlignmentAnnotation complementConsensus;
688 protected AlignmentAnnotation gapcounts;
690 protected AlignmentAnnotation strucConsensus;
692 protected AlignmentAnnotation conservation;
694 protected AlignmentAnnotation quality;
696 protected AlignmentAnnotation[] groupConsensus;
698 protected AlignmentAnnotation[] groupConservation;
701 * results of alignment consensus analysis for visible portion of view
703 protected ProfilesI hconsensus = null;
706 * results of cDNA complement consensus visible portion of view
708 protected Hashtable[] hcomplementConsensus = null;
711 * results of secondary structure base pair consensus for visible portion of
714 protected Hashtable[] hStrucConsensus = null;
716 protected Conservation hconservation = null;
719 public void setConservation(Conservation cons)
721 hconservation = cons;
725 * percentage gaps allowed in a column before all amino acid properties should
726 * be considered unconserved
728 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
731 public int getConsPercGaps()
737 public void setSequenceConsensusHash(ProfilesI hconsensus)
739 this.hconsensus = hconsensus;
743 public void setComplementConsensusHash(Hashtable[] hconsensus)
745 this.hcomplementConsensus = hconsensus;
749 public ProfilesI getSequenceConsensusHash()
755 public Hashtable[] getComplementConsensusHash()
757 return hcomplementConsensus;
761 public Hashtable[] getRnaStructureConsensusHash()
763 return hStrucConsensus;
767 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
769 this.hStrucConsensus = hStrucConsensus;
774 public AlignmentAnnotation getAlignmentQualityAnnot()
780 public AlignmentAnnotation getAlignmentConservationAnnotation()
786 public AlignmentAnnotation getAlignmentConsensusAnnotation()
792 public AlignmentAnnotation getAlignmentGapAnnotation()
798 public AlignmentAnnotation getComplementConsensusAnnotation()
800 return complementConsensus;
804 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
806 return strucConsensus;
809 protected AlignCalcManagerI calculator = new AlignCalcManager();
812 * trigger update of conservation annotation
814 public void updateConservation(final AlignmentViewPanel ap)
816 // see note in mantis : issue number 8585
817 if (alignment.isNucleotide()
818 || (conservation == null && quality == null)
819 || !autoCalculateConsensus)
824 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
826 calculator.registerWorker(new jalview.workers.ConservationThread(
832 * trigger update of consensus annotation
834 public void updateConsensus(final AlignmentViewPanel ap)
836 // see note in mantis : issue number 8585
837 if (consensus == null || !autoCalculateConsensus)
841 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
843 calculator.registerWorker(new ConsensusThread(this, ap));
847 * A separate thread to compute cDNA consensus for a protein alignment
848 * which has mapping to cDNA
850 final AlignmentI al = this.getAlignment();
851 if (!al.isNucleotide() && al.getCodonFrames() != null
852 && !al.getCodonFrames().isEmpty())
855 * fudge - check first for protein-to-nucleotide mappings
856 * (we don't want to do this for protein-to-protein)
858 boolean doConsensus = false;
859 for (AlignedCodonFrame mapping : al.getCodonFrames())
861 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
862 MapList[] mapLists = mapping.getdnaToProt();
863 // mapLists can be empty if project load has not finished resolving seqs
864 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
873 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
876 .registerWorker(new ComplementConsensusThread(this, ap));
882 // --------START Structure Conservation
883 public void updateStrucConsensus(final AlignmentViewPanel ap)
885 if (autoCalculateStrucConsensus && strucConsensus == null
886 && alignment.isNucleotide() && alignment.hasRNAStructure())
888 // secondary structure has been added - so init the consensus line
892 // see note in mantis : issue number 8585
893 if (strucConsensus == null || !autoCalculateStrucConsensus)
897 if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
899 calculator.registerWorker(new StrucConsensusThread(this, ap));
903 public boolean isCalcInProgress()
905 return calculator.isWorking();
909 public boolean isCalculationInProgress(
910 AlignmentAnnotation alignmentAnnotation)
912 if (!alignmentAnnotation.autoCalculated)
916 if (calculator.workingInvolvedWith(alignmentAnnotation))
918 // System.err.println("grey out ("+alignmentAnnotation.label+")");
924 public void setAlignment(AlignmentI align)
926 this.alignment = align;
930 * Clean up references when this viewport is closed
933 public void dispose()
936 * defensively null out references to large objects in case
937 * this object is not garbage collected (as if!)
940 complementConsensus = null;
941 strucConsensus = null;
944 groupConsensus = null;
945 groupConservation = null;
947 hcomplementConsensus = null;
948 // colour scheme may hold reference to consensus
949 residueShading = null;
950 // TODO remove listeners from changeSupport?
951 changeSupport = null;
956 public boolean isClosed()
958 // TODO: check that this isClosed is only true after panel is closed, not
959 // before it is fully constructed.
960 return alignment == null;
964 public AlignCalcManagerI getCalcManager()
970 * should conservation rows be shown for groups
972 protected boolean showGroupConservation = false;
975 * should consensus rows be shown for groups
977 protected boolean showGroupConsensus = false;
980 * should consensus profile be rendered by default
982 protected boolean showSequenceLogo = false;
985 * should consensus profile be rendered normalised to row height
987 protected boolean normaliseSequenceLogo = false;
990 * should consensus histograms be rendered by default
992 protected boolean showConsensusHistogram = true;
995 * @return the showConsensusProfile
998 public boolean isShowSequenceLogo()
1000 return showSequenceLogo;
1004 * @param showSequenceLogo
1007 public void setShowSequenceLogo(boolean showSequenceLogo)
1009 if (showSequenceLogo != this.showSequenceLogo)
1011 // TODO: decouple settings setting from calculation when refactoring
1012 // annotation update method from alignframe to viewport
1013 this.showSequenceLogo = showSequenceLogo;
1014 calculator.updateAnnotationFor(ConsensusThread.class);
1015 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1016 calculator.updateAnnotationFor(StrucConsensusThread.class);
1018 this.showSequenceLogo = showSequenceLogo;
1022 * @param showConsensusHistogram
1023 * the showConsensusHistogram to set
1025 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1027 this.showConsensusHistogram = showConsensusHistogram;
1031 * @return the showGroupConservation
1033 public boolean isShowGroupConservation()
1035 return showGroupConservation;
1039 * @param showGroupConservation
1040 * the showGroupConservation to set
1042 public void setShowGroupConservation(boolean showGroupConservation)
1044 this.showGroupConservation = showGroupConservation;
1048 * @return the showGroupConsensus
1050 public boolean isShowGroupConsensus()
1052 return showGroupConsensus;
1056 * @param showGroupConsensus
1057 * the showGroupConsensus to set
1059 public void setShowGroupConsensus(boolean showGroupConsensus)
1061 this.showGroupConsensus = showGroupConsensus;
1066 * @return flag to indicate if the consensus histogram should be rendered by
1070 public boolean isShowConsensusHistogram()
1072 return this.showConsensusHistogram;
1076 * when set, updateAlignment will always ensure sequences are of equal length
1078 private boolean padGaps = false;
1081 * when set, alignment should be reordered according to a newly opened tree
1083 public boolean sortByTree = false;
1088 * @return null or the currently selected sequence region
1091 public SequenceGroup getSelectionGroup()
1093 return selectionGroup;
1097 * Set the selection group for this window. Also sets the current alignment as
1098 * the context for the group, if it does not already have one.
1101 * - group holding references to sequences in this alignment view
1105 public void setSelectionGroup(SequenceGroup sg)
1107 selectionGroup = sg;
1108 if (sg != null && sg.getContext() == null)
1110 sg.setContext(alignment);
1114 public void setHiddenColumns(HiddenColumns hidden)
1116 this.alignment.setHiddenColumns(hidden);
1120 public ColumnSelection getColumnSelection()
1126 public void setColumnSelection(ColumnSelection colSel)
1128 this.colSel = colSel;
1131 updateHiddenColumns();
1133 isColSelChanged(true);
1141 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1143 return hiddenRepSequences;
1147 public void setHiddenRepSequences(
1148 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1150 this.hiddenRepSequences = hiddenRepSequences;
1154 public boolean hasSelectedColumns()
1156 ColumnSelection columnSelection = getColumnSelection();
1157 return columnSelection != null && columnSelection.hasSelectedColumns();
1161 public boolean hasHiddenColumns()
1163 return alignment.getHiddenColumns() != null
1164 && alignment.getHiddenColumns().hasHiddenColumns();
1167 public void updateHiddenColumns()
1169 // this method doesn't really do anything now. But - it could, since a
1170 // column Selection could be in the process of modification
1171 // hasHiddenColumns = colSel.hasHiddenColumns();
1175 public boolean hasHiddenRows()
1177 return alignment.getHiddenSequences().getSize() > 0;
1180 protected SequenceGroup selectionGroup;
1182 public void setSequenceSetId(String newid)
1184 if (sequenceSetID != null)
1187 .println("Warning - overwriting a sequenceSetId for a viewport!");
1189 sequenceSetID = new String(newid);
1193 public String getSequenceSetId()
1195 if (sequenceSetID == null)
1197 sequenceSetID = alignment.hashCode() + "";
1200 return sequenceSetID;
1204 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1207 protected String viewId = null;
1210 public String getViewId()
1214 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1219 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1221 ignoreGapsInConsensusCalculation = b;
1224 updateConsensus(ap);
1225 if (residueShading != null)
1227 residueShading.setThreshold(residueShading.getThreshold(),
1228 ignoreGapsInConsensusCalculation);
1234 private long sgrouphash = -1, colselhash = -1;
1237 * checks current SelectionGroup against record of last hash value, and
1241 * update the record of last hash value
1243 * @return true if SelectionGroup changed since last call (when b is true)
1245 public boolean isSelectionGroupChanged(boolean b)
1247 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1248 : selectionGroup.hashCode();
1249 if (hc != -1 && hc != sgrouphash)
1261 * checks current colsel against record of last hash value, and optionally
1265 * update the record of last hash value
1266 * @return true if colsel changed since last call (when b is true)
1268 public boolean isColSelChanged(boolean b)
1270 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1271 if (hc != -1 && hc != colselhash)
1283 public boolean isIgnoreGapsConsensus()
1285 return ignoreGapsInConsensusCalculation;
1288 // property change stuff
1289 // JBPNote Prolly only need this in the applet version.
1290 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1293 protected boolean showConservation = true;
1295 protected boolean showQuality = true;
1297 protected boolean showConsensus = true;
1299 protected boolean showOccupancy = true;
1301 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1303 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1305 protected boolean showAutocalculatedAbove;
1308 * when set, view will scroll to show the highlighted position
1310 private boolean followHighlight = true;
1313 * Property change listener for changes in alignment
1318 public void addPropertyChangeListener(
1319 java.beans.PropertyChangeListener listener)
1321 changeSupport.addPropertyChangeListener(listener);
1330 public void removePropertyChangeListener(
1331 java.beans.PropertyChangeListener listener)
1333 changeSupport.removePropertyChangeListener(listener);
1337 * Property change listener for changes in alignment
1346 public void firePropertyChange(String prop, Object oldvalue,
1349 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1352 // common hide/show column stuff
1354 public void hideSelectedColumns()
1356 if (colSel.isEmpty())
1361 colSel.hideSelectedColumns(alignment);
1362 setSelectionGroup(null);
1363 isColSelChanged(true);
1366 public void hideColumns(int start, int end)
1370 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1374 alignment.getHiddenColumns().hideColumns(start, end);
1376 isColSelChanged(true);
1379 public void showColumn(int col)
1381 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1382 isColSelChanged(true);
1385 public void showAllHiddenColumns()
1387 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1388 isColSelChanged(true);
1391 // common hide/show seq stuff
1392 public void showAllHiddenSeqs()
1394 int startSeq = ranges.getStartSeq();
1396 if (alignment.getHiddenSequences().getSize() > 0)
1398 if (selectionGroup == null)
1400 selectionGroup = new SequenceGroup();
1401 selectionGroup.setEndRes(alignment.getWidth() - 1);
1403 List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
1404 hiddenRepSequences);
1405 for (SequenceI seq : tmp)
1407 selectionGroup.addSequence(seq, false);
1408 setSequenceAnnotationsVisible(seq, true);
1411 hiddenRepSequences = null;
1413 ranges.setStartSeq(startSeq);
1415 firePropertyChange("alignment", null, alignment.getSequences());
1416 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1422 public void showSequence(int index)
1424 int startSeq = ranges.getStartSeq();
1426 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1427 index, hiddenRepSequences);
1430 if (selectionGroup == null)
1432 selectionGroup = new SequenceGroup();
1433 selectionGroup.setEndRes(alignment.getWidth() - 1);
1436 for (SequenceI seq : tmp)
1438 selectionGroup.addSequence(seq, false);
1439 setSequenceAnnotationsVisible(seq, true);
1441 ranges.setStartSeq(startSeq);
1442 firePropertyChange("alignment", null, alignment.getSequences());
1447 public void hideAllSelectedSeqs()
1449 if (selectionGroup == null || selectionGroup.getSize() < 1)
1454 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1458 setSelectionGroup(null);
1461 public void hideSequence(SequenceI[] seq)
1464 * cache offset to first visible sequence
1466 int startSeq = ranges.getStartSeq();
1470 for (int i = 0; i < seq.length; i++)
1472 alignment.getHiddenSequences().hideSequence(seq[i]);
1473 setSequenceAnnotationsVisible(seq[i], false);
1475 ranges.setStartSeq(startSeq);
1476 firePropertyChange("alignment", null, alignment.getSequences());
1481 * Hides the specified sequence, or the sequences it represents
1484 * the sequence to hide, or keep as representative
1485 * @param representGroup
1486 * if true, hide the current selection group except for the
1487 * representative sequence
1489 public void hideSequences(SequenceI sequence, boolean representGroup)
1491 if (selectionGroup == null || selectionGroup.getSize() < 1)
1493 hideSequence(new SequenceI[] { sequence });
1499 hideRepSequences(sequence, selectionGroup);
1500 setSelectionGroup(null);
1504 int gsize = selectionGroup.getSize();
1505 SequenceI[] hseqs = selectionGroup.getSequences().toArray(
1506 new SequenceI[gsize]);
1508 hideSequence(hseqs);
1509 setSelectionGroup(null);
1514 * Set visibility for any annotations for the given sequence.
1518 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1521 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1524 for (AlignmentAnnotation ann : anns)
1526 if (ann.sequenceRef == sequenceI)
1528 ann.visible = visible;
1534 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1536 int sSize = sg.getSize();
1542 if (hiddenRepSequences == null)
1544 hiddenRepSequences = new Hashtable<>();
1547 hiddenRepSequences.put(repSequence, sg);
1549 // Hide all sequences except the repSequence
1550 SequenceI[] seqs = new SequenceI[sSize - 1];
1552 for (int i = 0; i < sSize; i++)
1554 if (sg.getSequenceAt(i) != repSequence)
1556 if (index == sSize - 1)
1561 seqs[index++] = sg.getSequenceAt(i);
1564 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1565 sg.setHidereps(true); // note: not done in 2.7applet
1572 * @return null or the current reference sequence
1574 public SequenceI getReferenceSeq()
1576 return alignment.getSeqrep();
1581 * @return true iff seq is the reference for the alignment
1583 public boolean isReferenceSeq(SequenceI seq)
1585 return alignment.getSeqrep() == seq;
1591 * @return true if there are sequences represented by this sequence that are
1594 public boolean isHiddenRepSequence(SequenceI seq)
1596 return (hiddenRepSequences != null && hiddenRepSequences
1603 * @return null or a sequence group containing the sequences that seq
1606 public SequenceGroup getRepresentedSequences(SequenceI seq)
1608 return (SequenceGroup) (hiddenRepSequences == null ? null
1609 : hiddenRepSequences.get(seq));
1613 public int adjustForHiddenSeqs(int alignmentIndex)
1615 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1620 public void invertColumnSelection()
1622 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1626 public SequenceI[] getSelectionAsNewSequence()
1628 SequenceI[] sequences;
1629 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1630 // this was the only caller in the applet for this method
1631 // JBPNote: in applet, this method returned references to the alignment
1632 // sequences, and it did not honour the presence/absence of annotation
1633 // attached to the alignment (probably!)
1634 if (selectionGroup == null || selectionGroup.getSize() == 0)
1636 sequences = alignment.getSequencesArray();
1637 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1638 for (int i = 0; i < sequences.length; i++)
1640 // construct new sequence with subset of visible annotation
1641 sequences[i] = new Sequence(sequences[i], annots);
1646 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1653 public SequenceI[] getSequenceSelection()
1655 SequenceI[] sequences = null;
1656 if (selectionGroup != null)
1658 sequences = selectionGroup.getSequencesInOrder(alignment);
1660 if (sequences == null)
1662 sequences = alignment.getSequencesArray();
1668 public CigarArray getViewAsCigars(boolean selectedRegionOnly)
1670 return new CigarArray(alignment, alignment.getHiddenColumns(),
1671 (selectedRegionOnly ? selectionGroup : null));
1675 public jalview.datamodel.AlignmentView getAlignmentView(
1676 boolean selectedOnly)
1678 return getAlignmentView(selectedOnly, false);
1682 public jalview.datamodel.AlignmentView getAlignmentView(
1683 boolean selectedOnly, boolean markGroups)
1685 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1686 selectionGroup, alignment.getHiddenColumns() != null
1687 && alignment.getHiddenColumns().hasHiddenColumns(),
1693 public String[] getViewAsString(boolean selectedRegionOnly)
1695 return getViewAsString(selectedRegionOnly, true);
1699 public String[] getViewAsString(boolean selectedRegionOnly,
1700 boolean exportHiddenSeqs)
1702 String[] selection = null;
1703 SequenceI[] seqs = null;
1705 int start = 0, end = 0;
1706 if (selectedRegionOnly && selectionGroup != null)
1708 iSize = selectionGroup.getSize();
1709 seqs = selectionGroup.getSequencesInOrder(alignment);
1710 start = selectionGroup.getStartRes();
1711 end = selectionGroup.getEndRes() + 1;
1715 if (hasHiddenRows() && exportHiddenSeqs)
1717 AlignmentI fullAlignment = alignment.getHiddenSequences()
1718 .getFullAlignment();
1719 iSize = fullAlignment.getHeight();
1720 seqs = fullAlignment.getSequencesArray();
1721 end = fullAlignment.getWidth();
1725 iSize = alignment.getHeight();
1726 seqs = alignment.getSequencesArray();
1727 end = alignment.getWidth();
1731 selection = new String[iSize];
1732 if (alignment.getHiddenColumns() != null
1733 && alignment.getHiddenColumns().hasHiddenColumns())
1735 selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
1740 for (i = 0; i < iSize; i++)
1742 selection[i] = seqs[i].getSequenceAsString(start, end);
1750 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1752 ArrayList<int[]> regions = new ArrayList<>();
1758 HiddenColumns hidden = alignment.getHiddenColumns();
1759 if (hidden != null && hidden.hasHiddenColumns())
1763 start = hidden.adjustForHiddenColumns(start);
1766 end = hidden.getHiddenBoundaryRight(start);
1777 regions.add(new int[] { start, end });
1779 if (hidden != null && hidden.hasHiddenColumns())
1781 start = hidden.adjustForHiddenColumns(end);
1782 start = hidden.getHiddenBoundaryLeft(start) + 1;
1784 } while (end < max);
1786 int[][] startEnd = new int[regions.size()][2];
1792 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1793 boolean selectedOnly)
1795 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1796 AlignmentAnnotation[] aa;
1797 if ((aa = alignment.getAlignmentAnnotation()) != null)
1799 for (AlignmentAnnotation annot : aa)
1801 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1802 if (selectedOnly && selectionGroup != null)
1804 alignment.getHiddenColumns().makeVisibleAnnotation(
1805 selectionGroup.getStartRes(),
1806 selectionGroup.getEndRes(), clone);
1810 alignment.getHiddenColumns().makeVisibleAnnotation(clone);
1819 public boolean isPadGaps()
1825 public void setPadGaps(boolean padGaps)
1827 this.padGaps = padGaps;
1831 * apply any post-edit constraints and trigger any calculations needed after
1832 * an edit has been performed on the alignment
1837 public void alignmentChanged(AlignmentViewPanel ap)
1841 alignment.padGaps();
1843 if (autoCalculateConsensus)
1845 updateConsensus(ap);
1847 if (hconsensus != null && autoCalculateConsensus)
1849 updateConservation(ap);
1851 if (autoCalculateStrucConsensus)
1853 updateStrucConsensus(ap);
1856 // Reset endRes of groups if beyond alignment width
1857 int alWidth = alignment.getWidth();
1858 List<SequenceGroup> groups = alignment.getGroups();
1861 for (SequenceGroup sg : groups)
1863 if (sg.getEndRes() > alWidth)
1865 sg.setEndRes(alWidth - 1);
1870 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1872 selectionGroup.setEndRes(alWidth - 1);
1875 updateAllColourSchemes();
1876 calculator.restartWorkers();
1877 // alignment.adjustSequenceAnnotations();
1881 * reset scope and do calculations for all applied colourschemes on alignment
1883 void updateAllColourSchemes()
1885 ResidueShaderI rs = residueShading;
1888 rs.alignmentChanged(alignment, hiddenRepSequences);
1890 rs.setConsensus(hconsensus);
1891 if (rs.conservationApplied())
1893 rs.setConservation(Conservation.calculateConservation("All",
1894 alignment.getSequences(), 0, alignment.getWidth(), false,
1895 getConsPercGaps(), false));
1899 for (SequenceGroup sg : alignment.getGroups())
1903 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1905 sg.recalcConservation();
1909 protected void initAutoAnnotation()
1911 // TODO: add menu option action that nulls or creates consensus object
1912 // depending on if the user wants to see the annotation or not in a
1913 // specific alignment
1915 if (hconsensus == null && !isDataset)
1917 if (!alignment.isNucleotide())
1926 consensus = new AlignmentAnnotation("Consensus",
1927 MessageManager.getString("label.consensus_descr"),
1928 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1929 initConsensus(consensus);
1932 initComplementConsensus();
1937 * If this is a protein alignment and there are mappings to cDNA, adds the
1938 * cDNA consensus annotation and returns true, else returns false.
1940 public boolean initComplementConsensus()
1942 if (!alignment.isNucleotide())
1944 final List<AlignedCodonFrame> codonMappings = alignment
1946 if (codonMappings != null && !codonMappings.isEmpty())
1948 boolean doConsensus = false;
1949 for (AlignedCodonFrame mapping : codonMappings)
1951 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1952 MapList[] mapLists = mapping.getdnaToProt();
1953 // mapLists can be empty if project load has not finished resolving
1955 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1963 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1965 .getString("label.complement_consensus_descr"),
1966 new Annotation[1], 0f, 100f,
1967 AlignmentAnnotation.BAR_GRAPH);
1968 initConsensus(complementConsensus);
1976 private void initConsensus(AlignmentAnnotation aa)
1979 aa.autoCalculated = true;
1983 alignment.addAnnotation(aa);
1987 // these should be extracted from the view model - style and settings for
1988 // derived annotation
1989 private void initGapCounts()
1993 gapcounts = new AlignmentAnnotation("Occupancy",
1994 MessageManager.getString("label.occupancy_descr"),
1995 new Annotation[1], 0f,
1996 alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
1997 gapcounts.hasText = true;
1998 gapcounts.autoCalculated = true;
1999 gapcounts.scaleColLabel = true;
2000 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
2002 alignment.addAnnotation(gapcounts);
2006 private void initConservation()
2008 if (showConservation)
2010 if (conservation == null)
2012 conservation = new AlignmentAnnotation("Conservation",
2013 MessageManager.formatMessage("label.conservation_descr",
2014 getConsPercGaps()), new Annotation[1],
2015 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2016 conservation.hasText = true;
2017 conservation.autoCalculated = true;
2018 alignment.addAnnotation(conservation);
2023 private void initQuality()
2027 if (quality == null)
2029 quality = new AlignmentAnnotation("Quality",
2030 MessageManager.getString("label.quality_descr"),
2031 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2032 quality.hasText = true;
2033 quality.autoCalculated = true;
2034 alignment.addAnnotation(quality);
2039 private void initRNAStructure()
2041 if (alignment.hasRNAStructure() && strucConsensus == null)
2043 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2044 MessageManager.getString("label.strucconsensus_descr"),
2045 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2046 strucConsensus.hasText = true;
2047 strucConsensus.autoCalculated = true;
2051 alignment.addAnnotation(strucConsensus);
2059 * @see jalview.api.AlignViewportI#calcPanelHeight()
2062 public int calcPanelHeight()
2064 // setHeight of panels
2065 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2067 int charHeight = getCharHeight();
2070 BitSet graphgrp = new BitSet();
2071 for (AlignmentAnnotation aa : anns)
2075 System.err.println("Null annotation row: ignoring.");
2082 if (aa.graphGroup > -1)
2084 if (graphgrp.get(aa.graphGroup))
2090 graphgrp.set(aa.graphGroup);
2097 aa.height += charHeight;
2107 aa.height += aa.graphHeight;
2115 height += aa.height;
2127 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2128 boolean preserveNewGroupSettings)
2130 boolean updateCalcs = false;
2131 boolean conv = isShowGroupConservation();
2132 boolean cons = isShowGroupConsensus();
2133 boolean showprf = isShowSequenceLogo();
2134 boolean showConsHist = isShowConsensusHistogram();
2135 boolean normLogo = isNormaliseSequenceLogo();
2138 * TODO reorder the annotation rows according to group/sequence ordering on
2141 boolean sortg = true;
2143 // remove old automatic annotation
2144 // add any new annotation
2146 // intersect alignment annotation with alignment groups
2148 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2149 List<SequenceGroup> oldrfs = new ArrayList<>();
2152 for (int an = 0; an < aan.length; an++)
2154 if (aan[an].autoCalculated && aan[an].groupRef != null)
2156 oldrfs.add(aan[an].groupRef);
2157 alignment.deleteAnnotation(aan[an], false);
2161 if (alignment.getGroups() != null)
2163 for (SequenceGroup sg : alignment.getGroups())
2165 updateCalcs = false;
2166 if (applyGlobalSettings
2167 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2169 // set defaults for this group's conservation/consensus
2170 sg.setshowSequenceLogo(showprf);
2171 sg.setShowConsensusHistogram(showConsHist);
2172 sg.setNormaliseSequenceLogo(normLogo);
2177 alignment.addAnnotation(sg.getConservationRow(), 0);
2182 alignment.addAnnotation(sg.getConsensus(), 0);
2184 // refresh the annotation rows
2187 sg.recalcConservation();
2195 public boolean isDisplayReferenceSeq()
2197 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2201 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2203 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2207 public boolean isColourByReferenceSeq()
2209 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2213 public Color getSequenceColour(SequenceI seq)
2215 Color sqc = sequenceColours.get(seq);
2216 return (sqc == null ? Color.white : sqc);
2220 public void setSequenceColour(SequenceI seq, Color col)
2224 sequenceColours.remove(seq);
2228 sequenceColours.put(seq, col);
2233 public void updateSequenceIdColours()
2235 for (SequenceGroup sg : alignment.getGroups())
2237 if (sg.idColour != null)
2239 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2241 sequenceColours.put(s, sg.idColour);
2248 public void clearSequenceColours()
2250 sequenceColours.clear();
2254 public AlignViewportI getCodingComplement()
2256 return this.codingComplement;
2260 * Set this as the (cDna/protein) complement of the given viewport. Also
2261 * ensures the reverse relationship is set on the given viewport.
2264 public void setCodingComplement(AlignViewportI av)
2268 System.err.println("Ignoring recursive setCodingComplement request");
2272 this.codingComplement = av;
2273 // avoid infinite recursion!
2274 if (av.getCodingComplement() != this)
2276 av.setCodingComplement(this);
2282 public boolean isNucleotide()
2284 return getAlignment() == null ? false : getAlignment().isNucleotide();
2288 public FeaturesDisplayedI getFeaturesDisplayed()
2290 return featuresDisplayed;
2294 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2296 featuresDisplayed = featuresDisplayedI;
2300 public boolean areFeaturesDisplayed()
2302 return featuresDisplayed != null
2303 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2310 * features are displayed if true
2313 public void setShowSequenceFeatures(boolean b)
2315 viewStyle.setShowSequenceFeatures(b);
2319 public boolean isShowSequenceFeatures()
2321 return viewStyle.isShowSequenceFeatures();
2325 public void setShowSequenceFeaturesHeight(boolean selected)
2327 viewStyle.setShowSequenceFeaturesHeight(selected);
2331 public boolean isShowSequenceFeaturesHeight()
2333 return viewStyle.isShowSequenceFeaturesHeight();
2337 public void setShowAnnotation(boolean b)
2339 viewStyle.setShowAnnotation(b);
2343 public boolean isShowAnnotation()
2345 return viewStyle.isShowAnnotation();
2349 public boolean isRightAlignIds()
2351 return viewStyle.isRightAlignIds();
2355 public void setRightAlignIds(boolean rightAlignIds)
2357 viewStyle.setRightAlignIds(rightAlignIds);
2361 public boolean getConservationSelected()
2363 return viewStyle.getConservationSelected();
2367 public void setShowBoxes(boolean state)
2369 viewStyle.setShowBoxes(state);
2374 * @see jalview.api.ViewStyleI#getTextColour()
2377 public Color getTextColour()
2379 return viewStyle.getTextColour();
2384 * @see jalview.api.ViewStyleI#getTextColour2()
2387 public Color getTextColour2()
2389 return viewStyle.getTextColour2();
2394 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2397 public int getThresholdTextColour()
2399 return viewStyle.getThresholdTextColour();
2404 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2407 public boolean isConservationColourSelected()
2409 return viewStyle.isConservationColourSelected();
2414 * @see jalview.api.ViewStyleI#isRenderGaps()
2417 public boolean isRenderGaps()
2419 return viewStyle.isRenderGaps();
2424 * @see jalview.api.ViewStyleI#isShowColourText()
2427 public boolean isShowColourText()
2429 return viewStyle.isShowColourText();
2433 * @param conservationColourSelected
2434 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2437 public void setConservationColourSelected(
2438 boolean conservationColourSelected)
2440 viewStyle.setConservationColourSelected(conservationColourSelected);
2444 * @param showColourText
2445 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2448 public void setShowColourText(boolean showColourText)
2450 viewStyle.setShowColourText(showColourText);
2455 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2458 public void setTextColour(Color textColour)
2460 viewStyle.setTextColour(textColour);
2464 * @param thresholdTextColour
2465 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2468 public void setThresholdTextColour(int thresholdTextColour)
2470 viewStyle.setThresholdTextColour(thresholdTextColour);
2474 * @param textColour2
2475 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2478 public void setTextColour2(Color textColour2)
2480 viewStyle.setTextColour2(textColour2);
2484 public ViewStyleI getViewStyle()
2486 return new ViewStyle(viewStyle);
2490 public void setViewStyle(ViewStyleI settingsForView)
2492 viewStyle = new ViewStyle(settingsForView);
2493 if (residueShading != null)
2495 residueShading.setConservationApplied(settingsForView
2496 .isConservationColourSelected());
2501 public boolean sameStyle(ViewStyleI them)
2503 return viewStyle.sameStyle(them);
2508 * @see jalview.api.ViewStyleI#getIdWidth()
2511 public int getIdWidth()
2513 return viewStyle.getIdWidth();
2518 * @see jalview.api.ViewStyleI#setIdWidth(int)
2521 public void setIdWidth(int i)
2523 viewStyle.setIdWidth(i);
2528 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2531 public boolean isCentreColumnLabels()
2533 return viewStyle.isCentreColumnLabels();
2537 * @param centreColumnLabels
2538 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2541 public void setCentreColumnLabels(boolean centreColumnLabels)
2543 viewStyle.setCentreColumnLabels(centreColumnLabels);
2548 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2551 public void setShowDBRefs(boolean showdbrefs)
2553 viewStyle.setShowDBRefs(showdbrefs);
2558 * @see jalview.api.ViewStyleI#isShowDBRefs()
2561 public boolean isShowDBRefs()
2563 return viewStyle.isShowDBRefs();
2568 * @see jalview.api.ViewStyleI#isShowNPFeats()
2571 public boolean isShowNPFeats()
2573 return viewStyle.isShowNPFeats();
2577 * @param shownpfeats
2578 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2581 public void setShowNPFeats(boolean shownpfeats)
2583 viewStyle.setShowNPFeats(shownpfeats);
2586 public abstract StructureSelectionManager getStructureSelectionManager();
2589 * Add one command to the command history list.
2593 public void addToHistoryList(CommandI command)
2595 if (this.historyList != null)
2597 this.historyList.push(command);
2598 broadcastCommand(command, false);
2602 protected void broadcastCommand(CommandI command, boolean undo)
2604 getStructureSelectionManager().commandPerformed(command, undo,
2609 * Add one command to the command redo list.
2613 public void addToRedoList(CommandI command)
2615 if (this.redoList != null)
2617 this.redoList.push(command);
2619 broadcastCommand(command, true);
2623 * Clear the command redo list.
2625 public void clearRedoList()
2627 if (this.redoList != null)
2629 this.redoList.clear();
2633 public void setHistoryList(Deque<CommandI> list)
2635 this.historyList = list;
2638 public Deque<CommandI> getHistoryList()
2640 return this.historyList;
2643 public void setRedoList(Deque<CommandI> list)
2645 this.redoList = list;
2648 public Deque<CommandI> getRedoList()
2650 return this.redoList;
2654 public VamsasSource getVamsasSource()
2659 public SequenceAnnotationOrder getSortAnnotationsBy()
2661 return sortAnnotationsBy;
2664 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2666 this.sortAnnotationsBy = sortAnnotationsBy;
2669 public boolean isShowAutocalculatedAbove()
2671 return showAutocalculatedAbove;
2674 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2676 this.showAutocalculatedAbove = showAutocalculatedAbove;
2680 public boolean isScaleProteinAsCdna()
2682 return viewStyle.isScaleProteinAsCdna();
2686 public void setScaleProteinAsCdna(boolean b)
2688 viewStyle.setScaleProteinAsCdna(b);
2692 public boolean isProteinFontAsCdna()
2694 return viewStyle.isProteinFontAsCdna();
2698 public void setProteinFontAsCdna(boolean b)
2700 viewStyle.setProteinFontAsCdna(b);
2704 * @return true if view should scroll to show the highlighted region of a
2709 public final boolean isFollowHighlight()
2711 return followHighlight;
2715 public final void setFollowHighlight(boolean b)
2717 this.followHighlight = b;
2721 public ViewportRanges getRanges()
2727 * Helper method to populate the SearchResults with the location in the
2728 * complementary alignment to scroll to, in order to match this one.
2731 * the SearchResults to add to
2732 * @return the offset (below top of visible region) of the matched sequence
2734 protected int findComplementScrollTarget(SearchResultsI sr)
2736 final AlignViewportI complement = getCodingComplement();
2737 if (complement == null || !complement.isFollowHighlight())
2741 boolean iAmProtein = !getAlignment().isNucleotide();
2742 AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
2744 if (proteinAlignment == null)
2748 final List<AlignedCodonFrame> mappings = proteinAlignment
2752 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2753 * residue in the middle column of the visible region. Scroll the
2754 * complementary alignment to line up the corresponding residue.
2757 SequenceI sequence = null;
2760 * locate 'middle' column (true middle if an odd number visible, left of
2761 * middle if an even number visible)
2763 int middleColumn = ranges.getStartRes()
2764 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2765 final HiddenSequences hiddenSequences = getAlignment()
2766 .getHiddenSequences();
2769 * searching to the bottom of the alignment gives smoother scrolling across
2770 * all gapped visible regions
2772 int lastSeq = alignment.getHeight() - 1;
2773 List<AlignedCodonFrame> seqMappings = null;
2774 for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
2776 sequence = getAlignment().getSequenceAt(seqNo);
2777 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2781 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2785 seqMappings = MappingUtils
2786 .findMappingsForSequenceAndOthers(sequence, mappings,
2787 getCodingComplement().getAlignment().getSequences());
2788 if (!seqMappings.isEmpty())
2794 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2797 * No ungapped mapped sequence in middle column - do nothing
2801 MappingUtils.addSearchResults(sr, sequence,
2802 sequence.findPosition(middleColumn), seqMappings);
2807 * synthesize a column selection if none exists so it covers the given
2808 * selection group. if wholewidth is false, no column selection is made if the
2809 * selection group covers the whole alignment width.
2814 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2817 if (sg != null && (sgs = sg.getStartRes()) >= 0
2818 && sg.getStartRes() <= (sge = sg.getEndRes())
2819 && !this.hasSelectedColumns())
2821 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2828 colSel = new ColumnSelection();
2830 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2832 colSel.addElement(cspos);
2838 * hold status of current selection group - defined on alignment or not.
2840 private boolean selectionIsDefinedGroup = false;
2843 public boolean isSelectionDefinedGroup()
2845 if (selectionGroup == null)
2849 if (isSelectionGroupChanged(true))
2851 selectionIsDefinedGroup = false;
2852 List<SequenceGroup> gps = alignment.getGroups();
2853 if (gps == null || gps.size() == 0)
2855 selectionIsDefinedGroup = false;
2859 selectionIsDefinedGroup = gps.contains(selectionGroup);
2862 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2866 * null, or currently highlighted results on this view
2868 private SearchResultsI searchResults = null;
2871 public boolean hasSearchResults()
2873 return searchResults != null;
2877 public void setSearchResults(SearchResultsI results)
2879 searchResults = results;
2883 public SearchResultsI getSearchResults()
2885 return searchResults;
2889 * get the consensus sequence as displayed under the PID consensus annotation
2892 * @return consensus sequence as a new sequence object
2894 public SequenceI getConsensusSeq()
2896 if (consensus == null)
2898 updateConsensus(null);
2900 if (consensus == null)
2904 StringBuffer seqs = new StringBuffer();
2905 for (int i = 0; i < consensus.annotations.length; i++)
2907 Annotation annotation = consensus.annotations[i];
2908 if (annotation != null)
2910 String description = annotation.description;
2911 if (description != null && description.startsWith("["))
2913 // consensus is a tie - just pick the first one
2914 seqs.append(description.charAt(1));
2918 seqs.append(annotation.displayCharacter);
2923 SequenceI sq = new Sequence("Consensus", seqs.toString());
2924 sq.setDescription("Percentage Identity Consensus "
2925 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));