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.SearchResults;
40 import jalview.datamodel.Sequence;
41 import jalview.datamodel.SequenceCollectionI;
42 import jalview.datamodel.SequenceGroup;
43 import jalview.datamodel.SequenceI;
44 import jalview.schemes.Blosum62ColourScheme;
45 import jalview.schemes.ColourSchemeI;
46 import jalview.schemes.PIDColourScheme;
47 import jalview.schemes.ResidueProperties;
48 import jalview.structure.CommandListener;
49 import jalview.structure.StructureSelectionManager;
50 import jalview.structure.VamsasSource;
51 import jalview.util.Comparison;
52 import jalview.util.MappingUtils;
53 import jalview.viewmodel.styles.ViewStyle;
54 import jalview.workers.AlignCalcManager;
55 import jalview.workers.ComplementConsensusThread;
56 import jalview.workers.ConsensusThread;
57 import jalview.workers.StrucConsensusThread;
59 import java.awt.Color;
60 import java.util.ArrayDeque;
61 import java.util.ArrayList;
62 import java.util.BitSet;
63 import java.util.Deque;
64 import java.util.HashMap;
65 import java.util.Hashtable;
66 import java.util.List;
71 * base class holding visualization and analysis attributes and common logic for
72 * an active alignment view displayed in the GUI
77 public abstract class AlignmentViewport implements AlignViewportI,
78 CommandListener, VamsasSource
80 protected ViewStyleI viewStyle = new ViewStyle();
83 * A viewport that hosts the cDna view of this (protein), or vice versa (if
86 AlignViewportI codingComplement = null;
88 FeaturesDisplayedI featuresDisplayed = null;
90 protected Deque<CommandI> historyList = new ArrayDeque<CommandI>();
92 protected Deque<CommandI> redoList = new ArrayDeque<CommandI>();
96 * @see jalview.api.ViewStyleI#setFontName(java.lang.String)
98 public void setFontName(String name)
100 viewStyle.setFontName(name);
105 * @see jalview.api.ViewStyleI#setFontStyle(int)
107 public void setFontStyle(int style)
109 viewStyle.setFontStyle(style);
114 * @see jalview.api.ViewStyleI#setFontSize(int)
116 public void setFontSize(int size)
118 viewStyle.setFontSize(size);
123 * @see jalview.api.ViewStyleI#getFontStyle()
125 public int getFontStyle()
127 return viewStyle.getFontStyle();
132 * @see jalview.api.ViewStyleI#getFontName()
134 public String getFontName()
136 return viewStyle.getFontName();
141 * @see jalview.api.ViewStyleI#getFontSize()
143 public int getFontSize()
145 return viewStyle.getFontSize();
149 * @param upperCasebold
150 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
152 public void setUpperCasebold(boolean upperCasebold)
154 viewStyle.setUpperCasebold(upperCasebold);
159 * @see jalview.api.ViewStyleI#isUpperCasebold()
161 public boolean isUpperCasebold()
163 return viewStyle.isUpperCasebold();
168 * @see jalview.api.ViewStyleI#isSeqNameItalics()
170 public boolean isSeqNameItalics()
172 return viewStyle.isSeqNameItalics();
176 * @param colourByReferenceSeq
177 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
179 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
181 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
186 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
188 public void setColourAppliesToAllGroups(boolean b)
190 viewStyle.setColourAppliesToAllGroups(b);
195 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
197 public boolean getColourAppliesToAllGroups()
199 return viewStyle.getColourAppliesToAllGroups();
204 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
206 public boolean getAbovePIDThreshold()
208 return viewStyle.getAbovePIDThreshold();
213 * @see jalview.api.ViewStyleI#setIncrement(int)
215 public void setIncrement(int inc)
217 viewStyle.setIncrement(inc);
222 * @see jalview.api.ViewStyleI#getIncrement()
224 public int getIncrement()
226 return viewStyle.getIncrement();
231 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
233 public void setConservationSelected(boolean b)
235 viewStyle.setConservationSelected(b);
240 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
242 public void setShowHiddenMarkers(boolean show)
244 viewStyle.setShowHiddenMarkers(show);
249 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
251 public boolean getShowHiddenMarkers()
253 return viewStyle.getShowHiddenMarkers();
258 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
260 public void setScaleRightWrapped(boolean b)
262 viewStyle.setScaleRightWrapped(b);
267 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
269 public void setScaleLeftWrapped(boolean b)
271 viewStyle.setScaleLeftWrapped(b);
276 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
278 public void setScaleAboveWrapped(boolean b)
280 viewStyle.setScaleAboveWrapped(b);
285 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
287 public boolean getScaleLeftWrapped()
289 return viewStyle.getScaleLeftWrapped();
294 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
296 public boolean getScaleAboveWrapped()
298 return viewStyle.getScaleAboveWrapped();
303 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
305 public boolean getScaleRightWrapped()
307 return viewStyle.getScaleRightWrapped();
312 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
314 public void setAbovePIDThreshold(boolean b)
316 viewStyle.setAbovePIDThreshold(b);
321 * @see jalview.api.ViewStyleI#setThreshold(int)
323 public void setThreshold(int thresh)
325 viewStyle.setThreshold(thresh);
330 * @see jalview.api.ViewStyleI#getThreshold()
332 public int getThreshold()
334 return viewStyle.getThreshold();
339 * @see jalview.api.ViewStyleI#getShowJVSuffix()
341 public boolean getShowJVSuffix()
343 return viewStyle.getShowJVSuffix();
348 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
350 public void setShowJVSuffix(boolean b)
352 viewStyle.setShowJVSuffix(b);
357 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
359 public void setWrapAlignment(boolean state)
361 viewStyle.setWrapAlignment(state);
366 * @see jalview.api.ViewStyleI#setShowText(boolean)
368 public void setShowText(boolean state)
370 viewStyle.setShowText(state);
375 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
377 public void setRenderGaps(boolean state)
379 viewStyle.setRenderGaps(state);
384 * @see jalview.api.ViewStyleI#getColourText()
386 public boolean getColourText()
388 return viewStyle.getColourText();
393 * @see jalview.api.ViewStyleI#setColourText(boolean)
395 public void setColourText(boolean state)
397 viewStyle.setColourText(state);
402 * @see jalview.api.ViewStyleI#getWrapAlignment()
404 public boolean getWrapAlignment()
406 return viewStyle.getWrapAlignment();
411 * @see jalview.api.ViewStyleI#getShowText()
413 public boolean getShowText()
415 return viewStyle.getShowText();
420 * @see jalview.api.ViewStyleI#getWrappedWidth()
422 public int getWrappedWidth()
424 return viewStyle.getWrappedWidth();
429 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
431 public void setWrappedWidth(int w)
433 viewStyle.setWrappedWidth(w);
438 * @see jalview.api.ViewStyleI#getCharHeight()
440 public int getCharHeight()
442 return viewStyle.getCharHeight();
447 * @see jalview.api.ViewStyleI#setCharHeight(int)
449 public void setCharHeight(int h)
451 viewStyle.setCharHeight(h);
456 * @see jalview.api.ViewStyleI#getCharWidth()
458 public int getCharWidth()
460 return viewStyle.getCharWidth();
465 * @see jalview.api.ViewStyleI#setCharWidth(int)
467 public void setCharWidth(int w)
469 viewStyle.setCharWidth(w);
474 * @see jalview.api.ViewStyleI#getShowBoxes()
476 public boolean getShowBoxes()
478 return viewStyle.getShowBoxes();
483 * @see jalview.api.ViewStyleI#getShowUnconserved()
485 public boolean getShowUnconserved()
487 return viewStyle.getShowUnconserved();
491 * @param showunconserved
492 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
494 public void setShowUnconserved(boolean showunconserved)
496 viewStyle.setShowUnconserved(showunconserved);
501 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
503 public void setSeqNameItalics(boolean default1)
505 viewStyle.setSeqNameItalics(default1);
509 * alignment displayed in the viewport. Please use get/setter
511 protected AlignmentI alignment;
514 public AlignmentI getAlignment()
520 public char getGapCharacter()
522 return alignment.getGapCharacter();
525 protected String sequenceSetID;
528 * probably unused indicator that view is of a dataset rather than an
531 protected boolean isDataset = false;
533 public void setDataset(boolean b)
538 public boolean isDataset()
544 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
546 protected ColumnSelection colSel = new ColumnSelection();
548 public boolean autoCalculateConsensus = true;
550 protected boolean autoCalculateStrucConsensus = true;
552 protected boolean ignoreGapsInConsensusCalculation = false;
554 protected ColourSchemeI globalColourScheme = null;
558 public void setGlobalColourScheme(ColourSchemeI cs)
560 // TODO: logic refactored from AlignFrame changeColour -
561 // autorecalc stuff should be changed to rely on the worker system
562 // check to see if we should implement a changeColour(cs) method rather than
563 // put th logic in here
564 // - means that caller decides if they want to just modify state and defer
565 // calculation till later or to do all calculations in thread.
567 globalColourScheme = cs;
568 boolean recalc = false;
571 cs.setConservationApplied(recalc = getConservationSelected());
572 if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
573 || cs instanceof Blosum62ColourScheme)
576 cs.setThreshold(viewStyle.getThreshold(),
577 ignoreGapsInConsensusCalculation);
581 cs.setThreshold(0, ignoreGapsInConsensusCalculation);
585 cs.setConsensus(hconsensus);
586 cs.setConservation(hconservation);
588 cs.alignmentChanged(alignment, hiddenRepSequences);
590 if (getColourAppliesToAllGroups())
592 for (SequenceGroup sg : getAlignment().getGroups())
599 sg.cs = cs.applyTo(sg, getHiddenRepSequences());
600 sg.setConsPercGaps(ConsPercGaps);
601 if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
602 || cs instanceof Blosum62ColourScheme)
604 sg.cs.setThreshold(viewStyle.getThreshold(),
605 isIgnoreGapsConsensus());
610 sg.cs.setThreshold(0, isIgnoreGapsConsensus());
613 if (getConservationSelected())
615 sg.cs.setConservationApplied(true);
620 sg.cs.setConservation(null);
621 // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
625 sg.recalcConservation();
629 sg.cs.alignmentChanged(sg, hiddenRepSequences);
637 public ColourSchemeI getGlobalColourScheme()
639 return globalColourScheme;
642 protected AlignmentAnnotation consensus;
644 protected AlignmentAnnotation complementConsensus;
646 protected AlignmentAnnotation strucConsensus;
648 protected AlignmentAnnotation conservation;
650 protected AlignmentAnnotation quality;
652 protected AlignmentAnnotation[] groupConsensus;
654 protected AlignmentAnnotation[] groupConservation;
657 * results of alignment consensus analysis for visible portion of view
659 protected Hashtable[] hconsensus = null;
662 * results of cDNA complement consensus visible portion of view
664 protected Hashtable[] hcomplementConsensus = null;
667 * results of secondary structure base pair consensus for visible portion of
670 protected Hashtable[] hStrucConsensus = null;
672 protected Conservation hconservation = null;
675 public void setConservation(Conservation cons)
677 hconservation = cons;
681 * percentage gaps allowed in a column before all amino acid properties should
682 * be considered unconserved
684 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
687 public int getConsPercGaps()
693 public void setSequenceConsensusHash(Hashtable[] hconsensus)
695 this.hconsensus = hconsensus;
699 public void setComplementConsensusHash(Hashtable[] hconsensus)
701 this.hcomplementConsensus = hconsensus;
705 public Hashtable[] getSequenceConsensusHash()
711 public Hashtable[] getComplementConsensusHash()
713 return hcomplementConsensus;
717 public Hashtable[] getRnaStructureConsensusHash()
719 return hStrucConsensus;
723 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
725 this.hStrucConsensus = hStrucConsensus;
730 public AlignmentAnnotation getAlignmentQualityAnnot()
736 public AlignmentAnnotation getAlignmentConservationAnnotation()
742 public AlignmentAnnotation getAlignmentConsensusAnnotation()
748 public AlignmentAnnotation getComplementConsensusAnnotation()
750 return complementConsensus;
754 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
756 return strucConsensus;
759 protected AlignCalcManagerI calculator = new AlignCalcManager();
762 * trigger update of conservation annotation
764 public void updateConservation(final AlignmentViewPanel ap)
766 // see note in mantis : issue number 8585
767 if (alignment.isNucleotide() || conservation == null
768 || !autoCalculateConsensus)
773 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
775 calculator.registerWorker(new jalview.workers.ConservationThread(
781 * trigger update of consensus annotation
783 public void updateConsensus(final AlignmentViewPanel ap)
785 // see note in mantis : issue number 8585
786 if (consensus == null || !autoCalculateConsensus)
790 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
792 calculator.registerWorker(new ConsensusThread(this, ap));
796 * A separate thread to compute cDNA consensus for a protein alignment
798 final AlignmentI al = this.getAlignment();
799 if (!al.isNucleotide() && al.getCodonFrames() != null
800 && !al.getCodonFrames().isEmpty())
803 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
805 calculator.registerWorker(new ComplementConsensusThread(this, ap));
810 // --------START Structure Conservation
811 public void updateStrucConsensus(final AlignmentViewPanel ap)
813 if (autoCalculateStrucConsensus && strucConsensus == null
814 && alignment.isNucleotide() && alignment.hasRNAStructure())
816 // secondary structure has been added - so init the consensus line
820 // see note in mantis : issue number 8585
821 if (strucConsensus == null || !autoCalculateStrucConsensus)
825 if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
827 calculator.registerWorker(new StrucConsensusThread(this, ap));
831 public boolean isCalcInProgress()
833 return calculator.isWorking();
837 public boolean isCalculationInProgress(
838 AlignmentAnnotation alignmentAnnotation)
840 if (!alignmentAnnotation.autoCalculated)
844 if (calculator.workingInvolvedWith(alignmentAnnotation))
846 // System.err.println("grey out ("+alignmentAnnotation.label+")");
853 public boolean isClosed()
855 // TODO: check that this isClosed is only true after panel is closed, not
856 // before it is fully constructed.
857 return alignment == null;
861 public AlignCalcManagerI getCalcManager()
867 * should conservation rows be shown for groups
869 protected boolean showGroupConservation = false;
872 * should consensus rows be shown for groups
874 protected boolean showGroupConsensus = false;
877 * should consensus profile be rendered by default
879 protected boolean showSequenceLogo = false;
882 * should consensus profile be rendered normalised to row height
884 protected boolean normaliseSequenceLogo = false;
887 * should consensus histograms be rendered by default
889 protected boolean showConsensusHistogram = true;
892 * @return the showConsensusProfile
895 public boolean isShowSequenceLogo()
897 return showSequenceLogo;
901 * @param showSequenceLogo
904 public void setShowSequenceLogo(boolean showSequenceLogo)
906 if (showSequenceLogo != this.showSequenceLogo)
908 // TODO: decouple settings setting from calculation when refactoring
909 // annotation update method from alignframe to viewport
910 this.showSequenceLogo = showSequenceLogo;
911 calculator.updateAnnotationFor(ConsensusThread.class);
912 calculator.updateAnnotationFor(ComplementConsensusThread.class);
913 calculator.updateAnnotationFor(StrucConsensusThread.class);
915 this.showSequenceLogo = showSequenceLogo;
919 * @param showConsensusHistogram
920 * the showConsensusHistogram to set
922 public void setShowConsensusHistogram(boolean showConsensusHistogram)
924 this.showConsensusHistogram = showConsensusHistogram;
928 * @return the showGroupConservation
930 public boolean isShowGroupConservation()
932 return showGroupConservation;
936 * @param showGroupConservation
937 * the showGroupConservation to set
939 public void setShowGroupConservation(boolean showGroupConservation)
941 this.showGroupConservation = showGroupConservation;
945 * @return the showGroupConsensus
947 public boolean isShowGroupConsensus()
949 return showGroupConsensus;
953 * @param showGroupConsensus
954 * the showGroupConsensus to set
956 public void setShowGroupConsensus(boolean showGroupConsensus)
958 this.showGroupConsensus = showGroupConsensus;
963 * @return flag to indicate if the consensus histogram should be rendered by
967 public boolean isShowConsensusHistogram()
969 return this.showConsensusHistogram;
973 * when set, updateAlignment will always ensure sequences are of equal length
975 private boolean padGaps = false;
978 * when set, alignment should be reordered according to a newly opened tree
980 public boolean sortByTree = false;
986 * @return null or the currently selected sequence region
989 public SequenceGroup getSelectionGroup()
991 return selectionGroup;
995 * Set the selection group for this window.
998 * - group holding references to sequences in this alignment view
1002 public void setSelectionGroup(SequenceGroup sg)
1004 selectionGroup = sg;
1007 public void setHiddenColumns(ColumnSelection colsel)
1009 this.colSel = colsel;
1013 public ColumnSelection getColumnSelection()
1019 public void setColumnSelection(ColumnSelection colSel)
1021 this.colSel = colSel;
1024 updateHiddenColumns();
1033 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1035 return hiddenRepSequences;
1039 public void setHiddenRepSequences(
1040 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1042 this.hiddenRepSequences = hiddenRepSequences;
1046 public boolean hasHiddenColumns()
1048 return colSel != null && colSel.hasHiddenColumns();
1051 public void updateHiddenColumns()
1053 // this method doesn't really do anything now. But - it could, since a
1054 // column Selection could be in the process of modification
1055 // hasHiddenColumns = colSel.hasHiddenColumns();
1059 public boolean hasHiddenRows()
1061 return alignment.getHiddenSequences().getSize() > 0;
1065 protected SequenceGroup selectionGroup;
1067 public void setSequenceSetId(String newid)
1069 if (sequenceSetID != null)
1072 .println("Warning - overwriting a sequenceSetId for a viewport!");
1074 sequenceSetID = new String(newid);
1078 public String getSequenceSetId()
1080 if (sequenceSetID == null)
1082 sequenceSetID = alignment.hashCode() + "";
1085 return sequenceSetID;
1089 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1092 protected String viewId = null;
1095 public String getViewId()
1099 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1104 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1106 ignoreGapsInConsensusCalculation = b;
1109 updateConsensus(ap);
1110 if (globalColourScheme != null)
1112 globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
1113 ignoreGapsInConsensusCalculation);
1119 private long sgrouphash = -1, colselhash = -1;
1122 * checks current SelectionGroup against record of last hash value, and
1126 * update the record of last hash value
1128 * @return true if SelectionGroup changed since last call (when b is true)
1130 public boolean isSelectionGroupChanged(boolean b)
1132 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1133 : selectionGroup.hashCode();
1134 if (hc != -1 && hc != sgrouphash)
1146 * checks current colsel against record of last hash value, and optionally
1150 * update the record of last hash value
1151 * @return true if colsel changed since last call (when b is true)
1153 public boolean isColSelChanged(boolean b)
1155 int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
1157 if (hc != -1 && hc != colselhash)
1169 public boolean isIgnoreGapsConsensus()
1171 return ignoreGapsInConsensusCalculation;
1174 // / property change stuff
1176 // JBPNote Prolly only need this in the applet version.
1177 private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
1180 protected boolean showConservation = true;
1182 protected boolean showQuality = true;
1184 protected boolean showConsensus = true;
1186 private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
1188 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1190 protected boolean showAutocalculatedAbove;
1193 * when set, view will scroll to show the highlighted position
1195 private boolean followHighlight = true;
1197 // TODO private with getters and setters?
1198 public int startRes;
1202 public int startSeq;
1207 * Property change listener for changes in alignment
1212 public void addPropertyChangeListener(
1213 java.beans.PropertyChangeListener listener)
1215 changeSupport.addPropertyChangeListener(listener);
1224 public void removePropertyChangeListener(
1225 java.beans.PropertyChangeListener listener)
1227 changeSupport.removePropertyChangeListener(listener);
1231 * Property change listener for changes in alignment
1240 public void firePropertyChange(String prop, Object oldvalue,
1243 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1246 // common hide/show column stuff
1248 public void hideSelectedColumns()
1250 if (colSel.size() < 1)
1255 colSel.hideSelectedColumns();
1256 setSelectionGroup(null);
1260 public void hideColumns(int start, int end)
1264 colSel.hideColumns(start);
1268 colSel.hideColumns(start, end);
1272 public void showColumn(int col)
1274 colSel.revealHiddenColumns(col);
1278 public void showAllHiddenColumns()
1280 colSel.revealAllHiddenColumns();
1283 // common hide/show seq stuff
1284 public void showAllHiddenSeqs()
1286 if (alignment.getHiddenSequences().getSize() > 0)
1288 if (selectionGroup == null)
1290 selectionGroup = new SequenceGroup();
1291 selectionGroup.setEndRes(alignment.getWidth() - 1);
1293 List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
1294 hiddenRepSequences);
1295 for (SequenceI seq : tmp)
1297 selectionGroup.addSequence(seq, false);
1298 setSequenceAnnotationsVisible(seq, true);
1301 hiddenRepSequences = null;
1303 firePropertyChange("alignment", null, alignment.getSequences());
1304 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1310 public void showSequence(int index)
1312 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1314 hiddenRepSequences);
1317 if (selectionGroup == null)
1319 selectionGroup = new SequenceGroup();
1320 selectionGroup.setEndRes(alignment.getWidth() - 1);
1323 for (SequenceI seq : tmp)
1325 selectionGroup.addSequence(seq, false);
1326 setSequenceAnnotationsVisible(seq, true);
1328 firePropertyChange("alignment", null, alignment.getSequences());
1333 public void hideAllSelectedSeqs()
1335 if (selectionGroup == null || selectionGroup.getSize() < 1)
1340 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1344 setSelectionGroup(null);
1347 public void hideSequence(SequenceI[] seq)
1351 for (int i = 0; i < seq.length; i++)
1353 alignment.getHiddenSequences().hideSequence(seq[i]);
1354 setSequenceAnnotationsVisible(seq[i], false);
1356 firePropertyChange("alignment", null, alignment.getSequences());
1361 * Set visibility for any annotations for the given sequence.
1365 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1368 for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
1370 if (ann.sequenceRef == sequenceI)
1372 ann.visible = visible;
1377 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1379 int sSize = sg.getSize();
1385 if (hiddenRepSequences == null)
1387 hiddenRepSequences = new Hashtable();
1390 hiddenRepSequences.put(repSequence, sg);
1392 // Hide all sequences except the repSequence
1393 SequenceI[] seqs = new SequenceI[sSize - 1];
1395 for (int i = 0; i < sSize; i++)
1397 if (sg.getSequenceAt(i) != repSequence)
1399 if (index == sSize - 1)
1404 seqs[index++] = sg.getSequenceAt(i);
1407 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1408 sg.setHidereps(true); // note: not done in 2.7applet
1413 public boolean isHiddenRepSequence(SequenceI seq)
1415 return alignment.getSeqrep()==seq || (hiddenRepSequences != null
1416 && hiddenRepSequences.containsKey(seq));
1419 public SequenceGroup getRepresentedSequences(SequenceI seq)
1421 return (SequenceGroup) (hiddenRepSequences == null ? null
1422 : hiddenRepSequences.get(seq));
1426 public int adjustForHiddenSeqs(int alignmentIndex)
1428 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1433 public void invertColumnSelection()
1435 colSel.invertColumnSelection(0, alignment.getWidth());
1440 public SequenceI[] getSelectionAsNewSequence()
1442 SequenceI[] sequences;
1443 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1444 // this was the only caller in the applet for this method
1445 // JBPNote: in applet, this method returned references to the alignment
1446 // sequences, and it did not honour the presence/absence of annotation
1447 // attached to the alignment (probably!)
1448 if (selectionGroup == null || selectionGroup.getSize() == 0)
1450 sequences = alignment.getSequencesArray();
1451 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1452 for (int i = 0; i < sequences.length; i++)
1454 // construct new sequence with subset of visible annotation
1455 sequences[i] = new Sequence(sequences[i], annots);
1460 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1468 public SequenceI[] getSequenceSelection()
1470 SequenceI[] sequences = null;
1471 if (selectionGroup != null)
1473 sequences = selectionGroup.getSequencesInOrder(alignment);
1475 if (sequences == null)
1477 sequences = alignment.getSequencesArray();
1484 public CigarArray getViewAsCigars(
1485 boolean selectedRegionOnly)
1487 return new CigarArray(alignment, colSel,
1488 (selectedRegionOnly ? selectionGroup : null));
1493 public jalview.datamodel.AlignmentView getAlignmentView(
1494 boolean selectedOnly)
1496 return getAlignmentView(selectedOnly, false);
1501 public jalview.datamodel.AlignmentView getAlignmentView(
1502 boolean selectedOnly, boolean markGroups)
1504 return new AlignmentView(alignment, colSel, selectionGroup,
1505 colSel != null && colSel.hasHiddenColumns(), selectedOnly,
1511 public String[] getViewAsString(boolean selectedRegionOnly)
1513 String[] selection = null;
1514 SequenceI[] seqs = null;
1516 int start = 0, end = 0;
1517 if (selectedRegionOnly && selectionGroup != null)
1519 iSize = selectionGroup.getSize();
1520 seqs = selectionGroup.getSequencesInOrder(alignment);
1521 start = selectionGroup.getStartRes();
1522 end = selectionGroup.getEndRes() + 1;
1526 iSize = alignment.getHeight();
1527 seqs = alignment.getSequencesArray();
1528 end = alignment.getWidth();
1531 selection = new String[iSize];
1532 if (colSel != null && colSel.hasHiddenColumns())
1534 selection = colSel.getVisibleSequenceStrings(start, end, seqs);
1538 for (i = 0; i < iSize; i++)
1540 selection[i] = seqs[i].getSequenceAsString(start, end);
1549 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1551 ArrayList<int[]> regions = new ArrayList<int[]>();
1557 if (colSel != null && colSel.hasHiddenColumns())
1561 start = colSel.adjustForHiddenColumns(start);
1564 end = colSel.getHiddenBoundaryRight(start);
1575 regions.add(new int[]
1578 if (colSel != null && colSel.hasHiddenColumns())
1580 start = colSel.adjustForHiddenColumns(end);
1581 start = colSel.getHiddenBoundaryLeft(start) + 1;
1583 } while (end < max);
1585 int[][] startEnd = new int[regions.size()][2];
1591 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
1593 ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
1594 AlignmentAnnotation[] aa;
1595 if ((aa=alignment.getAlignmentAnnotation())!=null)
1597 for (AlignmentAnnotation annot:aa)
1599 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1600 if (selectedOnly && selectionGroup!=null)
1602 colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
1604 colSel.makeVisibleAnnotation(clone);
1614 public boolean isPadGaps()
1621 public void setPadGaps(boolean padGaps)
1623 this.padGaps = padGaps;
1627 * apply any post-edit constraints and trigger any calculations needed after
1628 * an edit has been performed on the alignment
1633 public void alignmentChanged(AlignmentViewPanel ap)
1637 alignment.padGaps();
1639 if (autoCalculateConsensus)
1641 updateConsensus(ap);
1643 if (hconsensus != null && autoCalculateConsensus)
1645 updateConservation(ap);
1647 if (autoCalculateStrucConsensus)
1649 updateStrucConsensus(ap);
1652 // Reset endRes of groups if beyond alignment width
1653 int alWidth = alignment.getWidth();
1654 List<SequenceGroup> groups = alignment.getGroups();
1657 for (SequenceGroup sg : groups)
1659 if (sg.getEndRes() > alWidth)
1661 sg.setEndRes(alWidth - 1);
1666 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1668 selectionGroup.setEndRes(alWidth - 1);
1671 resetAllColourSchemes();
1672 calculator.restartWorkers();
1673 // alignment.adjustSequenceAnnotations();
1677 * reset scope and do calculations for all applied colourschemes on alignment
1679 void resetAllColourSchemes()
1681 ColourSchemeI cs = globalColourScheme;
1684 cs.alignmentChanged(alignment, hiddenRepSequences);
1686 cs.setConsensus(hconsensus);
1687 if (cs.conservationApplied())
1689 cs.setConservation(Conservation.calculateConservation("All",
1690 ResidueProperties.propHash, 3, alignment.getSequences(), 0,
1691 alignment.getWidth(), false, getConsPercGaps(), false));
1695 for (SequenceGroup sg : alignment.getGroups())
1699 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1701 sg.recalcConservation();
1705 protected void initAutoAnnotation()
1707 // TODO: add menu option action that nulls or creates consensus object
1708 // depending on if the user wants to see the annotation or not in a
1709 // specific alignment
1711 if (hconsensus == null && !isDataset)
1713 if (!alignment.isNucleotide())
1722 consensus = new AlignmentAnnotation("Consensus", "PID",
1723 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1724 initConsensus(consensus);
1726 initComplementConsensus();
1731 * If this is a protein alignment and there are mappings to cDNA, add the cDNA
1732 * consensus annotation.
1734 public void initComplementConsensus()
1736 if (!alignment.isNucleotide())
1738 final Set<AlignedCodonFrame> codonMappings = alignment
1740 if (codonMappings != null && !codonMappings.isEmpty())
1742 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1743 "PID for cDNA", new Annotation[1], 0f, 100f,
1744 AlignmentAnnotation.BAR_GRAPH);
1745 initConsensus(complementConsensus);
1750 private void initConsensus(AlignmentAnnotation aa)
1753 aa.autoCalculated = true;
1757 alignment.addAnnotation(aa);
1761 private void initConservation()
1763 if (showConservation)
1765 if (conservation == null)
1767 conservation = new AlignmentAnnotation("Conservation",
1768 "Conservation of total alignment less than "
1769 + getConsPercGaps() + "% gaps", new Annotation[1],
1770 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1771 conservation.hasText = true;
1772 conservation.autoCalculated = true;
1773 alignment.addAnnotation(conservation);
1778 private void initQuality()
1782 if (quality == null)
1784 quality = new AlignmentAnnotation("Quality",
1785 "Alignment Quality based on Blosum62 scores",
1786 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1787 quality.hasText = true;
1788 quality.autoCalculated = true;
1789 alignment.addAnnotation(quality);
1794 private void initRNAStructure()
1796 if (alignment.hasRNAStructure() && strucConsensus == null)
1798 strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
1799 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1800 strucConsensus.hasText = true;
1801 strucConsensus.autoCalculated = true;
1805 alignment.addAnnotation(strucConsensus);
1813 * @see jalview.api.AlignViewportI#calcPanelHeight()
1816 public int calcPanelHeight()
1818 // setHeight of panels
1819 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
1821 int charHeight = getCharHeight();
1824 BitSet graphgrp = new BitSet();
1825 for (AlignmentAnnotation aa : anns)
1829 System.err.println("Null annotation row: ignoring.");
1836 if (aa.graphGroup > -1)
1838 if (graphgrp.get(aa.graphGroup))
1844 graphgrp.set(aa.graphGroup);
1851 aa.height += charHeight;
1861 aa.height += aa.graphHeight;
1869 height += aa.height;
1881 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
1882 boolean preserveNewGroupSettings)
1884 boolean updateCalcs = false;
1885 boolean conv = isShowGroupConservation();
1886 boolean cons = isShowGroupConsensus();
1887 boolean showprf = isShowSequenceLogo();
1888 boolean showConsHist = isShowConsensusHistogram();
1889 boolean normLogo = isNormaliseSequenceLogo();
1892 * TODO reorder the annotation rows according to group/sequence ordering on
1895 boolean sortg = true;
1897 // remove old automatic annotation
1898 // add any new annotation
1900 // intersect alignment annotation with alignment groups
1902 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
1903 List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
1906 for (int an = 0; an < aan.length; an++)
1908 if (aan[an].autoCalculated && aan[an].groupRef != null)
1910 oldrfs.add(aan[an].groupRef);
1911 alignment.deleteAnnotation(aan[an], false);
1915 if (alignment.getGroups() != null)
1917 for (SequenceGroup sg : alignment.getGroups())
1919 updateCalcs = false;
1920 if (applyGlobalSettings
1921 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
1923 // set defaults for this group's conservation/consensus
1924 sg.setshowSequenceLogo(showprf);
1925 sg.setShowConsensusHistogram(showConsHist);
1926 sg.setNormaliseSequenceLogo(normLogo);
1931 alignment.addAnnotation(sg.getConservationRow(), 0);
1936 alignment.addAnnotation(sg.getConsensus(), 0);
1938 // refresh the annotation rows
1941 sg.recalcConservation();
1948 public boolean isDisplayReferenceSeq()
1950 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
1954 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
1956 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
1960 public boolean isColourByReferenceSeq()
1962 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
1966 public Color getSequenceColour(SequenceI seq)
1968 Color sqc = sequenceColours.get(seq);
1969 return (sqc == null ? Color.white : sqc);
1973 public void setSequenceColour(SequenceI seq, Color col)
1977 sequenceColours.remove(seq);
1981 sequenceColours.put(seq, col);
1986 public void updateSequenceIdColours()
1988 for (SequenceGroup sg : alignment.getGroups())
1990 if (sg.idColour != null)
1992 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
1994 sequenceColours.put(s, sg.idColour);
2001 public void clearSequenceColours()
2003 sequenceColours.clear();
2007 public AlignViewportI getCodingComplement()
2009 return this.codingComplement;
2013 * Set this as the (cDna/protein) complement of the given viewport. Also
2014 * ensures the reverse relationship is set on the given viewport.
2017 public void setCodingComplement(AlignViewportI av)
2021 System.err.println("Ignoring recursive setCodingComplement request");
2025 this.codingComplement = av;
2026 // avoid infinite recursion!
2027 if (av.getCodingComplement() != this)
2029 av.setCodingComplement(this);
2035 public boolean isNucleotide()
2037 return getAlignment() == null ? false : getAlignment().isNucleotide();
2041 public FeaturesDisplayedI getFeaturesDisplayed()
2043 return featuresDisplayed;
2047 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2049 featuresDisplayed = featuresDisplayedI;
2053 public boolean areFeaturesDisplayed()
2055 return featuresDisplayed != null && featuresDisplayed.getRegisterdFeaturesCount()>0;
2062 * features are displayed if true
2065 public void setShowSequenceFeatures(boolean b)
2067 viewStyle.setShowSequenceFeatures(b);
2070 public boolean isShowSequenceFeatures()
2072 return viewStyle.isShowSequenceFeatures();
2076 public void setShowSequenceFeaturesHeight(boolean selected)
2078 viewStyle.setShowSequenceFeaturesHeight(selected);
2082 public boolean isShowSequenceFeaturesHeight()
2084 return viewStyle.isShowSequenceFeaturesHeight();
2090 public void setShowAnnotation(boolean b)
2092 viewStyle.setShowAnnotation(b);
2096 public boolean isShowAnnotation()
2098 return viewStyle.isShowAnnotation();
2102 public boolean isRightAlignIds()
2104 return viewStyle.isRightAlignIds();
2108 public void setRightAlignIds(boolean rightAlignIds)
2110 viewStyle.setRightAlignIds(rightAlignIds);
2114 public boolean getConservationSelected()
2116 return viewStyle.getConservationSelected();
2120 public void setShowBoxes(boolean state)
2122 viewStyle.setShowBoxes(state);
2127 * @see jalview.api.ViewStyleI#getTextColour()
2129 public Color getTextColour()
2131 return viewStyle.getTextColour();
2136 * @see jalview.api.ViewStyleI#getTextColour2()
2138 public Color getTextColour2()
2140 return viewStyle.getTextColour2();
2145 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2147 public int getThresholdTextColour()
2149 return viewStyle.getThresholdTextColour();
2154 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2156 public boolean isConservationColourSelected()
2158 return viewStyle.isConservationColourSelected();
2163 * @see jalview.api.ViewStyleI#isRenderGaps()
2165 public boolean isRenderGaps()
2167 return viewStyle.isRenderGaps();
2172 * @see jalview.api.ViewStyleI#isShowColourText()
2174 public boolean isShowColourText()
2176 return viewStyle.isShowColourText();
2180 * @param conservationColourSelected
2181 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2183 public void setConservationColourSelected(
2184 boolean conservationColourSelected)
2186 viewStyle.setConservationColourSelected(conservationColourSelected);
2190 * @param showColourText
2191 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2193 public void setShowColourText(boolean showColourText)
2195 viewStyle.setShowColourText(showColourText);
2200 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2202 public void setTextColour(Color textColour)
2204 viewStyle.setTextColour(textColour);
2208 * @param thresholdTextColour
2209 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2211 public void setThresholdTextColour(int thresholdTextColour)
2213 viewStyle.setThresholdTextColour(thresholdTextColour);
2217 * @param textColour2
2218 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2220 public void setTextColour2(Color textColour2)
2222 viewStyle.setTextColour2(textColour2);
2226 public ViewStyleI getViewStyle()
2228 return new ViewStyle(viewStyle);
2232 public void setViewStyle(ViewStyleI settingsForView)
2234 viewStyle = new ViewStyle(settingsForView);
2238 public boolean sameStyle(ViewStyleI them)
2240 return viewStyle.sameStyle(them);
2245 * @see jalview.api.ViewStyleI#getIdWidth()
2247 public int getIdWidth()
2249 return viewStyle.getIdWidth();
2254 * @see jalview.api.ViewStyleI#setIdWidth(int)
2256 public void setIdWidth(int i)
2258 viewStyle.setIdWidth(i);
2263 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2265 public boolean isCentreColumnLabels()
2267 return viewStyle.isCentreColumnLabels();
2271 * @param centreColumnLabels
2272 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2274 public void setCentreColumnLabels(boolean centreColumnLabels)
2276 viewStyle.setCentreColumnLabels(centreColumnLabels);
2281 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2283 public void setShowDBRefs(boolean showdbrefs)
2285 viewStyle.setShowDBRefs(showdbrefs);
2290 * @see jalview.api.ViewStyleI#isShowDBRefs()
2292 public boolean isShowDBRefs()
2294 return viewStyle.isShowDBRefs();
2299 * @see jalview.api.ViewStyleI#isShowNPFeats()
2301 public boolean isShowNPFeats()
2303 return viewStyle.isShowNPFeats();
2307 * @param shownpfeats
2308 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2310 public void setShowNPFeats(boolean shownpfeats)
2312 viewStyle.setShowNPFeats(shownpfeats);
2315 public abstract StructureSelectionManager getStructureSelectionManager();
2318 * Add one command to the command history list.
2322 public void addToHistoryList(CommandI command)
2324 if (this.historyList != null)
2326 this.historyList.push(command);
2327 broadcastCommand(command, false);
2331 protected void broadcastCommand(CommandI command, boolean undo)
2333 getStructureSelectionManager().commandPerformed(command, undo, getVamsasSource());
2337 * Add one command to the command redo list.
2341 public void addToRedoList(CommandI command)
2343 if (this.redoList != null)
2345 this.redoList.push(command);
2347 broadcastCommand(command, true);
2351 * Clear the command redo list.
2353 public void clearRedoList()
2355 if (this.redoList != null)
2357 this.redoList.clear();
2361 public void setHistoryList(Deque<CommandI> list)
2363 this.historyList = list;
2366 public Deque<CommandI> getHistoryList()
2368 return this.historyList;
2371 public void setRedoList(Deque<CommandI> list)
2373 this.redoList = list;
2376 public Deque<CommandI> getRedoList()
2378 return this.redoList;
2382 public VamsasSource getVamsasSource()
2387 public SequenceAnnotationOrder getSortAnnotationsBy()
2389 return sortAnnotationsBy;
2392 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2394 this.sortAnnotationsBy = sortAnnotationsBy;
2397 public boolean isShowAutocalculatedAbove()
2399 return showAutocalculatedAbove;
2402 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2404 this.showAutocalculatedAbove = showAutocalculatedAbove;
2408 public boolean isScaleProteinAsCdna()
2410 return viewStyle.isScaleProteinAsCdna();
2414 public void setScaleProteinAsCdna(boolean b)
2416 viewStyle.setScaleProteinAsCdna(b);
2420 * @return true if view should scroll to show the highlighted region of a
2425 public final boolean isFollowHighlight()
2427 return followHighlight;
2431 public final void setFollowHighlight(boolean b)
2433 this.followHighlight = b;
2436 public int getStartRes()
2441 public int getEndRes()
2446 public int getStartSeq()
2451 public void setStartRes(int res)
2453 this.startRes = res;
2456 public void setStartSeq(int seq)
2458 this.startSeq = seq;
2461 public void setEndRes(int res)
2463 if (res > alignment.getWidth() - 1)
2465 // log.System.out.println(" Corrected res from " + res + " to maximum " +
2466 // (alignment.getWidth()-1));
2467 res = alignment.getWidth() - 1;
2476 public void setEndSeq(int seq)
2478 if (seq > alignment.getHeight())
2480 seq = alignment.getHeight();
2489 public int getEndSeq()
2495 * Helper method to populate the SearchResults with the location in the
2496 * complementary alignment to scroll to, in order to match this one.
2499 * the SearchResults to add to
2500 * @return the offset (below top of visible region) of the matched sequence
2502 protected int findComplementScrollTarget(SearchResults sr)
2504 final AlignViewportI codingComplement = getCodingComplement();
2505 if (codingComplement == null || !codingComplement.isFollowHighlight())
2509 boolean iAmProtein = !getAlignment().isNucleotide();
2510 AlignmentI proteinAlignment = iAmProtein ? getAlignment()
2511 : codingComplement.getAlignment();
2512 if (proteinAlignment == null)
2516 final Set<AlignedCodonFrame> mappings = proteinAlignment
2520 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2521 * residue in the middle column of the visible region. Scroll the
2522 * complementary alignment to line up the corresponding residue.
2525 SequenceI sequence = null;
2528 * locate 'middle' column (true middle if an odd number visible, left of
2529 * middle if an even number visible)
2531 int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
2532 final HiddenSequences hiddenSequences = getAlignment()
2533 .getHiddenSequences();
2534 for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
2536 sequence = getAlignment().getSequenceAt(seqNo);
2537 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2541 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2545 List<AlignedCodonFrame> seqMappings = MappingUtils
2546 .findMappingsForSequence(sequence, mappings);
2547 if (!seqMappings.isEmpty())
2553 if (sequence == null)
2556 * No ungapped mapped sequence in middle column - do nothing
2560 MappingUtils.addSearchResults(sr, sequence,
2561 sequence.findPosition(middleColumn), mappings);