2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.viewmodel;
23 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
24 import jalview.analysis.Conservation;
25 import jalview.analysis.TreeModel;
26 import jalview.api.AlignCalcManagerI;
27 import jalview.api.AlignExportSettingsI;
28 import jalview.api.AlignViewportI;
29 import jalview.api.AlignmentViewPanel;
30 import jalview.api.FeaturesDisplayedI;
31 import jalview.api.ViewStyleI;
32 import jalview.commands.CommandI;
33 import jalview.datamodel.AlignedCodonFrame;
34 import jalview.datamodel.AlignmentAnnotation;
35 import jalview.datamodel.AlignmentExportData;
36 import jalview.datamodel.AlignmentI;
37 import jalview.datamodel.AlignmentView;
38 import jalview.datamodel.Annotation;
39 import jalview.datamodel.ColumnSelection;
40 import jalview.datamodel.HiddenColumns;
41 import jalview.datamodel.HiddenSequences;
42 import jalview.datamodel.ProfilesI;
43 import jalview.datamodel.SearchResultsI;
44 import jalview.datamodel.Sequence;
45 import jalview.datamodel.SequenceCollectionI;
46 import jalview.datamodel.SequenceGroup;
47 import jalview.datamodel.SequenceI;
48 import jalview.renderer.ResidueShader;
49 import jalview.renderer.ResidueShaderI;
50 import jalview.schemes.ColourSchemeI;
51 import jalview.structure.CommandListener;
52 import jalview.structure.StructureSelectionManager;
53 import jalview.structure.VamsasSource;
54 import jalview.util.Comparison;
55 import jalview.util.MapList;
56 import jalview.util.MappingUtils;
57 import jalview.util.MessageManager;
58 import jalview.viewmodel.styles.ViewStyle;
59 import jalview.workers.AlignCalcManager;
60 import jalview.workers.ComplementConsensusThread;
61 import jalview.workers.ConsensusThread;
62 import jalview.workers.StrucConsensusThread;
64 import java.awt.Color;
65 import java.beans.PropertyChangeSupport;
66 import java.util.ArrayDeque;
67 import java.util.ArrayList;
68 import java.util.BitSet;
69 import java.util.Deque;
70 import java.util.HashMap;
71 import java.util.Hashtable;
72 import java.util.Iterator;
73 import java.util.List;
77 * base class holding visualization and analysis attributes and common logic for
78 * an active alignment view displayed in the GUI
83 public abstract class AlignmentViewport
84 implements AlignViewportI, CommandListener, VamsasSource
86 protected ViewportRanges ranges;
88 protected ViewStyleI viewStyle = new ViewStyle();
91 * A viewport that hosts the cDna view of this (protein), or vice versa (if
94 AlignViewportI codingComplement = null;
96 FeaturesDisplayedI featuresDisplayed = null;
98 protected Deque<CommandI> historyList = new ArrayDeque<>();
100 protected Deque<CommandI> redoList = new ArrayDeque<>();
103 * alignment displayed in the viewport. Please use get/setter
105 protected AlignmentI alignment;
107 public AlignmentViewport(AlignmentI al)
110 ranges = new ViewportRanges(al);
115 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
118 public void setFontName(String name)
120 viewStyle.setFontName(name);
125 * @see jalview.api.ViewStyleI#setFontStyle(int)
128 public void setFontStyle(int style)
130 viewStyle.setFontStyle(style);
135 * @see jalview.api.ViewStyleI#setFontSize(int)
138 public void setFontSize(int size)
140 viewStyle.setFontSize(size);
145 * @see jalview.api.ViewStyleI#getFontStyle()
148 public int getFontStyle()
150 return viewStyle.getFontStyle();
155 * @see jalview.api.ViewStyleI#getFontName()
158 public String getFontName()
160 return viewStyle.getFontName();
165 * @see jalview.api.ViewStyleI#getFontSize()
168 public int getFontSize()
170 return viewStyle.getFontSize();
174 * @param upperCasebold
175 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
178 public void setUpperCasebold(boolean upperCasebold)
180 viewStyle.setUpperCasebold(upperCasebold);
185 * @see jalview.api.ViewStyleI#isUpperCasebold()
188 public boolean isUpperCasebold()
190 return viewStyle.isUpperCasebold();
195 * @see jalview.api.ViewStyleI#isSeqNameItalics()
198 public boolean isSeqNameItalics()
200 return viewStyle.isSeqNameItalics();
204 * @param colourByReferenceSeq
205 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
208 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
210 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
215 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
218 public void setColourAppliesToAllGroups(boolean b)
220 viewStyle.setColourAppliesToAllGroups(b);
225 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
228 public boolean getColourAppliesToAllGroups()
230 return viewStyle.getColourAppliesToAllGroups();
235 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
238 public boolean getAbovePIDThreshold()
240 return viewStyle.getAbovePIDThreshold();
245 * @see jalview.api.ViewStyleI#setIncrement(int)
248 public void setIncrement(int inc)
250 viewStyle.setIncrement(inc);
255 * @see jalview.api.ViewStyleI#getIncrement()
258 public int getIncrement()
260 return viewStyle.getIncrement();
265 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
268 public void setConservationSelected(boolean b)
270 viewStyle.setConservationSelected(b);
275 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
278 public void setShowHiddenMarkers(boolean show)
280 viewStyle.setShowHiddenMarkers(show);
285 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
288 public boolean getShowHiddenMarkers()
290 return viewStyle.getShowHiddenMarkers();
295 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
298 public void setScaleRightWrapped(boolean b)
300 viewStyle.setScaleRightWrapped(b);
305 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
308 public void setScaleLeftWrapped(boolean b)
310 viewStyle.setScaleLeftWrapped(b);
315 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
318 public void setScaleAboveWrapped(boolean b)
320 viewStyle.setScaleAboveWrapped(b);
325 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
328 public boolean getScaleLeftWrapped()
330 return viewStyle.getScaleLeftWrapped();
335 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
338 public boolean getScaleAboveWrapped()
340 return viewStyle.getScaleAboveWrapped();
345 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
348 public boolean getScaleRightWrapped()
350 return viewStyle.getScaleRightWrapped();
355 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
358 public void setAbovePIDThreshold(boolean b)
360 viewStyle.setAbovePIDThreshold(b);
365 * @see jalview.api.ViewStyleI#setThreshold(int)
368 public void setThreshold(int thresh)
370 viewStyle.setThreshold(thresh);
375 * @see jalview.api.ViewStyleI#getThreshold()
378 public int getThreshold()
380 return viewStyle.getThreshold();
385 * @see jalview.api.ViewStyleI#getShowJVSuffix()
388 public boolean getShowJVSuffix()
390 return viewStyle.getShowJVSuffix();
395 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
398 public void setShowJVSuffix(boolean b)
400 viewStyle.setShowJVSuffix(b);
405 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
408 public void setWrapAlignment(boolean state)
410 viewStyle.setWrapAlignment(state);
411 ranges.setWrappedMode(state);
416 * @see jalview.api.ViewStyleI#setShowText(boolean)
419 public void setShowText(boolean state)
421 viewStyle.setShowText(state);
426 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
429 public void setRenderGaps(boolean state)
431 viewStyle.setRenderGaps(state);
436 * @see jalview.api.ViewStyleI#getColourText()
439 public boolean getColourText()
441 return viewStyle.getColourText();
446 * @see jalview.api.ViewStyleI#setColourText(boolean)
449 public void setColourText(boolean state)
451 viewStyle.setColourText(state);
456 * @see jalview.api.ViewStyleI#getWrapAlignment()
459 public boolean getWrapAlignment()
461 return viewStyle.getWrapAlignment();
466 * @see jalview.api.ViewStyleI#getShowText()
469 public boolean getShowText()
471 return viewStyle.getShowText();
476 * @see jalview.api.ViewStyleI#getWrappedWidth()
479 public int getWrappedWidth()
481 return viewStyle.getWrappedWidth();
486 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
489 public void setWrappedWidth(int w)
491 viewStyle.setWrappedWidth(w);
496 * @see jalview.api.ViewStyleI#getCharHeight()
499 public int getCharHeight()
501 return viewStyle.getCharHeight();
506 * @see jalview.api.ViewStyleI#setCharHeight(int)
509 public void setCharHeight(int h)
511 viewStyle.setCharHeight(h);
516 * @see jalview.api.ViewStyleI#getCharWidth()
519 public int getCharWidth()
521 return viewStyle.getCharWidth();
526 * @see jalview.api.ViewStyleI#setCharWidth(int)
529 public void setCharWidth(int w)
531 viewStyle.setCharWidth(w);
536 * @see jalview.api.ViewStyleI#getShowBoxes()
539 public boolean getShowBoxes()
541 return viewStyle.getShowBoxes();
546 * @see jalview.api.ViewStyleI#getShowUnconserved()
549 public boolean getShowUnconserved()
551 return viewStyle.getShowUnconserved();
555 * @param showunconserved
556 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
559 public void setShowUnconserved(boolean showunconserved)
561 viewStyle.setShowUnconserved(showunconserved);
566 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
569 public void setSeqNameItalics(boolean default1)
571 viewStyle.setSeqNameItalics(default1);
575 public AlignmentI getAlignment()
581 public char getGapCharacter()
583 return alignment.getGapCharacter();
586 protected String sequenceSetID;
589 * probably unused indicator that view is of a dataset rather than an
592 protected boolean isDataset = false;
594 public void setDataset(boolean b)
599 public boolean isDataset()
604 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
606 protected ColumnSelection colSel = new ColumnSelection();
608 public boolean autoCalculateConsensus = true;
610 protected boolean autoCalculateStrucConsensus = true;
612 protected boolean ignoreGapsInConsensusCalculation = false;
614 protected ResidueShaderI residueShading = new ResidueShader();
617 public void setGlobalColourScheme(ColourSchemeI cs)
619 // TODO: logic refactored from AlignFrame changeColour -
620 // TODO: autorecalc stuff should be changed to rely on the worker system
621 // check to see if we should implement a changeColour(cs) method rather than
622 // put the logic in here
623 // - means that caller decides if they want to just modify state and defer
624 // calculation till later or to do all calculations in thread.
628 * only instantiate alignment colouring once, thereafter update it;
629 * this means that any conservation or PID threshold settings
630 * persist when the alignment colour scheme is changed
632 if (residueShading == null)
634 residueShading = new ResidueShader(viewStyle);
636 residueShading.setColourScheme(cs);
638 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
639 // ...problem: groups need these, but do not currently have a ViewStyle
643 if (getConservationSelected())
645 residueShading.setConservation(hconservation);
648 * reset conservation flag in case just set to false if
649 * Conservation was null (calculation still in progress)
651 residueShading.setConservationApplied(getConservationSelected());
652 residueShading.alignmentChanged(alignment, hiddenRepSequences);
656 * if 'apply colour to all groups' is selected... do so
657 * (but don't transfer any colour threshold settings to groups)
659 if (getColourAppliesToAllGroups())
661 for (SequenceGroup sg : getAlignment().getGroups())
664 * retain any colour thresholds per group while
665 * changing choice of colour scheme (JAL-2386)
668 cs == null ? null : cs.getInstance(this, sg));
671 sg.getGroupColourScheme().alignmentChanged(sg,
679 public ColourSchemeI getGlobalColourScheme()
681 return residueShading == null ? null : residueShading.getColourScheme();
685 public ResidueShaderI getResidueShading()
687 return residueShading;
690 protected AlignmentAnnotation consensus;
692 protected AlignmentAnnotation complementConsensus;
694 protected AlignmentAnnotation gapcounts;
696 protected AlignmentAnnotation strucConsensus;
698 protected AlignmentAnnotation conservation;
700 protected AlignmentAnnotation quality;
702 protected AlignmentAnnotation[] groupConsensus;
704 protected AlignmentAnnotation[] groupConservation;
707 * results of alignment consensus analysis for visible portion of view
709 protected ProfilesI hconsensus = null;
712 * results of cDNA complement consensus visible portion of view
714 protected Hashtable<String, Object>[] hcomplementConsensus = null;
717 * results of secondary structure base pair consensus for visible portion of
720 protected Hashtable<String, Object>[] hStrucConsensus = null;
722 protected Conservation hconservation = null;
725 public void setConservation(Conservation cons)
727 hconservation = cons;
731 * percentage gaps allowed in a column before all amino acid properties should
732 * be considered unconserved
734 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
737 public int getConsPercGaps()
743 public void setSequenceConsensusHash(ProfilesI hconsensus)
745 this.hconsensus = hconsensus;
749 public void setComplementConsensusHash(
750 Hashtable<String, Object>[] hconsensus)
752 this.hcomplementConsensus = hconsensus;
756 public ProfilesI getSequenceConsensusHash()
762 public Hashtable<String, Object>[] getComplementConsensusHash()
764 return hcomplementConsensus;
768 public Hashtable<String, Object>[] getRnaStructureConsensusHash()
770 return hStrucConsensus;
774 public void setRnaStructureConsensusHash(
775 Hashtable<String, Object>[] hStrucConsensus)
777 this.hStrucConsensus = hStrucConsensus;
782 public AlignmentAnnotation getAlignmentQualityAnnot()
788 public AlignmentAnnotation getAlignmentConservationAnnotation()
794 public AlignmentAnnotation getAlignmentConsensusAnnotation()
800 public AlignmentAnnotation getAlignmentGapAnnotation()
806 public AlignmentAnnotation getComplementConsensusAnnotation()
808 return complementConsensus;
812 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
814 return strucConsensus;
817 protected AlignCalcManagerI calculator = new AlignCalcManager();
820 * trigger update of conservation annotation
822 public void updateConservation(final AlignmentViewPanel ap)
824 // see note in mantis : issue number 8585
825 if (alignment.isNucleotide()
826 || (conservation == null && quality == null)
827 || !autoCalculateConsensus)
831 if (calculator.getRegisteredWorkersOfClass(
832 jalview.workers.ConservationThread.class) == null)
834 calculator.registerWorker(
835 new jalview.workers.ConservationThread(this, ap));
840 * trigger update of consensus annotation
842 public void updateConsensus(final AlignmentViewPanel ap)
844 // see note in mantis : issue number 8585
845 if (consensus == null || !autoCalculateConsensus)
850 .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
852 calculator.registerWorker(new ConsensusThread(this, ap));
856 * A separate thread to compute cDNA consensus for a protein alignment
857 * which has mapping to cDNA
859 final AlignmentI al = this.getAlignment();
860 if (!al.isNucleotide() && al.getCodonFrames() != null
861 && !al.getCodonFrames().isEmpty())
864 * fudge - check first for protein-to-nucleotide mappings
865 * (we don't want to do this for protein-to-protein)
867 boolean doConsensus = false;
868 for (AlignedCodonFrame mapping : al.getCodonFrames())
870 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
871 MapList[] mapLists = mapping.getdnaToProt();
872 // mapLists can be empty if project load has not finished resolving seqs
873 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
881 if (calculator.getRegisteredWorkersOfClass(
882 ComplementConsensusThread.class) == null)
885 .registerWorker(new ComplementConsensusThread(this, ap));
891 // --------START Structure Conservation
892 public void updateStrucConsensus(final AlignmentViewPanel ap)
894 if (autoCalculateStrucConsensus && strucConsensus == null
895 && alignment.isNucleotide() && alignment.hasRNAStructure())
897 // secondary structure has been added - so init the consensus line
901 // see note in mantis : issue number 8585
902 if (strucConsensus == null || !autoCalculateStrucConsensus)
906 if (calculator.getRegisteredWorkersOfClass(
907 StrucConsensusThread.class) == null)
909 calculator.registerWorker(new StrucConsensusThread(this, ap));
913 public boolean isCalcInProgress()
915 return calculator.isWorking();
919 public boolean isCalculationInProgress(
920 AlignmentAnnotation alignmentAnnotation)
922 if (!alignmentAnnotation.autoCalculated)
926 if (calculator.workingInvolvedWith(alignmentAnnotation))
928 // System.err.println("grey out ("+alignmentAnnotation.label+")");
934 public void setAlignment(AlignmentI align)
936 this.alignment = align;
940 * Clean up references when this viewport is closed
943 public void dispose()
946 * defensively null out references to large objects in case
947 * this object is not garbage collected (as if!)
950 complementConsensus = null;
951 strucConsensus = null;
954 groupConsensus = null;
955 groupConservation = null;
957 hconservation = null;
958 hcomplementConsensus = null;
961 residueShading = null; // may hold a reference to Consensus
962 changeSupport = null;
965 selectionGroup = null;
970 public boolean isClosed()
972 // TODO: check that this isClosed is only true after panel is closed, not
973 // before it is fully constructed.
974 return alignment == null;
978 public AlignCalcManagerI getCalcManager()
984 * should conservation rows be shown for groups
986 protected boolean showGroupConservation = false;
989 * should consensus rows be shown for groups
991 protected boolean showGroupConsensus = false;
994 * should consensus profile be rendered by default
996 protected boolean showSequenceLogo = false;
999 * should consensus profile be rendered normalised to row height
1001 protected boolean normaliseSequenceLogo = false;
1004 * should consensus histograms be rendered by default
1006 protected boolean showConsensusHistogram = true;
1009 * @return the showConsensusProfile
1012 public boolean isShowSequenceLogo()
1014 return showSequenceLogo;
1018 * @param showSequenceLogo
1021 public void setShowSequenceLogo(boolean showSequenceLogo)
1023 if (showSequenceLogo != this.showSequenceLogo)
1025 // TODO: decouple settings setting from calculation when refactoring
1026 // annotation update method from alignframe to viewport
1027 this.showSequenceLogo = showSequenceLogo;
1028 calculator.updateAnnotationFor(ConsensusThread.class);
1029 calculator.updateAnnotationFor(ComplementConsensusThread.class);
1030 calculator.updateAnnotationFor(StrucConsensusThread.class);
1032 this.showSequenceLogo = showSequenceLogo;
1036 * @param showConsensusHistogram
1037 * the showConsensusHistogram to set
1039 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1041 this.showConsensusHistogram = showConsensusHistogram;
1045 * @return the showGroupConservation
1047 public boolean isShowGroupConservation()
1049 return showGroupConservation;
1053 * @param showGroupConservation
1054 * the showGroupConservation to set
1056 public void setShowGroupConservation(boolean showGroupConservation)
1058 this.showGroupConservation = showGroupConservation;
1062 * @return the showGroupConsensus
1064 public boolean isShowGroupConsensus()
1066 return showGroupConsensus;
1070 * @param showGroupConsensus
1071 * the showGroupConsensus to set
1073 public void setShowGroupConsensus(boolean showGroupConsensus)
1075 this.showGroupConsensus = showGroupConsensus;
1080 * @return flag to indicate if the consensus histogram should be rendered by
1084 public boolean isShowConsensusHistogram()
1086 return this.showConsensusHistogram;
1090 * when set, updateAlignment will always ensure sequences are of equal length
1092 private boolean padGaps = false;
1095 * when set, alignment should be reordered according to a newly opened tree
1097 public boolean sortByTree = false;
1102 * @return null or the currently selected sequence region
1105 public SequenceGroup getSelectionGroup()
1107 return selectionGroup;
1111 * Set the selection group for this window. Also sets the current alignment as
1112 * the context for the group, if it does not already have one.
1115 * - group holding references to sequences in this alignment view
1119 public void setSelectionGroup(SequenceGroup sg)
1121 selectionGroup = sg;
1122 if (sg != null && sg.getContext() == null)
1124 sg.setContext(alignment);
1128 public void setHiddenColumns(HiddenColumns hidden)
1130 this.alignment.setHiddenColumns(hidden);
1134 public ColumnSelection getColumnSelection()
1140 public void setColumnSelection(ColumnSelection colSel)
1142 this.colSel = colSel;
1145 updateHiddenColumns();
1147 isColSelChanged(true);
1155 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1157 return hiddenRepSequences;
1161 public void setHiddenRepSequences(
1162 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1164 this.hiddenRepSequences = hiddenRepSequences;
1168 public boolean hasSelectedColumns()
1170 ColumnSelection columnSelection = getColumnSelection();
1171 return columnSelection != null && columnSelection.hasSelectedColumns();
1175 public boolean hasHiddenColumns()
1177 return alignment.getHiddenColumns() != null
1178 && alignment.getHiddenColumns().hasHiddenColumns();
1181 public void updateHiddenColumns()
1183 // this method doesn't really do anything now. But - it could, since a
1184 // column Selection could be in the process of modification
1185 // hasHiddenColumns = colSel.hasHiddenColumns();
1189 public boolean hasHiddenRows()
1191 return alignment.getHiddenSequences().getSize() > 0;
1194 protected SequenceGroup selectionGroup;
1196 public void setSequenceSetId(String newid)
1198 if (sequenceSetID != null)
1201 "Warning - overwriting a sequenceSetId for a viewport!");
1203 sequenceSetID = new String(newid);
1207 public String getSequenceSetId()
1209 if (sequenceSetID == null)
1211 sequenceSetID = alignment.hashCode() + "";
1214 return sequenceSetID;
1218 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1221 protected String viewId = null;
1224 public String getViewId()
1228 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1233 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1235 ignoreGapsInConsensusCalculation = b;
1238 updateConsensus(ap);
1239 if (residueShading != null)
1241 residueShading.setThreshold(residueShading.getThreshold(),
1242 ignoreGapsInConsensusCalculation);
1248 private long sgrouphash = -1, colselhash = -1;
1251 * checks current SelectionGroup against record of last hash value, and
1255 * update the record of last hash value
1257 * @return true if SelectionGroup changed since last call (when b is true)
1259 public boolean isSelectionGroupChanged(boolean b)
1261 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1262 : selectionGroup.hashCode();
1263 if (hc != -1 && hc != sgrouphash)
1275 * checks current colsel against record of last hash value, and optionally
1279 * update the record of last hash value
1280 * @return true if colsel changed since last call (when b is true)
1282 public boolean isColSelChanged(boolean b)
1284 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1285 if (hc != -1 && hc != colselhash)
1297 public boolean isIgnoreGapsConsensus()
1299 return ignoreGapsInConsensusCalculation;
1302 // property change stuff
1303 // JBPNote Prolly only need this in the applet version.
1304 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1307 protected boolean showConservation = true;
1309 protected boolean showQuality = true;
1311 protected boolean showConsensus = true;
1313 protected boolean showOccupancy = true;
1315 private Map<SequenceI, Color> sequenceColours = new HashMap<>();
1317 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1319 protected boolean showAutocalculatedAbove;
1322 * when set, view will scroll to show the highlighted position
1324 private boolean followHighlight = true;
1326 private boolean disableFastPaint; // BH 2019.04.18
1329 * BH 2019.04.18 When gap filling is on and a modification is made to fill
1330 * those, we need to disallow fast painting for paste just once
1334 public boolean isFastPaintDisabled()
1336 boolean ret = disableFastPaint;
1337 disableFastPaint = false;
1342 * Property change listener for changes in alignment
1347 public void addPropertyChangeListener(
1348 java.beans.PropertyChangeListener listener)
1350 changeSupport.addPropertyChangeListener(listener);
1359 public void removePropertyChangeListener(
1360 java.beans.PropertyChangeListener listener)
1362 if (changeSupport != null)
1364 changeSupport.removePropertyChangeListener(listener);
1369 * Property change listener for changes in alignment
1378 public void firePropertyChange(String prop, Object oldvalue,
1381 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1384 // common hide/show column stuff
1386 public void hideSelectedColumns()
1388 if (colSel.isEmpty())
1393 colSel.hideSelectedColumns(alignment);
1394 setSelectionGroup(null);
1395 isColSelChanged(true);
1398 public void hideColumns(int start, int end)
1402 colSel.hideSelectedColumns(start, alignment.getHiddenColumns());
1406 alignment.getHiddenColumns().hideColumns(start, end);
1408 isColSelChanged(true);
1411 public void showColumn(int col)
1413 alignment.getHiddenColumns().revealHiddenColumns(col, colSel);
1414 isColSelChanged(true);
1417 public void showAllHiddenColumns()
1419 alignment.getHiddenColumns().revealAllHiddenColumns(colSel);
1420 isColSelChanged(true);
1423 // common hide/show seq stuff
1424 public void showAllHiddenSeqs()
1426 int startSeq = ranges.getStartSeq();
1427 int endSeq = ranges.getEndSeq();
1429 if (alignment.getHiddenSequences().getSize() > 0)
1431 if (selectionGroup == null)
1433 selectionGroup = new SequenceGroup();
1434 selectionGroup.setEndRes(alignment.getWidth() - 1);
1436 List<SequenceI> tmp = alignment.getHiddenSequences()
1437 .showAll(hiddenRepSequences);
1438 for (SequenceI seq : tmp)
1440 selectionGroup.addSequence(seq, false);
1441 setSequenceAnnotationsVisible(seq, true);
1444 hiddenRepSequences = null;
1446 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1448 firePropertyChange("alignment", null, alignment.getSequences());
1449 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1455 public void showSequence(int index)
1457 int startSeq = ranges.getStartSeq();
1458 int endSeq = ranges.getEndSeq();
1460 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
1461 hiddenRepSequences);
1464 if (selectionGroup == null)
1466 selectionGroup = new SequenceGroup();
1467 selectionGroup.setEndRes(alignment.getWidth() - 1);
1470 for (SequenceI seq : tmp)
1472 selectionGroup.addSequence(seq, false);
1473 setSequenceAnnotationsVisible(seq, true);
1476 ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
1478 firePropertyChange("alignment", null, alignment.getSequences());
1483 public void hideAllSelectedSeqs()
1485 if (selectionGroup == null || selectionGroup.getSize() < 1)
1490 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1494 setSelectionGroup(null);
1497 public void hideSequence(SequenceI[] seq)
1500 * cache offset to first visible sequence
1502 int startSeq = ranges.getStartSeq();
1506 for (int i = 0; i < seq.length; i++)
1508 alignment.getHiddenSequences().hideSequence(seq[i]);
1509 setSequenceAnnotationsVisible(seq[i], false);
1511 ranges.setStartSeq(startSeq);
1512 firePropertyChange("alignment", null, alignment.getSequences());
1517 * Hides the specified sequence, or the sequences it represents
1520 * the sequence to hide, or keep as representative
1521 * @param representGroup
1522 * if true, hide the current selection group except for the
1523 * representative sequence
1525 public void hideSequences(SequenceI sequence, boolean representGroup)
1527 if (selectionGroup == null || selectionGroup.getSize() < 1)
1529 hideSequence(new SequenceI[] { sequence });
1535 hideRepSequences(sequence, selectionGroup);
1536 setSelectionGroup(null);
1540 int gsize = selectionGroup.getSize();
1541 SequenceI[] hseqs = selectionGroup.getSequences()
1542 .toArray(new SequenceI[gsize]);
1544 hideSequence(hseqs);
1545 setSelectionGroup(null);
1550 * Set visibility for any annotations for the given sequence.
1554 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1557 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1560 for (AlignmentAnnotation ann : anns)
1562 if (ann.sequenceRef == sequenceI)
1564 ann.visible = visible;
1570 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1572 int sSize = sg.getSize();
1578 if (hiddenRepSequences == null)
1580 hiddenRepSequences = new Hashtable<>();
1583 hiddenRepSequences.put(repSequence, sg);
1585 // Hide all sequences except the repSequence
1586 SequenceI[] seqs = new SequenceI[sSize - 1];
1588 for (int i = 0; i < sSize; i++)
1590 if (sg.getSequenceAt(i) != repSequence)
1592 if (index == sSize - 1)
1597 seqs[index++] = sg.getSequenceAt(i);
1600 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1601 sg.setHidereps(true); // note: not done in 2.7applet
1608 * @return null or the current reference sequence
1610 public SequenceI getReferenceSeq()
1612 return alignment.getSeqrep();
1617 * @return true iff seq is the reference for the alignment
1619 public boolean isReferenceSeq(SequenceI seq)
1621 return alignment.getSeqrep() == seq;
1627 * @return true if there are sequences represented by this sequence that are
1630 public boolean isHiddenRepSequence(SequenceI seq)
1632 return (hiddenRepSequences != null
1633 && hiddenRepSequences.containsKey(seq));
1639 * @return null or a sequence group containing the sequences that seq
1642 public SequenceGroup getRepresentedSequences(SequenceI seq)
1644 return (SequenceGroup) (hiddenRepSequences == null ? null
1645 : hiddenRepSequences.get(seq));
1649 public int adjustForHiddenSeqs(int alignmentIndex)
1651 return alignment.getHiddenSequences()
1652 .adjustForHiddenSeqs(alignmentIndex);
1656 public void invertColumnSelection()
1658 colSel.invertColumnSelection(0, alignment.getWidth(), alignment);
1659 isColSelChanged(true);
1663 public SequenceI[] getSelectionAsNewSequence()
1665 SequenceI[] sequences;
1666 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1667 // this was the only caller in the applet for this method
1668 // JBPNote: in applet, this method returned references to the alignment
1669 // sequences, and it did not honour the presence/absence of annotation
1670 // attached to the alignment (probably!)
1671 if (selectionGroup == null || selectionGroup.getSize() == 0)
1673 sequences = alignment.getSequencesArray();
1674 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1675 for (int i = 0; i < sequences.length; i++)
1677 // construct new sequence with subset of visible annotation
1678 sequences[i] = new Sequence(sequences[i], annots);
1683 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1690 public SequenceI[] getSequenceSelection()
1692 SequenceI[] sequences = null;
1693 if (selectionGroup != null)
1695 sequences = selectionGroup.getSequencesInOrder(alignment);
1697 if (sequences == null)
1699 sequences = alignment.getSequencesArray();
1705 public jalview.datamodel.AlignmentView getAlignmentView(
1706 boolean selectedOnly)
1708 return getAlignmentView(selectedOnly, false);
1712 public jalview.datamodel.AlignmentView getAlignmentView(
1713 boolean selectedOnly, boolean markGroups)
1715 return new AlignmentView(alignment, alignment.getHiddenColumns(),
1717 alignment.getHiddenColumns() != null
1718 && alignment.getHiddenColumns().hasHiddenColumns(),
1719 selectedOnly, markGroups);
1723 public String[] getViewAsString(boolean selectedRegionOnly)
1725 return getViewAsString(selectedRegionOnly, true);
1729 public String[] getViewAsString(boolean selectedRegionOnly,
1730 boolean exportHiddenSeqs)
1732 String[] selection = null;
1733 SequenceI[] seqs = null;
1735 int start = 0, end = 0;
1736 if (selectedRegionOnly && selectionGroup != null)
1738 iSize = selectionGroup.getSize();
1739 seqs = selectionGroup.getSequencesInOrder(alignment);
1740 start = selectionGroup.getStartRes();
1741 end = selectionGroup.getEndRes() + 1;
1745 if (hasHiddenRows() && exportHiddenSeqs)
1747 AlignmentI fullAlignment = alignment.getHiddenSequences()
1748 .getFullAlignment();
1749 iSize = fullAlignment.getHeight();
1750 seqs = fullAlignment.getSequencesArray();
1751 end = fullAlignment.getWidth();
1755 iSize = alignment.getHeight();
1756 seqs = alignment.getSequencesArray();
1757 end = alignment.getWidth();
1761 selection = new String[iSize];
1762 if (alignment.getHiddenColumns() != null
1763 && alignment.getHiddenColumns().hasHiddenColumns())
1765 for (i = 0; i < iSize; i++)
1767 Iterator<int[]> blocks = alignment.getHiddenColumns()
1768 .getVisContigsIterator(start, end + 1, false);
1769 selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
1774 for (i = 0; i < iSize; i++)
1776 selection[i] = seqs[i].getSequenceAsString(start, end);
1784 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1786 ArrayList<int[]> regions = new ArrayList<>();
1792 HiddenColumns hidden = alignment.getHiddenColumns();
1793 if (hidden != null && hidden.hasHiddenColumns())
1797 start = hidden.visibleToAbsoluteColumn(start);
1800 end = hidden.getNextHiddenBoundary(false, start);
1811 regions.add(new int[] { start, end });
1813 if (hidden != null && hidden.hasHiddenColumns())
1815 start = hidden.visibleToAbsoluteColumn(end);
1816 start = hidden.getNextHiddenBoundary(true, start) + 1;
1818 } while (end < max);
1820 // int[][] startEnd = new int[regions.size()][2];
1826 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1827 boolean selectedOnly)
1829 ArrayList<AlignmentAnnotation> ala = new ArrayList<>();
1830 AlignmentAnnotation[] aa;
1831 if ((aa = alignment.getAlignmentAnnotation()) != null)
1833 for (AlignmentAnnotation annot : aa)
1835 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1836 if (selectedOnly && selectionGroup != null)
1838 clone.makeVisibleAnnotation(
1839 selectionGroup.getStartRes(), selectionGroup.getEndRes(),
1840 alignment.getHiddenColumns());
1844 clone.makeVisibleAnnotation(alignment.getHiddenColumns());
1853 public boolean isPadGaps()
1859 public void setPadGaps(boolean padGaps)
1861 this.padGaps = padGaps;
1865 * apply any post-edit constraints and trigger any calculations needed after
1866 * an edit has been performed on the alignment
1871 public void alignmentChanged(AlignmentViewPanel ap)
1875 if (alignment.padGaps())
1877 // the new alignment has been modified -- can't fast paint
1878 disableFastPaint = true;
1881 if (autoCalculateConsensus)
1883 updateConsensus(ap);
1885 if (hconsensus != null && autoCalculateConsensus)
1887 updateConservation(ap);
1889 if (autoCalculateStrucConsensus)
1891 updateStrucConsensus(ap);
1894 // Reset endRes of groups if beyond alignment width
1895 int alWidth = alignment.getWidth();
1896 List<SequenceGroup> groups = alignment.getGroups();
1899 for (SequenceGroup sg : groups)
1901 if (sg.getEndRes() > alWidth)
1903 sg.setEndRes(alWidth - 1);
1908 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1910 selectionGroup.setEndRes(alWidth - 1);
1913 updateAllColourSchemes();
1914 calculator.restartWorkers();
1915 // alignment.adjustSequenceAnnotations();
1919 * reset scope and do calculations for all applied colourschemes on alignment
1921 void updateAllColourSchemes()
1923 ResidueShaderI rs = residueShading;
1926 rs.alignmentChanged(alignment, hiddenRepSequences);
1928 rs.setConsensus(hconsensus);
1929 if (rs.conservationApplied())
1931 rs.setConservation(Conservation.calculateConservation("All",
1932 alignment.getSequences(), 0, alignment.getWidth(), false,
1933 getConsPercGaps(), false));
1937 for (SequenceGroup sg : alignment.getGroups())
1941 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1943 sg.recalcConservation();
1947 protected void initAutoAnnotation()
1949 // TODO: add menu option action that nulls or creates consensus object
1950 // depending on if the user wants to see the annotation or not in a
1951 // specific alignment
1953 if (hconsensus == null && !isDataset)
1955 if (!alignment.isNucleotide())
1964 consensus = new AlignmentAnnotation("Consensus",
1965 MessageManager.getString("label.consensus_descr"),
1966 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1967 initConsensus(consensus);
1970 initComplementConsensus();
1975 * If this is a protein alignment and there are mappings to cDNA, adds the
1976 * cDNA consensus annotation and returns true, else returns false.
1978 public boolean initComplementConsensus()
1980 if (!alignment.isNucleotide())
1982 final List<AlignedCodonFrame> codonMappings = alignment
1984 if (codonMappings != null && !codonMappings.isEmpty())
1986 boolean doConsensus = false;
1987 for (AlignedCodonFrame mapping : codonMappings)
1989 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1990 MapList[] mapLists = mapping.getdnaToProt();
1991 // mapLists can be empty if project load has not finished resolving
1993 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
2001 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
2003 .getString("label.complement_consensus_descr"),
2004 new Annotation[1], 0f, 100f,
2005 AlignmentAnnotation.BAR_GRAPH);
2006 initConsensus(complementConsensus);
2014 private void initConsensus(AlignmentAnnotation aa)
2017 aa.autoCalculated = true;
2021 alignment.addAnnotation(aa);
2025 // these should be extracted from the view model - style and settings for
2026 // derived annotation
2027 private void initGapCounts()
2031 gapcounts = new AlignmentAnnotation("Occupancy",
2032 MessageManager.getString("label.occupancy_descr"),
2033 new Annotation[1], 0f, alignment.getHeight(),
2034 AlignmentAnnotation.BAR_GRAPH);
2035 gapcounts.hasText = true;
2036 gapcounts.autoCalculated = true;
2037 gapcounts.scaleColLabel = true;
2038 gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
2040 alignment.addAnnotation(gapcounts);
2044 private void initConservation()
2046 if (showConservation)
2048 if (conservation == null)
2050 conservation = new AlignmentAnnotation("Conservation",
2051 MessageManager.formatMessage("label.conservation_descr",
2053 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2054 conservation.hasText = true;
2055 conservation.autoCalculated = true;
2056 alignment.addAnnotation(conservation);
2061 private void initQuality()
2065 if (quality == null)
2067 quality = new AlignmentAnnotation("Quality",
2068 MessageManager.getString("label.quality_descr"),
2069 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
2070 quality.hasText = true;
2071 quality.autoCalculated = true;
2072 alignment.addAnnotation(quality);
2077 private void initRNAStructure()
2079 if (alignment.hasRNAStructure() && strucConsensus == null)
2081 strucConsensus = new AlignmentAnnotation("StrucConsensus",
2082 MessageManager.getString("label.strucconsensus_descr"),
2083 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
2084 strucConsensus.hasText = true;
2085 strucConsensus.autoCalculated = true;
2089 alignment.addAnnotation(strucConsensus);
2097 * @see jalview.api.AlignViewportI#calcPanelHeight()
2100 public int calcPanelHeight()
2102 // setHeight of panels
2103 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2105 int charHeight = getCharHeight();
2108 BitSet graphgrp = new BitSet();
2109 for (AlignmentAnnotation aa : anns)
2113 System.err.println("Null annotation row: ignoring.");
2120 if (aa.graphGroup > -1)
2122 if (graphgrp.get(aa.graphGroup))
2128 graphgrp.set(aa.graphGroup);
2135 aa.height += charHeight;
2145 aa.height += aa.graphHeight;
2153 height += aa.height;
2165 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2166 boolean preserveNewGroupSettings)
2168 boolean updateCalcs = false;
2169 boolean conv = isShowGroupConservation();
2170 boolean cons = isShowGroupConsensus();
2171 boolean showprf = isShowSequenceLogo();
2172 boolean showConsHist = isShowConsensusHistogram();
2173 boolean normLogo = isNormaliseSequenceLogo();
2176 * TODO reorder the annotation rows according to group/sequence ordering on
2179 // boolean sortg = true;
2181 // remove old automatic annotation
2182 // add any new annotation
2184 // intersect alignment annotation with alignment groups
2186 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2187 List<SequenceGroup> oldrfs = new ArrayList<>();
2190 for (int an = 0; an < aan.length; an++)
2192 if (aan[an].autoCalculated && aan[an].groupRef != null)
2194 oldrfs.add(aan[an].groupRef);
2195 alignment.deleteAnnotation(aan[an], false);
2199 if (alignment.getGroups() != null)
2201 for (SequenceGroup sg : alignment.getGroups())
2203 updateCalcs = false;
2204 if (applyGlobalSettings
2205 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2207 // set defaults for this group's conservation/consensus
2208 sg.setshowSequenceLogo(showprf);
2209 sg.setShowConsensusHistogram(showConsHist);
2210 sg.setNormaliseSequenceLogo(normLogo);
2215 alignment.addAnnotation(sg.getConservationRow(), 0);
2220 alignment.addAnnotation(sg.getConsensus(), 0);
2222 // refresh the annotation rows
2225 sg.recalcConservation();
2233 public boolean isDisplayReferenceSeq()
2235 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2239 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2241 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2245 public boolean isColourByReferenceSeq()
2247 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2251 public Color getSequenceColour(SequenceI seq)
2253 Color sqc = sequenceColours.get(seq);
2254 return (sqc == null ? Color.white : sqc);
2258 public void setSequenceColour(SequenceI seq, Color col)
2262 sequenceColours.remove(seq);
2266 sequenceColours.put(seq, col);
2271 public void updateSequenceIdColours()
2273 for (SequenceGroup sg : alignment.getGroups())
2275 if (sg.idColour != null)
2277 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2279 sequenceColours.put(s, sg.idColour);
2286 public void clearSequenceColours()
2288 sequenceColours.clear();
2292 public AlignViewportI getCodingComplement()
2294 return this.codingComplement;
2298 * Set this as the (cDna/protein) complement of the given viewport. Also
2299 * ensures the reverse relationship is set on the given viewport.
2302 public void setCodingComplement(AlignViewportI av)
2306 System.err.println("Ignoring recursive setCodingComplement request");
2310 this.codingComplement = av;
2311 // avoid infinite recursion!
2312 if (av.getCodingComplement() != this)
2314 av.setCodingComplement(this);
2320 public boolean isNucleotide()
2322 return getAlignment() == null ? false : getAlignment().isNucleotide();
2326 public FeaturesDisplayedI getFeaturesDisplayed()
2328 return featuresDisplayed;
2332 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2334 featuresDisplayed = featuresDisplayedI;
2338 public boolean areFeaturesDisplayed()
2340 return featuresDisplayed != null
2341 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2348 * features are displayed if true
2351 public void setShowSequenceFeatures(boolean b)
2353 viewStyle.setShowSequenceFeatures(b);
2357 public boolean isShowSequenceFeatures()
2359 return viewStyle.isShowSequenceFeatures();
2363 public void setShowSequenceFeaturesHeight(boolean selected)
2365 viewStyle.setShowSequenceFeaturesHeight(selected);
2369 public boolean isShowSequenceFeaturesHeight()
2371 return viewStyle.isShowSequenceFeaturesHeight();
2375 public void setShowAnnotation(boolean b)
2377 viewStyle.setShowAnnotation(b);
2381 public boolean isShowAnnotation()
2383 return viewStyle.isShowAnnotation();
2387 public boolean isRightAlignIds()
2389 return viewStyle.isRightAlignIds();
2393 public void setRightAlignIds(boolean rightAlignIds)
2395 viewStyle.setRightAlignIds(rightAlignIds);
2399 public boolean getConservationSelected()
2401 return viewStyle.getConservationSelected();
2405 public void setShowBoxes(boolean state)
2407 viewStyle.setShowBoxes(state);
2412 * @see jalview.api.ViewStyleI#getTextColour()
2415 public Color getTextColour()
2417 return viewStyle.getTextColour();
2422 * @see jalview.api.ViewStyleI#getTextColour2()
2425 public Color getTextColour2()
2427 return viewStyle.getTextColour2();
2432 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2435 public int getThresholdTextColour()
2437 return viewStyle.getThresholdTextColour();
2442 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2445 public boolean isConservationColourSelected()
2447 return viewStyle.isConservationColourSelected();
2452 * @see jalview.api.ViewStyleI#isRenderGaps()
2455 public boolean isRenderGaps()
2457 return viewStyle.isRenderGaps();
2462 * @see jalview.api.ViewStyleI#isShowColourText()
2465 public boolean isShowColourText()
2467 return viewStyle.isShowColourText();
2471 * @param conservationColourSelected
2472 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2475 public void setConservationColourSelected(
2476 boolean conservationColourSelected)
2478 viewStyle.setConservationColourSelected(conservationColourSelected);
2482 * @param showColourText
2483 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2486 public void setShowColourText(boolean showColourText)
2488 viewStyle.setShowColourText(showColourText);
2493 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2496 public void setTextColour(Color textColour)
2498 viewStyle.setTextColour(textColour);
2502 * @param thresholdTextColour
2503 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2506 public void setThresholdTextColour(int thresholdTextColour)
2508 viewStyle.setThresholdTextColour(thresholdTextColour);
2512 * @param textColour2
2513 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2516 public void setTextColour2(Color textColour2)
2518 viewStyle.setTextColour2(textColour2);
2522 public ViewStyleI getViewStyle()
2524 return new ViewStyle(viewStyle);
2528 public void setViewStyle(ViewStyleI settingsForView)
2530 viewStyle = new ViewStyle(settingsForView);
2531 if (residueShading != null)
2533 residueShading.setConservationApplied(
2534 settingsForView.isConservationColourSelected());
2539 public boolean sameStyle(ViewStyleI them)
2541 return viewStyle.sameStyle(them);
2546 * @see jalview.api.ViewStyleI#getIdWidth()
2549 public int getIdWidth()
2551 return viewStyle.getIdWidth();
2556 * @see jalview.api.ViewStyleI#setIdWidth(int)
2559 public void setIdWidth(int i)
2561 viewStyle.setIdWidth(i);
2566 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2569 public boolean isCentreColumnLabels()
2571 return viewStyle.isCentreColumnLabels();
2575 * @param centreColumnLabels
2576 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2579 public void setCentreColumnLabels(boolean centreColumnLabels)
2581 viewStyle.setCentreColumnLabels(centreColumnLabels);
2586 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2589 public void setShowDBRefs(boolean showdbrefs)
2591 viewStyle.setShowDBRefs(showdbrefs);
2596 * @see jalview.api.ViewStyleI#isShowDBRefs()
2599 public boolean isShowDBRefs()
2601 return viewStyle.isShowDBRefs();
2606 * @see jalview.api.ViewStyleI#isShowNPFeats()
2609 public boolean isShowNPFeats()
2611 return viewStyle.isShowNPFeats();
2615 * @param shownpfeats
2616 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2619 public void setShowNPFeats(boolean shownpfeats)
2621 viewStyle.setShowNPFeats(shownpfeats);
2624 public abstract StructureSelectionManager getStructureSelectionManager();
2627 * Add one command to the command history list.
2631 public void addToHistoryList(CommandI command)
2633 if (this.historyList != null)
2635 this.historyList.push(command);
2636 broadcastCommand(command, false);
2640 protected void broadcastCommand(CommandI command, boolean undo)
2642 getStructureSelectionManager().commandPerformed(command, undo,
2647 * Add one command to the command redo list.
2651 public void addToRedoList(CommandI command)
2653 if (this.redoList != null)
2655 this.redoList.push(command);
2657 broadcastCommand(command, true);
2661 * Clear the command redo list.
2663 public void clearRedoList()
2665 if (this.redoList != null)
2667 this.redoList.clear();
2671 public void setHistoryList(Deque<CommandI> list)
2673 this.historyList = list;
2676 public Deque<CommandI> getHistoryList()
2678 return this.historyList;
2681 public void setRedoList(Deque<CommandI> list)
2683 this.redoList = list;
2686 public Deque<CommandI> getRedoList()
2688 return this.redoList;
2692 public VamsasSource getVamsasSource()
2697 public SequenceAnnotationOrder getSortAnnotationsBy()
2699 return sortAnnotationsBy;
2702 public void setSortAnnotationsBy(
2703 SequenceAnnotationOrder sortAnnotationsBy)
2705 this.sortAnnotationsBy = sortAnnotationsBy;
2708 public boolean isShowAutocalculatedAbove()
2710 return showAutocalculatedAbove;
2713 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2715 this.showAutocalculatedAbove = showAutocalculatedAbove;
2719 public boolean isScaleProteinAsCdna()
2721 return viewStyle.isScaleProteinAsCdna();
2725 public void setScaleProteinAsCdna(boolean b)
2727 viewStyle.setScaleProteinAsCdna(b);
2731 public boolean isProteinFontAsCdna()
2733 return viewStyle.isProteinFontAsCdna();
2737 public void setProteinFontAsCdna(boolean b)
2739 viewStyle.setProteinFontAsCdna(b);
2743 * @return true if view should scroll to show the highlighted region of a
2748 public final boolean isFollowHighlight()
2750 return followHighlight;
2754 public final void setFollowHighlight(boolean b)
2756 this.followHighlight = b;
2760 public ViewportRanges getRanges()
2766 * Helper method to populate the SearchResults with the location in the
2767 * complementary alignment to scroll to, in order to match this one.
2770 * the SearchResults to add to
2771 * @return the offset (below top of visible region) of the matched sequence
2773 protected int findComplementScrollTarget(SearchResultsI sr)
2775 final AlignViewportI complement = getCodingComplement();
2776 if (complement == null || !complement.isFollowHighlight())
2780 boolean iAmProtein = !getAlignment().isNucleotide();
2781 AlignmentI proteinAlignment = iAmProtein ? getAlignment()
2782 : complement.getAlignment();
2783 if (proteinAlignment == null)
2787 final List<AlignedCodonFrame> mappings = proteinAlignment
2791 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2792 * residue in the middle column of the visible region. Scroll the
2793 * complementary alignment to line up the corresponding residue.
2796 SequenceI sequence = null;
2799 * locate 'middle' column (true middle if an odd number visible, left of
2800 * middle if an even number visible)
2802 int middleColumn = ranges.getStartRes()
2803 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2804 final HiddenSequences hiddenSequences = getAlignment()
2805 .getHiddenSequences();
2808 * searching to the bottom of the alignment gives smoother scrolling across
2809 * all gapped visible regions
2811 int lastSeq = alignment.getHeight() - 1;
2812 List<AlignedCodonFrame> seqMappings = null;
2813 for (int seqNo = ranges
2814 .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
2816 sequence = getAlignment().getSequenceAt(seqNo);
2817 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2821 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2825 seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
2827 getCodingComplement().getAlignment().getSequences());
2828 if (!seqMappings.isEmpty())
2834 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2837 * No ungapped mapped sequence in middle column - do nothing
2841 MappingUtils.addSearchResults(sr, sequence,
2842 sequence.findPosition(middleColumn), seqMappings);
2847 * synthesize a column selection if none exists so it covers the given
2848 * selection group. if wholewidth is false, no column selection is made if the
2849 * selection group covers the whole alignment width.
2854 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2857 if (sg != null && (sgs = sg.getStartRes()) >= 0
2858 && sg.getStartRes() <= (sge = sg.getEndRes())
2859 && !this.hasSelectedColumns())
2861 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2868 colSel = new ColumnSelection();
2870 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2872 colSel.addElement(cspos);
2878 * hold status of current selection group - defined on alignment or not.
2880 private boolean selectionIsDefinedGroup = false;
2883 public boolean isSelectionDefinedGroup()
2885 if (selectionGroup == null)
2889 if (isSelectionGroupChanged(true))
2891 selectionIsDefinedGroup = false;
2892 List<SequenceGroup> gps = alignment.getGroups();
2893 if (gps == null || gps.size() == 0)
2895 selectionIsDefinedGroup = false;
2899 selectionIsDefinedGroup = gps.contains(selectionGroup);
2902 return selectionGroup.isDefined() || selectionIsDefinedGroup;
2906 * null, or currently highlighted results on this view
2908 private SearchResultsI searchResults = null;
2910 protected TreeModel currentTree = null;
2913 public boolean hasSearchResults()
2915 return searchResults != null;
2919 public void setSearchResults(SearchResultsI results)
2921 searchResults = results;
2925 public SearchResultsI getSearchResults()
2927 return searchResults;
2931 * get the consensus sequence as displayed under the PID consensus annotation
2934 * @return consensus sequence as a new sequence object
2936 public SequenceI getConsensusSeq()
2938 if (consensus == null)
2940 updateConsensus(null);
2942 if (consensus == null)
2946 StringBuffer seqs = new StringBuffer();
2947 for (int i = 0; i < consensus.annotations.length; i++)
2949 Annotation annotation = consensus.annotations[i];
2950 if (annotation != null)
2952 String description = annotation.description;
2953 if (description != null && description.startsWith("["))
2955 // consensus is a tie - just pick the first one
2956 seqs.append(description.charAt(1));
2960 seqs.append(annotation.displayCharacter);
2965 SequenceI sq = new Sequence("Consensus", seqs.toString());
2966 sq.setDescription("Percentage Identity Consensus "
2967 + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
2972 public void setCurrentTree(TreeModel tree)
2978 public TreeModel getCurrentTree()
2984 public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
2986 AlignmentI alignmentToExport = null;
2987 String[] omitHidden = null;
2988 alignmentToExport = null;
2990 if (hasHiddenColumns() && !options.isExportHiddenColumns())
2992 omitHidden = getViewAsString(false,
2993 options.isExportHiddenSequences());
2996 int[] alignmentStartEnd = new int[2];
2997 if (hasHiddenRows() && options.isExportHiddenSequences())
2999 alignmentToExport = getAlignment().getHiddenSequences()
3000 .getFullAlignment();
3004 alignmentToExport = getAlignment();
3006 alignmentStartEnd = getAlignment().getHiddenColumns()
3007 .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
3008 AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
3009 omitHidden, alignmentStartEnd);
3014 * flag set to indicate if structure views might be out of sync with sequences
3018 private boolean needToUpdateStructureViews = false;
3021 public boolean isUpdateStructures()
3023 return needToUpdateStructureViews;
3027 public void setUpdateStructures(boolean update)
3029 needToUpdateStructureViews = update;
3033 public boolean needToUpdateStructureViews()
3035 boolean update = needToUpdateStructureViews;
3036 needToUpdateStructureViews = false;
3041 public void addSequenceGroup(SequenceGroup sequenceGroup)
3043 alignment.addGroup(sequenceGroup);
3045 Color col = sequenceGroup.idColour;
3048 col = col.brighter();
3050 for (SequenceI sq : sequenceGroup.getSequences())
3052 setSequenceColour(sq, col);
3056 if (codingComplement != null)
3058 SequenceGroup mappedGroup = MappingUtils
3059 .mapSequenceGroup(sequenceGroup, this, codingComplement);
3060 if (mappedGroup.getSequences().size() > 0)
3062 codingComplement.getAlignment().addGroup(mappedGroup);
3066 for (SequenceI seq : mappedGroup.getSequences())
3068 codingComplement.setSequenceColour(seq, col);
3072 // propagate the structure view update flag according to our own setting
3073 codingComplement.setUpdateStructures(needToUpdateStructureViews);