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);
412 * @see jalview.api.ViewStyleI#setShowText(boolean)
415 public void setShowText(boolean state)
417 viewStyle.setShowText(state);
422 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
425 public void setRenderGaps(boolean state)
427 viewStyle.setRenderGaps(state);
432 * @see jalview.api.ViewStyleI#getColourText()
435 public boolean getColourText()
437 return viewStyle.getColourText();
442 * @see jalview.api.ViewStyleI#setColourText(boolean)
445 public void setColourText(boolean state)
447 viewStyle.setColourText(state);
452 * @see jalview.api.ViewStyleI#getWrapAlignment()
455 public boolean getWrapAlignment()
457 return viewStyle.getWrapAlignment();
462 * @see jalview.api.ViewStyleI#getShowText()
465 public boolean getShowText()
467 return viewStyle.getShowText();
472 * @see jalview.api.ViewStyleI#getWrappedWidth()
475 public int getWrappedWidth()
477 return viewStyle.getWrappedWidth();
482 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
485 public void setWrappedWidth(int w)
487 viewStyle.setWrappedWidth(w);
492 * @see jalview.api.ViewStyleI#getCharHeight()
495 public int getCharHeight()
497 return viewStyle.getCharHeight();
502 * @see jalview.api.ViewStyleI#setCharHeight(int)
505 public void setCharHeight(int h)
507 viewStyle.setCharHeight(h);
512 * @see jalview.api.ViewStyleI#getCharWidth()
515 public int getCharWidth()
517 return viewStyle.getCharWidth();
522 * @see jalview.api.ViewStyleI#setCharWidth(int)
525 public void setCharWidth(int w)
527 viewStyle.setCharWidth(w);
532 * @see jalview.api.ViewStyleI#getShowBoxes()
535 public boolean getShowBoxes()
537 return viewStyle.getShowBoxes();
542 * @see jalview.api.ViewStyleI#getShowUnconserved()
545 public boolean getShowUnconserved()
547 return viewStyle.getShowUnconserved();
551 * @param showunconserved
552 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
555 public void setShowUnconserved(boolean showunconserved)
557 viewStyle.setShowUnconserved(showunconserved);
562 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
565 public void setSeqNameItalics(boolean default1)
567 viewStyle.setSeqNameItalics(default1);
573 public AlignmentI getAlignment()
579 public char getGapCharacter()
581 return alignment.getGapCharacter();
584 protected String sequenceSetID;
587 * probably unused indicator that view is of a dataset rather than an
590 protected boolean isDataset = false;
592 public void setDataset(boolean b)
597 public boolean isDataset()
602 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
604 protected ColumnSelection colSel = new ColumnSelection();
606 public boolean autoCalculateConsensus = true;
608 protected boolean autoCalculateStrucConsensus = true;
610 protected boolean ignoreGapsInConsensusCalculation = false;
612 protected ResidueShaderI residueShading = new ResidueShader();
615 public void setGlobalColourScheme(ColourSchemeI cs)
617 // TODO: logic refactored from AlignFrame changeColour -
618 // TODO: autorecalc stuff should be changed to rely on the worker system
619 // check to see if we should implement a changeColour(cs) method rather than
620 // put the logic in here
621 // - means that caller decides if they want to just modify state and defer
622 // calculation till later or to do all calculations in thread.
626 * only instantiate alignment colouring once, thereafter update it;
627 * this means that any conservation or PID threshold settings
628 * persist when the alignment colour scheme is changed
630 if (residueShading == null)
632 residueShading = new ResidueShader(viewStyle);
634 residueShading.setColourScheme(cs);
636 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
637 // ...problem: groups need these, but do not currently have a ViewStyle
641 if (getConservationSelected())
643 residueShading.setConservation(hconservation);
645 residueShading.alignmentChanged(alignment, hiddenRepSequences);
649 * if 'apply colour to all groups' is selected... do so
650 * (but don't transfer any colour threshold settings to groups)
652 if (getColourAppliesToAllGroups())
654 for (SequenceGroup sg : getAlignment().getGroups())
657 * retain any colour thresholds per group while
658 * changing choice of colour scheme (JAL-2386)
660 sg.setColourScheme(cs);
663 sg.getGroupColourScheme()
664 .alignmentChanged(sg, hiddenRepSequences);
671 public ColourSchemeI getGlobalColourScheme()
673 return residueShading == null ? null : residueShading
678 public ResidueShaderI getResidueShading()
680 return residueShading;
683 protected AlignmentAnnotation consensus;
685 protected AlignmentAnnotation complementConsensus;
687 protected AlignmentAnnotation gapcounts;
689 protected AlignmentAnnotation strucConsensus;
691 protected AlignmentAnnotation conservation;
693 protected AlignmentAnnotation quality;
695 protected AlignmentAnnotation[] groupConsensus;
697 protected AlignmentAnnotation[] groupConservation;
700 * results of alignment consensus analysis for visible portion of view
702 protected ProfilesI hconsensus = null;
705 * results of cDNA complement consensus visible portion of view
707 protected Hashtable[] hcomplementConsensus = null;
710 * results of secondary structure base pair consensus for visible portion of
713 protected Hashtable[] hStrucConsensus = null;
715 protected Conservation hconservation = null;
718 public void setConservation(Conservation cons)
720 hconservation = cons;
724 * percentage gaps allowed in a column before all amino acid properties should
725 * be considered unconserved
727 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
730 public int getConsPercGaps()
736 public void setSequenceConsensusHash(ProfilesI hconsensus)
738 this.hconsensus = hconsensus;
742 public void setComplementConsensusHash(Hashtable[] hconsensus)
744 this.hcomplementConsensus = hconsensus;
748 public ProfilesI getSequenceConsensusHash()
754 public Hashtable[] getComplementConsensusHash()
756 return hcomplementConsensus;
760 public Hashtable[] getRnaStructureConsensusHash()
762 return hStrucConsensus;
766 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
768 this.hStrucConsensus = hStrucConsensus;
773 public AlignmentAnnotation getAlignmentQualityAnnot()
779 public AlignmentAnnotation getAlignmentConservationAnnotation()
785 public AlignmentAnnotation getAlignmentConsensusAnnotation()
791 public AlignmentAnnotation getAlignmentGapAnnotation()
797 public AlignmentAnnotation getComplementConsensusAnnotation()
799 return complementConsensus;
803 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
805 return strucConsensus;
808 protected AlignCalcManagerI calculator = new AlignCalcManager();
811 * trigger update of conservation annotation
813 public void updateConservation(final AlignmentViewPanel ap)
815 // see note in mantis : issue number 8585
816 if (alignment.isNucleotide()
817 || (conservation == null && quality == null)
818 || !autoCalculateConsensus)
823 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
825 calculator.registerWorker(new jalview.workers.ConservationThread(
831 * trigger update of consensus annotation
833 public void updateConsensus(final AlignmentViewPanel ap)
835 // see note in mantis : issue number 8585
836 if (consensus == null || !autoCalculateConsensus)
840 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
842 calculator.registerWorker(new ConsensusThread(this, ap));
846 * A separate thread to compute cDNA consensus for a protein alignment
847 * which has mapping to cDNA
849 final AlignmentI al = this.getAlignment();
850 if (!al.isNucleotide() && al.getCodonFrames() != null
851 && !al.getCodonFrames().isEmpty())
854 * fudge - check first for protein-to-nucleotide mappings
855 * (we don't want to do this for protein-to-protein)
857 boolean doConsensus = false;
858 for (AlignedCodonFrame mapping : al.getCodonFrames())
860 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
861 MapList[] mapLists = mapping.getdnaToProt();
862 // mapLists can be empty if project load has not finished resolving seqs
863 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
872 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
875 .registerWorker(new ComplementConsensusThread(this, ap));
881 // --------START Structure Conservation
882 public void updateStrucConsensus(final AlignmentViewPanel ap)
884 if (autoCalculateStrucConsensus && strucConsensus == null
885 && alignment.isNucleotide() && alignment.hasRNAStructure())
887 // secondary structure has been added - so init the consensus line
891 // see note in mantis : issue number 8585
892 if (strucConsensus == null || !autoCalculateStrucConsensus)
896 if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
898 calculator.registerWorker(new StrucConsensusThread(this, ap));
902 public boolean isCalcInProgress()
904 return calculator.isWorking();
908 public boolean isCalculationInProgress(
909 AlignmentAnnotation alignmentAnnotation)
911 if (!alignmentAnnotation.autoCalculated)
915 if (calculator.workingInvolvedWith(alignmentAnnotation))
917 // System.err.println("grey out ("+alignmentAnnotation.label+")");
923 public void setAlignment(AlignmentI align)
925 this.alignment = align;
929 * Clean up references when this viewport is closed
932 public void dispose()
935 * defensively null out references to large objects in case
936 * this object is not garbage collected (as if!)
939 complementConsensus = null;
940 strucConsensus = null;
943 groupConsensus = null;
944 groupConservation = null;
946 hcomplementConsensus = null;
947 // colour scheme may hold reference to consensus
948 residueShading = null;
949 // TODO remove listeners from changeSupport?
950 changeSupport = null;
955 public boolean isClosed()
957 // TODO: check that this isClosed is only true after panel is closed, not
958 // before it is fully constructed.
959 return alignment == null;
963 public AlignCalcManagerI getCalcManager()
969 * should conservation rows be shown for groups
971 protected boolean showGroupConservation = false;
974 * should consensus rows be shown for groups
976 protected boolean showGroupConsensus = false;
979 * should consensus profile be rendered by default
981 protected boolean showSequenceLogo = false;
984 * should consensus profile be rendered normalised to row height
986 protected boolean normaliseSequenceLogo = false;
989 * should consensus histograms be rendered by default
991 protected boolean showConsensusHistogram = true;
994 * @return the showConsensusProfile
997 public boolean isShowSequenceLogo()
999 return showSequenceLogo;
1003 * @param showSequenceLogo
1006 public void setShowSequenceLogo(boolean showSequenceLogo)
1008 if (showSequenceLogo != this.showSequenceLogo)
1010 // TODO: decouple settings setting from calculation when refactoring
1011 // annotation update method from alignframe to viewport
1012 this.showSequenceLogo = showSequenceLogo;
1013 calculator.updateAnnotationFor(ConsensusThread.class);
1014 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1015 calculator.updateAnnotationFor(StrucConsensusThread.class);
1017 this.showSequenceLogo = showSequenceLogo;
1021 * @param showConsensusHistogram
1022 * the showConsensusHistogram to set
1024 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1026 this.showConsensusHistogram = showConsensusHistogram;
1030 * @return the showGroupConservation
1032 public boolean isShowGroupConservation()
1034 return showGroupConservation;
1038 * @param showGroupConservation
1039 * the showGroupConservation to set
1041 public void setShowGroupConservation(boolean showGroupConservation)
1043 this.showGroupConservation = showGroupConservation;
1047 * @return the showGroupConsensus
1049 public boolean isShowGroupConsensus()
1051 return showGroupConsensus;
1055 * @param showGroupConsensus
1056 * the showGroupConsensus to set
1058 public void setShowGroupConsensus(boolean showGroupConsensus)
1060 this.showGroupConsensus = showGroupConsensus;
1065 * @return flag to indicate if the consensus histogram should be rendered by
1069 public boolean isShowConsensusHistogram()
1071 return this.showConsensusHistogram;
1075 * when set, updateAlignment will always ensure sequences are of equal length
1077 private boolean padGaps = false;
1080 * when set, alignment should be reordered according to a newly opened tree
1082 public boolean sortByTree = false;
1087 * @return null or the currently selected sequence region
1090 public SequenceGroup getSelectionGroup()
1092 return selectionGroup;
1096 * Set the selection group for this window. Also sets the current alignment as
1097 * the context for the group, if it does not already have one.
1100 * - group holding references to sequences in this alignment view
1104 public void setSelectionGroup(SequenceGroup sg)
1106 selectionGroup = sg;
1107 if (sg != null && sg.getContext() == null)
1109 sg.setContext(alignment);
1113 public void setHiddenColumns(HiddenColumns hidden)
1115 this.alignment.setHiddenColumns(hidden);
1119 public ColumnSelection getColumnSelection()
1125 public void setColumnSelection(ColumnSelection colSel)
1127 this.colSel = colSel;
1130 updateHiddenColumns();
1132 isColSelChanged(true);
1140 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1142 return hiddenRepSequences;
1146 public void setHiddenRepSequences(
1147 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1149 this.hiddenRepSequences = hiddenRepSequences;
1153 public boolean hasSelectedColumns()
1155 ColumnSelection columnSelection = getColumnSelection();
1156 return columnSelection != null && columnSelection.hasSelectedColumns();
1160 public boolean hasHiddenColumns()
1162 return alignment.getHiddenColumns() != null
1163 && alignment.getHiddenColumns().hasHiddenColumns();
1166 public void updateHiddenColumns()
1168 // this method doesn't really do anything now. But - it could, since a
1169 // column Selection could be in the process of modification
1170 // hasHiddenColumns = colSel.hasHiddenColumns();
1174 public boolean hasHiddenRows()
1176 return alignment.getHiddenSequences().getSize() > 0;
1179 protected SequenceGroup selectionGroup;
1181 public void setSequenceSetId(String newid)
1183 if (sequenceSetID != null)
1186 .println("Warning - overwriting a sequenceSetId for a viewport!");
1188 sequenceSetID = new String(newid);
1192 public String getSequenceSetId()
1194 if (sequenceSetID == null)
1196 sequenceSetID = alignment.hashCode() + "";
1199 return sequenceSetID;
1203 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1206 protected String viewId = null;
1209 public String getViewId()
1213 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1218 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1220 ignoreGapsInConsensusCalculation = b;
1223 updateConsensus(ap);
1224 if (residueShading != null)
1226 residueShading.setThreshold(residueShading.getThreshold(),
1227 ignoreGapsInConsensusCalculation);
1233 private long sgrouphash = -1, colselhash = -1;
1236 * checks current SelectionGroup against record of last hash value, and
1240 * update the record of last hash value
1242 * @return true if SelectionGroup changed since last call (when b is true)
1244 public boolean isSelectionGroupChanged(boolean b)
1246 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1247 : selectionGroup.hashCode();
1248 if (hc != -1 && hc != sgrouphash)
1260 * checks current colsel against record of last hash value, and optionally
1264 * update the record of last hash value
1265 * @return true if colsel changed since last call (when b is true)
1267 public boolean isColSelChanged(boolean b)
1269 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1270 if (hc != -1 && hc != colselhash)
1282 public boolean isIgnoreGapsConsensus()
1284 return ignoreGapsInConsensusCalculation;
1287 // property change stuff
1288 // JBPNote Prolly only need this in the applet version.
1289 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1292 protected boolean showConservation = true;
1294 protected boolean showQuality = true;
1296 protected boolean showConsensus = true;
1298 protected boolean showOccupancy = true;
1300 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1302 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1304 protected boolean showAutocalculatedAbove;
1307 * when set, view will scroll to show the highlighted position
1309 private boolean followHighlight = true;
1312 * Property change listener for changes in alignment
1317 public void addPropertyChangeListener(
1318 java.beans.PropertyChangeListener listener)
1320 changeSupport.addPropertyChangeListener(listener);
1329 public void removePropertyChangeListener(
1330 java.beans.PropertyChangeListener listener)
1332 changeSupport.removePropertyChangeListener(listener);
1336 * Property change listener for changes in alignment
1345 public void firePropertyChange(String prop, Object oldvalue,
1348 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1351 // common hide/show column stuff
1353 public void hideSelectedColumns()
1355 if (colSel.isEmpty())
1360 colSel.hideSelectedColumns(alignment);
1361 setSelectionGroup(null);
1362 isColSelChanged(true);
1365 public void hideColumns(int start, int end)
1369 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1373 alignment.getHiddenColumns().hideColumns(start, end);
1375 isColSelChanged(true);
1378 public void showColumn(int col)
1380 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1381 isColSelChanged(true);
1384 public void showAllHiddenColumns()
1386 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1387 isColSelChanged(true);
1390 // common hide/show seq stuff
1391 public void showAllHiddenSeqs()
1393 if (alignment.getHiddenSequences().getSize() > 0)
1395 if (selectionGroup == null)
1397 selectionGroup = new SequenceGroup();
1398 selectionGroup.setEndRes(alignment.getWidth() - 1);
1400 List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
1401 hiddenRepSequences);
1402 for (SequenceI seq : tmp)
1404 selectionGroup.addSequence(seq, false);
1405 setSequenceAnnotationsVisible(seq, true);
1408 hiddenRepSequences = null;
1410 firePropertyChange("alignment", null, alignment.getSequences());
1411 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1417 public void showSequence(int index)
1419 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1420 index, hiddenRepSequences);
1423 if (selectionGroup == null)
1425 selectionGroup = new SequenceGroup();
1426 selectionGroup.setEndRes(alignment.getWidth() - 1);
1429 for (SequenceI seq : tmp)
1431 selectionGroup.addSequence(seq, false);
1432 setSequenceAnnotationsVisible(seq, true);
1434 firePropertyChange("alignment", null, alignment.getSequences());
1439 public void hideAllSelectedSeqs()
1441 if (selectionGroup == null || selectionGroup.getSize() < 1)
1446 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1450 setSelectionGroup(null);
1453 public void hideSequence(SequenceI[] seq)
1457 for (int i = 0; i < seq.length; i++)
1459 alignment.getHiddenSequences().hideSequence(seq[i]);
1460 setSequenceAnnotationsVisible(seq[i], false);
1462 firePropertyChange("alignment", null, alignment.getSequences());
1467 * Hides the specified sequence, or the sequences it represents
1470 * the sequence to hide, or keep as representative
1471 * @param representGroup
1472 * if true, hide the current selection group except for the
1473 * representative sequence
1475 public void hideSequences(SequenceI sequence, boolean representGroup)
1477 if (selectionGroup == null || selectionGroup.getSize() < 1)
1479 hideSequence(new SequenceI[] { sequence });
1485 hideRepSequences(sequence, selectionGroup);
1486 setSelectionGroup(null);
1490 int gsize = selectionGroup.getSize();
1491 SequenceI[] hseqs = selectionGroup.getSequences().toArray(
1492 new SequenceI[gsize]);
1494 hideSequence(hseqs);
1495 setSelectionGroup(null);
1500 * Set visibility for any annotations for the given sequence.
1504 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1507 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1510 for (AlignmentAnnotation ann : anns)
1512 if (ann.sequenceRef == sequenceI)
1514 ann.visible = visible;
1520 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1522 int sSize = sg.getSize();
1528 if (hiddenRepSequences == null)
1530 hiddenRepSequences = new Hashtable<>();
1533 hiddenRepSequences.put(repSequence, sg);
1535 // Hide all sequences except the repSequence
1536 SequenceI[] seqs = new SequenceI[sSize - 1];
1538 for (int i = 0; i < sSize; i++)
1540 if (sg.getSequenceAt(i) != repSequence)
1542 if (index == sSize - 1)
1547 seqs[index++] = sg.getSequenceAt(i);
1550 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1551 sg.setHidereps(true); // note: not done in 2.7applet
1558 * @return null or the current reference sequence
1560 public SequenceI getReferenceSeq()
1562 return alignment.getSeqrep();
1567 * @return true iff seq is the reference for the alignment
1569 public boolean isReferenceSeq(SequenceI seq)
1571 return alignment.getSeqrep() == seq;
1577 * @return true if there are sequences represented by this sequence that are
1580 public boolean isHiddenRepSequence(SequenceI seq)
1582 return (hiddenRepSequences != null && hiddenRepSequences
1589 * @return null or a sequence group containing the sequences that seq
1592 public SequenceGroup getRepresentedSequences(SequenceI seq)
1594 return (SequenceGroup) (hiddenRepSequences == null ? null
1595 : hiddenRepSequences.get(seq));
1599 public int adjustForHiddenSeqs(int alignmentIndex)
1601 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1606 public void invertColumnSelection()
1608 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1612 public SequenceI[] getSelectionAsNewSequence()
1614 SequenceI[] sequences;
1615 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1616 // this was the only caller in the applet for this method
1617 // JBPNote: in applet, this method returned references to the alignment
1618 // sequences, and it did not honour the presence/absence of annotation
1619 // attached to the alignment (probably!)
1620 if (selectionGroup == null || selectionGroup.getSize() == 0)
1622 sequences = alignment.getSequencesArray();
1623 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1624 for (int i = 0; i < sequences.length; i++)
1626 // construct new sequence with subset of visible annotation
1627 sequences[i] = new Sequence(sequences[i], annots);
1632 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1639 public SequenceI[] getSequenceSelection()
1641 SequenceI[] sequences = null;
1642 if (selectionGroup != null)
1644 sequences = selectionGroup.getSequencesInOrder(alignment);
1646 if (sequences == null)
1648 sequences = alignment.getSequencesArray();
1654 public CigarArray getViewAsCigars(boolean selectedRegionOnly)
1656 return new CigarArray(alignment, alignment.getHiddenColumns(),
1657 (selectedRegionOnly ? selectionGroup : null));
1661 public jalview.datamodel.AlignmentView getAlignmentView(
1662 boolean selectedOnly)
1664 return getAlignmentView(selectedOnly, false);
1668 public jalview.datamodel.AlignmentView getAlignmentView(
1669 boolean selectedOnly, boolean markGroups)
1671 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1672 selectionGroup, alignment.getHiddenColumns() != null
1673 && alignment.getHiddenColumns().hasHiddenColumns(),
1679 public String[] getViewAsString(boolean selectedRegionOnly)
1681 return getViewAsString(selectedRegionOnly, true);
1685 public String[] getViewAsString(boolean selectedRegionOnly,
1686 boolean exportHiddenSeqs)
1688 String[] selection = null;
1689 SequenceI[] seqs = null;
1691 int start = 0, end = 0;
1692 if (selectedRegionOnly && selectionGroup != null)
1694 iSize = selectionGroup.getSize();
1695 seqs = selectionGroup.getSequencesInOrder(alignment);
1696 start = selectionGroup.getStartRes();
1697 end = selectionGroup.getEndRes() + 1;
1701 if (hasHiddenRows() && exportHiddenSeqs)
1703 AlignmentI fullAlignment = alignment.getHiddenSequences()
1704 .getFullAlignment();
1705 iSize = fullAlignment.getHeight();
1706 seqs = fullAlignment.getSequencesArray();
1707 end = fullAlignment.getWidth();
1711 iSize = alignment.getHeight();
1712 seqs = alignment.getSequencesArray();
1713 end = alignment.getWidth();
1717 selection = new String[iSize];
1718 if (alignment.getHiddenColumns() != null
1719 && alignment.getHiddenColumns().hasHiddenColumns())
1721 selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
1726 for (i = 0; i < iSize; i++)
1728 selection[i] = seqs[i].getSequenceAsString(start, end);
1736 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1738 ArrayList<int[]> regions = new ArrayList<>();
1744 HiddenColumns hidden = alignment.getHiddenColumns();
1745 if (hidden != null && hidden.hasHiddenColumns())
1749 start = hidden.adjustForHiddenColumns(start);
1752 end = hidden.getHiddenBoundaryRight(start);
1763 regions.add(new int[] { start, end });
1765 if (hidden != null && hidden.hasHiddenColumns())
1767 start = hidden.adjustForHiddenColumns(end);
1768 start = hidden.getHiddenBoundaryLeft(start) + 1;
1770 } while (end < max);
1772 int[][] startEnd = new int[regions.size()][2];
1778 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1779 boolean selectedOnly)
1781 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1782 AlignmentAnnotation[] aa;
1783 if ((aa = alignment.getAlignmentAnnotation()) != null)
1785 for (AlignmentAnnotation annot : aa)
1787 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1788 if (selectedOnly && selectionGroup != null)
1790 alignment.getHiddenColumns().makeVisibleAnnotation(
1791 selectionGroup.getStartRes(),
1792 selectionGroup.getEndRes(), clone);
1796 alignment.getHiddenColumns().makeVisibleAnnotation(clone);
1805 public boolean isPadGaps()
1811 public void setPadGaps(boolean padGaps)
1813 this.padGaps = padGaps;
1817 * apply any post-edit constraints and trigger any calculations needed after
1818 * an edit has been performed on the alignment
1823 public void alignmentChanged(AlignmentViewPanel ap)
1827 alignment.padGaps();
1829 if (autoCalculateConsensus)
1831 updateConsensus(ap);
1833 if (hconsensus != null && autoCalculateConsensus)
1835 updateConservation(ap);
1837 if (autoCalculateStrucConsensus)
1839 updateStrucConsensus(ap);
1842 // Reset endRes of groups if beyond alignment width
1843 int alWidth = alignment.getWidth();
1844 List<SequenceGroup> groups = alignment.getGroups();
1847 for (SequenceGroup sg : groups)
1849 if (sg.getEndRes() > alWidth)
1851 sg.setEndRes(alWidth - 1);
1856 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1858 selectionGroup.setEndRes(alWidth - 1);
1861 updateAllColourSchemes();
1862 calculator.restartWorkers();
1863 // alignment.adjustSequenceAnnotations();
1867 * reset scope and do calculations for all applied colourschemes on alignment
1869 void updateAllColourSchemes()
1871 ResidueShaderI rs = residueShading;
1874 rs.alignmentChanged(alignment, hiddenRepSequences);
1876 rs.setConsensus(hconsensus);
1877 if (rs.conservationApplied())
1879 rs.setConservation(Conservation.calculateConservation("All",
1880 alignment.getSequences(), 0, alignment.getWidth(), false,
1881 getConsPercGaps(), false));
1885 for (SequenceGroup sg : alignment.getGroups())
1889 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1891 sg.recalcConservation();
1895 protected void initAutoAnnotation()
1897 // TODO: add menu option action that nulls or creates consensus object
1898 // depending on if the user wants to see the annotation or not in a
1899 // specific alignment
1901 if (hconsensus == null && !isDataset)
1903 if (!alignment.isNucleotide())
1912 consensus = new AlignmentAnnotation("Consensus",
1913 MessageManager.getString("label.consensus_descr"),
1914 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1915 initConsensus(consensus);
1918 initComplementConsensus();
1923 * If this is a protein alignment and there are mappings to cDNA, adds the
1924 * cDNA consensus annotation and returns true, else returns false.
1926 public boolean initComplementConsensus()
1928 if (!alignment.isNucleotide())
1930 final List<AlignedCodonFrame> codonMappings = alignment
1932 if (codonMappings != null && !codonMappings.isEmpty())
1934 boolean doConsensus = false;
1935 for (AlignedCodonFrame mapping : codonMappings)
1937 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1938 MapList[] mapLists = mapping.getdnaToProt();
1939 // mapLists can be empty if project load has not finished resolving
1941 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1949 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1951 .getString("label.complement_consensus_descr"),
1952 new Annotation[1], 0f, 100f,
1953 AlignmentAnnotation.BAR_GRAPH);
1954 initConsensus(complementConsensus);
1962 private void initConsensus(AlignmentAnnotation aa)
1965 aa.autoCalculated = true;
1969 alignment.addAnnotation(aa);
1973 // these should be extracted from the view model - style and settings for
1974 // derived annotation
1975 private void initGapCounts()
1979 gapcounts = new AlignmentAnnotation("Occupancy",
1980 MessageManager.getString("label.occupancy_descr"),
1981 new Annotation[1], 0f,
1982 alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
1983 gapcounts.hasText = true;
1984 gapcounts.autoCalculated = true;
1985 gapcounts.scaleColLabel = true;
1986 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
1988 alignment.addAnnotation(gapcounts);
1992 private void initConservation()
1994 if (showConservation)
1996 if (conservation == null)
1998 conservation = new AlignmentAnnotation("Conservation",
1999 MessageManager.formatMessage("label.conservation_descr",
2000 getConsPercGaps()), new Annotation[1],
2001 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2002 conservation.hasText = true;
2003 conservation.autoCalculated = true;
2004 alignment.addAnnotation(conservation);
2009 private void initQuality()
2013 if (quality == null)
2015 quality = new AlignmentAnnotation("Quality",
2016 MessageManager.getString("label.quality_descr"),
2017 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2018 quality.hasText = true;
2019 quality.autoCalculated = true;
2020 alignment.addAnnotation(quality);
2025 private void initRNAStructure()
2027 if (alignment.hasRNAStructure() && strucConsensus == null)
2029 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2030 MessageManager.getString("label.strucconsensus_descr"),
2031 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2032 strucConsensus.hasText = true;
2033 strucConsensus.autoCalculated = true;
2037 alignment.addAnnotation(strucConsensus);
2045 * @see jalview.api.AlignViewportI#calcPanelHeight()
2048 public int calcPanelHeight()
2050 // setHeight of panels
2051 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2053 int charHeight = getCharHeight();
2056 BitSet graphgrp = new BitSet();
2057 for (AlignmentAnnotation aa : anns)
2061 System.err.println("Null annotation row: ignoring.");
2068 if (aa.graphGroup > -1)
2070 if (graphgrp.get(aa.graphGroup))
2076 graphgrp.set(aa.graphGroup);
2083 aa.height += charHeight;
2093 aa.height += aa.graphHeight;
2101 height += aa.height;
2113 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2114 boolean preserveNewGroupSettings)
2116 boolean updateCalcs = false;
2117 boolean conv = isShowGroupConservation();
2118 boolean cons = isShowGroupConsensus();
2119 boolean showprf = isShowSequenceLogo();
2120 boolean showConsHist = isShowConsensusHistogram();
2121 boolean normLogo = isNormaliseSequenceLogo();
2124 * TODO reorder the annotation rows according to group/sequence ordering on
2127 boolean sortg = true;
2129 // remove old automatic annotation
2130 // add any new annotation
2132 // intersect alignment annotation with alignment groups
2134 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2135 List<SequenceGroup> oldrfs = new ArrayList<>();
2138 for (int an = 0; an < aan.length; an++)
2140 if (aan[an].autoCalculated && aan[an].groupRef != null)
2142 oldrfs.add(aan[an].groupRef);
2143 alignment.deleteAnnotation(aan[an], false);
2147 if (alignment.getGroups() != null)
2149 for (SequenceGroup sg : alignment.getGroups())
2151 updateCalcs = false;
2152 if (applyGlobalSettings
2153 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2155 // set defaults for this group's conservation/consensus
2156 sg.setshowSequenceLogo(showprf);
2157 sg.setShowConsensusHistogram(showConsHist);
2158 sg.setNormaliseSequenceLogo(normLogo);
2163 alignment.addAnnotation(sg.getConservationRow(), 0);
2168 alignment.addAnnotation(sg.getConsensus(), 0);
2170 // refresh the annotation rows
2173 sg.recalcConservation();
2181 public boolean isDisplayReferenceSeq()
2183 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2187 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2189 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2193 public boolean isColourByReferenceSeq()
2195 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2199 public Color getSequenceColour(SequenceI seq)
2201 Color sqc = sequenceColours.get(seq);
2202 return (sqc == null ? Color.white : sqc);
2206 public void setSequenceColour(SequenceI seq, Color col)
2210 sequenceColours.remove(seq);
2214 sequenceColours.put(seq, col);
2219 public void updateSequenceIdColours()
2221 for (SequenceGroup sg : alignment.getGroups())
2223 if (sg.idColour != null)
2225 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2227 sequenceColours.put(s, sg.idColour);
2234 public void clearSequenceColours()
2236 sequenceColours.clear();
2240 public AlignViewportI getCodingComplement()
2242 return this.codingComplement;
2246 * Set this as the (cDna/protein) complement of the given viewport. Also
2247 * ensures the reverse relationship is set on the given viewport.
2250 public void setCodingComplement(AlignViewportI av)
2254 System.err.println("Ignoring recursive setCodingComplement request");
2258 this.codingComplement = av;
2259 // avoid infinite recursion!
2260 if (av.getCodingComplement() != this)
2262 av.setCodingComplement(this);
2268 public boolean isNucleotide()
2270 return getAlignment() == null ? false : getAlignment().isNucleotide();
2274 public FeaturesDisplayedI getFeaturesDisplayed()
2276 return featuresDisplayed;
2280 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2282 featuresDisplayed = featuresDisplayedI;
2286 public boolean areFeaturesDisplayed()
2288 return featuresDisplayed != null
2289 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2296 * features are displayed if true
2299 public void setShowSequenceFeatures(boolean b)
2301 viewStyle.setShowSequenceFeatures(b);
2305 public boolean isShowSequenceFeatures()
2307 return viewStyle.isShowSequenceFeatures();
2311 public void setShowSequenceFeaturesHeight(boolean selected)
2313 viewStyle.setShowSequenceFeaturesHeight(selected);
2317 public boolean isShowSequenceFeaturesHeight()
2319 return viewStyle.isShowSequenceFeaturesHeight();
2323 public void setShowAnnotation(boolean b)
2325 viewStyle.setShowAnnotation(b);
2329 public boolean isShowAnnotation()
2331 return viewStyle.isShowAnnotation();
2335 public boolean isRightAlignIds()
2337 return viewStyle.isRightAlignIds();
2341 public void setRightAlignIds(boolean rightAlignIds)
2343 viewStyle.setRightAlignIds(rightAlignIds);
2347 public boolean getConservationSelected()
2349 return viewStyle.getConservationSelected();
2353 public void setShowBoxes(boolean state)
2355 viewStyle.setShowBoxes(state);
2360 * @see jalview.api.ViewStyleI#getTextColour()
2363 public Color getTextColour()
2365 return viewStyle.getTextColour();
2370 * @see jalview.api.ViewStyleI#getTextColour2()
2373 public Color getTextColour2()
2375 return viewStyle.getTextColour2();
2380 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2383 public int getThresholdTextColour()
2385 return viewStyle.getThresholdTextColour();
2390 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2393 public boolean isConservationColourSelected()
2395 return viewStyle.isConservationColourSelected();
2400 * @see jalview.api.ViewStyleI#isRenderGaps()
2403 public boolean isRenderGaps()
2405 return viewStyle.isRenderGaps();
2410 * @see jalview.api.ViewStyleI#isShowColourText()
2413 public boolean isShowColourText()
2415 return viewStyle.isShowColourText();
2419 * @param conservationColourSelected
2420 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2423 public void setConservationColourSelected(
2424 boolean conservationColourSelected)
2426 viewStyle.setConservationColourSelected(conservationColourSelected);
2430 * @param showColourText
2431 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2434 public void setShowColourText(boolean showColourText)
2436 viewStyle.setShowColourText(showColourText);
2441 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2444 public void setTextColour(Color textColour)
2446 viewStyle.setTextColour(textColour);
2450 * @param thresholdTextColour
2451 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2454 public void setThresholdTextColour(int thresholdTextColour)
2456 viewStyle.setThresholdTextColour(thresholdTextColour);
2460 * @param textColour2
2461 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2464 public void setTextColour2(Color textColour2)
2466 viewStyle.setTextColour2(textColour2);
2470 public ViewStyleI getViewStyle()
2472 return new ViewStyle(viewStyle);
2476 public void setViewStyle(ViewStyleI settingsForView)
2478 viewStyle = new ViewStyle(settingsForView);
2479 if (residueShading != null)
2481 residueShading.setConservationApplied(settingsForView
2482 .isConservationColourSelected());
2487 public boolean sameStyle(ViewStyleI them)
2489 return viewStyle.sameStyle(them);
2494 * @see jalview.api.ViewStyleI#getIdWidth()
2497 public int getIdWidth()
2499 return viewStyle.getIdWidth();
2504 * @see jalview.api.ViewStyleI#setIdWidth(int)
2507 public void setIdWidth(int i)
2509 viewStyle.setIdWidth(i);
2514 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2517 public boolean isCentreColumnLabels()
2519 return viewStyle.isCentreColumnLabels();
2523 * @param centreColumnLabels
2524 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2527 public void setCentreColumnLabels(boolean centreColumnLabels)
2529 viewStyle.setCentreColumnLabels(centreColumnLabels);
2534 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2537 public void setShowDBRefs(boolean showdbrefs)
2539 viewStyle.setShowDBRefs(showdbrefs);
2544 * @see jalview.api.ViewStyleI#isShowDBRefs()
2547 public boolean isShowDBRefs()
2549 return viewStyle.isShowDBRefs();
2554 * @see jalview.api.ViewStyleI#isShowNPFeats()
2557 public boolean isShowNPFeats()
2559 return viewStyle.isShowNPFeats();
2563 * @param shownpfeats
2564 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2567 public void setShowNPFeats(boolean shownpfeats)
2569 viewStyle.setShowNPFeats(shownpfeats);
2572 public abstract StructureSelectionManager getStructureSelectionManager();
2575 * Add one command to the command history list.
2579 public void addToHistoryList(CommandI command)
2581 if (this.historyList != null)
2583 this.historyList.push(command);
2584 broadcastCommand(command, false);
2588 protected void broadcastCommand(CommandI command, boolean undo)
2590 getStructureSelectionManager().commandPerformed(command, undo,
2595 * Add one command to the command redo list.
2599 public void addToRedoList(CommandI command)
2601 if (this.redoList != null)
2603 this.redoList.push(command);
2605 broadcastCommand(command, true);
2609 * Clear the command redo list.
2611 public void clearRedoList()
2613 if (this.redoList != null)
2615 this.redoList.clear();
2619 public void setHistoryList(Deque<CommandI> list)
2621 this.historyList = list;
2624 public Deque<CommandI> getHistoryList()
2626 return this.historyList;
2629 public void setRedoList(Deque<CommandI> list)
2631 this.redoList = list;
2634 public Deque<CommandI> getRedoList()
2636 return this.redoList;
2640 public VamsasSource getVamsasSource()
2645 public SequenceAnnotationOrder getSortAnnotationsBy()
2647 return sortAnnotationsBy;
2650 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2652 this.sortAnnotationsBy = sortAnnotationsBy;
2655 public boolean isShowAutocalculatedAbove()
2657 return showAutocalculatedAbove;
2660 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2662 this.showAutocalculatedAbove = showAutocalculatedAbove;
2666 public boolean isScaleProteinAsCdna()
2668 return viewStyle.isScaleProteinAsCdna();
2672 public void setScaleProteinAsCdna(boolean b)
2674 viewStyle.setScaleProteinAsCdna(b);
2678 public boolean isProteinFontAsCdna()
2680 return viewStyle.isProteinFontAsCdna();
2684 public void setProteinFontAsCdna(boolean b)
2686 viewStyle.setProteinFontAsCdna(b);
2690 * @return true if view should scroll to show the highlighted region of a
2695 public final boolean isFollowHighlight()
2697 return followHighlight;
2701 public final void setFollowHighlight(boolean b)
2703 this.followHighlight = b;
2707 public ViewportRanges getRanges()
2713 * Helper method to populate the SearchResults with the location in the
2714 * complementary alignment to scroll to, in order to match this one.
2717 * the SearchResults to add to
2718 * @return the offset (below top of visible region) of the matched sequence
2720 protected int findComplementScrollTarget(SearchResultsI sr)
2722 final AlignViewportI complement = getCodingComplement();
2723 if (complement == null || !complement.isFollowHighlight())
2727 boolean iAmProtein = !getAlignment().isNucleotide();
2728 AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
2730 if (proteinAlignment == null)
2734 final List<AlignedCodonFrame> mappings = proteinAlignment
2738 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2739 * residue in the middle column of the visible region. Scroll the
2740 * complementary alignment to line up the corresponding residue.
2743 SequenceI sequence = null;
2746 * locate 'middle' column (true middle if an odd number visible, left of
2747 * middle if an even number visible)
2749 int middleColumn = ranges.getStartRes()
2750 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2751 final HiddenSequences hiddenSequences = getAlignment()
2752 .getHiddenSequences();
2755 * searching to the bottom of the alignment gives smoother scrolling across
2756 * all gapped visible regions
2758 int lastSeq = alignment.getHeight() - 1;
2759 List<AlignedCodonFrame> seqMappings = null;
2760 for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
2762 sequence = getAlignment().getSequenceAt(seqNo);
2763 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2767 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2771 seqMappings = MappingUtils
2772 .findMappingsForSequenceAndOthers(sequence, mappings,
2773 getCodingComplement().getAlignment().getSequences());
2774 if (!seqMappings.isEmpty())
2780 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2783 * No ungapped mapped sequence in middle column - do nothing
2787 MappingUtils.addSearchResults(sr, sequence,
2788 sequence.findPosition(middleColumn), seqMappings);
2793 * synthesize a column selection if none exists so it covers the given
2794 * selection group. if wholewidth is false, no column selection is made if the
2795 * selection group covers the whole alignment width.
2800 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2803 if (sg != null && (sgs = sg.getStartRes()) >= 0
2804 && sg.getStartRes() <= (sge = sg.getEndRes())
2805 && !this.hasSelectedColumns())
2807 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2814 colSel = new ColumnSelection();
2816 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2818 colSel.addElement(cspos);
2824 * hold status of current selection group - defined on alignment or not.
2826 private boolean selectionIsDefinedGroup = false;
2829 public boolean isSelectionDefinedGroup()
2831 if (selectionGroup == null)
2835 if (isSelectionGroupChanged(true))
2837 selectionIsDefinedGroup = false;
2838 List<SequenceGroup> gps = alignment.getGroups();
2839 if (gps == null || gps.size() == 0)
2841 selectionIsDefinedGroup = false;
2845 selectionIsDefinedGroup = gps.contains(selectionGroup);
2848 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2852 * null, or currently highlighted results on this view
2854 private SearchResultsI searchResults = null;
2857 public boolean hasSearchResults()
2859 return searchResults != null;
2863 public void setSearchResults(SearchResultsI results)
2865 searchResults = results;
2869 public SearchResultsI getSearchResults()
2871 return searchResults;