2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
20 package jalview.appletgui;
\r
26 import jalview.analysis.*;
\r
27 import jalview.bin.*;
\r
28 import jalview.datamodel.*;
\r
29 import jalview.schemes.*;
\r
31 public class AlignViewport
\r
40 boolean cursorMode = false;
\r
42 boolean showJVSuffix = true;
\r
43 boolean showText = true;
\r
44 boolean showColourText = false;
\r
45 boolean showBoxes = true;
\r
46 boolean wrapAlignment = false;
\r
47 boolean renderGaps = true;
\r
48 boolean showSequenceFeatures = false;
\r
49 boolean showAnnotation = true;
\r
50 boolean showConservation = true;
\r
51 boolean showQuality = true;
\r
52 boolean showConsensus = true;
\r
53 boolean upperCasebold = false;
\r
55 boolean colourAppliesToAllGroups = true;
\r
56 ColourSchemeI globalColourScheme = null;
\r
57 boolean conservationColourSelected = false;
\r
58 boolean abovePIDThreshold = false;
\r
60 SequenceGroup selectionGroup;
\r
66 Font font = new Font("SansSerif", Font.PLAIN, 10);
\r
67 boolean validCharWidth = true;
\r
68 AlignmentI alignment;
\r
70 ColumnSelection colSel = new ColumnSelection();
\r
75 NJTree currentTree = null;
\r
77 boolean scaleAboveWrapped = true;
\r
78 boolean scaleLeftWrapped = true;
\r
79 boolean scaleRightWrapped = true;
\r
81 // The following vector holds the features which are
\r
82 // currently visible, in the correct order or rendering
\r
83 public Hashtable featuresDisplayed;
\r
85 boolean hasHiddenColumns = false;
\r
86 boolean hasHiddenRows = false;
\r
87 boolean showHiddenMarkers = true;
\r
90 public Vector vconsensus;
\r
91 AlignmentAnnotation consensus;
\r
92 AlignmentAnnotation conservation;
\r
93 AlignmentAnnotation quality;
\r
95 boolean autocalculateConsensus = true;
\r
97 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
\r
99 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
\r
101 boolean ignoreGapsInConsensusCalculation = false;
\r
103 jalview.bin.JalviewLite applet;
\r
105 boolean MAC = false;
\r
107 public AlignViewport(AlignmentI al, JalviewLite applet)
\r
109 this.applet = applet;
\r
112 this.endRes = al.getWidth() - 1;
\r
114 this.endSeq = al.getHeight() - 1;
\r
117 if(System.getProperty("os.name").startsWith("Mac"))
\r
120 if (applet != null)
\r
122 String param = applet.getParameter("showFullId");
\r
125 showJVSuffix = Boolean.valueOf(param).booleanValue();
\r
128 param = applet.getParameter("showAnnotation");
\r
131 showAnnotation = Boolean.valueOf(param).booleanValue();
\r
134 param = applet.getParameter("showConservation");
\r
137 showConservation = Boolean.valueOf(param).booleanValue();
\r
140 param = applet.getParameter("showQuality");
\r
143 showQuality = Boolean.valueOf(param).booleanValue();
\r
146 param = applet.getParameter("showConsensus");
\r
149 showConsensus = Boolean.valueOf(param).booleanValue();
\r
152 param = applet.getParameter("upperCase");
\r
155 if(param.equalsIgnoreCase("bold"))
\r
156 upperCasebold = true;
\r
160 // We must set conservation and consensus before setting colour,
\r
161 // as Blosum and Clustal require this to be done
\r
162 updateConservation();
\r
166 if (applet != null)
\r
168 String colour = applet.getParameter("defaultColour");
\r
172 colour = applet.getParameter("userDefinedColour");
\r
174 colour = "User Defined";
\r
179 globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
\r
180 if (globalColourScheme != null)
\r
182 globalColourScheme.setConsensus(vconsensus);
\r
186 if(applet.getParameter("userDefinedColour")!=null)
\r
188 ((UserColourScheme)globalColourScheme).parseAppletParameter(
\r
189 applet.getParameter("userDefinedColour"));
\r
196 public void showSequenceFeatures(boolean b)
\r
198 showSequenceFeatures = b;
\r
201 public boolean getShowSequenceFeatures()
\r
203 return showSequenceFeatures;
\r
207 public void updateConservation()
\r
209 if(alignment.isNucleotide())
\r
212 Conservation cons = new jalview.analysis.Conservation("All",
\r
213 jalview.schemes.ResidueProperties.propHash, 3,
\r
214 alignment.getSequences(), 0,
\r
215 alignment.getWidth() - 1);
\r
217 cons.verdict(false, ConsPercGaps);
\r
218 cons.findQuality();
\r
219 int alWidth = alignment.getWidth();
\r
220 Annotation[] annotations = new Annotation[alWidth];
\r
221 Annotation[] qannotations = new Annotation[alWidth];
\r
222 String sequence = cons.getConsSequence().getSequence();
\r
223 float minR, minG, minB, maxR, maxG, maxB;
\r
227 maxR = 1.0f - minR;
\r
228 maxG = 0.9f - minG;
\r
229 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
\r
232 float qmin = cons.qualityRange[0].floatValue();
\r
233 float qmax = cons.qualityRange[1].floatValue();
\r
235 for (int i = 0; i < alWidth; i++)
\r
240 value = Integer.parseInt(sequence.charAt(i) + "");
\r
242 catch (Exception ex)
\r
244 if (sequence.charAt(i) == '*')
\r
248 if (sequence.charAt(i) == '+')
\r
253 float vprop = value - min;
\r
256 annotations[i] = new Annotation(sequence.charAt(i) + "",
\r
258 new Color(minR + maxR * vprop,
\r
259 minG + maxG * vprop,
\r
260 minB + maxB * vprop));
\r
262 value = ( (Double) cons.quality.elementAt(i)).floatValue();
\r
263 vprop = value - qmin;
\r
265 qannotations[i] = new Annotation(" ",
\r
266 String.valueOf(value), ' ', value,
\r
268 Color(minR + maxR * vprop,
\r
269 minG + maxG * vprop,
\r
270 minB + maxB * vprop));
\r
273 if (conservation == null)
\r
275 conservation = new AlignmentAnnotation("Conservation",
\r
276 "Conservation of total alignment less than " +
\r
277 ConsPercGaps + "% gaps",
\r
279 0f, // cons.qualityRange[0].floatValue(),
\r
280 11f, // cons.qualityRange[1].floatValue()
\r
281 AlignmentAnnotation.BAR_GRAPH);
\r
282 if (showConservation)
\r
284 alignment.addAnnotation(conservation);
\r
286 quality = new AlignmentAnnotation("Quality",
\r
287 "Alignment Quality based on Blosum62 scores",
\r
289 cons.qualityRange[0].floatValue(),
\r
290 cons.qualityRange[1].floatValue(),
\r
291 AlignmentAnnotation.BAR_GRAPH);
\r
294 alignment.addAnnotation(quality);
\r
299 conservation.annotations = annotations;
\r
300 quality.annotations = qannotations;
\r
301 quality.graphMax = cons.qualityRange[1].floatValue();
\r
306 public void updateConsensus()
\r
308 Annotation[] annotations = new Annotation[alignment.getWidth()];
\r
310 // this routine prevents vconsensus becoming a new object each time
\r
311 // consenus is calculated. Important for speed of Blosum62
\r
312 // and PID colouring of alignment
\r
313 if (vconsensus == null)
\r
315 vconsensus = alignment.getAAFrequency();
\r
319 Vector temp = alignment.getAAFrequency();
\r
320 vconsensus.removeAllElements();
\r
321 Enumeration e = temp.elements();
\r
322 while (e.hasMoreElements())
\r
324 vconsensus.addElement(e.nextElement());
\r
327 Hashtable hash = null;
\r
328 for (int i = 0; i < alignment.getWidth(); i++)
\r
330 hash = (Hashtable) vconsensus.elementAt(i);
\r
332 if(ignoreGapsInConsensusCalculation)
\r
333 value = ((Float)hash.get("pid_nogaps")).floatValue();
\r
335 value = ((Float)hash.get("pid_gaps")).floatValue();
\r
337 String maxRes = hash.get("maxResidue").toString();
\r
338 String mouseOver = hash.get("maxResidue") + " ";
\r
339 if (maxRes.length() > 1)
\r
341 mouseOver = "[" + maxRes + "] ";
\r
346 mouseOver += (int) value + "%";
\r
347 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
\r
351 if (consensus == null)
\r
353 consensus = new AlignmentAnnotation("Consensus",
\r
354 "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
\r
357 alignment.addAnnotation(consensus);
\r
362 consensus.annotations = annotations;
\r
365 if(globalColourScheme!=null)
\r
366 globalColourScheme.setConsensus(vconsensus);
\r
370 * get the consensus sequence as displayed under the PID consensus annotation row.
\r
371 * @return consensus sequence as a new sequence object
\r
374 * get the consensus sequence as displayed under the PID consensus annotation row.
\r
375 * @return consensus sequence as a new sequence object
\r
377 public SequenceI getConsensusSeq() {
\r
378 if (consensus==null)
\r
380 if (consensus==null)
\r
382 StringBuffer seqs=new StringBuffer();
\r
383 for (int i=0; i<consensus.annotations.length; i++) {
\r
384 if (consensus.annotations[i]!=null) {
\r
385 if (consensus.annotations[i].description.charAt(0) == '[')
\r
386 seqs.append(consensus.annotations[i].description.charAt(1));
\r
388 seqs.append(consensus.annotations[i].displayCharacter);
\r
391 SequenceI sq = new Sequence("Consensus", seqs.toString());
\r
392 sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
\r
395 public SequenceGroup getSelectionGroup()
\r
397 return selectionGroup;
\r
400 public void setSelectionGroup(SequenceGroup sg)
\r
402 selectionGroup = sg;
\r
405 public boolean getConservationSelected()
\r
407 return conservationColourSelected;
\r
410 public void setConservationSelected(boolean b)
\r
412 conservationColourSelected = b;
\r
415 public boolean getAbovePIDThreshold()
\r
417 return abovePIDThreshold;
\r
420 public void setAbovePIDThreshold(boolean b)
\r
422 abovePIDThreshold = b;
\r
425 public int getStartRes()
\r
430 public int getEndRes()
\r
435 public int getStartSeq()
\r
440 public void setGlobalColourScheme(ColourSchemeI cs)
\r
442 globalColourScheme = cs;
\r
445 public ColourSchemeI getGlobalColourScheme()
\r
447 return globalColourScheme;
\r
450 public void setStartRes(int res)
\r
452 this.startRes = res;
\r
455 public void setStartSeq(int seq)
\r
457 this.startSeq = seq;
\r
460 public void setEndRes(int res)
\r
462 if (res > alignment.getWidth() - 1)
\r
464 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
\r
465 res = alignment.getWidth() - 1;
\r
474 public void setEndSeq(int seq)
\r
476 if (seq > alignment.getHeight())
\r
478 seq = alignment.getHeight();
\r
487 public int getEndSeq()
\r
492 java.awt.Frame nullFrame;
\r
493 public void setFont(Font f)
\r
496 if(nullFrame == null)
\r
498 nullFrame = new java.awt.Frame();
\r
499 nullFrame.addNotify();
\r
502 java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
\r
503 setCharHeight(fm.getHeight());
\r
504 charWidth = fm.charWidth('M');
\r
508 Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
\r
509 fm = nullFrame.getGraphics().getFontMetrics(f2);
\r
510 charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
\r
514 public Font getFont()
\r
519 public int getCharWidth()
\r
524 public void setCharHeight(int h)
\r
526 this.charHeight = h;
\r
529 public int getCharHeight()
\r
534 public void setWrappedWidth(int w)
\r
536 this.wrappedWidth = w;
\r
539 public int getwrappedWidth()
\r
541 return wrappedWidth;
\r
544 public AlignmentI getAlignment()
\r
549 public void setAlignment(AlignmentI align)
\r
551 this.alignment = align;
\r
554 public void setWrapAlignment(boolean state)
\r
556 wrapAlignment = state;
\r
559 public void setShowText(boolean state)
\r
564 public void setRenderGaps(boolean state)
\r
566 renderGaps = state;
\r
569 public boolean getColourText()
\r
571 return showColourText;
\r
574 public void setColourText(boolean state)
\r
576 showColourText = state;
\r
579 public void setShowBoxes(boolean state)
\r
584 public boolean getWrapAlignment()
\r
586 return wrapAlignment;
\r
589 public boolean getShowText()
\r
594 public boolean getShowBoxes()
\r
599 public char getGapCharacter()
\r
601 return getAlignment().getGapCharacter();
\r
604 public void setGapCharacter(char gap)
\r
606 if (getAlignment() != null)
\r
608 getAlignment().setGapCharacter(gap);
\r
612 public void setThreshold(int thresh)
\r
614 threshold = thresh;
\r
617 public int getThreshold()
\r
622 public void setIncrement(int inc)
\r
627 public int getIncrement()
\r
632 public void setHiddenColumns(ColumnSelection colsel)
\r
634 this.colSel = colsel;
\r
635 if(colSel.getHiddenColumns()!=null)
\r
636 hasHiddenColumns = true;
\r
639 public ColumnSelection getColumnSelection()
\r
644 public void resetSeqLimits(int height)
\r
646 setEndSeq(height / getCharHeight());
\r
649 public void setCurrentTree(NJTree tree)
\r
651 currentTree = tree;
\r
654 public NJTree getCurrentTree()
\r
656 return currentTree;
\r
659 public void setColourAppliesToAllGroups(boolean b)
\r
661 colourAppliesToAllGroups = b;
\r
664 public boolean getColourAppliesToAllGroups()
\r
666 return colourAppliesToAllGroups;
\r
669 public boolean getShowJVSuffix()
\r
671 return showJVSuffix;
\r
674 public void setShowJVSuffix(boolean b)
\r
679 public boolean getShowAnnotation()
\r
681 return showAnnotation;
\r
684 public void setShowAnnotation(boolean b)
\r
686 showAnnotation = b;
\r
689 public boolean getScaleAboveWrapped()
\r
691 return scaleAboveWrapped;
\r
694 public boolean getScaleLeftWrapped()
\r
696 return scaleLeftWrapped;
\r
699 public boolean getScaleRightWrapped()
\r
701 return scaleRightWrapped;
\r
704 public void setScaleAboveWrapped(boolean b)
\r
706 scaleAboveWrapped = b;
\r
709 public void setScaleLeftWrapped(boolean b)
\r
711 scaleLeftWrapped = b;
\r
714 public void setScaleRightWrapped(boolean b)
\r
716 scaleRightWrapped = b;
\r
719 public void setIgnoreGapsConsensus(boolean b)
\r
721 ignoreGapsInConsensusCalculation = b;
\r
723 if (globalColourScheme!=null)
\r
725 globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
\r
726 ignoreGapsInConsensusCalculation);
\r
732 * Property change listener for changes in alignment
\r
734 * @param listener DOCUMENT ME!
\r
736 public void addPropertyChangeListener(
\r
737 java.beans.PropertyChangeListener listener)
\r
739 changeSupport.addPropertyChangeListener(listener);
\r
745 * @param listener DOCUMENT ME!
\r
747 public void removePropertyChangeListener(
\r
748 java.beans.PropertyChangeListener listener)
\r
750 changeSupport.removePropertyChangeListener(listener);
\r
754 * Property change listener for changes in alignment
\r
756 * @param prop DOCUMENT ME!
\r
757 * @param oldvalue DOCUMENT ME!
\r
758 * @param newvalue DOCUMENT ME!
\r
760 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
\r
762 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
\r
767 public boolean getIgnoreGapsConsensus()
\r
769 return ignoreGapsInConsensusCalculation;
\r
771 public void hideSelectedColumns()
\r
773 if (colSel.size() < 1)
\r
776 colSel.hideSelectedColumns();
\r
777 setSelectionGroup(null);
\r
779 hasHiddenColumns = true;
\r
782 public void invertColumnSelection()
\r
785 for (int i = 0; i < alignment.getWidth(); i++)
\r
789 if (colSel.contains(column))
\r
790 colSel.removeElement(column);
\r
792 colSel.addElement(column);
\r
798 public void hideColumns(int start, int end)
\r
801 colSel.hideColumns(start);
\r
803 colSel.hideColumns(start, end);
\r
805 hasHiddenColumns = true;
\r
808 public void hideAllSelectedSeqs()
\r
810 if (selectionGroup == null)
\r
813 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
\r
815 hideSequence(seqs);
\r
817 setSelectionGroup(null);
\r
820 public void hideSequence(SequenceI [] seq)
\r
824 for (int i = 0; i < seq.length; i++)
\r
825 alignment.getHiddenSequences().hideSequence(seq[i]);
\r
827 hasHiddenRows = true;
\r
828 firePropertyChange("alignment", null, alignment.getSequences());
\r
832 public void showColumn(int col)
\r
834 colSel.revealHiddenColumns(col);
\r
835 if(colSel.getHiddenColumns()==null)
\r
836 hasHiddenColumns = false;
\r
839 public void showAllHiddenColumns()
\r
841 colSel.revealAllHiddenColumns();
\r
842 hasHiddenColumns = false;
\r
845 public void showAllHiddenSeqs()
\r
847 if(alignment.getHiddenSequences().getSize()>0)
\r
849 if(selectionGroup==null)
\r
851 selectionGroup = new SequenceGroup();
\r
852 selectionGroup.setEndRes(alignment.getWidth()-1);
\r
854 Vector tmp = alignment.getHiddenSequences().showAll();
\r
855 for(int t=0; t<tmp.size(); t++)
\r
857 selectionGroup.addSequence(
\r
858 (SequenceI)tmp.elementAt(t), false
\r
861 firePropertyChange("alignment", null, alignment.getSequences());
\r
862 hasHiddenRows = false;
\r
866 public int adjustForHiddenSeqs(int alignmentIndex)
\r
868 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
\r
872 * This method returns the a new SequenceI [] with
\r
873 * the selection sequence and start and end points adjusted
\r
876 public SequenceI[] getSelectionAsNewSequence()
\r
878 SequenceI[] sequences;
\r
880 if (selectionGroup == null)
\r
881 sequences = alignment.getSequencesArray();
\r
883 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
\r
889 * This method returns the visible alignment as text, as
\r
890 * seen on the GUI, ie if columns are hidden they will not
\r
891 * be returned in the result.
\r
892 * Use this for calculating trees, PCA, redundancy etc on views
\r
893 * which contain hidden columns.
\r
896 public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
\r
898 CigarArray selection=null;
\r
899 SequenceI [] seqs= null;
\r
901 int start = 0, end = 0;
\r
902 if(selectedRegionOnly && selectionGroup!=null)
\r
904 iSize = selectionGroup.getSize(false);
\r
905 seqs = selectionGroup.getSequencesInOrder(alignment);
\r
906 start = selectionGroup.getStartRes();
\r
907 end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
\r
911 iSize = alignment.getHeight();
\r
912 seqs = alignment.getSequencesArray();
\r
913 end = alignment.getWidth()-1;
\r
915 SeqCigar[] selseqs = new SeqCigar[iSize];
\r
916 for(i=0; i<iSize; i++)
\r
918 selseqs[i] = new SeqCigar(seqs[i], start, end);
\r
920 selection=new CigarArray(selseqs);
\r
921 // now construct the CigarArray operations
\r
922 if (hasHiddenColumns) {
\r
923 Vector regions = colSel.getHiddenColumns();
\r
925 int hideStart, hideEnd;
\r
927 for (int j = 0; last<end & j < regions.size(); j++)
\r
929 region = (int[]) regions.elementAt(j);
\r
930 hideStart = region[0];
\r
931 hideEnd = region[1];
\r
932 // edit hidden regions to selection range
\r
933 if(hideStart<last) {
\r
934 if (hideEnd > last)
\r
947 if (hideStart>hideEnd)
\r
950 * form operations...
\r
952 if (last<hideStart)
\r
953 selection.addOperation(CigarArray.M, hideStart-last);
\r
954 selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
\r
957 // Final match if necessary.
\r
959 selection.addOperation(CigarArray.M, end-last+1);
\r
961 selection.addOperation(CigarArray.M, end-start+1);
\r
966 * return a compact representation of the current alignment selection to
\r
967 * pass to an analysis function
\r
968 * @param selectedOnly boolean true to just return the selected view
\r
969 * @return AlignmentView
\r
971 jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
\r
973 // this is here because the AlignmentView constructor modifies the CigarArray
\r
974 // object. Refactoring of Cigar and alignment view representation should
\r
975 // be done to remove redundancy.
\r
976 CigarArray aligview = getViewAsCigars(selectedOnly);
\r
977 if (aligview!=null)
\r
978 return new AlignmentView(aligview);
\r
982 * This method returns the visible alignment as text, as
\r
983 * seen on the GUI, ie if columns are hidden they will not
\r
984 * be returned in the result.
\r
985 * Use this for calculating trees, PCA, redundancy etc on views
\r
986 * which contain hidden columns.
\r
989 public String [] getViewAsString(boolean selectedRegionOnly)
\r
991 String [] selection = null;
\r
992 SequenceI [] seqs= null;
\r
994 int start = 0, end = 0;
\r
995 if(selectedRegionOnly && selectionGroup!=null)
\r
997 iSize = selectionGroup.getSize(false);
\r
998 seqs = selectionGroup.getSequencesInOrder(alignment);
\r
999 start = selectionGroup.getStartRes();
\r
1000 end = selectionGroup.getEndRes()+1;
\r
1004 iSize = alignment.getHeight();
\r
1005 seqs = alignment.getSequencesArray();
\r
1006 end = alignment.getWidth();
\r
1009 selection = new String[iSize];
\r
1012 for(i=0; i<iSize; i++)
\r
1014 if (hasHiddenColumns)
\r
1016 StringBuffer visibleSeq = new StringBuffer();
\r
1017 Vector regions = colSel.getHiddenColumns();
\r
1019 int blockStart = start, blockEnd=end;
\r
1021 int hideStart, hideEnd;
\r
1023 for (int j = 0; j < regions.size(); j++)
\r
1025 region = (int[]) regions.elementAt(j);
\r
1026 hideStart = region[0];
\r
1027 hideEnd = region[1];
\r
1029 if(hideStart < start)
\r
1034 blockStart = Math.min(blockStart, hideEnd+1);
\r
1035 blockEnd = Math.min(blockEnd, hideStart);
\r
1037 if(blockStart>blockEnd)
\r
1043 visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
\r
1045 blockStart = hideEnd+1;
\r
1049 if(end>blockStart)
\r
1050 visibleSeq.append(seqs[i].getSequence(blockStart, end));
\r
1052 selection[i] = visibleSeq.toString();
\r
1056 selection[i] = seqs[i].getSequence(start, end);
\r
1063 public boolean getShowHiddenMarkers()
\r
1065 return showHiddenMarkers;
\r
1068 public void setShowHiddenMarkers(boolean show)
\r
1070 showHiddenMarkers = show;
\r