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.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.util.ArrayDeque;
62 import java.util.ArrayList;
63 import java.util.BitSet;
64 import java.util.Deque;
65 import java.util.HashMap;
66 import java.util.Hashtable;
67 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)
99 public void setFontName(String name)
101 viewStyle.setFontName(name);
106 * @see jalview.api.ViewStyleI#setFontStyle(int)
109 public void setFontStyle(int style)
111 viewStyle.setFontStyle(style);
116 * @see jalview.api.ViewStyleI#setFontSize(int)
119 public void setFontSize(int size)
121 viewStyle.setFontSize(size);
126 * @see jalview.api.ViewStyleI#getFontStyle()
129 public int getFontStyle()
131 return viewStyle.getFontStyle();
136 * @see jalview.api.ViewStyleI#getFontName()
139 public String getFontName()
141 return viewStyle.getFontName();
146 * @see jalview.api.ViewStyleI#getFontSize()
149 public int getFontSize()
151 return viewStyle.getFontSize();
155 * @param upperCasebold
156 * @see jalview.api.ViewStyleI#setUpperCasebold(boolean)
159 public void setUpperCasebold(boolean upperCasebold)
161 viewStyle.setUpperCasebold(upperCasebold);
166 * @see jalview.api.ViewStyleI#isUpperCasebold()
169 public boolean isUpperCasebold()
171 return viewStyle.isUpperCasebold();
176 * @see jalview.api.ViewStyleI#isSeqNameItalics()
179 public boolean isSeqNameItalics()
181 return viewStyle.isSeqNameItalics();
185 * @param colourByReferenceSeq
186 * @see jalview.api.ViewStyleI#setColourByReferenceSeq(boolean)
189 public void setColourByReferenceSeq(boolean colourByReferenceSeq)
191 viewStyle.setColourByReferenceSeq(colourByReferenceSeq);
196 * @see jalview.api.ViewStyleI#setColourAppliesToAllGroups(boolean)
199 public void setColourAppliesToAllGroups(boolean b)
201 viewStyle.setColourAppliesToAllGroups(b);
206 * @see jalview.api.ViewStyleI#getColourAppliesToAllGroups()
209 public boolean getColourAppliesToAllGroups()
211 return viewStyle.getColourAppliesToAllGroups();
216 * @see jalview.api.ViewStyleI#getAbovePIDThreshold()
219 public boolean getAbovePIDThreshold()
221 return viewStyle.getAbovePIDThreshold();
226 * @see jalview.api.ViewStyleI#setIncrement(int)
229 public void setIncrement(int inc)
231 viewStyle.setIncrement(inc);
236 * @see jalview.api.ViewStyleI#getIncrement()
239 public int getIncrement()
241 return viewStyle.getIncrement();
246 * @see jalview.api.ViewStyleI#setConservationSelected(boolean)
249 public void setConservationSelected(boolean b)
251 viewStyle.setConservationSelected(b);
256 * @see jalview.api.ViewStyleI#setShowHiddenMarkers(boolean)
259 public void setShowHiddenMarkers(boolean show)
261 viewStyle.setShowHiddenMarkers(show);
266 * @see jalview.api.ViewStyleI#getShowHiddenMarkers()
269 public boolean getShowHiddenMarkers()
271 return viewStyle.getShowHiddenMarkers();
276 * @see jalview.api.ViewStyleI#setScaleRightWrapped(boolean)
279 public void setScaleRightWrapped(boolean b)
281 viewStyle.setScaleRightWrapped(b);
286 * @see jalview.api.ViewStyleI#setScaleLeftWrapped(boolean)
289 public void setScaleLeftWrapped(boolean b)
291 viewStyle.setScaleLeftWrapped(b);
296 * @see jalview.api.ViewStyleI#setScaleAboveWrapped(boolean)
299 public void setScaleAboveWrapped(boolean b)
301 viewStyle.setScaleAboveWrapped(b);
306 * @see jalview.api.ViewStyleI#getScaleLeftWrapped()
309 public boolean getScaleLeftWrapped()
311 return viewStyle.getScaleLeftWrapped();
316 * @see jalview.api.ViewStyleI#getScaleAboveWrapped()
319 public boolean getScaleAboveWrapped()
321 return viewStyle.getScaleAboveWrapped();
326 * @see jalview.api.ViewStyleI#getScaleRightWrapped()
329 public boolean getScaleRightWrapped()
331 return viewStyle.getScaleRightWrapped();
336 * @see jalview.api.ViewStyleI#setAbovePIDThreshold(boolean)
339 public void setAbovePIDThreshold(boolean b)
341 viewStyle.setAbovePIDThreshold(b);
346 * @see jalview.api.ViewStyleI#setThreshold(int)
349 public void setThreshold(int thresh)
351 viewStyle.setThreshold(thresh);
356 * @see jalview.api.ViewStyleI#getThreshold()
359 public int getThreshold()
361 return viewStyle.getThreshold();
366 * @see jalview.api.ViewStyleI#getShowJVSuffix()
369 public boolean getShowJVSuffix()
371 return viewStyle.getShowJVSuffix();
376 * @see jalview.api.ViewStyleI#setShowJVSuffix(boolean)
379 public void setShowJVSuffix(boolean b)
381 viewStyle.setShowJVSuffix(b);
386 * @see jalview.api.ViewStyleI#setWrapAlignment(boolean)
389 public void setWrapAlignment(boolean state)
391 viewStyle.setWrapAlignment(state);
396 * @see jalview.api.ViewStyleI#setShowText(boolean)
399 public void setShowText(boolean state)
401 viewStyle.setShowText(state);
406 * @see jalview.api.ViewStyleI#setRenderGaps(boolean)
409 public void setRenderGaps(boolean state)
411 viewStyle.setRenderGaps(state);
416 * @see jalview.api.ViewStyleI#getColourText()
419 public boolean getColourText()
421 return viewStyle.getColourText();
426 * @see jalview.api.ViewStyleI#setColourText(boolean)
429 public void setColourText(boolean state)
431 viewStyle.setColourText(state);
436 * @see jalview.api.ViewStyleI#getWrapAlignment()
439 public boolean getWrapAlignment()
441 return viewStyle.getWrapAlignment();
446 * @see jalview.api.ViewStyleI#getShowText()
449 public boolean getShowText()
451 return viewStyle.getShowText();
456 * @see jalview.api.ViewStyleI#getWrappedWidth()
459 public int getWrappedWidth()
461 return viewStyle.getWrappedWidth();
466 * @see jalview.api.ViewStyleI#setWrappedWidth(int)
469 public void setWrappedWidth(int w)
471 viewStyle.setWrappedWidth(w);
476 * @see jalview.api.ViewStyleI#getCharHeight()
479 public int getCharHeight()
481 return viewStyle.getCharHeight();
486 * @see jalview.api.ViewStyleI#setCharHeight(int)
489 public void setCharHeight(int h)
491 viewStyle.setCharHeight(h);
496 * @see jalview.api.ViewStyleI#getCharWidth()
499 public int getCharWidth()
501 return viewStyle.getCharWidth();
506 * @see jalview.api.ViewStyleI#setCharWidth(int)
509 public void setCharWidth(int w)
511 viewStyle.setCharWidth(w);
516 * @see jalview.api.ViewStyleI#getShowBoxes()
519 public boolean getShowBoxes()
521 return viewStyle.getShowBoxes();
526 * @see jalview.api.ViewStyleI#getShowUnconserved()
529 public boolean getShowUnconserved()
531 return viewStyle.getShowUnconserved();
535 * @param showunconserved
536 * @see jalview.api.ViewStyleI#setShowUnconserved(boolean)
539 public void setShowUnconserved(boolean showunconserved)
541 viewStyle.setShowUnconserved(showunconserved);
546 * @see jalview.api.ViewStyleI#setSeqNameItalics(boolean)
549 public void setSeqNameItalics(boolean default1)
551 viewStyle.setSeqNameItalics(default1);
555 * alignment displayed in the viewport. Please use get/setter
557 protected AlignmentI alignment;
560 public AlignmentI getAlignment()
566 public char getGapCharacter()
568 return alignment.getGapCharacter();
571 protected String sequenceSetID;
574 * probably unused indicator that view is of a dataset rather than an
577 protected boolean isDataset = false;
579 public void setDataset(boolean b)
584 public boolean isDataset()
589 private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
591 protected ColumnSelection colSel = new ColumnSelection();
593 public boolean autoCalculateConsensus = true;
595 protected boolean autoCalculateStrucConsensus = true;
597 protected boolean ignoreGapsInConsensusCalculation = false;
599 protected ColourSchemeI globalColourScheme = null;
602 public void setGlobalColourScheme(ColourSchemeI cs)
604 // TODO: logic refactored from AlignFrame changeColour -
605 // TODO: autorecalc stuff should be changed to rely on the worker system
606 // check to see if we should implement a changeColour(cs) method rather than
607 // put th logic in here
608 // - means that caller decides if they want to just modify state and defer
609 // calculation till later or to do all calculations in thread.
611 globalColourScheme = cs;
612 boolean recalc = false;
615 cs.setConservationApplied(recalc = getConservationSelected());
616 if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
617 || cs instanceof Blosum62ColourScheme)
620 cs.setThreshold(viewStyle.getThreshold(),
621 ignoreGapsInConsensusCalculation);
625 cs.setThreshold(0, ignoreGapsInConsensusCalculation);
629 cs.setConsensus(hconsensus);
630 cs.setConservation(hconservation);
632 cs.alignmentChanged(alignment, hiddenRepSequences);
634 if (getColourAppliesToAllGroups())
636 for (SequenceGroup sg : getAlignment().getGroups())
643 sg.cs = cs.applyTo(sg, getHiddenRepSequences());
644 sg.setConsPercGaps(ConsPercGaps);
645 if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
646 || cs instanceof Blosum62ColourScheme)
648 sg.cs.setThreshold(viewStyle.getThreshold(),
649 isIgnoreGapsConsensus());
654 sg.cs.setThreshold(0, isIgnoreGapsConsensus());
657 if (getConservationSelected())
659 sg.cs.setConservationApplied(true);
664 sg.cs.setConservation(null);
665 // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
669 sg.recalcConservation();
673 sg.cs.alignmentChanged(sg, hiddenRepSequences);
680 public ColourSchemeI getGlobalColourScheme()
682 return globalColourScheme;
685 protected AlignmentAnnotation consensus;
687 protected AlignmentAnnotation complementConsensus;
689 protected AlignmentAnnotation strucConsensus;
691 protected AlignmentAnnotation conservation;
693 protected AlignmentAnnotation quality;
695 protected AlignmentAnnotation[] groupConsensus;
697 protected AlignmentAnnotation[] groupConservation;
700 * results of alignment consensus analysis for visible portion of view
702 protected Hashtable[] hconsensus = null;
705 * results of cDNA complement consensus visible portion of view
707 protected Hashtable[] hcomplementConsensus = null;
710 * results of secondary structure base pair consensus for visible portion of
713 protected Hashtable[] hStrucConsensus = null;
715 protected Conservation hconservation = null;
718 public void setConservation(Conservation cons)
720 hconservation = cons;
724 * percentage gaps allowed in a column before all amino acid properties should
725 * be considered unconserved
727 int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
730 public int getConsPercGaps()
736 public void setSequenceConsensusHash(Hashtable[] hconsensus)
738 this.hconsensus = hconsensus;
742 public void setComplementConsensusHash(Hashtable[] hconsensus)
744 this.hcomplementConsensus = hconsensus;
748 public Hashtable[] getSequenceConsensusHash()
754 public Hashtable[] getComplementConsensusHash()
756 return hcomplementConsensus;
760 public Hashtable[] getRnaStructureConsensusHash()
762 return hStrucConsensus;
766 public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
768 this.hStrucConsensus = hStrucConsensus;
773 public AlignmentAnnotation getAlignmentQualityAnnot()
779 public AlignmentAnnotation getAlignmentConservationAnnotation()
785 public AlignmentAnnotation getAlignmentConsensusAnnotation()
791 public AlignmentAnnotation getComplementConsensusAnnotation()
793 return complementConsensus;
797 public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
799 return strucConsensus;
802 protected AlignCalcManagerI calculator = new AlignCalcManager();
805 * trigger update of conservation annotation
807 public void updateConservation(final AlignmentViewPanel ap)
809 // see note in mantis : issue number 8585
810 if (alignment.isNucleotide() || conservation == null
811 || !autoCalculateConsensus)
816 .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
818 calculator.registerWorker(new jalview.workers.ConservationThread(
824 * trigger update of consensus annotation
826 public void updateConsensus(final AlignmentViewPanel ap)
828 // see note in mantis : issue number 8585
829 if (consensus == null || !autoCalculateConsensus)
833 if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
835 calculator.registerWorker(new ConsensusThread(this, ap));
839 * A separate thread to compute cDNA consensus for a protein alignment
840 * which has mapping to cDNA
842 final AlignmentI al = this.getAlignment();
843 if (!al.isNucleotide() && al.getCodonFrames() != null
844 && !al.getCodonFrames().isEmpty())
847 * fudge - check first mapping is protein-to-nucleotide
848 * (we don't want to do this for protein-to-protein)
850 AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
851 // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
852 MapList[] mapLists = mapping.getdnaToProt();
853 // mapLists can be empty if project load has not finished resolving seqs
854 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
857 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
860 .registerWorker(new ComplementConsensusThread(this, ap));
866 // --------START Structure Conservation
867 public void updateStrucConsensus(final AlignmentViewPanel ap)
869 if (autoCalculateStrucConsensus && strucConsensus == null
870 && alignment.isNucleotide() && alignment.hasRNAStructure())
872 // secondary structure has been added - so init the consensus line
876 // see note in mantis : issue number 8585
877 if (strucConsensus == null || !autoCalculateStrucConsensus)
881 if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
883 calculator.registerWorker(new StrucConsensusThread(this, ap));
887 public boolean isCalcInProgress()
889 return calculator.isWorking();
893 public boolean isCalculationInProgress(
894 AlignmentAnnotation alignmentAnnotation)
896 if (!alignmentAnnotation.autoCalculated)
900 if (calculator.workingInvolvedWith(alignmentAnnotation))
902 // System.err.println("grey out ("+alignmentAnnotation.label+")");
909 public boolean isClosed()
911 // TODO: check that this isClosed is only true after panel is closed, not
912 // before it is fully constructed.
913 return alignment == null;
917 public AlignCalcManagerI getCalcManager()
923 * should conservation rows be shown for groups
925 protected boolean showGroupConservation = false;
928 * should consensus rows be shown for groups
930 protected boolean showGroupConsensus = false;
933 * should consensus profile be rendered by default
935 protected boolean showSequenceLogo = false;
938 * should consensus profile be rendered normalised to row height
940 protected boolean normaliseSequenceLogo = false;
943 * should consensus histograms be rendered by default
945 protected boolean showConsensusHistogram = true;
948 * @return the showConsensusProfile
951 public boolean isShowSequenceLogo()
953 return showSequenceLogo;
957 * @param showSequenceLogo
960 public void setShowSequenceLogo(boolean showSequenceLogo)
962 if (showSequenceLogo != this.showSequenceLogo)
964 // TODO: decouple settings setting from calculation when refactoring
965 // annotation update method from alignframe to viewport
966 this.showSequenceLogo = showSequenceLogo;
967 calculator.updateAnnotationFor(ConsensusThread.class);
968 calculator.updateAnnotationFor(ComplementConsensusThread.class);
969 calculator.updateAnnotationFor(StrucConsensusThread.class);
971 this.showSequenceLogo = showSequenceLogo;
975 * @param showConsensusHistogram
976 * the showConsensusHistogram to set
978 public void setShowConsensusHistogram(boolean showConsensusHistogram)
980 this.showConsensusHistogram = showConsensusHistogram;
984 * @return the showGroupConservation
986 public boolean isShowGroupConservation()
988 return showGroupConservation;
992 * @param showGroupConservation
993 * the showGroupConservation to set
995 public void setShowGroupConservation(boolean showGroupConservation)
997 this.showGroupConservation = showGroupConservation;
1001 * @return the showGroupConsensus
1003 public boolean isShowGroupConsensus()
1005 return showGroupConsensus;
1009 * @param showGroupConsensus
1010 * the showGroupConsensus to set
1012 public void setShowGroupConsensus(boolean showGroupConsensus)
1014 this.showGroupConsensus = showGroupConsensus;
1019 * @return flag to indicate if the consensus histogram should be rendered by
1023 public boolean isShowConsensusHistogram()
1025 return this.showConsensusHistogram;
1029 * when set, updateAlignment will always ensure sequences are of equal length
1031 private boolean padGaps = false;
1034 * when set, alignment should be reordered according to a newly opened tree
1036 public boolean sortByTree = false;
1041 * @return null or the currently selected sequence region
1044 public SequenceGroup getSelectionGroup()
1046 return selectionGroup;
1050 * Set the selection group for this window.
1053 * - group holding references to sequences in this alignment view
1057 public void setSelectionGroup(SequenceGroup sg)
1059 selectionGroup = sg;
1062 public void setHiddenColumns(ColumnSelection colsel)
1064 this.colSel = colsel;
1068 public ColumnSelection getColumnSelection()
1074 public void setColumnSelection(ColumnSelection colSel)
1076 this.colSel = colSel;
1079 updateHiddenColumns();
1081 isColSelChanged(true);
1089 public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
1091 return hiddenRepSequences;
1095 public void setHiddenRepSequences(
1096 Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
1098 this.hiddenRepSequences = hiddenRepSequences;
1102 public boolean hasHiddenColumns()
1104 return colSel != null && colSel.hasHiddenColumns();
1107 public void updateHiddenColumns()
1109 // this method doesn't really do anything now. But - it could, since a
1110 // column Selection could be in the process of modification
1111 // hasHiddenColumns = colSel.hasHiddenColumns();
1115 public boolean hasHiddenRows()
1117 return alignment.getHiddenSequences().getSize() > 0;
1120 protected SequenceGroup selectionGroup;
1122 public void setSequenceSetId(String newid)
1124 if (sequenceSetID != null)
1127 .println("Warning - overwriting a sequenceSetId for a viewport!");
1129 sequenceSetID = new String(newid);
1133 public String getSequenceSetId()
1135 if (sequenceSetID == null)
1137 sequenceSetID = alignment.hashCode() + "";
1140 return sequenceSetID;
1144 * unique viewId for synchronizing state (e.g. with stored Jalview Project)
1147 protected String viewId = null;
1150 public String getViewId()
1154 viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
1159 public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap)
1161 ignoreGapsInConsensusCalculation = b;
1164 updateConsensus(ap);
1165 if (globalColourScheme != null)
1167 globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
1168 ignoreGapsInConsensusCalculation);
1174 private long sgrouphash = -1, colselhash = -1;
1177 * checks current SelectionGroup against record of last hash value, and
1181 * update the record of last hash value
1183 * @return true if SelectionGroup changed since last call (when b is true)
1185 public boolean isSelectionGroupChanged(boolean b)
1187 int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
1188 : selectionGroup.hashCode();
1189 if (hc != -1 && hc != sgrouphash)
1201 * checks current colsel against record of last hash value, and optionally
1205 * update the record of last hash value
1206 * @return true if colsel changed since last call (when b is true)
1208 public boolean isColSelChanged(boolean b)
1210 int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
1211 if (hc != -1 && hc != colselhash)
1223 public boolean isIgnoreGapsConsensus()
1225 return ignoreGapsInConsensusCalculation;
1228 // / property change stuff
1230 // JBPNote Prolly only need this in the applet version.
1231 private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
1234 protected boolean showConservation = true;
1236 protected boolean showQuality = true;
1238 protected boolean showConsensus = true;
1240 private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
1242 protected SequenceAnnotationOrder sortAnnotationsBy = null;
1244 protected boolean showAutocalculatedAbove;
1247 * when set, view will scroll to show the highlighted position
1249 private boolean followHighlight = true;
1251 // TODO private with getters and setters?
1252 public int startRes;
1256 public int startSeq;
1261 * Property change listener for changes in alignment
1266 public void addPropertyChangeListener(
1267 java.beans.PropertyChangeListener listener)
1269 changeSupport.addPropertyChangeListener(listener);
1278 public void removePropertyChangeListener(
1279 java.beans.PropertyChangeListener listener)
1281 changeSupport.removePropertyChangeListener(listener);
1285 * Property change listener for changes in alignment
1294 public void firePropertyChange(String prop, Object oldvalue,
1297 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1300 // common hide/show column stuff
1302 public void hideSelectedColumns()
1304 if (colSel.isEmpty())
1309 colSel.hideSelectedColumns();
1310 setSelectionGroup(null);
1311 isColSelChanged(true);
1314 public void hideColumns(int start, int end)
1318 colSel.hideColumns(start);
1322 colSel.hideColumns(start, end);
1324 isColSelChanged(true);
1327 public void showColumn(int col)
1329 colSel.revealHiddenColumns(col);
1330 isColSelChanged(true);
1333 public void showAllHiddenColumns()
1335 colSel.revealAllHiddenColumns();
1336 isColSelChanged(true);
1339 // common hide/show seq stuff
1340 public void showAllHiddenSeqs()
1342 if (alignment.getHiddenSequences().getSize() > 0)
1344 if (selectionGroup == null)
1346 selectionGroup = new SequenceGroup();
1347 selectionGroup.setEndRes(alignment.getWidth() - 1);
1349 List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
1350 hiddenRepSequences);
1351 for (SequenceI seq : tmp)
1353 selectionGroup.addSequence(seq, false);
1354 setSequenceAnnotationsVisible(seq, true);
1357 hiddenRepSequences = null;
1359 firePropertyChange("alignment", null, alignment.getSequences());
1360 // used to set hasHiddenRows/hiddenRepSequences here, after the property
1366 public void showSequence(int index)
1368 List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
1369 index, hiddenRepSequences);
1372 if (selectionGroup == null)
1374 selectionGroup = new SequenceGroup();
1375 selectionGroup.setEndRes(alignment.getWidth() - 1);
1378 for (SequenceI seq : tmp)
1380 selectionGroup.addSequence(seq, false);
1381 setSequenceAnnotationsVisible(seq, true);
1383 firePropertyChange("alignment", null, alignment.getSequences());
1388 public void hideAllSelectedSeqs()
1390 if (selectionGroup == null || selectionGroup.getSize() < 1)
1395 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1399 setSelectionGroup(null);
1402 public void hideSequence(SequenceI[] seq)
1406 for (int i = 0; i < seq.length; i++)
1408 alignment.getHiddenSequences().hideSequence(seq[i]);
1409 setSequenceAnnotationsVisible(seq[i], false);
1411 firePropertyChange("alignment", null, alignment.getSequences());
1416 * Set visibility for any annotations for the given sequence.
1420 protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
1423 for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
1425 if (ann.sequenceRef == sequenceI)
1427 ann.visible = visible;
1432 public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
1434 int sSize = sg.getSize();
1440 if (hiddenRepSequences == null)
1442 hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
1445 hiddenRepSequences.put(repSequence, sg);
1447 // Hide all sequences except the repSequence
1448 SequenceI[] seqs = new SequenceI[sSize - 1];
1450 for (int i = 0; i < sSize; i++)
1452 if (sg.getSequenceAt(i) != repSequence)
1454 if (index == sSize - 1)
1459 seqs[index++] = sg.getSequenceAt(i);
1462 sg.setSeqrep(repSequence); // note: not done in 2.7applet
1463 sg.setHidereps(true); // note: not done in 2.7applet
1470 * @return null or the current reference sequence
1472 public SequenceI getReferenceSeq()
1474 return alignment.getSeqrep();
1479 * @return true iff seq is the reference for the alignment
1481 public boolean isReferenceSeq(SequenceI seq)
1483 return alignment.getSeqrep() == seq;
1489 * @return true if there are sequences represented by this sequence that are
1492 public boolean isHiddenRepSequence(SequenceI seq)
1494 return (hiddenRepSequences != null && hiddenRepSequences
1501 * @return null or a sequence group containing the sequences that seq
1504 public SequenceGroup getRepresentedSequences(SequenceI seq)
1506 return (SequenceGroup) (hiddenRepSequences == null ? null
1507 : hiddenRepSequences.get(seq));
1511 public int adjustForHiddenSeqs(int alignmentIndex)
1513 return alignment.getHiddenSequences().adjustForHiddenSeqs(
1518 public void invertColumnSelection()
1520 colSel.invertColumnSelection(0, alignment.getWidth());
1524 public SequenceI[] getSelectionAsNewSequence()
1526 SequenceI[] sequences;
1527 // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom -
1528 // this was the only caller in the applet for this method
1529 // JBPNote: in applet, this method returned references to the alignment
1530 // sequences, and it did not honour the presence/absence of annotation
1531 // attached to the alignment (probably!)
1532 if (selectionGroup == null || selectionGroup.getSize() == 0)
1534 sequences = alignment.getSequencesArray();
1535 AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
1536 for (int i = 0; i < sequences.length; i++)
1538 // construct new sequence with subset of visible annotation
1539 sequences[i] = new Sequence(sequences[i], annots);
1544 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1551 public SequenceI[] getSequenceSelection()
1553 SequenceI[] sequences = null;
1554 if (selectionGroup != null)
1556 sequences = selectionGroup.getSequencesInOrder(alignment);
1558 if (sequences == null)
1560 sequences = alignment.getSequencesArray();
1566 public CigarArray getViewAsCigars(boolean selectedRegionOnly)
1568 return new CigarArray(alignment, colSel,
1569 (selectedRegionOnly ? selectionGroup : null));
1573 public jalview.datamodel.AlignmentView getAlignmentView(
1574 boolean selectedOnly)
1576 return getAlignmentView(selectedOnly, false);
1580 public jalview.datamodel.AlignmentView getAlignmentView(
1581 boolean selectedOnly, boolean markGroups)
1583 return new AlignmentView(alignment, colSel, selectionGroup,
1584 colSel != null && colSel.hasHiddenColumns(), selectedOnly,
1589 public String[] getViewAsString(boolean selectedRegionOnly)
1591 return getViewAsString(selectedRegionOnly, true);
1595 public String[] getViewAsString(boolean selectedRegionOnly,
1596 boolean exportHiddenSeqs)
1598 String[] selection = null;
1599 SequenceI[] seqs = null;
1601 int start = 0, end = 0;
1602 if (selectedRegionOnly && selectionGroup != null)
1604 iSize = selectionGroup.getSize();
1605 seqs = selectionGroup.getSequencesInOrder(alignment);
1606 start = selectionGroup.getStartRes();
1607 end = selectionGroup.getEndRes() + 1;
1611 if (hasHiddenRows() && exportHiddenSeqs)
1613 AlignmentI fullAlignment = alignment.getHiddenSequences()
1614 .getFullAlignment();
1615 iSize = fullAlignment.getHeight();
1616 seqs = fullAlignment.getSequencesArray();
1617 end = fullAlignment.getWidth();
1621 iSize = alignment.getHeight();
1622 seqs = alignment.getSequencesArray();
1623 end = alignment.getWidth();
1627 selection = new String[iSize];
1628 if (colSel != null && colSel.hasHiddenColumns())
1630 selection = colSel.getVisibleSequenceStrings(start, end, seqs);
1634 for (i = 0; i < iSize; i++)
1636 selection[i] = seqs[i].getSequenceAsString(start, end);
1644 public List<int[]> getVisibleRegionBoundaries(int min, int max)
1646 ArrayList<int[]> regions = new ArrayList<int[]>();
1652 if (colSel != null && colSel.hasHiddenColumns())
1656 start = colSel.adjustForHiddenColumns(start);
1659 end = colSel.getHiddenBoundaryRight(start);
1670 regions.add(new int[] { start, end });
1672 if (colSel != null && colSel.hasHiddenColumns())
1674 start = colSel.adjustForHiddenColumns(end);
1675 start = colSel.getHiddenBoundaryLeft(start) + 1;
1677 } while (end < max);
1679 int[][] startEnd = new int[regions.size()][2];
1685 public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
1686 boolean selectedOnly)
1688 ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
1689 AlignmentAnnotation[] aa;
1690 if ((aa = alignment.getAlignmentAnnotation()) != null)
1692 for (AlignmentAnnotation annot : aa)
1694 AlignmentAnnotation clone = new AlignmentAnnotation(annot);
1695 if (selectedOnly && selectionGroup != null)
1697 colSel.makeVisibleAnnotation(selectionGroup.getStartRes(),
1698 selectionGroup.getEndRes(), clone);
1702 colSel.makeVisibleAnnotation(clone);
1711 public boolean isPadGaps()
1717 public void setPadGaps(boolean padGaps)
1719 this.padGaps = padGaps;
1723 * apply any post-edit constraints and trigger any calculations needed after
1724 * an edit has been performed on the alignment
1729 public void alignmentChanged(AlignmentViewPanel ap)
1733 alignment.padGaps();
1735 if (autoCalculateConsensus)
1737 updateConsensus(ap);
1739 if (hconsensus != null && autoCalculateConsensus)
1741 updateConservation(ap);
1743 if (autoCalculateStrucConsensus)
1745 updateStrucConsensus(ap);
1748 // Reset endRes of groups if beyond alignment width
1749 int alWidth = alignment.getWidth();
1750 List<SequenceGroup> groups = alignment.getGroups();
1753 for (SequenceGroup sg : groups)
1755 if (sg.getEndRes() > alWidth)
1757 sg.setEndRes(alWidth - 1);
1762 if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
1764 selectionGroup.setEndRes(alWidth - 1);
1767 resetAllColourSchemes();
1768 calculator.restartWorkers();
1769 // alignment.adjustSequenceAnnotations();
1773 * reset scope and do calculations for all applied colourschemes on alignment
1775 void resetAllColourSchemes()
1777 ColourSchemeI cs = globalColourScheme;
1780 cs.alignmentChanged(alignment, hiddenRepSequences);
1782 cs.setConsensus(hconsensus);
1783 if (cs.conservationApplied())
1785 cs.setConservation(Conservation.calculateConservation("All",
1786 ResidueProperties.propHash, 3, alignment.getSequences(), 0,
1787 alignment.getWidth(), false, getConsPercGaps(), false));
1791 for (SequenceGroup sg : alignment.getGroups())
1795 sg.cs.alignmentChanged(sg, hiddenRepSequences);
1797 sg.recalcConservation();
1801 protected void initAutoAnnotation()
1803 // TODO: add menu option action that nulls or creates consensus object
1804 // depending on if the user wants to see the annotation or not in a
1805 // specific alignment
1807 if (hconsensus == null && !isDataset)
1809 if (!alignment.isNucleotide())
1818 consensus = new AlignmentAnnotation("Consensus", "PID",
1819 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1820 initConsensus(consensus);
1822 initComplementConsensus();
1827 * If this is a protein alignment and there are mappings to cDNA, add the cDNA
1828 * consensus annotation.
1830 public void initComplementConsensus()
1832 if (!alignment.isNucleotide())
1834 final List<AlignedCodonFrame> codonMappings = alignment
1836 if (codonMappings != null && !codonMappings.isEmpty())
1838 // fudge: check mappings are not protein-to-protein
1840 AlignedCodonFrame mapping = codonMappings.iterator().next();
1841 MapList[] mapLists = mapping.getdnaToProt();
1842 // mapLists can be empty if project load has not finished resolving seqs
1843 if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
1845 complementConsensus = new AlignmentAnnotation("cDNA Consensus",
1846 "PID for cDNA", new Annotation[1], 0f, 100f,
1847 AlignmentAnnotation.BAR_GRAPH);
1848 initConsensus(complementConsensus);
1854 private void initConsensus(AlignmentAnnotation aa)
1857 aa.autoCalculated = true;
1861 alignment.addAnnotation(aa);
1865 private void initConservation()
1867 if (showConservation)
1869 if (conservation == null)
1871 conservation = new AlignmentAnnotation("Conservation",
1872 "Conservation of total alignment less than "
1873 + getConsPercGaps() + "% gaps", new Annotation[1],
1874 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1875 conservation.hasText = true;
1876 conservation.autoCalculated = true;
1877 alignment.addAnnotation(conservation);
1882 private void initQuality()
1886 if (quality == null)
1888 quality = new AlignmentAnnotation("Quality",
1889 "Alignment Quality based on Blosum62 scores",
1890 new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
1891 quality.hasText = true;
1892 quality.autoCalculated = true;
1893 alignment.addAnnotation(quality);
1898 private void initRNAStructure()
1900 if (alignment.hasRNAStructure() && strucConsensus == null)
1902 strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
1903 new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
1904 strucConsensus.hasText = true;
1905 strucConsensus.autoCalculated = true;
1909 alignment.addAnnotation(strucConsensus);
1917 * @see jalview.api.AlignViewportI#calcPanelHeight()
1920 public int calcPanelHeight()
1922 // setHeight of panels
1923 AlignmentAnnotation[] anns = getAlignment().getAlignmentAnnotation();
1925 int charHeight = getCharHeight();
1928 BitSet graphgrp = new BitSet();
1929 for (AlignmentAnnotation aa : anns)
1933 System.err.println("Null annotation row: ignoring.");
1940 if (aa.graphGroup > -1)
1942 if (graphgrp.get(aa.graphGroup))
1948 graphgrp.set(aa.graphGroup);
1955 aa.height += charHeight;
1965 aa.height += aa.graphHeight;
1973 height += aa.height;
1985 public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
1986 boolean preserveNewGroupSettings)
1988 boolean updateCalcs = false;
1989 boolean conv = isShowGroupConservation();
1990 boolean cons = isShowGroupConsensus();
1991 boolean showprf = isShowSequenceLogo();
1992 boolean showConsHist = isShowConsensusHistogram();
1993 boolean normLogo = isNormaliseSequenceLogo();
1996 * TODO reorder the annotation rows according to group/sequence ordering on
1999 boolean sortg = true;
2001 // remove old automatic annotation
2002 // add any new annotation
2004 // intersect alignment annotation with alignment groups
2006 AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
2007 List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
2010 for (int an = 0; an < aan.length; an++)
2012 if (aan[an].autoCalculated && aan[an].groupRef != null)
2014 oldrfs.add(aan[an].groupRef);
2015 alignment.deleteAnnotation(aan[an], false);
2019 if (alignment.getGroups() != null)
2021 for (SequenceGroup sg : alignment.getGroups())
2023 updateCalcs = false;
2024 if (applyGlobalSettings
2025 || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
2027 // set defaults for this group's conservation/consensus
2028 sg.setshowSequenceLogo(showprf);
2029 sg.setShowConsensusHistogram(showConsHist);
2030 sg.setNormaliseSequenceLogo(normLogo);
2035 alignment.addAnnotation(sg.getConservationRow(), 0);
2040 alignment.addAnnotation(sg.getConsensus(), 0);
2042 // refresh the annotation rows
2045 sg.recalcConservation();
2053 public boolean isDisplayReferenceSeq()
2055 return alignment.hasSeqrep() && viewStyle.isDisplayReferenceSeq();
2059 public void setDisplayReferenceSeq(boolean displayReferenceSeq)
2061 viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
2065 public boolean isColourByReferenceSeq()
2067 return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
2071 public Color getSequenceColour(SequenceI seq)
2073 Color sqc = sequenceColours.get(seq);
2074 return (sqc == null ? Color.white : sqc);
2078 public void setSequenceColour(SequenceI seq, Color col)
2082 sequenceColours.remove(seq);
2086 sequenceColours.put(seq, col);
2091 public void updateSequenceIdColours()
2093 for (SequenceGroup sg : alignment.getGroups())
2095 if (sg.idColour != null)
2097 for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
2099 sequenceColours.put(s, sg.idColour);
2106 public void clearSequenceColours()
2108 sequenceColours.clear();
2112 public AlignViewportI getCodingComplement()
2114 return this.codingComplement;
2118 * Set this as the (cDna/protein) complement of the given viewport. Also
2119 * ensures the reverse relationship is set on the given viewport.
2122 public void setCodingComplement(AlignViewportI av)
2126 System.err.println("Ignoring recursive setCodingComplement request");
2130 this.codingComplement = av;
2131 // avoid infinite recursion!
2132 if (av.getCodingComplement() != this)
2134 av.setCodingComplement(this);
2140 public boolean isNucleotide()
2142 return getAlignment() == null ? false : getAlignment().isNucleotide();
2146 public FeaturesDisplayedI getFeaturesDisplayed()
2148 return featuresDisplayed;
2152 public void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI)
2154 featuresDisplayed = featuresDisplayedI;
2158 public boolean areFeaturesDisplayed()
2160 return featuresDisplayed != null
2161 && featuresDisplayed.getRegisteredFeaturesCount() > 0;
2168 * features are displayed if true
2171 public void setShowSequenceFeatures(boolean b)
2173 viewStyle.setShowSequenceFeatures(b);
2177 public boolean isShowSequenceFeatures()
2179 return viewStyle.isShowSequenceFeatures();
2183 public void setShowSequenceFeaturesHeight(boolean selected)
2185 viewStyle.setShowSequenceFeaturesHeight(selected);
2189 public boolean isShowSequenceFeaturesHeight()
2191 return viewStyle.isShowSequenceFeaturesHeight();
2195 public void setShowAnnotation(boolean b)
2197 viewStyle.setShowAnnotation(b);
2201 public boolean isShowAnnotation()
2203 return viewStyle.isShowAnnotation();
2207 public boolean isRightAlignIds()
2209 return viewStyle.isRightAlignIds();
2213 public void setRightAlignIds(boolean rightAlignIds)
2215 viewStyle.setRightAlignIds(rightAlignIds);
2219 public boolean getConservationSelected()
2221 return viewStyle.getConservationSelected();
2225 public void setShowBoxes(boolean state)
2227 viewStyle.setShowBoxes(state);
2232 * @see jalview.api.ViewStyleI#getTextColour()
2235 public Color getTextColour()
2237 return viewStyle.getTextColour();
2242 * @see jalview.api.ViewStyleI#getTextColour2()
2245 public Color getTextColour2()
2247 return viewStyle.getTextColour2();
2252 * @see jalview.api.ViewStyleI#getThresholdTextColour()
2255 public int getThresholdTextColour()
2257 return viewStyle.getThresholdTextColour();
2262 * @see jalview.api.ViewStyleI#isConservationColourSelected()
2265 public boolean isConservationColourSelected()
2267 return viewStyle.isConservationColourSelected();
2272 * @see jalview.api.ViewStyleI#isRenderGaps()
2275 public boolean isRenderGaps()
2277 return viewStyle.isRenderGaps();
2282 * @see jalview.api.ViewStyleI#isShowColourText()
2285 public boolean isShowColourText()
2287 return viewStyle.isShowColourText();
2291 * @param conservationColourSelected
2292 * @see jalview.api.ViewStyleI#setConservationColourSelected(boolean)
2295 public void setConservationColourSelected(
2296 boolean conservationColourSelected)
2298 viewStyle.setConservationColourSelected(conservationColourSelected);
2302 * @param showColourText
2303 * @see jalview.api.ViewStyleI#setShowColourText(boolean)
2306 public void setShowColourText(boolean showColourText)
2308 viewStyle.setShowColourText(showColourText);
2313 * @see jalview.api.ViewStyleI#setTextColour(java.awt.Color)
2316 public void setTextColour(Color textColour)
2318 viewStyle.setTextColour(textColour);
2322 * @param thresholdTextColour
2323 * @see jalview.api.ViewStyleI#setThresholdTextColour(int)
2326 public void setThresholdTextColour(int thresholdTextColour)
2328 viewStyle.setThresholdTextColour(thresholdTextColour);
2332 * @param textColour2
2333 * @see jalview.api.ViewStyleI#setTextColour2(java.awt.Color)
2336 public void setTextColour2(Color textColour2)
2338 viewStyle.setTextColour2(textColour2);
2342 public ViewStyleI getViewStyle()
2344 return new ViewStyle(viewStyle);
2348 public void setViewStyle(ViewStyleI settingsForView)
2350 viewStyle = new ViewStyle(settingsForView);
2354 public boolean sameStyle(ViewStyleI them)
2356 return viewStyle.sameStyle(them);
2361 * @see jalview.api.ViewStyleI#getIdWidth()
2364 public int getIdWidth()
2366 return viewStyle.getIdWidth();
2371 * @see jalview.api.ViewStyleI#setIdWidth(int)
2374 public void setIdWidth(int i)
2376 viewStyle.setIdWidth(i);
2381 * @see jalview.api.ViewStyleI#isCentreColumnLabels()
2384 public boolean isCentreColumnLabels()
2386 return viewStyle.isCentreColumnLabels();
2390 * @param centreColumnLabels
2391 * @see jalview.api.ViewStyleI#setCentreColumnLabels(boolean)
2394 public void setCentreColumnLabels(boolean centreColumnLabels)
2396 viewStyle.setCentreColumnLabels(centreColumnLabels);
2401 * @see jalview.api.ViewStyleI#setShowDBRefs(boolean)
2404 public void setShowDBRefs(boolean showdbrefs)
2406 viewStyle.setShowDBRefs(showdbrefs);
2411 * @see jalview.api.ViewStyleI#isShowDBRefs()
2414 public boolean isShowDBRefs()
2416 return viewStyle.isShowDBRefs();
2421 * @see jalview.api.ViewStyleI#isShowNPFeats()
2424 public boolean isShowNPFeats()
2426 return viewStyle.isShowNPFeats();
2430 * @param shownpfeats
2431 * @see jalview.api.ViewStyleI#setShowNPFeats(boolean)
2434 public void setShowNPFeats(boolean shownpfeats)
2436 viewStyle.setShowNPFeats(shownpfeats);
2439 public abstract StructureSelectionManager getStructureSelectionManager();
2442 * Add one command to the command history list.
2446 public void addToHistoryList(CommandI command)
2448 if (this.historyList != null)
2450 this.historyList.push(command);
2451 broadcastCommand(command, false);
2455 protected void broadcastCommand(CommandI command, boolean undo)
2457 getStructureSelectionManager().commandPerformed(command, undo,
2462 * Add one command to the command redo list.
2466 public void addToRedoList(CommandI command)
2468 if (this.redoList != null)
2470 this.redoList.push(command);
2472 broadcastCommand(command, true);
2476 * Clear the command redo list.
2478 public void clearRedoList()
2480 if (this.redoList != null)
2482 this.redoList.clear();
2486 public void setHistoryList(Deque<CommandI> list)
2488 this.historyList = list;
2491 public Deque<CommandI> getHistoryList()
2493 return this.historyList;
2496 public void setRedoList(Deque<CommandI> list)
2498 this.redoList = list;
2501 public Deque<CommandI> getRedoList()
2503 return this.redoList;
2507 public VamsasSource getVamsasSource()
2512 public SequenceAnnotationOrder getSortAnnotationsBy()
2514 return sortAnnotationsBy;
2517 public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
2519 this.sortAnnotationsBy = sortAnnotationsBy;
2522 public boolean isShowAutocalculatedAbove()
2524 return showAutocalculatedAbove;
2527 public void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
2529 this.showAutocalculatedAbove = showAutocalculatedAbove;
2533 public boolean isScaleProteinAsCdna()
2535 return viewStyle.isScaleProteinAsCdna();
2539 public void setScaleProteinAsCdna(boolean b)
2541 viewStyle.setScaleProteinAsCdna(b);
2545 * @return true if view should scroll to show the highlighted region of a
2550 public final boolean isFollowHighlight()
2552 return followHighlight;
2556 public final void setFollowHighlight(boolean b)
2558 this.followHighlight = b;
2561 public int getStartRes()
2567 public int getEndRes()
2572 public int getStartSeq()
2577 public void setStartRes(int res)
2579 this.startRes = res;
2582 public void setStartSeq(int seq)
2584 this.startSeq = seq;
2587 public void setEndRes(int res)
2589 if (res > alignment.getWidth() - 1)
2591 // log.System.out.println(" Corrected res from " + res + " to maximum " +
2592 // (alignment.getWidth()-1));
2593 res = alignment.getWidth() - 1;
2602 public void setEndSeq(int seq)
2604 if (seq > alignment.getHeight())
2606 seq = alignment.getHeight();
2615 public int getEndSeq()
2621 * Helper method to populate the SearchResults with the location in the
2622 * complementary alignment to scroll to, in order to match this one.
2625 * the SearchResults to add to
2626 * @return the offset (below top of visible region) of the matched sequence
2628 protected int findComplementScrollTarget(SearchResults sr)
2630 final AlignViewportI complement = getCodingComplement();
2631 if (complement == null || !complement.isFollowHighlight())
2635 boolean iAmProtein = !getAlignment().isNucleotide();
2636 AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
2638 if (proteinAlignment == null)
2642 final List<AlignedCodonFrame> mappings = proteinAlignment
2646 * Heuristic: find the first mapped sequence (if any) with a non-gapped
2647 * residue in the middle column of the visible region. Scroll the
2648 * complementary alignment to line up the corresponding residue.
2651 SequenceI sequence = null;
2654 * locate 'middle' column (true middle if an odd number visible, left of
2655 * middle if an even number visible)
2657 int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
2658 final HiddenSequences hiddenSequences = getAlignment()
2659 .getHiddenSequences();
2662 * searching to the bottom of the alignment gives smoother scrolling across
2663 * all gapped visible regions
2665 int lastSeq = alignment.getHeight() - 1;
2666 for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
2668 sequence = getAlignment().getSequenceAt(seqNo);
2669 if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
2673 if (Comparison.isGap(sequence.getCharAt(middleColumn)))
2677 List<AlignedCodonFrame> seqMappings = MappingUtils
2678 .findMappingsForSequence(sequence, mappings);
2679 if (!seqMappings.isEmpty())
2685 if (sequence == null)
2688 * No ungapped mapped sequence in middle column - do nothing
2692 MappingUtils.addSearchResults(sr, sequence,
2693 sequence.findPosition(middleColumn), mappings);
2698 * synthesize a column selection if none exists so it covers the given
2699 * selection group. if wholewidth is false, no column selection is made if the
2700 * selection group covers the whole alignment width.
2705 public void expandColSelection(SequenceGroup sg, boolean wholewidth)
2709 && (sgs = sg.getStartRes()) >= 0
2710 && sg.getStartRes() <= (sge = sg.getEndRes())
2711 && (colSel == null || colSel.getSelected() == null || colSel
2712 .getSelected().size() == 0))
2714 if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
2721 colSel = new ColumnSelection();
2723 for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
2725 colSel.addElement(cspos);