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<>();
101 * alignment displayed in the viewport. Please use get/setter
103 protected AlignmentI alignment;
105 public AlignmentViewport(AlignmentI al)
108 ranges = new ViewportRanges(al);
113 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
116 public void setFontName(String name)
118 viewStyle.setFontName(name);
123 * @see jalview.api.ViewStyleI#setFontStyle(int)
126 public void setFontStyle(int style)
128 viewStyle.setFontStyle(style);
133 * @see jalview.api.ViewStyleI#setFontSize(int)
136 public void setFontSize(int size)
138 viewStyle.setFontSize(size);
143 * @see jalview.api.ViewStyleI#getFontStyle()
146 public int getFontStyle()
148 return viewStyle.getFontStyle();
153 * @see jalview.api.ViewStyleI#getFontName()
156 public String getFontName()
158 return viewStyle.getFontName();
163 * @see jalview.api.ViewStyleI#getFontSize()
166 public int getFontSize()
168 return viewStyle.getFontSize();
172 * @param upperCasebold
173 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
176 public void setUpperCasebold(boolean upperCasebold)
178 viewStyle.setUpperCasebold(upperCasebold);
183 * @see jalview.api.ViewStyleI#isUpperCasebold()
186 public boolean isUpperCasebold()
188 return viewStyle.isUpperCasebold();
193 * @see jalview.api.ViewStyleI#isSeqNameItalics()
196 public boolean isSeqNameItalics()
198 return viewStyle.isSeqNameItalics();
202 * @param colourByReferenceSeq
203 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
206 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
208 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
213 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
216 public void setColourAppliesToAllGroups(boolean b)
218 viewStyle.setColourAppliesToAllGroups(b);
223 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
226 public boolean getColourAppliesToAllGroups()
228 return viewStyle.getColourAppliesToAllGroups();
233 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
236 public boolean getAbovePIDThreshold()
238 return viewStyle.getAbovePIDThreshold();
243 * @see jalview.api.ViewStyleI#setIncrement(int)
246 public void setIncrement(int inc)
248 viewStyle.setIncrement(inc);
253 * @see jalview.api.ViewStyleI#getIncrement()
256 public int getIncrement()
258 return viewStyle.getIncrement();
263 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
266 public void setConservationSelected(boolean b)
268 viewStyle.setConservationSelected(b);
273 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
276 public void setShowHiddenMarkers(boolean show)
278 viewStyle.setShowHiddenMarkers(show);
283 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
286 public boolean getShowHiddenMarkers()
288 return viewStyle.getShowHiddenMarkers();
293 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
296 public void setScaleRightWrapped(boolean b)
298 viewStyle.setScaleRightWrapped(b);
303 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
306 public void setScaleLeftWrapped(boolean b)
308 viewStyle.setScaleLeftWrapped(b);
313 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
316 public void setScaleAboveWrapped(boolean b)
318 viewStyle.setScaleAboveWrapped(b);
323 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
326 public boolean getScaleLeftWrapped()
328 return viewStyle.getScaleLeftWrapped();
333 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
336 public boolean getScaleAboveWrapped()
338 return viewStyle.getScaleAboveWrapped();
343 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
346 public boolean getScaleRightWrapped()
348 return viewStyle.getScaleRightWrapped();
353 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
356 public void setAbovePIDThreshold(boolean b)
358 viewStyle.setAbovePIDThreshold(b);
363 * @see jalview.api.ViewStyleI#setThreshold(int)
366 public void setThreshold(int thresh)
368 viewStyle.setThreshold(thresh);
373 * @see jalview.api.ViewStyleI#getThreshold()
376 public int getThreshold()
378 return viewStyle.getThreshold();
383 * @see jalview.api.ViewStyleI#getShowJVSuffix()
386 public boolean getShowJVSuffix()
388 return viewStyle.getShowJVSuffix();
393 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
396 public void setShowJVSuffix(boolean b)
398 viewStyle.setShowJVSuffix(b);
403 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
406 public void setWrapAlignment(boolean state)
408 viewStyle.setWrapAlignment(state);
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;
700 protected AlignmentAnnotation hmmConsensus;
703 * results of alignment consensus analysis for visible portion of view
705 protected ProfilesI hconsensus = null;
708 * results of cDNA complement consensus visible portion of view
710 protected Hashtable[] hcomplementConsensus = null;
713 * results of secondary structure base pair consensus for visible portion of
716 protected Hashtable[] hStrucConsensus = null;
718 protected Conservation hconservation = null;
721 public void setConservation(Conservation cons)
723 hconservation = cons;
727 * percentage gaps allowed in a column before all amino acid properties should
728 * be considered unconserved
730 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
733 public int getConsPercGaps()
739 public void setSequenceConsensusHash(ProfilesI hconsensus)
741 this.hconsensus = hconsensus;
745 public void setComplementConsensusHash(Hashtable[] hconsensus)
747 this.hcomplementConsensus = hconsensus;
751 public ProfilesI getSequenceConsensusHash()
757 public Hashtable[] getComplementConsensusHash()
759 return hcomplementConsensus;
763 public Hashtable[] getRnaStructureConsensusHash()
765 return hStrucConsensus;
769 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
771 this.hStrucConsensus = hStrucConsensus;
776 public AlignmentAnnotation getAlignmentQualityAnnot()
782 public AlignmentAnnotation getAlignmentConservationAnnotation()
788 public AlignmentAnnotation getAlignmentConsensusAnnotation()
794 public AlignmentAnnotation getAlignmentGapAnnotation()
800 public AlignmentAnnotation getComplementConsensusAnnotation()
802 return complementConsensus;
806 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
808 return strucConsensus;
811 protected AlignCalcManagerI calculator = new AlignCalcManager();
814 * trigger update of conservation annotation
816 public void updateConservation(final AlignmentViewPanel ap)
818 // see note in mantis : issue number 8585
819 if (alignment.isNucleotide()
820 || (conservation == null && quality == null)
821 || !autoCalculateConsensus)
826 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
828 calculator.registerWorker(new jalview.workers.ConservationThread(
834 * trigger update of consensus annotation
836 public void updateConsensus(final AlignmentViewPanel ap)
838 // see note in mantis : issue number 8585
839 if (consensus == null || !autoCalculateConsensus)
843 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
845 calculator.registerWorker(new ConsensusThread(this, ap));
849 * A separate thread to compute cDNA consensus for a protein alignment
850 * which has mapping to cDNA
852 final AlignmentI al = this.getAlignment();
853 if (!al.isNucleotide() && al.getCodonFrames() != null
854 && !al.getCodonFrames().isEmpty())
857 * fudge - check first for protein-to-nucleotide mappings
858 * (we don't want to do this for protein-to-protein)
860 boolean doConsensus = false;
861 for (AlignedCodonFrame mapping : al.getCodonFrames())
863 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
864 MapList[] mapLists = mapping.getdnaToProt();
865 // mapLists can be empty if project load has not finished resolving seqs
866 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
875 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
878 .registerWorker(new ComplementConsensusThread(this, ap));
884 // --------START Structure Conservation
885 public void updateStrucConsensus(final AlignmentViewPanel ap)
887 if (autoCalculateStrucConsensus && strucConsensus == null
888 && alignment.isNucleotide() && alignment.hasRNAStructure())
890 // secondary structure has been added - so init the consensus line
894 // see note in mantis : issue number 8585
895 if (strucConsensus == null || !autoCalculateStrucConsensus)
899 if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
901 calculator.registerWorker(new StrucConsensusThread(this, ap));
905 public boolean isCalcInProgress()
907 return calculator.isWorking();
911 public boolean isCalculationInProgress(
912 AlignmentAnnotation alignmentAnnotation)
914 if (!alignmentAnnotation.autoCalculated)
918 if (calculator.workingInvolvedWith(alignmentAnnotation))
920 // System.err.println("grey out ("+alignmentAnnotation.label+")");
926 public void setAlignment(AlignmentI align)
928 this.alignment = align;
932 * Clean up references when this viewport is closed
935 public void dispose()
938 * defensively null out references to large objects in case
939 * this object is not garbage collected (as if!)
942 complementConsensus = null;
943 strucConsensus = null;
946 groupConsensus = null;
947 groupConservation = null;
949 hcomplementConsensus = null;
950 // colour scheme may hold reference to consensus
951 residueShading = null;
952 // TODO remove listeners from changeSupport?
953 changeSupport = null;
958 public boolean isClosed()
960 // TODO: check that this isClosed is only true after panel is closed, not
961 // before it is fully constructed.
962 return alignment == null;
966 public AlignCalcManagerI getCalcManager()
972 * should conservation rows be shown for groups
974 protected boolean showGroupConservation = false;
977 * should consensus rows be shown for groups
979 protected boolean showGroupConsensus = false;
982 * should consensus profile be rendered by default
984 protected boolean showSequenceLogo = false;
987 * should consensus profile be rendered normalised to row height
989 protected boolean normaliseSequenceLogo = false;
992 * should consensus histograms be rendered by default
994 protected boolean showConsensusHistogram = true;
997 * @return the showConsensusProfile
1000 public boolean isShowSequenceLogo()
1002 return showSequenceLogo;
1006 * @param showSequenceLogo
1009 public void setShowSequenceLogo(boolean showSequenceLogo)
1011 if (showSequenceLogo != this.showSequenceLogo)
1013 // TODO: decouple settings setting from calculation when refactoring
1014 // annotation update method from alignframe to viewport
1015 this.showSequenceLogo = showSequenceLogo;
1016 calculator.updateAnnotationFor(ConsensusThread.class);
1017 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1018 calculator.updateAnnotationFor(StrucConsensusThread.class);
1020 this.showSequenceLogo = showSequenceLogo;
1024 * @param showConsensusHistogram
1025 * the showConsensusHistogram to set
1027 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1029 this.showConsensusHistogram = showConsensusHistogram;
1033 * @return the showGroupConservation
1035 public boolean isShowGroupConservation()
1037 return showGroupConservation;
1041 * @param showGroupConservation
1042 * the showGroupConservation to set
1044 public void setShowGroupConservation(boolean showGroupConservation)
1046 this.showGroupConservation = showGroupConservation;
1050 * @return the showGroupConsensus
1052 public boolean isShowGroupConsensus()
1054 return showGroupConsensus;
1058 * @param showGroupConsensus
1059 * the showGroupConsensus to set
1061 public void setShowGroupConsensus(boolean showGroupConsensus)
1063 this.showGroupConsensus = showGroupConsensus;
1068 * @return flag to indicate if the consensus histogram should be rendered by
1072 public boolean isShowConsensusHistogram()
1074 return this.showConsensusHistogram;
1078 * when set, updateAlignment will always ensure sequences are of equal length
1080 private boolean padGaps = false;
1083 * when set, alignment should be reordered according to a newly opened tree
1085 public boolean sortByTree = false;
1090 * @return null or the currently selected sequence region
1093 public SequenceGroup getSelectionGroup()
1095 return selectionGroup;
1099 * Set the selection group for this window. Also sets the current alignment as
1100 * the context for the group, if it does not already have one.
1103 * - group holding references to sequences in this alignment view
1107 public void setSelectionGroup(SequenceGroup sg)
1109 selectionGroup = sg;
1110 if (sg != null && sg.getContext() == null)
1112 sg.setContext(alignment);
1116 public void setHiddenColumns(HiddenColumns hidden)
1118 this.alignment.setHiddenColumns(hidden);
1122 public ColumnSelection getColumnSelection()
1128 public void setColumnSelection(ColumnSelection colSel)
1130 this.colSel = colSel;
1133 updateHiddenColumns();
1135 isColSelChanged(true);
1143 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1145 return hiddenRepSequences;
1149 public void setHiddenRepSequences(
1150 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1152 this.hiddenRepSequences = hiddenRepSequences;
1156 public boolean hasSelectedColumns()
1158 ColumnSelection columnSelection = getColumnSelection();
1159 return columnSelection != null && columnSelection.hasSelectedColumns();
1163 public boolean hasHiddenColumns()
1165 return colSel != null
1166 && alignment.getHiddenColumns().hasHiddenColumns();
1169 public void updateHiddenColumns()
1171 // this method doesn't really do anything now. But - it could, since a
1172 // column Selection could be in the process of modification
1173 // hasHiddenColumns = colSel.hasHiddenColumns();
1177 public boolean hasHiddenRows()
1179 return alignment.getHiddenSequences().getSize() > 0;
1182 protected SequenceGroup selectionGroup;
1184 public void setSequenceSetId(String newid)
1186 if (sequenceSetID != null)
1189 .println("Warning - overwriting a sequenceSetId for a viewport!");
1191 sequenceSetID = new String(newid);
1195 public String getSequenceSetId()
1197 if (sequenceSetID == null)
1199 sequenceSetID = alignment.hashCode() + "";
1202 return sequenceSetID;
1206 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1209 protected String viewId = null;
1212 public String getViewId()
1216 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1221 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1223 ignoreGapsInConsensusCalculation = b;
1226 updateConsensus(ap);
1227 if (residueShading != null)
1229 residueShading.setThreshold(residueShading.getThreshold(),
1230 ignoreGapsInConsensusCalculation);
1236 private long sgrouphash = -1, colselhash = -1;
1239 * checks current SelectionGroup against record of last hash value, and
1243 * update the record of last hash value
1245 * @return true if SelectionGroup changed since last call (when b is true)
1247 public boolean isSelectionGroupChanged(boolean b)
1249 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1250 : selectionGroup.hashCode();
1251 if (hc != -1 && hc != sgrouphash)
1263 * checks current colsel against record of last hash value, and optionally
1267 * update the record of last hash value
1268 * @return true if colsel changed since last call (when b is true)
1270 public boolean isColSelChanged(boolean b)
1272 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1273 if (hc != -1 && hc != colselhash)
1285 public boolean isIgnoreGapsConsensus()
1287 return ignoreGapsInConsensusCalculation;
1290 // property change stuff
1291 // JBPNote Prolly only need this in the applet version.
1292 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1295 protected boolean showConservation = true;
1297 protected boolean showQuality = true;
1299 protected boolean showConsensus = true;
1301 protected boolean showOccupancy = true;
1303 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1305 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1307 protected boolean showAutocalculatedAbove;
1310 * when set, view will scroll to show the highlighted position
1312 private boolean followHighlight = true;
1315 * Property change listener for changes in alignment
1320 public void addPropertyChangeListener(
1321 java.beans.PropertyChangeListener listener)
1323 changeSupport.addPropertyChangeListener(listener);
1332 public void removePropertyChangeListener(
1333 java.beans.PropertyChangeListener listener)
1335 changeSupport.removePropertyChangeListener(listener);
1339 * Property change listener for changes in alignment
1348 public void firePropertyChange(String prop, Object oldvalue,
1351 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1354 // common hide/show column stuff
1356 public void hideSelectedColumns()
1358 if (colSel.isEmpty())
1363 colSel.hideSelectedColumns(alignment);
1364 setSelectionGroup(null);
1365 isColSelChanged(true);
1368 public void hideColumns(int start, int end)
1372 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1376 alignment.getHiddenColumns().hideColumns(start, end);
1378 isColSelChanged(true);
1381 public void showColumn(int col)
1383 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1384 isColSelChanged(true);
1387 public void showAllHiddenColumns()
1389 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1390 isColSelChanged(true);
1393 // common hide/show seq stuff
1394 public void showAllHiddenSeqs()
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 firePropertyChange("alignment", null, alignment.getSequences());
1414 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1420 public void showSequence(int index)
1422 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1423 index, hiddenRepSequences);
1426 if (selectionGroup == null)
1428 selectionGroup = new SequenceGroup();
1429 selectionGroup.setEndRes(alignment.getWidth() - 1);
1432 for (SequenceI seq : tmp)
1434 selectionGroup.addSequence(seq, false);
1435 setSequenceAnnotationsVisible(seq, true);
1437 firePropertyChange("alignment", null, alignment.getSequences());
1442 public void hideAllSelectedSeqs()
1444 if (selectionGroup == null || selectionGroup.getSize() < 1)
1449 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1453 setSelectionGroup(null);
1456 public void hideSequence(SequenceI[] seq)
1460 for (int i = 0; i < seq.length; i++)
1462 alignment.getHiddenSequences().hideSequence(seq[i]);
1463 setSequenceAnnotationsVisible(seq[i], false);
1465 firePropertyChange("alignment", null, alignment.getSequences());
1470 * Hides the specified sequence, or the sequences it represents
1473 * the sequence to hide, or keep as representative
1474 * @param representGroup
1475 * if true, hide the current selection group except for the
1476 * representative sequence
1478 public void hideSequences(SequenceI sequence, boolean representGroup)
1480 if (selectionGroup == null || selectionGroup.getSize() < 1)
1482 hideSequence(new SequenceI[] { sequence });
1488 hideRepSequences(sequence, selectionGroup);
1489 setSelectionGroup(null);
1493 int gsize = selectionGroup.getSize();
1494 SequenceI[] hseqs = selectionGroup.getSequences().toArray(
1495 new SequenceI[gsize]);
1497 hideSequence(hseqs);
1498 setSelectionGroup(null);
1503 * Set visibility for any annotations for the given sequence.
1507 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1510 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1513 for (AlignmentAnnotation ann : anns)
1515 if (ann.sequenceRef == sequenceI)
1517 ann.visible = visible;
1523 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1525 int sSize = sg.getSize();
1531 if (hiddenRepSequences == null)
1533 hiddenRepSequences = new Hashtable<>();
1536 hiddenRepSequences.put(repSequence, sg);
1538 // Hide all sequences except the repSequence
1539 SequenceI[] seqs = new SequenceI[sSize - 1];
1541 for (int i = 0; i < sSize; i++)
1543 if (sg.getSequenceAt(i) != repSequence)
1545 if (index == sSize - 1)
1550 seqs[index++] = sg.getSequenceAt(i);
1553 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1554 sg.setHidereps(true); // note: not done in 2.7applet
1561 * @return null or the current reference sequence
1563 public SequenceI getReferenceSeq()
1565 return alignment.getSeqrep();
1570 * @return true iff seq is the reference for the alignment
1572 public boolean isReferenceSeq(SequenceI seq)
1574 return alignment.getSeqrep() == seq;
1580 * @return true if there are sequences represented by this sequence that are
1583 public boolean isHiddenRepSequence(SequenceI seq)
1585 return (hiddenRepSequences != null && hiddenRepSequences
1592 * @return null or a sequence group containing the sequences that seq
1595 public SequenceGroup getRepresentedSequences(SequenceI seq)
1597 return (SequenceGroup) (hiddenRepSequences == null ? null
1598 : hiddenRepSequences.get(seq));
1602 public int adjustForHiddenSeqs(int alignmentIndex)
1604 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1609 public void invertColumnSelection()
1611 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1615 public SequenceI[] getSelectionAsNewSequence()
1617 SequenceI[] sequences;
1618 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1619 // this was the only caller in the applet for this method
1620 // JBPNote: in applet, this method returned references to the alignment
1621 // sequences, and it did not honour the presence/absence of annotation
1622 // attached to the alignment (probably!)
1623 if (selectionGroup == null || selectionGroup.getSize() == 0)
1625 sequences = alignment.getSequencesArray();
1626 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1627 for (int i = 0; i < sequences.length; i++)
1629 // construct new sequence with subset of visible annotation
1630 sequences[i] = new Sequence(sequences[i], annots);
1635 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1642 public SequenceI[] getSequenceSelection()
1644 SequenceI[] sequences = null;
1645 if (selectionGroup != null)
1647 sequences = selectionGroup.getSequencesInOrder(alignment);
1649 if (sequences == null)
1651 sequences = alignment.getSequencesArray();
1657 public CigarArray getViewAsCigars(boolean selectedRegionOnly)
1659 return new CigarArray(alignment, alignment.getHiddenColumns(),
1660 (selectedRegionOnly ? selectionGroup : null));
1664 public jalview.datamodel.AlignmentView getAlignmentView(
1665 boolean selectedOnly)
1667 return getAlignmentView(selectedOnly, false);
1671 public jalview.datamodel.AlignmentView getAlignmentView(
1672 boolean selectedOnly, boolean markGroups)
1674 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1675 selectionGroup, alignment.getHiddenColumns() != null
1676 && alignment.getHiddenColumns().hasHiddenColumns(),
1682 public String[] getViewAsString(boolean selectedRegionOnly)
1684 return getViewAsString(selectedRegionOnly, true);
1688 public String[] getViewAsString(boolean selectedRegionOnly,
1689 boolean exportHiddenSeqs)
1691 String[] selection = null;
1692 SequenceI[] seqs = null;
1694 int start = 0, end = 0;
1695 if (selectedRegionOnly && selectionGroup != null)
1697 iSize = selectionGroup.getSize();
1698 seqs = selectionGroup.getSequencesInOrder(alignment);
1699 start = selectionGroup.getStartRes();
1700 end = selectionGroup.getEndRes() + 1;
1704 if (hasHiddenRows() && exportHiddenSeqs)
1706 AlignmentI fullAlignment = alignment.getHiddenSequences()
1707 .getFullAlignment();
1708 iSize = fullAlignment.getHeight();
1709 seqs = fullAlignment.getSequencesArray();
1710 end = fullAlignment.getWidth();
1714 iSize = alignment.getHeight();
1715 seqs = alignment.getSequencesArray();
1716 end = alignment.getWidth();
1720 selection = new String[iSize];
1721 if (alignment.getHiddenColumns() != null
1722 && alignment.getHiddenColumns().hasHiddenColumns())
1724 selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
1729 for (i = 0; i < iSize; i++)
1731 selection[i] = seqs[i].getSequenceAsString(start, end);
1739 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1741 ArrayList<int[]> regions = new ArrayList<>();
1747 HiddenColumns hidden = alignment.getHiddenColumns();
1748 if (hidden != null && hidden.hasHiddenColumns())
1752 start = hidden.adjustForHiddenColumns(start);
1755 end = hidden.getHiddenBoundaryRight(start);
1766 regions.add(new int[] { start, end });
1768 if (hidden != null && hidden.hasHiddenColumns())
1770 start = hidden.adjustForHiddenColumns(end);
1771 start = hidden.getHiddenBoundaryLeft(start) + 1;
1773 } while (end < max);
1775 int[][] startEnd = new int[regions.size()][2];
1781 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1782 boolean selectedOnly)
1784 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1785 AlignmentAnnotation[] aa;
1786 if ((aa = alignment.getAlignmentAnnotation()) != null)
1788 for (AlignmentAnnotation annot : aa)
1790 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1791 if (selectedOnly && selectionGroup != null)
1793 alignment.getHiddenColumns().makeVisibleAnnotation(
1794 selectionGroup.getStartRes(),
1795 selectionGroup.getEndRes(), clone);
1799 alignment.getHiddenColumns().makeVisibleAnnotation(clone);
1808 public boolean isPadGaps()
1814 public void setPadGaps(boolean padGaps)
1816 this.padGaps = padGaps;
1820 * apply any post-edit constraints and trigger any calculations needed after
1821 * an edit has been performed on the alignment
1826 public void alignmentChanged(AlignmentViewPanel ap)
1830 alignment.padGaps();
1832 if (autoCalculateConsensus)
1834 updateConsensus(ap);
1836 if (hconsensus != null && autoCalculateConsensus)
1838 updateConservation(ap);
1840 if (autoCalculateStrucConsensus)
1842 updateStrucConsensus(ap);
1845 // Reset endRes of groups if beyond alignment width
1846 int alWidth = alignment.getWidth();
1847 List<SequenceGroup> groups = alignment.getGroups();
1850 for (SequenceGroup sg : groups)
1852 if (sg.getEndRes() > alWidth)
1854 sg.setEndRes(alWidth - 1);
1859 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1861 selectionGroup.setEndRes(alWidth - 1);
1864 updateAllColourSchemes();
1865 calculator.restartWorkers();
1866 // alignment.adjustSequenceAnnotations();
1870 * reset scope and do calculations for all applied colourschemes on alignment
1872 void updateAllColourSchemes()
1874 ResidueShaderI rs = residueShading;
1877 rs.alignmentChanged(alignment, hiddenRepSequences);
1879 rs.setConsensus(hconsensus);
1880 if (rs.conservationApplied())
1882 rs.setConservation(Conservation.calculateConservation("All",
1883 alignment.getSequences(), 0, alignment.getWidth(), false,
1884 getConsPercGaps(), false));
1888 for (SequenceGroup sg : alignment.getGroups())
1892 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1894 sg.recalcConservation();
1898 protected void initAutoAnnotation()
1900 // TODO: add menu option action that nulls or creates consensus object
1901 // depending on if the user wants to see the annotation or not in a
1902 // specific alignment
1904 if (hconsensus == null && !isDataset)
1906 if (!alignment.isNucleotide())
1915 consensus = new AlignmentAnnotation("Consensus",
1916 MessageManager.getString("label.consensus_descr"),
1917 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1918 initConsensus(consensus);
1922 initComplementConsensus();
1927 * If this is a protein alignment and there are mappings to cDNA, adds the
1928 * cDNA consensus annotation and returns true, else returns false.
1930 public boolean initComplementConsensus()
1932 if (!alignment.isNucleotide())
1934 final List<AlignedCodonFrame> codonMappings = alignment
1936 if (codonMappings != null && !codonMappings.isEmpty())
1938 boolean doConsensus = false;
1939 for (AlignedCodonFrame mapping : codonMappings)
1941 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1942 MapList[] mapLists = mapping.getdnaToProt();
1943 // mapLists can be empty if project load has not finished resolving
1945 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1953 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1955 .getString("label.complement_consensus_descr"),
1956 new Annotation[1], 0f, 100f,
1957 AlignmentAnnotation.BAR_GRAPH);
1958 initConsensus(complementConsensus);
1966 private void initConsensus(AlignmentAnnotation aa)
1969 aa.autoCalculated = true;
1973 alignment.addAnnotation(aa);
1977 // these should be extracted from the view model - style and settings for
1978 // derived annotation
1979 private void initGapCounts()
1983 gapcounts = new AlignmentAnnotation("Occupancy",
1984 MessageManager.getString("label.occupancy_descr"),
1985 new Annotation[1], 0f,
1986 alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
1987 gapcounts.hasText = true;
1988 gapcounts.autoCalculated = true;
1989 gapcounts.scaleColLabel = true;
1990 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
1992 alignment.addAnnotation(gapcounts);
1996 private void initConservation()
1998 if (showConservation)
2000 if (conservation == null)
2002 conservation = new AlignmentAnnotation("Conservation",
2003 MessageManager.formatMessage("label.conservation_descr",
2004 getConsPercGaps()), new Annotation[1],
2005 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2006 conservation.hasText = true;
2007 conservation.autoCalculated = true;
2008 alignment.addAnnotation(conservation);
2013 private void initQuality()
2017 if (quality == null)
2019 quality = new AlignmentAnnotation("Quality",
2020 MessageManager.getString("label.quality_descr"),
2021 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2022 quality.hasText = true;
2023 quality.autoCalculated = true;
2024 alignment.addAnnotation(quality);
2029 private void initRNAStructure()
2031 if (alignment.hasRNAStructure() && strucConsensus == null)
2033 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2034 MessageManager.getString("label.strucconsensus_descr"),
2035 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2036 strucConsensus.hasText = true;
2037 strucConsensus.autoCalculated = true;
2041 alignment.addAnnotation(strucConsensus);
2049 * @see jalview.api.AlignViewportI#calcPanelHeight()
2052 public int calcPanelHeight()
2054 // setHeight of panels
2055 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2057 int charHeight = getCharHeight();
2060 BitSet graphgrp = new BitSet();
2061 for (AlignmentAnnotation aa : anns)
2065 System.err.println("Null annotation row: ignoring.");
2072 if (aa.graphGroup > -1)
2074 if (graphgrp.get(aa.graphGroup))
2080 graphgrp.set(aa.graphGroup);
2087 aa.height += charHeight;
2097 aa.height += aa.graphHeight;
2105 height += aa.height;
2117 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2118 boolean preserveNewGroupSettings)
2120 boolean updateCalcs = false;
2121 boolean conv = isShowGroupConservation();
2122 boolean cons = isShowGroupConsensus();
2123 boolean showprf = isShowSequenceLogo();
2124 boolean showConsHist = isShowConsensusHistogram();
2125 boolean normLogo = isNormaliseSequenceLogo();
2128 * TODO reorder the annotation rows according to group/sequence ordering on
2131 boolean sortg = true;
2133 // remove old automatic annotation
2134 // add any new annotation
2136 // intersect alignment annotation with alignment groups
2138 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2139 List<SequenceGroup> oldrfs = new ArrayList<>();
2142 for (int an = 0; an < aan.length; an++)
2144 if (aan[an].autoCalculated && aan[an].groupRef != null)
2146 oldrfs.add(aan[an].groupRef);
2147 alignment.deleteAnnotation(aan[an], false);
2151 if (alignment.getGroups() != null)
2153 for (SequenceGroup sg : alignment.getGroups())
2155 updateCalcs = false;
2156 if (applyGlobalSettings
2157 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2159 // set defaults for this group's conservation/consensus
2160 sg.setshowSequenceLogo(showprf);
2161 sg.setShowConsensusHistogram(showConsHist);
2162 sg.setNormaliseSequenceLogo(normLogo);
2167 alignment.addAnnotation(sg.getConservationRow(), 0);
2172 alignment.addAnnotation(sg.getConsensus(), 0);
2174 // refresh the annotation rows
2177 sg.recalcConservation();
2185 public boolean isDisplayReferenceSeq()
2187 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2191 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2193 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2197 public boolean isColourByReferenceSeq()
2199 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2203 public Color getSequenceColour(SequenceI seq)
2205 Color sqc = sequenceColours.get(seq);
2206 return (sqc == null ? Color.white : sqc);
2210 public void setSequenceColour(SequenceI seq, Color col)
2214 sequenceColours.remove(seq);
2218 sequenceColours.put(seq, col);
2223 public void updateSequenceIdColours()
2225 for (SequenceGroup sg : alignment.getGroups())
2227 if (sg.idColour != null)
2229 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2231 sequenceColours.put(s, sg.idColour);
2238 public void clearSequenceColours()
2240 sequenceColours.clear();
2244 public AlignViewportI getCodingComplement()
2246 return this.codingComplement;
2250 * Set this as the (cDna/protein) complement of the given viewport. Also
2251 * ensures the reverse relationship is set on the given viewport.
2254 public void setCodingComplement(AlignViewportI av)
2258 System.err.println("Ignoring recursive setCodingComplement request");
2262 this.codingComplement = av;
2263 // avoid infinite recursion!
2264 if (av.getCodingComplement() != this)
2266 av.setCodingComplement(this);
2272 public boolean isNucleotide()
2274 return getAlignment() == null ? false : getAlignment().isNucleotide();
2278 public FeaturesDisplayedI getFeaturesDisplayed()
2280 return featuresDisplayed;
2284 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2286 featuresDisplayed = featuresDisplayedI;
2290 public boolean areFeaturesDisplayed()
2292 return featuresDisplayed != null
2293 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2300 * features are displayed if true
2303 public void setShowSequenceFeatures(boolean b)
2305 viewStyle.setShowSequenceFeatures(b);
2309 public boolean isShowSequenceFeatures()
2311 return viewStyle.isShowSequenceFeatures();
2315 public void setShowSequenceFeaturesHeight(boolean selected)
2317 viewStyle.setShowSequenceFeaturesHeight(selected);
2321 public boolean isShowSequenceFeaturesHeight()
2323 return viewStyle.isShowSequenceFeaturesHeight();
2327 public void setShowAnnotation(boolean b)
2329 viewStyle.setShowAnnotation(b);
2333 public boolean isShowAnnotation()
2335 return viewStyle.isShowAnnotation();
2339 public boolean isRightAlignIds()
2341 return viewStyle.isRightAlignIds();
2345 public void setRightAlignIds(boolean rightAlignIds)
2347 viewStyle.setRightAlignIds(rightAlignIds);
2351 public boolean getConservationSelected()
2353 return viewStyle.getConservationSelected();
2357 public void setShowBoxes(boolean state)
2359 viewStyle.setShowBoxes(state);
2364 * @see jalview.api.ViewStyleI#getTextColour()
2367 public Color getTextColour()
2369 return viewStyle.getTextColour();
2374 * @see jalview.api.ViewStyleI#getTextColour2()
2377 public Color getTextColour2()
2379 return viewStyle.getTextColour2();
2384 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2387 public int getThresholdTextColour()
2389 return viewStyle.getThresholdTextColour();
2394 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2397 public boolean isConservationColourSelected()
2399 return viewStyle.isConservationColourSelected();
2404 * @see jalview.api.ViewStyleI#isRenderGaps()
2407 public boolean isRenderGaps()
2409 return viewStyle.isRenderGaps();
2414 * @see jalview.api.ViewStyleI#isShowColourText()
2417 public boolean isShowColourText()
2419 return viewStyle.isShowColourText();
2423 * @param conservationColourSelected
2424 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2427 public void setConservationColourSelected(
2428 boolean conservationColourSelected)
2430 viewStyle.setConservationColourSelected(conservationColourSelected);
2434 * @param showColourText
2435 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2438 public void setShowColourText(boolean showColourText)
2440 viewStyle.setShowColourText(showColourText);
2445 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2448 public void setTextColour(Color textColour)
2450 viewStyle.setTextColour(textColour);
2454 * @param thresholdTextColour
2455 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2458 public void setThresholdTextColour(int thresholdTextColour)
2460 viewStyle.setThresholdTextColour(thresholdTextColour);
2464 * @param textColour2
2465 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2468 public void setTextColour2(Color textColour2)
2470 viewStyle.setTextColour2(textColour2);
2474 public ViewStyleI getViewStyle()
2476 return new ViewStyle(viewStyle);
2480 public void setViewStyle(ViewStyleI settingsForView)
2482 viewStyle = new ViewStyle(settingsForView);
2483 if (residueShading != null)
2485 residueShading.setConservationApplied(settingsForView
2486 .isConservationColourSelected());
2491 public boolean sameStyle(ViewStyleI them)
2493 return viewStyle.sameStyle(them);
2498 * @see jalview.api.ViewStyleI#getIdWidth()
2501 public int getIdWidth()
2503 return viewStyle.getIdWidth();
2508 * @see jalview.api.ViewStyleI#setIdWidth(int)
2511 public void setIdWidth(int i)
2513 viewStyle.setIdWidth(i);
2518 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2521 public boolean isCentreColumnLabels()
2523 return viewStyle.isCentreColumnLabels();
2527 * @param centreColumnLabels
2528 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2531 public void setCentreColumnLabels(boolean centreColumnLabels)
2533 viewStyle.setCentreColumnLabels(centreColumnLabels);
2538 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2541 public void setShowDBRefs(boolean showdbrefs)
2543 viewStyle.setShowDBRefs(showdbrefs);
2548 * @see jalview.api.ViewStyleI#isShowDBRefs()
2551 public boolean isShowDBRefs()
2553 return viewStyle.isShowDBRefs();
2558 * @see jalview.api.ViewStyleI#isShowNPFeats()
2561 public boolean isShowNPFeats()
2563 return viewStyle.isShowNPFeats();
2567 * @param shownpfeats
2568 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2571 public void setShowNPFeats(boolean shownpfeats)
2573 viewStyle.setShowNPFeats(shownpfeats);
2576 public abstract StructureSelectionManager getStructureSelectionManager();
2579 * Add one command to the command history list.
2583 public void addToHistoryList(CommandI command)
2585 if (this.historyList != null)
2587 this.historyList.push(command);
2588 broadcastCommand(command, false);
2592 protected void broadcastCommand(CommandI command, boolean undo)
2594 getStructureSelectionManager().commandPerformed(command, undo,
2599 * Add one command to the command redo list.
2603 public void addToRedoList(CommandI command)
2605 if (this.redoList != null)
2607 this.redoList.push(command);
2609 broadcastCommand(command, true);
2613 * Clear the command redo list.
2615 public void clearRedoList()
2617 if (this.redoList != null)
2619 this.redoList.clear();
2623 public void setHistoryList(Deque<CommandI> list)
2625 this.historyList = list;
2628 public Deque<CommandI> getHistoryList()
2630 return this.historyList;
2633 public void setRedoList(Deque<CommandI> list)
2635 this.redoList = list;
2638 public Deque<CommandI> getRedoList()
2640 return this.redoList;
2644 public VamsasSource getVamsasSource()
2649 public SequenceAnnotationOrder getSortAnnotationsBy()
2651 return sortAnnotationsBy;
2654 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2656 this.sortAnnotationsBy = sortAnnotationsBy;
2659 public boolean isShowAutocalculatedAbove()
2661 return showAutocalculatedAbove;
2664 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2666 this.showAutocalculatedAbove = showAutocalculatedAbove;
2670 public boolean isScaleProteinAsCdna()
2672 return viewStyle.isScaleProteinAsCdna();
2676 public void setScaleProteinAsCdna(boolean b)
2678 viewStyle.setScaleProteinAsCdna(b);
2682 public boolean isProteinFontAsCdna()
2684 return viewStyle.isProteinFontAsCdna();
2688 public void setProteinFontAsCdna(boolean b)
2690 viewStyle.setProteinFontAsCdna(b);
2694 * @return true if view should scroll to show the highlighted region of a
2699 public final boolean isFollowHighlight()
2701 return followHighlight;
2705 public final void setFollowHighlight(boolean b)
2707 this.followHighlight = b;
2711 public ViewportRanges getRanges()
2717 * Helper method to populate the SearchResults with the location in the
2718 * complementary alignment to scroll to, in order to match this one.
2721 * the SearchResults to add to
2722 * @return the offset (below top of visible region) of the matched sequence
2724 protected int findComplementScrollTarget(SearchResultsI sr)
2726 final AlignViewportI complement = getCodingComplement();
2727 if (complement == null || !complement.isFollowHighlight())
2731 boolean iAmProtein = !getAlignment().isNucleotide();
2732 AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
2734 if (proteinAlignment == null)
2738 final List<AlignedCodonFrame> mappings = proteinAlignment
2742 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2743 * residue in the middle column of the visible region. Scroll the
2744 * complementary alignment to line up the corresponding residue.
2747 SequenceI sequence = null;
2750 * locate 'middle' column (true middle if an odd number visible, left of
2751 * middle if an even number visible)
2753 int middleColumn = ranges.getStartRes()
2754 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2755 final HiddenSequences hiddenSequences = getAlignment()
2756 .getHiddenSequences();
2759 * searching to the bottom of the alignment gives smoother scrolling across
2760 * all gapped visible regions
2762 int lastSeq = alignment.getHeight() - 1;
2763 List<AlignedCodonFrame> seqMappings = null;
2764 for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
2766 sequence = getAlignment().getSequenceAt(seqNo);
2767 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2771 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2775 seqMappings = MappingUtils
2776 .findMappingsForSequenceAndOthers(sequence, mappings,
2777 getCodingComplement().getAlignment().getSequences());
2778 if (!seqMappings.isEmpty())
2784 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2787 * No ungapped mapped sequence in middle column - do nothing
2791 MappingUtils.addSearchResults(sr, sequence,
2792 sequence.findPosition(middleColumn), seqMappings);
2797 * synthesize a column selection if none exists so it covers the given
2798 * selection group. if wholewidth is false, no column selection is made if the
2799 * selection group covers the whole alignment width.
2804 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2807 if (sg != null && (sgs = sg.getStartRes()) >= 0
2808 && sg.getStartRes() <= (sge = sg.getEndRes())
2809 && !this.hasSelectedColumns())
2811 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2818 colSel = new ColumnSelection();
2820 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2822 colSel.addElement(cspos);
2828 * hold status of current selection group - defined on alignment or not.
2830 private boolean selectionIsDefinedGroup = false;
2833 public boolean isSelectionDefinedGroup()
2835 if (selectionGroup == null)
2839 if (isSelectionGroupChanged(true))
2841 selectionIsDefinedGroup = false;
2842 List<SequenceGroup> gps = alignment.getGroups();
2843 if (gps == null || gps.size() == 0)
2845 selectionIsDefinedGroup = false;
2849 selectionIsDefinedGroup = gps.contains(selectionGroup);
2852 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2856 * null, or currently highlighted results on this view
2858 private SearchResultsI searchResults = null;
2861 public boolean hasSearchResults()
2863 return searchResults != null;
2867 public void setSearchResults(SearchResultsI results)
2869 searchResults = results;
2873 public SearchResultsI getSearchResults()
2875 return searchResults;