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.HiddenSequences;
39 import jalview.datamodel.ProfilesI;
40 import jalview.datamodel.SearchResultsI;
41 import jalview.datamodel.Sequence;
42 import jalview.datamodel.SequenceCollectionI;
43 import jalview.datamodel.SequenceGroup;
44 import jalview.datamodel.SequenceI;
45 import jalview.renderer.ResidueShader;
46 import jalview.renderer.ResidueShaderI;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.structure.CommandListener;
49 import jalview.structure.StructureSelectionManager;
50 import jalview.structure.VamsasSource;
51 import jalview.util.Comparison;
52 import jalview.util.MapList;
53 import jalview.util.MappingUtils;
54 import jalview.viewmodel.styles.ViewStyle;
55 import jalview.workers.AlignCalcManager;
56 import jalview.workers.ComplementConsensusThread;
57 import jalview.workers.ConsensusThread;
58 import jalview.workers.StrucConsensusThread;
60 import java.awt.Color;
61 import java.beans.PropertyChangeSupport;
62 import java.util.ArrayDeque;
63 import java.util.ArrayList;
64 import java.util.BitSet;
65 import java.util.Deque;
66 import java.util.HashMap;
67 import java.util.Hashtable;
68 import java.util.List;
72 * base class holding visualization and analysis attributes and common logic for
73 * an active alignment view displayed in the GUI
78 public abstract class AlignmentViewport implements AlignViewportI,
79 CommandListener, VamsasSource
81 protected ViewportRanges ranges;
83 protected ViewStyleI viewStyle = new ViewStyle();
86 * A viewport that hosts the cDna view of this (protein), or vice versa (if
89 AlignViewportI codingComplement = null;
91 FeaturesDisplayedI featuresDisplayed = null;
93 protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
95 protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
99 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
102 public void setFontName(String name)
104 viewStyle.setFontName(name);
109 * @see jalview.api.ViewStyleI#setFontStyle(int)
112 public void setFontStyle(int style)
114 viewStyle.setFontStyle(style);
119 * @see jalview.api.ViewStyleI#setFontSize(int)
122 public void setFontSize(int size)
124 viewStyle.setFontSize(size);
129 * @see jalview.api.ViewStyleI#getFontStyle()
132 public int getFontStyle()
134 return viewStyle.getFontStyle();
139 * @see jalview.api.ViewStyleI#getFontName()
142 public String getFontName()
144 return viewStyle.getFontName();
149 * @see jalview.api.ViewStyleI#getFontSize()
152 public int getFontSize()
154 return viewStyle.getFontSize();
158 * @param upperCasebold
159 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
162 public void setUpperCasebold(boolean upperCasebold)
164 viewStyle.setUpperCasebold(upperCasebold);
169 * @see jalview.api.ViewStyleI#isUpperCasebold()
172 public boolean isUpperCasebold()
174 return viewStyle.isUpperCasebold();
179 * @see jalview.api.ViewStyleI#isSeqNameItalics()
182 public boolean isSeqNameItalics()
184 return viewStyle.isSeqNameItalics();
188 * @param colourByReferenceSeq
189 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
192 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
194 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
199 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
202 public void setColourAppliesToAllGroups(boolean b)
204 viewStyle.setColourAppliesToAllGroups(b);
209 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
212 public boolean getColourAppliesToAllGroups()
214 return viewStyle.getColourAppliesToAllGroups();
219 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
222 public boolean getAbovePIDThreshold()
224 return viewStyle.getAbovePIDThreshold();
229 * @see jalview.api.ViewStyleI#setIncrement(int)
232 public void setIncrement(int inc)
234 viewStyle.setIncrement(inc);
239 * @see jalview.api.ViewStyleI#getIncrement()
242 public int getIncrement()
244 return viewStyle.getIncrement();
249 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
252 public void setConservationSelected(boolean b)
254 viewStyle.setConservationSelected(b);
259 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
262 public void setShowHiddenMarkers(boolean show)
264 viewStyle.setShowHiddenMarkers(show);
269 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
272 public boolean getShowHiddenMarkers()
274 return viewStyle.getShowHiddenMarkers();
279 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
282 public void setScaleRightWrapped(boolean b)
284 viewStyle.setScaleRightWrapped(b);
289 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
292 public void setScaleLeftWrapped(boolean b)
294 viewStyle.setScaleLeftWrapped(b);
299 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
302 public void setScaleAboveWrapped(boolean b)
304 viewStyle.setScaleAboveWrapped(b);
309 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
312 public boolean getScaleLeftWrapped()
314 return viewStyle.getScaleLeftWrapped();
319 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
322 public boolean getScaleAboveWrapped()
324 return viewStyle.getScaleAboveWrapped();
329 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
332 public boolean getScaleRightWrapped()
334 return viewStyle.getScaleRightWrapped();
339 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
342 public void setAbovePIDThreshold(boolean b)
344 viewStyle.setAbovePIDThreshold(b);
349 * @see jalview.api.ViewStyleI#setThreshold(int)
352 public void setThreshold(int thresh)
354 viewStyle.setThreshold(thresh);
359 * @see jalview.api.ViewStyleI#getThreshold()
362 public int getThreshold()
364 return viewStyle.getThreshold();
369 * @see jalview.api.ViewStyleI#getShowJVSuffix()
372 public boolean getShowJVSuffix()
374 return viewStyle.getShowJVSuffix();
379 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
382 public void setShowJVSuffix(boolean b)
384 viewStyle.setShowJVSuffix(b);
389 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
392 public void setWrapAlignment(boolean state)
394 viewStyle.setWrapAlignment(state);
399 * @see jalview.api.ViewStyleI#setShowText(boolean)
402 public void setShowText(boolean state)
404 viewStyle.setShowText(state);
409 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
412 public void setRenderGaps(boolean state)
414 viewStyle.setRenderGaps(state);
419 * @see jalview.api.ViewStyleI#getColourText()
422 public boolean getColourText()
424 return viewStyle.getColourText();
429 * @see jalview.api.ViewStyleI#setColourText(boolean)
432 public void setColourText(boolean state)
434 viewStyle.setColourText(state);
439 * @see jalview.api.ViewStyleI#getWrapAlignment()
442 public boolean getWrapAlignment()
444 return viewStyle.getWrapAlignment();
449 * @see jalview.api.ViewStyleI#getShowText()
452 public boolean getShowText()
454 return viewStyle.getShowText();
459 * @see jalview.api.ViewStyleI#getWrappedWidth()
462 public int getWrappedWidth()
464 return viewStyle.getWrappedWidth();
469 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
472 public void setWrappedWidth(int w)
474 viewStyle.setWrappedWidth(w);
479 * @see jalview.api.ViewStyleI#getCharHeight()
482 public int getCharHeight()
484 return viewStyle.getCharHeight();
489 * @see jalview.api.ViewStyleI#setCharHeight(int)
492 public void setCharHeight(int h)
494 viewStyle.setCharHeight(h);
499 * @see jalview.api.ViewStyleI#getCharWidth()
502 public int getCharWidth()
504 return viewStyle.getCharWidth();
509 * @see jalview.api.ViewStyleI#setCharWidth(int)
512 public void setCharWidth(int w)
514 viewStyle.setCharWidth(w);
519 * @see jalview.api.ViewStyleI#getShowBoxes()
522 public boolean getShowBoxes()
524 return viewStyle.getShowBoxes();
529 * @see jalview.api.ViewStyleI#getShowUnconserved()
532 public boolean getShowUnconserved()
534 return viewStyle.getShowUnconserved();
538 * @param showunconserved
539 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
542 public void setShowUnconserved(boolean showunconserved)
544 viewStyle.setShowUnconserved(showunconserved);
549 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
552 public void setSeqNameItalics(boolean default1)
554 viewStyle.setSeqNameItalics(default1);
558 * alignment displayed in the viewport. Please use get/setter
560 protected AlignmentI alignment;
563 public AlignmentI getAlignment()
569 public char getGapCharacter()
571 return alignment.getGapCharacter();
574 protected String sequenceSetID;
577 * probably unused indicator that view is of a dataset rather than an
580 protected boolean isDataset = false;
582 public void setDataset(boolean b)
587 public boolean isDataset()
592 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
594 protected ColumnSelection colSel = new ColumnSelection();
596 public boolean autoCalculateConsensus = true;
598 protected boolean autoCalculateStrucConsensus = true;
600 protected boolean ignoreGapsInConsensusCalculation = false;
602 protected ResidueShaderI residueShading;
605 public void setGlobalColourScheme(ColourSchemeI cs)
607 // TODO: logic refactored from AlignFrame changeColour -
608 // TODO: autorecalc stuff should be changed to rely on the worker system
609 // check to see if we should implement a changeColour(cs) method rather than
610 // put the logic in here
611 // - means that caller decides if they want to just modify state and defer
612 // calculation till later or to do all calculations in thread.
616 * only instantiate alignment colouring once, thereafter update it;
617 * this means that any conservation or PID threshold settings
618 * persist when the alignment colour scheme is changed
620 if (residueShading == null)
622 residueShading = new ResidueShader(viewStyle);
624 residueShading.setColourScheme(cs);
626 // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
627 // ...problem: groups need these, but do not currently have a ViewStyle
631 if (getConservationSelected())
633 residueShading.setConservation(hconservation);
635 residueShading.alignmentChanged(alignment, hiddenRepSequences);
639 * if 'apply colour to all groups' is selected... do so
640 * (but don't transfer any colour threshold settings to groups)
642 if (getColourAppliesToAllGroups())
644 for (SequenceGroup sg : getAlignment().getGroups())
647 * retain any colour thresholds per group while
648 * changing choice of colour scheme (JAL-2386)
650 sg.setColourScheme(cs);
653 sg.getGroupColourScheme()
654 .alignmentChanged(sg, hiddenRepSequences);
661 public ColourSchemeI getGlobalColourScheme()
663 return residueShading == null ? null : residueShading
668 public ResidueShaderI getResidueShading()
670 return residueShading;
673 protected AlignmentAnnotation consensus;
675 protected AlignmentAnnotation complementConsensus;
677 protected AlignmentAnnotation strucConsensus;
679 protected AlignmentAnnotation conservation;
681 protected AlignmentAnnotation quality;
683 protected AlignmentAnnotation[] groupConsensus;
685 protected AlignmentAnnotation[] groupConservation;
688 * results of alignment consensus analysis for visible portion of view
690 protected ProfilesI hconsensus = null;
693 * results of cDNA complement consensus visible portion of view
695 protected Hashtable[] hcomplementConsensus = null;
698 * results of secondary structure base pair consensus for visible portion of
701 protected Hashtable[] hStrucConsensus = null;
703 protected Conservation hconservation = null;
706 public void setConservation(Conservation cons)
708 hconservation = cons;
712 * percentage gaps allowed in a column before all amino acid properties should
713 * be considered unconserved
715 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
718 public int getConsPercGaps()
724 public void setSequenceConsensusHash(ProfilesI hconsensus)
726 this.hconsensus = hconsensus;
730 public void setComplementConsensusHash(Hashtable[] hconsensus)
732 this.hcomplementConsensus = hconsensus;
736 public ProfilesI getSequenceConsensusHash()
742 public Hashtable[] getComplementConsensusHash()
744 return hcomplementConsensus;
748 public Hashtable[] getRnaStructureConsensusHash()
750 return hStrucConsensus;
754 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
756 this.hStrucConsensus = hStrucConsensus;
761 public AlignmentAnnotation getAlignmentQualityAnnot()
767 public AlignmentAnnotation getAlignmentConservationAnnotation()
773 public AlignmentAnnotation getAlignmentConsensusAnnotation()
779 public AlignmentAnnotation getComplementConsensusAnnotation()
781 return complementConsensus;
785 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
787 return strucConsensus;
790 protected AlignCalcManagerI calculator = new AlignCalcManager();
793 * trigger update of conservation annotation
795 public void updateConservation(final AlignmentViewPanel ap)
797 // see note in mantis : issue number 8585
798 if (alignment.isNucleotide()
799 || (conservation == null && quality == null)
800 || !autoCalculateConsensus)
805 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
807 calculator.registerWorker(new jalview.workers.ConservationThread(
813 * trigger update of consensus annotation
815 public void updateConsensus(final AlignmentViewPanel ap)
817 // see note in mantis : issue number 8585
818 if (consensus == null || !autoCalculateConsensus)
822 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
824 calculator.registerWorker(new ConsensusThread(this, ap));
828 * A separate thread to compute cDNA consensus for a protein alignment
829 * which has mapping to cDNA
831 final AlignmentI al = this.getAlignment();
832 if (!al.isNucleotide() && al.getCodonFrames() != null
833 && !al.getCodonFrames().isEmpty())
836 * fudge - check first for protein-to-nucleotide mappings
837 * (we don't want to do this for protein-to-protein)
839 boolean doConsensus = false;
840 for (AlignedCodonFrame mapping : al.getCodonFrames())
842 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
843 MapList[] mapLists = mapping.getdnaToProt();
844 // mapLists can be empty if project load has not finished resolving seqs
845 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
854 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
857 .registerWorker(new ComplementConsensusThread(this, ap));
863 // --------START Structure Conservation
864 public void updateStrucConsensus(final AlignmentViewPanel ap)
866 if (autoCalculateStrucConsensus && strucConsensus == null
867 && alignment.isNucleotide() && alignment.hasRNAStructure())
869 // secondary structure has been added - so init the consensus line
873 // see note in mantis : issue number 8585
874 if (strucConsensus == null || !autoCalculateStrucConsensus)
878 if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
880 calculator.registerWorker(new StrucConsensusThread(this, ap));
884 public boolean isCalcInProgress()
886 return calculator.isWorking();
890 public boolean isCalculationInProgress(
891 AlignmentAnnotation alignmentAnnotation)
893 if (!alignmentAnnotation.autoCalculated)
897 if (calculator.workingInvolvedWith(alignmentAnnotation))
899 // System.err.println("grey out ("+alignmentAnnotation.label+")");
905 public void setAlignment(AlignmentI align)
907 this.alignment = align;
911 * Clean up references when this viewport is closed
914 public void dispose()
917 * defensively null out references to large objects in case
918 * this object is not garbage collected (as if!)
921 complementConsensus = null;
922 strucConsensus = null;
925 groupConsensus = null;
926 groupConservation = null;
928 hcomplementConsensus = null;
929 // colour scheme may hold reference to consensus
930 residueShading = null;
931 // TODO remove listeners from changeSupport?
932 changeSupport = null;
937 public boolean isClosed()
939 // TODO: check that this isClosed is only true after panel is closed, not
940 // before it is fully constructed.
941 return alignment == null;
945 public AlignCalcManagerI getCalcManager()
951 * should conservation rows be shown for groups
953 protected boolean showGroupConservation = false;
956 * should consensus rows be shown for groups
958 protected boolean showGroupConsensus = false;
961 * should consensus profile be rendered by default
963 protected boolean showSequenceLogo = false;
966 * should consensus profile be rendered normalised to row height
968 protected boolean normaliseSequenceLogo = false;
971 * should consensus histograms be rendered by default
973 protected boolean showConsensusHistogram = true;
976 * @return the showConsensusProfile
979 public boolean isShowSequenceLogo()
981 return showSequenceLogo;
985 * @param showSequenceLogo
988 public void setShowSequenceLogo(boolean showSequenceLogo)
990 if (showSequenceLogo != this.showSequenceLogo)
992 // TODO: decouple settings setting from calculation when refactoring
993 // annotation update method from alignframe to viewport
994 this.showSequenceLogo = showSequenceLogo;
995 calculator.updateAnnotationFor(ConsensusThread.class);
996 calculator.updateAnnotationFor(ComplementConsensusThread.class);
997 calculator.updateAnnotationFor(StrucConsensusThread.class);
999 this.showSequenceLogo = showSequenceLogo;
1003 * @param showConsensusHistogram
1004 * the showConsensusHistogram to set
1006 public void setShowConsensusHistogram(boolean showConsensusHistogram)
1008 this.showConsensusHistogram = showConsensusHistogram;
1012 * @return the showGroupConservation
1014 public boolean isShowGroupConservation()
1016 return showGroupConservation;
1020 * @param showGroupConservation
1021 * the showGroupConservation to set
1023 public void setShowGroupConservation(boolean showGroupConservation)
1025 this.showGroupConservation = showGroupConservation;
1029 * @return the showGroupConsensus
1031 public boolean isShowGroupConsensus()
1033 return showGroupConsensus;
1037 * @param showGroupConsensus
1038 * the showGroupConsensus to set
1040 public void setShowGroupConsensus(boolean showGroupConsensus)
1042 this.showGroupConsensus = showGroupConsensus;
1047 * @return flag to indicate if the consensus histogram should be rendered by
1051 public boolean isShowConsensusHistogram()
1053 return this.showConsensusHistogram;
1057 * when set, updateAlignment will always ensure sequences are of equal length
1059 private boolean padGaps = false;
1062 * when set, alignment should be reordered according to a newly opened tree
1064 public boolean sortByTree = false;
1069 * @return null or the currently selected sequence region
1072 public SequenceGroup getSelectionGroup()
1074 return selectionGroup;
1078 * Set the selection group for this window. Also sets the current alignment as
1079 * the context for the group, if it does not already have one.
1082 * - group holding references to sequences in this alignment view
1086 public void setSelectionGroup(SequenceGroup sg)
1088 selectionGroup = sg;
1089 if (sg != null && sg.getContext() == null)
1091 sg.setContext(alignment);
1095 public void setHiddenColumns(ColumnSelection colsel)
1097 this.colSel = colsel;
1101 public ColumnSelection getColumnSelection()
1107 public void setColumnSelection(ColumnSelection colSel)
1109 this.colSel = colSel;
1112 updateHiddenColumns();
1114 isColSelChanged(true);
1122 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1124 return hiddenRepSequences;
1128 public void setHiddenRepSequences(
1129 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1131 this.hiddenRepSequences = hiddenRepSequences;
1135 public boolean hasSelectedColumns()
1137 ColumnSelection columnSelection = getColumnSelection();
1138 return columnSelection != null && columnSelection.hasSelectedColumns();
1142 public boolean hasHiddenColumns()
1144 return colSel != null && colSel.hasHiddenColumns();
1147 public void updateHiddenColumns()
1149 // this method doesn't really do anything now. But - it could, since a
1150 // column Selection could be in the process of modification
1151 // hasHiddenColumns = colSel.hasHiddenColumns();
1155 public boolean hasHiddenRows()
1157 return alignment.getHiddenSequences().getSize() > 0;
1160 protected SequenceGroup selectionGroup;
1162 public void setSequenceSetId(String newid)
1164 if (sequenceSetID != null)
1167 .println("Warning - overwriting a sequenceSetId for a viewport!");
1169 sequenceSetID = new String(newid);
1173 public String getSequenceSetId()
1175 if (sequenceSetID == null)
1177 sequenceSetID = alignment.hashCode() + "";
1180 return sequenceSetID;
1184 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1187 protected String viewId = null;
1190 public String getViewId()
1194 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1199 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1201 ignoreGapsInConsensusCalculation = b;
1204 updateConsensus(ap);
1205 if (residueShading != null)
1207 residueShading.setThreshold(residueShading.getThreshold(),
1208 ignoreGapsInConsensusCalculation);
1214 private long sgrouphash = -1, colselhash = -1;
1217 * checks current SelectionGroup against record of last hash value, and
1221 * update the record of last hash value
1223 * @return true if SelectionGroup changed since last call (when b is true)
1225 public boolean isSelectionGroupChanged(boolean b)
1227 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1228 : selectionGroup.hashCode();
1229 if (hc != -1 && hc != sgrouphash)
1241 * checks current colsel against record of last hash value, and optionally
1245 * update the record of last hash value
1246 * @return true if colsel changed since last call (when b is true)
1248 public boolean isColSelChanged(boolean b)
1250 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1251 if (hc != -1 && hc != colselhash)
1263 public boolean isIgnoreGapsConsensus()
1265 return ignoreGapsInConsensusCalculation;
1268 // property change stuff
1269 // JBPNote Prolly only need this in the applet version.
1270 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
1273 protected boolean showConservation = true;
1275 protected boolean showQuality = true;
1277 protected boolean showConsensus = true;
1279 private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
1281 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1283 protected boolean showAutocalculatedAbove;
1286 * when set, view will scroll to show the highlighted position
1288 private boolean followHighlight = true;
1291 * Property change listener for changes in alignment
1296 public void addPropertyChangeListener(
1297 java.beans.PropertyChangeListener listener)
1299 changeSupport.addPropertyChangeListener(listener);
1308 public void removePropertyChangeListener(
1309 java.beans.PropertyChangeListener listener)
1311 changeSupport.removePropertyChangeListener(listener);
1315 * Property change listener for changes in alignment
1324 public void firePropertyChange(String prop, Object oldvalue,
1327 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1330 // common hide/show column stuff
1332 public void hideSelectedColumns()
1334 if (colSel.isEmpty())
1339 colSel.hideSelectedColumns();
1340 setSelectionGroup(null);
1341 isColSelChanged(true);
1344 public void hideColumns(int start, int end)
1348 colSel.hideColumns(start);
1352 colSel.hideColumns(start, end);
1354 isColSelChanged(true);
1357 public void showColumn(int col)
1359 colSel.revealHiddenColumns(col);
1360 isColSelChanged(true);
1363 public void showAllHiddenColumns()
1365 colSel.revealAllHiddenColumns();
1366 isColSelChanged(true);
1369 // common hide/show seq stuff
1370 public void showAllHiddenSeqs()
1372 if (alignment.getHiddenSequences().getSize() > 0)
1374 if (selectionGroup == null)
1376 selectionGroup = new SequenceGroup();
1377 selectionGroup.setEndRes(alignment.getWidth() - 1);
1379 List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
1380 hiddenRepSequences);
1381 for (SequenceI seq : tmp)
1383 selectionGroup.addSequence(seq, false);
1384 setSequenceAnnotationsVisible(seq, true);
1387 hiddenRepSequences = null;
1389 firePropertyChange("alignment", null, alignment.getSequences());
1390 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1396 public void showSequence(int index)
1398 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1399 index, hiddenRepSequences);
1402 if (selectionGroup == null)
1404 selectionGroup = new SequenceGroup();
1405 selectionGroup.setEndRes(alignment.getWidth() - 1);
1408 for (SequenceI seq : tmp)
1410 selectionGroup.addSequence(seq, false);
1411 setSequenceAnnotationsVisible(seq, true);
1413 firePropertyChange("alignment", null, alignment.getSequences());
1418 public void hideAllSelectedSeqs()
1420 if (selectionGroup == null || selectionGroup.getSize() < 1)
1425 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1429 setSelectionGroup(null);
1432 public void hideSequence(SequenceI[] seq)
1436 for (int i = 0; i < seq.length; i++)
1438 alignment.getHiddenSequences().hideSequence(seq[i]);
1439 setSequenceAnnotationsVisible(seq[i], false);
1441 firePropertyChange("alignment", null, alignment.getSequences());
1446 * Hides the specified sequence, or the sequences it represents
1449 * the sequence to hide, or keep as representative
1450 * @param representGroup
1451 * if true, hide the current selection group except for the
1452 * representative sequence
1454 public void hideSequences(SequenceI sequence, boolean representGroup)
1456 if (selectionGroup == null || selectionGroup.getSize() < 1)
1458 hideSequence(new SequenceI[] { sequence });
1464 hideRepSequences(sequence, selectionGroup);
1465 setSelectionGroup(null);
1469 int gsize = selectionGroup.getSize();
1470 SequenceI[] hseqs = selectionGroup.getSequences().toArray(
1471 new SequenceI[gsize]);
1473 hideSequence(hseqs);
1474 setSelectionGroup(null);
1479 * Set visibility for any annotations for the given sequence.
1483 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1486 AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
1489 for (AlignmentAnnotation ann : anns)
1491 if (ann.sequenceRef == sequenceI)
1493 ann.visible = visible;
1499 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1501 int sSize = sg.getSize();
1507 if (hiddenRepSequences == null)
1509 hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
1512 hiddenRepSequences.put(repSequence, sg);
1514 // Hide all sequences except the repSequence
1515 SequenceI[] seqs = new SequenceI[sSize - 1];
1517 for (int i = 0; i < sSize; i++)
1519 if (sg.getSequenceAt(i) != repSequence)
1521 if (index == sSize - 1)
1526 seqs[index++] = sg.getSequenceAt(i);
1529 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1530 sg.setHidereps(true); // note: not done in 2.7applet
1537 * @return null or the current reference sequence
1539 public SequenceI getReferenceSeq()
1541 return alignment.getSeqrep();
1546 * @return true iff seq is the reference for the alignment
1548 public boolean isReferenceSeq(SequenceI seq)
1550 return alignment.getSeqrep() == seq;
1556 * @return true if there are sequences represented by this sequence that are
1559 public boolean isHiddenRepSequence(SequenceI seq)
1561 return (hiddenRepSequences != null && hiddenRepSequences
1568 * @return null or a sequence group containing the sequences that seq
1571 public SequenceGroup getRepresentedSequences(SequenceI seq)
1573 return (SequenceGroup) (hiddenRepSequences == null ? null
1574 : hiddenRepSequences.get(seq));
1578 public int adjustForHiddenSeqs(int alignmentIndex)
1580 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1585 public void invertColumnSelection()
1587 colSel.invertColumnSelection(0, alignment.getWidth());
1591 public SequenceI[] getSelectionAsNewSequence()
1593 SequenceI[] sequences;
1594 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1595 // this was the only caller in the applet for this method
1596 // JBPNote: in applet, this method returned references to the alignment
1597 // sequences, and it did not honour the presence/absence of annotation
1598 // attached to the alignment (probably!)
1599 if (selectionGroup == null || selectionGroup.getSize() == 0)
1601 sequences = alignment.getSequencesArray();
1602 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1603 for (int i = 0; i < sequences.length; i++)
1605 // construct new sequence with subset of visible annotation
1606 sequences[i] = new Sequence(sequences[i], annots);
1611 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1618 public SequenceI[] getSequenceSelection()
1620 SequenceI[] sequences = null;
1621 if (selectionGroup != null)
1623 sequences = selectionGroup.getSequencesInOrder(alignment);
1625 if (sequences == null)
1627 sequences = alignment.getSequencesArray();
1633 public CigarArray getViewAsCigars(boolean selectedRegionOnly)
1635 return new CigarArray(alignment, colSel,
1636 (selectedRegionOnly ? selectionGroup : null));
1640 public jalview.datamodel.AlignmentView getAlignmentView(
1641 boolean selectedOnly)
1643 return getAlignmentView(selectedOnly, false);
1647 public jalview.datamodel.AlignmentView getAlignmentView(
1648 boolean selectedOnly, boolean markGroups)
1650 return new AlignmentView(alignment, colSel, selectionGroup,
1651 colSel != null && colSel.hasHiddenColumns(), selectedOnly,
1656 public String[] getViewAsString(boolean selectedRegionOnly)
1658 return getViewAsString(selectedRegionOnly, true);
1662 public String[] getViewAsString(boolean selectedRegionOnly,
1663 boolean exportHiddenSeqs)
1665 String[] selection = null;
1666 SequenceI[] seqs = null;
1668 int start = 0, end = 0;
1669 if (selectedRegionOnly && selectionGroup != null)
1671 iSize = selectionGroup.getSize();
1672 seqs = selectionGroup.getSequencesInOrder(alignment);
1673 start = selectionGroup.getStartRes();
1674 end = selectionGroup.getEndRes() + 1;
1678 if (hasHiddenRows() && exportHiddenSeqs)
1680 AlignmentI fullAlignment = alignment.getHiddenSequences()
1681 .getFullAlignment();
1682 iSize = fullAlignment.getHeight();
1683 seqs = fullAlignment.getSequencesArray();
1684 end = fullAlignment.getWidth();
1688 iSize = alignment.getHeight();
1689 seqs = alignment.getSequencesArray();
1690 end = alignment.getWidth();
1694 selection = new String[iSize];
1695 if (colSel != null && colSel.hasHiddenColumns())
1697 selection = colSel.getVisibleSequenceStrings(start, end, seqs);
1701 for (i = 0; i < iSize; i++)
1703 selection[i] = seqs[i].getSequenceAsString(start, end);
1711 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1713 ArrayList<int[]> regions = new ArrayList<int[]>();
1719 if (colSel != null && colSel.hasHiddenColumns())
1723 start = colSel.adjustForHiddenColumns(start);
1726 end = colSel.getHiddenBoundaryRight(start);
1737 regions.add(new int[] { start, end });
1739 if (colSel != null && colSel.hasHiddenColumns())
1741 start = colSel.adjustForHiddenColumns(end);
1742 start = colSel.getHiddenBoundaryLeft(start) + 1;
1744 } while (end < max);
1746 int[][] startEnd = new int[regions.size()][2];
1752 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1753 boolean selectedOnly)
1755 ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
1756 AlignmentAnnotation[] aa;
1757 if ((aa = alignment.getAlignmentAnnotation()) != null)
1759 for (AlignmentAnnotation annot : aa)
1761 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1762 if (selectedOnly && selectionGroup != null)
1764 colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
1765 selectionGroup.getEndRes(), clone);
1769 colSel.makeVisibleAnnotation(clone);
1778 public boolean isPadGaps()
1784 public void setPadGaps(boolean padGaps)
1786 this.padGaps = padGaps;
1790 * apply any post-edit constraints and trigger any calculations needed after
1791 * an edit has been performed on the alignment
1796 public void alignmentChanged(AlignmentViewPanel ap)
1800 alignment.padGaps();
1802 if (autoCalculateConsensus)
1804 updateConsensus(ap);
1806 if (hconsensus != null && autoCalculateConsensus)
1808 updateConservation(ap);
1810 if (autoCalculateStrucConsensus)
1812 updateStrucConsensus(ap);
1815 // Reset endRes of groups if beyond alignment width
1816 int alWidth = alignment.getWidth();
1817 List<SequenceGroup> groups = alignment.getGroups();
1820 for (SequenceGroup sg : groups)
1822 if (sg.getEndRes() > alWidth)
1824 sg.setEndRes(alWidth - 1);
1829 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1831 selectionGroup.setEndRes(alWidth - 1);
1834 updateAllColourSchemes();
1835 calculator.restartWorkers();
1836 // alignment.adjustSequenceAnnotations();
1840 * reset scope and do calculations for all applied colourschemes on alignment
1842 void updateAllColourSchemes()
1844 ResidueShaderI rs = residueShading;
1847 rs.alignmentChanged(alignment, hiddenRepSequences);
1849 rs.setConsensus(hconsensus);
1850 if (rs.conservationApplied())
1852 rs.setConservation(Conservation.calculateConservation("All",
1853 alignment.getSequences(), 0, alignment.getWidth(), false,
1854 getConsPercGaps(), false));
1858 for (SequenceGroup sg : alignment.getGroups())
1862 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1864 sg.recalcConservation();
1868 protected void initAutoAnnotation()
1870 // TODO: add menu option action that nulls or creates consensus object
1871 // depending on if the user wants to see the annotation or not in a
1872 // specific alignment
1874 if (hconsensus == null && !isDataset)
1876 if (!alignment.isNucleotide())
1885 consensus = new AlignmentAnnotation("Consensus", "PID",
1886 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1887 initConsensus(consensus);
1889 initComplementConsensus();
1894 * If this is a protein alignment and there are mappings to cDNA, add the cDNA
1895 * consensus annotation.
1897 public void initComplementConsensus()
1899 if (!alignment.isNucleotide())
1901 final List<AlignedCodonFrame> codonMappings = alignment
1903 if (codonMappings != null && !codonMappings.isEmpty())
1905 boolean doConsensus = false;
1906 for (AlignedCodonFrame mapping : codonMappings)
1908 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
1909 MapList[] mapLists = mapping.getdnaToProt();
1910 // mapLists can be empty if project load has not finished resolving
1912 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1920 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1921 "PID for cDNA", new Annotation[1], 0f, 100f,
1922 AlignmentAnnotation.BAR_GRAPH);
1923 initConsensus(complementConsensus);
1929 private void initConsensus(AlignmentAnnotation aa)
1932 aa.autoCalculated = true;
1936 alignment.addAnnotation(aa);
1940 private void initConservation()
1942 if (showConservation)
1944 if (conservation == null)
1946 conservation = new AlignmentAnnotation("Conservation",
1947 "Conservation of total alignment less than "
1948 + getConsPercGaps() + "% gaps", new Annotation[1],
1949 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1950 conservation.hasText = true;
1951 conservation.autoCalculated = true;
1952 alignment.addAnnotation(conservation);
1957 private void initQuality()
1961 if (quality == null)
1963 quality = new AlignmentAnnotation("Quality",
1964 "Alignment Quality based on Blosum62 scores",
1965 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1966 quality.hasText = true;
1967 quality.autoCalculated = true;
1968 alignment.addAnnotation(quality);
1973 private void initRNAStructure()
1975 if (alignment.hasRNAStructure() && strucConsensus == null)
1977 strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
1978 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1979 strucConsensus.hasText = true;
1980 strucConsensus.autoCalculated = true;
1984 alignment.addAnnotation(strucConsensus);
1992 * @see jalview.api.AlignViewportI#calcPanelHeight()
1995 public int calcPanelHeight()
1997 // setHeight of panels
1998 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
2000 int charHeight = getCharHeight();
2003 BitSet graphgrp = new BitSet();
2004 for (AlignmentAnnotation aa : anns)
2008 System.err.println("Null annotation row: ignoring.");
2015 if (aa.graphGroup > -1)
2017 if (graphgrp.get(aa.graphGroup))
2023 graphgrp.set(aa.graphGroup);
2030 aa.height += charHeight;
2040 aa.height += aa.graphHeight;
2048 height += aa.height;
2060 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
2061 boolean preserveNewGroupSettings)
2063 boolean updateCalcs = false;
2064 boolean conv = isShowGroupConservation();
2065 boolean cons = isShowGroupConsensus();
2066 boolean showprf = isShowSequenceLogo();
2067 boolean showConsHist = isShowConsensusHistogram();
2068 boolean normLogo = isNormaliseSequenceLogo();
2071 * TODO reorder the annotation rows according to group/sequence ordering on
2074 boolean sortg = true;
2076 // remove old automatic annotation
2077 // add any new annotation
2079 // intersect alignment annotation with alignment groups
2081 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2082 List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
2085 for (int an = 0; an < aan.length; an++)
2087 if (aan[an].autoCalculated && aan[an].groupRef != null)
2089 oldrfs.add(aan[an].groupRef);
2090 alignment.deleteAnnotation(aan[an], false);
2094 if (alignment.getGroups() != null)
2096 for (SequenceGroup sg : alignment.getGroups())
2098 updateCalcs = false;
2099 if (applyGlobalSettings
2100 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2102 // set defaults for this group's conservation/consensus
2103 sg.setshowSequenceLogo(showprf);
2104 sg.setShowConsensusHistogram(showConsHist);
2105 sg.setNormaliseSequenceLogo(normLogo);
2110 alignment.addAnnotation(sg.getConservationRow(), 0);
2115 alignment.addAnnotation(sg.getConsensus(), 0);
2117 // refresh the annotation rows
2120 sg.recalcConservation();
2128 public boolean isDisplayReferenceSeq()
2130 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2134 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2136 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2140 public boolean isColourByReferenceSeq()
2142 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2146 public Color getSequenceColour(SequenceI seq)
2148 Color sqc = sequenceColours.get(seq);
2149 return (sqc == null ? Color.white : sqc);
2153 public void setSequenceColour(SequenceI seq, Color col)
2157 sequenceColours.remove(seq);
2161 sequenceColours.put(seq, col);
2166 public void updateSequenceIdColours()
2168 for (SequenceGroup sg : alignment.getGroups())
2170 if (sg.idColour != null)
2172 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2174 sequenceColours.put(s, sg.idColour);
2181 public void clearSequenceColours()
2183 sequenceColours.clear();
2187 public AlignViewportI getCodingComplement()
2189 return this.codingComplement;
2193 * Set this as the (cDna/protein) complement of the given viewport. Also
2194 * ensures the reverse relationship is set on the given viewport.
2197 public void setCodingComplement(AlignViewportI av)
2201 System.err.println("Ignoring recursive setCodingComplement request");
2205 this.codingComplement = av;
2206 // avoid infinite recursion!
2207 if (av.getCodingComplement() != this)
2209 av.setCodingComplement(this);
2215 public boolean isNucleotide()
2217 return getAlignment() == null ? false : getAlignment().isNucleotide();
2221 public FeaturesDisplayedI getFeaturesDisplayed()
2223 return featuresDisplayed;
2227 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2229 featuresDisplayed = featuresDisplayedI;
2233 public boolean areFeaturesDisplayed()
2235 return featuresDisplayed != null
2236 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2243 * features are displayed if true
2246 public void setShowSequenceFeatures(boolean b)
2248 viewStyle.setShowSequenceFeatures(b);
2252 public boolean isShowSequenceFeatures()
2254 return viewStyle.isShowSequenceFeatures();
2258 public void setShowSequenceFeaturesHeight(boolean selected)
2260 viewStyle.setShowSequenceFeaturesHeight(selected);
2264 public boolean isShowSequenceFeaturesHeight()
2266 return viewStyle.isShowSequenceFeaturesHeight();
2270 public void setShowAnnotation(boolean b)
2272 viewStyle.setShowAnnotation(b);
2276 public boolean isShowAnnotation()
2278 return viewStyle.isShowAnnotation();
2282 public boolean isRightAlignIds()
2284 return viewStyle.isRightAlignIds();
2288 public void setRightAlignIds(boolean rightAlignIds)
2290 viewStyle.setRightAlignIds(rightAlignIds);
2294 public boolean getConservationSelected()
2296 return viewStyle.getConservationSelected();
2300 public void setShowBoxes(boolean state)
2302 viewStyle.setShowBoxes(state);
2307 * @see jalview.api.ViewStyleI#getTextColour()
2310 public Color getTextColour()
2312 return viewStyle.getTextColour();
2317 * @see jalview.api.ViewStyleI#getTextColour2()
2320 public Color getTextColour2()
2322 return viewStyle.getTextColour2();
2327 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2330 public int getThresholdTextColour()
2332 return viewStyle.getThresholdTextColour();
2337 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2340 public boolean isConservationColourSelected()
2342 return viewStyle.isConservationColourSelected();
2347 * @see jalview.api.ViewStyleI#isRenderGaps()
2350 public boolean isRenderGaps()
2352 return viewStyle.isRenderGaps();
2357 * @see jalview.api.ViewStyleI#isShowColourText()
2360 public boolean isShowColourText()
2362 return viewStyle.isShowColourText();
2366 * @param conservationColourSelected
2367 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2370 public void setConservationColourSelected(
2371 boolean conservationColourSelected)
2373 viewStyle.setConservationColourSelected(conservationColourSelected);
2377 * @param showColourText
2378 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2381 public void setShowColourText(boolean showColourText)
2383 viewStyle.setShowColourText(showColourText);
2388 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2391 public void setTextColour(Color textColour)
2393 viewStyle.setTextColour(textColour);
2397 * @param thresholdTextColour
2398 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2401 public void setThresholdTextColour(int thresholdTextColour)
2403 viewStyle.setThresholdTextColour(thresholdTextColour);
2407 * @param textColour2
2408 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2411 public void setTextColour2(Color textColour2)
2413 viewStyle.setTextColour2(textColour2);
2417 public ViewStyleI getViewStyle()
2419 return new ViewStyle(viewStyle);
2423 public void setViewStyle(ViewStyleI settingsForView)
2425 viewStyle = new ViewStyle(settingsForView);
2426 if (residueShading != null)
2428 residueShading.setConservationApplied(settingsForView
2429 .isConservationColourSelected());
2434 public boolean sameStyle(ViewStyleI them)
2436 return viewStyle.sameStyle(them);
2441 * @see jalview.api.ViewStyleI#getIdWidth()
2444 public int getIdWidth()
2446 return viewStyle.getIdWidth();
2451 * @see jalview.api.ViewStyleI#setIdWidth(int)
2454 public void setIdWidth(int i)
2456 viewStyle.setIdWidth(i);
2461 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2464 public boolean isCentreColumnLabels()
2466 return viewStyle.isCentreColumnLabels();
2470 * @param centreColumnLabels
2471 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2474 public void setCentreColumnLabels(boolean centreColumnLabels)
2476 viewStyle.setCentreColumnLabels(centreColumnLabels);
2481 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2484 public void setShowDBRefs(boolean showdbrefs)
2486 viewStyle.setShowDBRefs(showdbrefs);
2491 * @see jalview.api.ViewStyleI#isShowDBRefs()
2494 public boolean isShowDBRefs()
2496 return viewStyle.isShowDBRefs();
2501 * @see jalview.api.ViewStyleI#isShowNPFeats()
2504 public boolean isShowNPFeats()
2506 return viewStyle.isShowNPFeats();
2510 * @param shownpfeats
2511 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2514 public void setShowNPFeats(boolean shownpfeats)
2516 viewStyle.setShowNPFeats(shownpfeats);
2519 public abstract StructureSelectionManager getStructureSelectionManager();
2522 * Add one command to the command history list.
2526 public void addToHistoryList(CommandI command)
2528 if (this.historyList != null)
2530 this.historyList.push(command);
2531 broadcastCommand(command, false);
2535 protected void broadcastCommand(CommandI command, boolean undo)
2537 getStructureSelectionManager().commandPerformed(command, undo,
2542 * Add one command to the command redo list.
2546 public void addToRedoList(CommandI command)
2548 if (this.redoList != null)
2550 this.redoList.push(command);
2552 broadcastCommand(command, true);
2556 * Clear the command redo list.
2558 public void clearRedoList()
2560 if (this.redoList != null)
2562 this.redoList.clear();
2566 public void setHistoryList(Deque<CommandI> list)
2568 this.historyList = list;
2571 public Deque<CommandI> getHistoryList()
2573 return this.historyList;
2576 public void setRedoList(Deque<CommandI> list)
2578 this.redoList = list;
2581 public Deque<CommandI> getRedoList()
2583 return this.redoList;
2587 public VamsasSource getVamsasSource()
2592 public SequenceAnnotationOrder getSortAnnotationsBy()
2594 return sortAnnotationsBy;
2597 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2599 this.sortAnnotationsBy = sortAnnotationsBy;
2602 public boolean isShowAutocalculatedAbove()
2604 return showAutocalculatedAbove;
2607 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2609 this.showAutocalculatedAbove = showAutocalculatedAbove;
2613 public boolean isScaleProteinAsCdna()
2615 return viewStyle.isScaleProteinAsCdna();
2619 public void setScaleProteinAsCdna(boolean b)
2621 viewStyle.setScaleProteinAsCdna(b);
2625 * @return true if view should scroll to show the highlighted region of a
2630 public final boolean isFollowHighlight()
2632 return followHighlight;
2636 public final void setFollowHighlight(boolean b)
2638 this.followHighlight = b;
2642 public ViewportRanges getRanges()
2648 * Helper method to populate the SearchResults with the location in the
2649 * complementary alignment to scroll to, in order to match this one.
2652 * the SearchResults to add to
2653 * @return the offset (below top of visible region) of the matched sequence
2655 protected int findComplementScrollTarget(SearchResultsI sr)
2657 final AlignViewportI complement = getCodingComplement();
2658 if (complement == null || !complement.isFollowHighlight())
2662 boolean iAmProtein = !getAlignment().isNucleotide();
2663 AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
2665 if (proteinAlignment == null)
2669 final List<AlignedCodonFrame> mappings = proteinAlignment
2673 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2674 * residue in the middle column of the visible region. Scroll the
2675 * complementary alignment to line up the corresponding residue.
2678 SequenceI sequence = null;
2681 * locate 'middle' column (true middle if an odd number visible, left of
2682 * middle if an even number visible)
2684 int middleColumn = ranges.getStartRes()
2685 + (ranges.getEndRes() - ranges.getStartRes()) / 2;
2686 final HiddenSequences hiddenSequences = getAlignment()
2687 .getHiddenSequences();
2690 * searching to the bottom of the alignment gives smoother scrolling across
2691 * all gapped visible regions
2693 int lastSeq = alignment.getHeight() - 1;
2694 List<AlignedCodonFrame> seqMappings = null;
2695 for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
2697 sequence = getAlignment().getSequenceAt(seqNo);
2698 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2702 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2706 seqMappings = MappingUtils
2707 .findMappingsForSequenceAndOthers(sequence, mappings,
2708 getCodingComplement().getAlignment().getSequences());
2709 if (!seqMappings.isEmpty())
2715 if (sequence == null || seqMappings == null || seqMappings.isEmpty())
2718 * No ungapped mapped sequence in middle column - do nothing
2722 MappingUtils.addSearchResults(sr, sequence,
2723 sequence.findPosition(middleColumn), seqMappings);
2728 * synthesize a column selection if none exists so it covers the given
2729 * selection group. if wholewidth is false, no column selection is made if the
2730 * selection group covers the whole alignment width.
2735 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2738 if (sg != null && (sgs = sg.getStartRes()) >= 0
2739 && sg.getStartRes() <= (sge = sg.getEndRes())
2740 && !this.hasSelectedColumns())
2742 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2749 colSel = new ColumnSelection();
2751 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2753 colSel.addElement(cspos);
2759 * hold status of current selection group - defined on alignment or not.
2761 private boolean selectionIsDefinedGroup = false;
2765 public boolean isSelectionDefinedGroup()
2767 if (selectionGroup == null)
2771 if (isSelectionGroupChanged(true))
2773 selectionIsDefinedGroup = false;
2774 List<SequenceGroup> gps = alignment.getGroups();
2775 if (gps == null || gps.size() == 0)
2777 selectionIsDefinedGroup = false;
2781 selectionIsDefinedGroup = gps.contains(selectionGroup);
2784 return selectionGroup.getContext() == alignment
2785 || selectionIsDefinedGroup;
2789 * null, or currently highlighted results on this view
2791 private SearchResultsI searchResults = null;
2794 public boolean hasSearchResults()
2796 return searchResults != null;
2800 public void setSearchResults(SearchResultsI results)
2802 searchResults = results;
2806 public SearchResultsI getSearchResults()
2808 return searchResults;