2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
21 import jalview.analysis.*;
25 import jalview.datamodel.*;
27 import jalview.schemes.*;
40 public class AlignViewport
46 boolean showJVSuffix = true;
47 boolean showText = true;
48 boolean showColourText = false;
49 boolean showBoxes = true;
50 boolean wrapAlignment = false;
51 boolean renderGaps = true;
52 boolean showSequenceFeatures = false;
53 boolean showAnnotation = true;
54 boolean showConservation = true;
55 boolean showQuality = true;
56 boolean showIdentity = true;
57 boolean colourAppliesToAllGroups = true;
58 ColourSchemeI globalColourScheme = null;
59 boolean conservationColourSelected = false;
60 boolean abovePIDThreshold = false;
61 SequenceGroup selectionGroup;
64 boolean validCharWidth;
68 ColumnSelection colSel = new ColumnSelection();
71 NJTree currentTree = null;
72 boolean scaleAboveWrapped = false;
73 boolean scaleLeftWrapped = true;
74 boolean scaleRightWrapped = true;
75 boolean hasHiddenColumns = false;
76 boolean hasHiddenRows = false;
77 boolean showHiddenMarkers = true;
79 boolean cursorMode = false;
81 // The following vector holds the features which are
82 // currently visible, in the correct order or rendering
83 Hashtable featuresDisplayed = null;
87 public Vector vconsensus;
88 AlignmentAnnotation consensus;
89 AlignmentAnnotation conservation;
90 AlignmentAnnotation quality;
91 boolean autoCalculateConsensus = true;
94 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
96 // JBPNote Prolly only need this in the applet version.
97 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
99 boolean ignoreGapsInConsensusCalculation = false;
101 boolean isDataset = false;
103 boolean antiAlias = false;
105 boolean padGaps = false;
107 Rectangle explodedPosition;
111 String sequenceSetID;
113 boolean gatherViewsHere = false;
116 public AlignViewport(AlignmentI al, boolean dataset)
123 * Creates a new AlignViewport object.
125 * @param al DOCUMENT ME!
127 public AlignViewport(AlignmentI al)
133 * Create a new AlignViewport with hidden regions
134 * @param al AlignmentI
135 * @param hiddenColumns ColumnSelection
137 public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
139 if (hiddenColumns!=null) {
140 this.colSel = hiddenColumns;
141 if (hiddenColumns.getHiddenColumns() != null)
142 hasHiddenColumns = true;
150 this.endRes = alignment.getWidth() - 1;
152 this.endSeq = alignment.getHeight() - 1;
154 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
156 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
157 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
158 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
160 showQuality = Cache.getDefault("SHOW_QUALITY", true);
161 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
163 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
165 padGaps = Cache.getDefault("PAD_GAPS", false);
167 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
168 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
169 String fontSize = Cache.getDefault("FONT_SIZE", "10");
173 if (fontStyle.equals("bold"))
177 else if (fontStyle.equals("italic"))
182 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
185 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
188 // We must set conservation and consensus before setting colour,
189 // as Blosum and Clustal require this to be done
190 if(vconsensus==null && !isDataset)
192 updateConservation();
196 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
198 globalColourScheme = ColourSchemeProperty.getColour(alignment,
199 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
201 if (globalColourScheme instanceof UserColourScheme)
203 globalColourScheme = UserDefinedColours.loadDefaultColours();
204 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
207 if (globalColourScheme != null)
209 globalColourScheme.setConsensus(vconsensus);
219 * @param b DOCUMENT ME!
221 public void setShowSequenceFeatures(boolean b)
223 showSequenceFeatures = b;
226 public boolean getShowSequenceFeatures()
228 return showSequenceFeatures;
234 public void updateConservation()
236 if(alignment.isNucleotide())
240 Conservation cons = new jalview.analysis.Conservation("All",
241 jalview.schemes.ResidueProperties.propHash, 3,
242 alignment.getSequences(), 0, alignment.getWidth() - 1);
244 cons.verdict(false, ConsPercGaps);
247 int alWidth = alignment.getWidth();
248 Annotation[] annotations = new Annotation[alWidth];
249 Annotation[] qannotations = new Annotation[alWidth];
250 String sequence = cons.getConsSequence().getSequence();
262 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
266 float qmin = cons.qualityRange[0].floatValue();
267 float qmax = cons.qualityRange[1].floatValue();
269 for (int i = 0; i < alWidth; i++)
275 value = Integer.parseInt(sequence.charAt(i) + "");
279 if (sequence.charAt(i) == '*')
284 if (sequence.charAt(i) == '+')
290 float vprop = value - min;
292 annotations[i] = new Annotation(sequence.charAt(i) + "",
293 String.valueOf(value), ' ', value,
294 new Color(minR + (maxR * vprop),
295 minG + (maxG * vprop),
296 minB + (maxB * vprop)));
299 value = ( (Double) cons.quality.get(i)).floatValue();
300 vprop = value - qmin;
302 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
304 new Color(minR + (maxR * vprop),
305 minG + (maxG * vprop),
306 minB + (maxB * vprop)));
309 if (conservation == null)
311 conservation = new AlignmentAnnotation("Conservation",
312 "Conservation of total alignment less than " +
313 ConsPercGaps + "% gaps",
314 annotations, 0f, // cons.qualityRange[0].floatValue(),
315 11f, // cons.qualityRange[1].floatValue()
316 AlignmentAnnotation.BAR_GRAPH);
318 if (showConservation)
320 alignment.addAnnotation(conservation);
323 quality = new AlignmentAnnotation("Quality",
324 "Alignment Quality based on Blosum62 scores",
326 cons.qualityRange[0].floatValue(),
327 cons.qualityRange[1].floatValue(),
328 AlignmentAnnotation.BAR_GRAPH);
332 alignment.addAnnotation(quality);
337 conservation.annotations = annotations;
338 quality.annotations = qannotations;
339 quality.graphMax = cons.qualityRange[1].floatValue();
342 catch (OutOfMemoryError error)
344 javax.swing.SwingUtilities.invokeLater(new Runnable()
348 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
349 "Out of memory calculating conservation!!"
351 "\nSee help files for increasing Java Virtual Machine memory."
353 javax.swing.JOptionPane.WARNING_MESSAGE);
357 System.out.println("Conservation calculation: " + error);
366 public void updateConsensus()
369 Annotation[] annotations = new Annotation[alignment.getWidth()];
371 // this routine prevents vconsensus becoming a new object each time
372 // consenus is calculated. Important for speed of Blosum62
373 // and PID colouring of alignment
374 if (vconsensus == null)
376 vconsensus = alignment.getAAFrequency();
380 Vector temp = alignment.getAAFrequency();
383 Enumeration e = temp.elements();
385 while (e.hasMoreElements())
387 vconsensus.add(e.nextElement());
391 Hashtable hash = null;
393 for (int i = 0; i < alignment.getWidth(); i++)
395 hash = (Hashtable) vconsensus.elementAt(i);
398 if (ignoreGapsInConsensusCalculation)
399 value = ( (Float) hash.get("pid_nogaps")).floatValue();
401 value = ( (Float) hash.get("pid_gaps")).floatValue();
403 String maxRes = hash.get("maxResidue").toString();
404 String mouseOver = hash.get("maxResidue") + " ";
406 if (maxRes.length() > 1)
408 mouseOver = "[" + maxRes + "] ";
412 mouseOver += ( (int) value + "%");
413 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
416 if (consensus == null)
418 consensus = new AlignmentAnnotation("Consensus", "PID",
419 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
423 alignment.addAnnotation(consensus);
428 consensus.annotations = annotations;
431 if (globalColourScheme != null)
432 globalColourScheme.setConsensus(vconsensus);
434 }catch(OutOfMemoryError error)
436 javax.swing.SwingUtilities.invokeLater(new Runnable()
440 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
441 "Out of memory calculating consensus!!"
443 "\nSee help files for increasing Java Virtual Machine memory."
445 javax.swing.JOptionPane.WARNING_MESSAGE);
450 System.out.println("Consensus calculation: " + error);
456 * get the consensus sequence as displayed under the PID consensus annotation row.
457 * @return consensus sequence as a new sequence object
459 public SequenceI getConsensusSeq() {
464 StringBuffer seqs=new StringBuffer();
465 for (int i=0; i<consensus.annotations.length; i++) {
466 if (consensus.annotations[i]!=null) {
467 if (consensus.annotations[i].description.charAt(0) == '[')
468 seqs.append(consensus.annotations[i].description.charAt(1));
470 seqs.append(consensus.annotations[i].displayCharacter);
473 SequenceI sq = new Sequence("Consensus", seqs.toString());
474 sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
480 * @return DOCUMENT ME!
482 public SequenceGroup getSelectionGroup()
484 return selectionGroup;
490 * @param sg DOCUMENT ME!
492 public void setSelectionGroup(SequenceGroup sg)
500 * @return DOCUMENT ME!
502 public boolean getConservationSelected()
504 return conservationColourSelected;
510 * @param b DOCUMENT ME!
512 public void setConservationSelected(boolean b)
514 conservationColourSelected = b;
520 * @return DOCUMENT ME!
522 public boolean getAbovePIDThreshold()
524 return abovePIDThreshold;
530 * @param b DOCUMENT ME!
532 public void setAbovePIDThreshold(boolean b)
534 abovePIDThreshold = b;
540 * @return DOCUMENT ME!
542 public int getStartRes()
550 * @return DOCUMENT ME!
552 public int getEndRes()
560 * @return DOCUMENT ME!
562 public int getStartSeq()
570 * @param cs DOCUMENT ME!
572 public void setGlobalColourScheme(ColourSchemeI cs)
574 globalColourScheme = cs;
580 * @return DOCUMENT ME!
582 public ColourSchemeI getGlobalColourScheme()
584 return globalColourScheme;
590 * @param res DOCUMENT ME!
592 public void setStartRes(int res)
600 * @param seq DOCUMENT ME!
602 public void setStartSeq(int seq)
610 * @param res DOCUMENT ME!
612 public void setEndRes(int res)
614 if (res > (alignment.getWidth() - 1))
616 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
617 res = alignment.getWidth() - 1;
631 * @param seq DOCUMENT ME!
633 public void setEndSeq(int seq)
635 if (seq > alignment.getHeight())
637 seq = alignment.getHeight();
651 * @return DOCUMENT ME!
653 public int getEndSeq()
661 * @param f DOCUMENT ME!
663 public void setFont(Font f)
667 Container c = new Container();
669 java.awt.FontMetrics fm = c.getFontMetrics(font);
670 setCharHeight(fm.getHeight());
671 setCharWidth(fm.charWidth('M'));
672 validCharWidth = true;
678 * @return DOCUMENT ME!
680 public Font getFont()
688 * @param w DOCUMENT ME!
690 public void setCharWidth(int w)
698 * @return DOCUMENT ME!
700 public int getCharWidth()
708 * @param h DOCUMENT ME!
710 public void setCharHeight(int h)
718 * @return DOCUMENT ME!
720 public int getCharHeight()
728 * @param w DOCUMENT ME!
730 public void setWrappedWidth(int w)
732 this.wrappedWidth = w;
738 * @return DOCUMENT ME!
740 public int getWrappedWidth()
749 * @return DOCUMENT ME!
751 public AlignmentI getAlignment()
759 * @param align DOCUMENT ME!
761 public void setAlignment(AlignmentI align)
763 this.alignment = align;
769 * @param state DOCUMENT ME!
771 public void setWrapAlignment(boolean state)
773 wrapAlignment = state;
779 * @param state DOCUMENT ME!
781 public void setShowText(boolean state)
789 * @param state DOCUMENT ME!
791 public void setRenderGaps(boolean state)
799 * @return DOCUMENT ME!
801 public boolean getColourText()
803 return showColourText;
809 * @param state DOCUMENT ME!
811 public void setColourText(boolean state)
813 showColourText = state;
819 * @param state DOCUMENT ME!
821 public void setShowBoxes(boolean state)
829 * @return DOCUMENT ME!
831 public boolean getWrapAlignment()
833 return wrapAlignment;
839 * @return DOCUMENT ME!
841 public boolean getShowText()
849 * @return DOCUMENT ME!
851 public boolean getShowBoxes()
859 * @return DOCUMENT ME!
861 public char getGapCharacter()
863 return getAlignment().getGapCharacter();
869 * @param gap DOCUMENT ME!
871 public void setGapCharacter(char gap)
873 if (getAlignment() != null)
875 getAlignment().setGapCharacter(gap);
882 * @param thresh DOCUMENT ME!
884 public void setThreshold(int thresh)
892 * @return DOCUMENT ME!
894 public int getThreshold()
902 * @param inc DOCUMENT ME!
904 public void setIncrement(int inc)
912 * @return DOCUMENT ME!
914 public int getIncrement()
923 * @return DOCUMENT ME!
925 public ColumnSelection getColumnSelection()
934 * @param tree DOCUMENT ME!
936 public void setCurrentTree(NJTree tree)
944 * @return DOCUMENT ME!
946 public NJTree getCurrentTree()
954 * @param b DOCUMENT ME!
956 public void setColourAppliesToAllGroups(boolean b)
958 colourAppliesToAllGroups = b;
964 * @return DOCUMENT ME!
966 public boolean getColourAppliesToAllGroups()
968 return colourAppliesToAllGroups;
974 * @return DOCUMENT ME!
976 public boolean getShowJVSuffix()
984 * @param b DOCUMENT ME!
986 public void setShowJVSuffix(boolean b)
995 * @return DOCUMENT ME!
997 public boolean getShowAnnotation()
999 return showAnnotation;
1005 * @param b DOCUMENT ME!
1007 public void setShowAnnotation(boolean b)
1015 * @return DOCUMENT ME!
1017 public boolean getScaleAboveWrapped()
1019 return scaleAboveWrapped;
1025 * @return DOCUMENT ME!
1027 public boolean getScaleLeftWrapped()
1029 return scaleLeftWrapped;
1035 * @return DOCUMENT ME!
1037 public boolean getScaleRightWrapped()
1039 return scaleRightWrapped;
1045 * @param b DOCUMENT ME!
1047 public void setScaleAboveWrapped(boolean b)
1049 scaleAboveWrapped = b;
1055 * @param b DOCUMENT ME!
1057 public void setScaleLeftWrapped(boolean b)
1059 scaleLeftWrapped = b;
1065 * @param b DOCUMENT ME!
1067 public void setScaleRightWrapped(boolean b)
1069 scaleRightWrapped = b;
1073 * Property change listener for changes in alignment
1075 * @param listener DOCUMENT ME!
1077 public void addPropertyChangeListener(
1078 java.beans.PropertyChangeListener listener)
1080 changeSupport.addPropertyChangeListener(listener);
1086 * @param listener DOCUMENT ME!
1088 public void removePropertyChangeListener(
1089 java.beans.PropertyChangeListener listener)
1091 changeSupport.removePropertyChangeListener(listener);
1095 * Property change listener for changes in alignment
1097 * @param prop DOCUMENT ME!
1098 * @param oldvalue DOCUMENT ME!
1099 * @param newvalue DOCUMENT ME!
1101 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
1103 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1106 public void setIgnoreGapsConsensus(boolean b)
1108 ignoreGapsInConsensusCalculation = b;
1110 if(globalColourScheme!=null)
1112 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
1116 public boolean getIgnoreGapsConsensus()
1118 return ignoreGapsInConsensusCalculation;
1121 public void setDataset(boolean b)
1126 public boolean isDataset()
1132 public void hideSelectedColumns()
1134 if (colSel.size() < 1)
1137 colSel.hideSelectedColumns();
1138 setSelectionGroup(null);
1140 hasHiddenColumns = true;
1144 public void hideColumns(int start, int end)
1147 colSel.hideColumns(start);
1149 colSel.hideColumns(start, end);
1151 hasHiddenColumns = true;
1154 public void hideAllSelectedSeqs()
1156 if (selectionGroup == null)
1159 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1163 setSelectionGroup(null);
1166 public void hideSequence(SequenceI [] seq)
1170 for (int i = 0; i < seq.length; i++)
1171 alignment.getHiddenSequences().hideSequence(seq[i]);
1173 hasHiddenRows = true;
1174 firePropertyChange("alignment", null, alignment.getSequences());
1178 public void showSequence(int index)
1180 Vector tmp = alignment.getHiddenSequences().showSequence(index);
1183 if(selectionGroup==null)
1185 selectionGroup = new SequenceGroup();
1186 selectionGroup.setEndRes(alignment.getWidth()-1);
1189 for (int t = 0; t < tmp.size(); t++)
1191 selectionGroup.addSequence(
1192 (SequenceI) tmp.elementAt(t), false
1195 firePropertyChange("alignment", null, alignment.getSequences());
1198 if(alignment.getHiddenSequences().getSize()<1)
1199 hasHiddenRows = false;
1202 public void showColumn(int col)
1204 colSel.revealHiddenColumns(col);
1205 if(colSel.getHiddenColumns()==null)
1206 hasHiddenColumns = false;
1209 public void showAllHiddenColumns()
1211 colSel.revealAllHiddenColumns();
1212 hasHiddenColumns = false;
1215 public void showAllHiddenSeqs()
1217 if(alignment.getHiddenSequences().getSize()>0)
1219 if(selectionGroup==null)
1221 selectionGroup = new SequenceGroup();
1222 selectionGroup.setEndRes(alignment.getWidth()-1);
1224 Vector tmp = alignment.getHiddenSequences().showAll();
1225 for(int t=0; t<tmp.size(); t++)
1227 selectionGroup.addSequence(
1228 (SequenceI)tmp.elementAt(t), false
1231 firePropertyChange("alignment", null, alignment.getSequences());
1232 hasHiddenRows = false;
1236 public void invertColumnSelection()
1239 for(int i=0; i<alignment.getWidth(); i++)
1243 if(colSel.contains(column))
1244 colSel.removeElement(column);
1246 colSel.addElement(column);
1252 public int adjustForHiddenSeqs(int alignmentIndex)
1254 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
1258 * This method returns the a new SequenceI [] with
1259 * the selection sequence and start and end points adjusted
1262 public SequenceI[] getSelectionAsNewSequence()
1264 SequenceI[] sequences;
1266 if (selectionGroup == null)
1267 sequences = alignment.getSequencesArray();
1269 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1275 * This method returns the visible alignment as text, as
1276 * seen on the GUI, ie if columns are hidden they will not
1277 * be returned in the result.
1278 * Use this for calculating trees, PCA, redundancy etc on views
1279 * which contain hidden columns.
1282 public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
1284 CigarArray selection=null;
1285 SequenceI [] seqs= null;
1287 int start = 0, end = 0;
1288 if(selectedRegionOnly && selectionGroup!=null)
1290 iSize = selectionGroup.getSize(false);
1291 seqs = selectionGroup.getSequencesInOrder(alignment);
1292 start = selectionGroup.getStartRes();
1293 end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
1297 iSize = alignment.getHeight();
1298 seqs = alignment.getSequencesArray();
1299 end = alignment.getWidth()-1;
1301 SeqCigar[] selseqs = new SeqCigar[iSize];
1302 for(i=0; i<iSize; i++)
1304 selseqs[i] = new SeqCigar(seqs[i], start, end);
1306 selection=new CigarArray(selseqs);
1307 // now construct the CigarArray operations
1308 if (hasHiddenColumns) {
1309 Vector regions = colSel.getHiddenColumns();
1311 int hideStart, hideEnd;
1313 for (int j = 0; last<end & j < regions.size(); j++)
1315 region = (int[]) regions.elementAt(j);
1316 hideStart = region[0];
1317 hideEnd = region[1];
1318 // edit hidden regions to selection range
1319 if(hideStart<last) {
1333 if (hideStart>hideEnd)
1336 * form operations...
1339 selection.addOperation(CigarArray.M, hideStart-last);
1340 selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
1343 // Final match if necessary.
1345 selection.addOperation(CigarArray.M, end-last+1);
1347 selection.addOperation(CigarArray.M, end-start+1);
1352 * return a compact representation of the current alignment selection to
1353 * pass to an analysis function
1354 * @param selectedOnly boolean true to just return the selected view
1355 * @return AlignmentView
1357 jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
1359 // this is here because the AlignmentView constructor modifies the CigarArray
1360 // object. Refactoring of Cigar and alignment view representation should
1361 // be done to remove redundancy.
1362 CigarArray aligview = getViewAsCigars(selectedOnly);
1364 return new AlignmentView(aligview);
1368 * This method returns the visible alignment as text, as
1369 * seen on the GUI, ie if columns are hidden they will not
1370 * be returned in the result.
1371 * Use this for calculating trees, PCA, redundancy etc on views
1372 * which contain hidden columns.
1375 public String [] getViewAsString(boolean selectedRegionOnly)
1377 String [] selection = null;
1378 SequenceI [] seqs= null;
1380 int start = 0, end = 0;
1381 if(selectedRegionOnly && selectionGroup!=null)
1383 iSize = selectionGroup.getSize(false);
1384 seqs = selectionGroup.getSequencesInOrder(alignment);
1385 start = selectionGroup.getStartRes();
1386 end = selectionGroup.getEndRes()+1;
1390 iSize = alignment.getHeight();
1391 seqs = alignment.getSequencesArray();
1392 end = alignment.getWidth();
1395 selection = new String[iSize];
1396 if (hasHiddenColumns) {
1397 selection = colSel.getVisibleSequenceStrings(start, end, seqs);
1399 for(i=0; i<iSize; i++)
1401 selection[i] = seqs[i].getSequence(start, end);
1408 public boolean getShowHiddenMarkers()
1410 return showHiddenMarkers;
1413 public void setShowHiddenMarkers(boolean show)
1415 showHiddenMarkers = show;
1418 public String getSequenceSetId()
1420 if(sequenceSetID==null)
1421 sequenceSetID = alignment.hashCode()+"";
1423 return sequenceSetID;