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 Hashtable [] hconsensus;
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(hconsensus==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(hconsensus);
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())
239 // System.out.println("UPDATING CONSERVATION");
242 Conservation cons = new jalview.analysis.Conservation("All",
243 jalview.schemes.ResidueProperties.propHash, 3,
244 alignment.getSequences(), 0, alignment.getWidth() - 1);
246 cons.verdict(false, ConsPercGaps);
249 int alWidth = alignment.getWidth();
250 Annotation[] annotations = new Annotation[alWidth];
251 Annotation[] qannotations = new Annotation[alWidth];
252 String sequence = cons.getConsSequence().getSequence();
264 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
268 float qmin = cons.qualityRange[0].floatValue();
269 float qmax = cons.qualityRange[1].floatValue();
271 for (int i = 0; i < alWidth; i++)
277 value = Integer.parseInt(sequence.charAt(i) + "");
281 if (sequence.charAt(i) == '*')
286 if (sequence.charAt(i) == '+')
292 float vprop = value - min;
294 annotations[i] = new Annotation(sequence.charAt(i) + "",
295 String.valueOf(value), ' ', value,
296 new Color(minR + (maxR * vprop),
297 minG + (maxG * vprop),
298 minB + (maxB * vprop)));
301 value = ( (Double) cons.quality.get(i)).floatValue();
302 vprop = value - qmin;
304 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
306 new Color(minR + (maxR * vprop),
307 minG + (maxG * vprop),
308 minB + (maxB * vprop)));
311 if (conservation == null)
313 conservation = new AlignmentAnnotation("Conservation",
314 "Conservation of total alignment less than " +
315 ConsPercGaps + "% gaps",
316 annotations, 0f, // cons.qualityRange[0].floatValue(),
317 11f, // cons.qualityRange[1].floatValue()
318 AlignmentAnnotation.BAR_GRAPH);
320 if (showConservation)
322 alignment.addAnnotation(conservation);
325 quality = new AlignmentAnnotation("Quality",
326 "Alignment Quality based on Blosum62 scores",
328 cons.qualityRange[0].floatValue(),
329 cons.qualityRange[1].floatValue(),
330 AlignmentAnnotation.BAR_GRAPH);
334 alignment.addAnnotation(quality);
339 conservation.annotations = annotations;
340 quality.annotations = qannotations;
341 quality.graphMax = cons.qualityRange[1].floatValue();
344 catch (OutOfMemoryError error)
346 javax.swing.SwingUtilities.invokeLater(new Runnable()
350 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
351 "Out of memory calculating conservation!!"
353 "\nSee help files for increasing Java Virtual Machine memory."
355 javax.swing.JOptionPane.WARNING_MESSAGE);
359 System.out.println("Conservation calculation: " + error);
369 public void updateConsensus()
372 int aWidth = alignment.getWidth();
374 Annotation[] annotations = new Annotation[aWidth];
376 hconsensus = new Hashtable[aWidth];
377 AAFrequency.calculate(alignment.getSequencesArray(),
379 alignment.getWidth(),
382 for (int i = 0; i < aWidth; i++)
385 if (ignoreGapsInConsensusCalculation)
386 value = ( (Float) hconsensus[i].get("pid_nogaps")).floatValue();
388 value = ( (Float) hconsensus[i].get("pid_gaps")).floatValue();
390 String maxRes = hconsensus[i].get("maxResidue").toString();
391 String mouseOver = hconsensus[i].get("maxResidue") + " ";
393 if (maxRes.length() > 1)
395 mouseOver = "[" + maxRes + "] ";
399 mouseOver += ( (int) value + "%");
400 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
403 if (consensus == null)
405 consensus = new AlignmentAnnotation("Consensus", "PID",
406 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
410 alignment.addAnnotation(consensus);
415 consensus.annotations = annotations;
418 if (globalColourScheme != null)
419 globalColourScheme.setConsensus(hconsensus);
421 }catch(OutOfMemoryError error)
423 javax.swing.SwingUtilities.invokeLater(new Runnable()
427 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
428 "Out of memory calculating consensus!!"
430 "\nSee help files for increasing Java Virtual Machine memory."
432 javax.swing.JOptionPane.WARNING_MESSAGE);
437 System.out.println("Consensus calculation: " + error);
443 * get the consensus sequence as displayed under the PID consensus annotation row.
444 * @return consensus sequence as a new sequence object
446 public SequenceI getConsensusSeq() {
451 StringBuffer seqs=new StringBuffer();
452 for (int i=0; i<consensus.annotations.length; i++) {
453 if (consensus.annotations[i]!=null) {
454 if (consensus.annotations[i].description.charAt(0) == '[')
455 seqs.append(consensus.annotations[i].description.charAt(1));
457 seqs.append(consensus.annotations[i].displayCharacter);
460 SequenceI sq = new Sequence("Consensus", seqs.toString());
461 sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
467 * @return DOCUMENT ME!
469 public SequenceGroup getSelectionGroup()
471 return selectionGroup;
477 * @param sg DOCUMENT ME!
479 public void setSelectionGroup(SequenceGroup sg)
487 * @return DOCUMENT ME!
489 public boolean getConservationSelected()
491 return conservationColourSelected;
497 * @param b DOCUMENT ME!
499 public void setConservationSelected(boolean b)
501 conservationColourSelected = b;
507 * @return DOCUMENT ME!
509 public boolean getAbovePIDThreshold()
511 return abovePIDThreshold;
517 * @param b DOCUMENT ME!
519 public void setAbovePIDThreshold(boolean b)
521 abovePIDThreshold = b;
527 * @return DOCUMENT ME!
529 public int getStartRes()
537 * @return DOCUMENT ME!
539 public int getEndRes()
547 * @return DOCUMENT ME!
549 public int getStartSeq()
557 * @param cs DOCUMENT ME!
559 public void setGlobalColourScheme(ColourSchemeI cs)
561 globalColourScheme = cs;
567 * @return DOCUMENT ME!
569 public ColourSchemeI getGlobalColourScheme()
571 return globalColourScheme;
577 * @param res DOCUMENT ME!
579 public void setStartRes(int res)
587 * @param seq DOCUMENT ME!
589 public void setStartSeq(int seq)
597 * @param res DOCUMENT ME!
599 public void setEndRes(int res)
601 if (res > (alignment.getWidth() - 1))
603 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
604 res = alignment.getWidth() - 1;
618 * @param seq DOCUMENT ME!
620 public void setEndSeq(int seq)
622 if (seq > alignment.getHeight())
624 seq = alignment.getHeight();
638 * @return DOCUMENT ME!
640 public int getEndSeq()
648 * @param f DOCUMENT ME!
650 public void setFont(Font f)
654 Container c = new Container();
656 java.awt.FontMetrics fm = c.getFontMetrics(font);
657 setCharHeight(fm.getHeight());
658 setCharWidth(fm.charWidth('M'));
659 validCharWidth = true;
665 * @return DOCUMENT ME!
667 public Font getFont()
675 * @param w DOCUMENT ME!
677 public void setCharWidth(int w)
685 * @return DOCUMENT ME!
687 public int getCharWidth()
695 * @param h DOCUMENT ME!
697 public void setCharHeight(int h)
705 * @return DOCUMENT ME!
707 public int getCharHeight()
715 * @param w DOCUMENT ME!
717 public void setWrappedWidth(int w)
719 this.wrappedWidth = w;
725 * @return DOCUMENT ME!
727 public int getWrappedWidth()
736 * @return DOCUMENT ME!
738 public AlignmentI getAlignment()
746 * @param align DOCUMENT ME!
748 public void setAlignment(AlignmentI align)
750 this.alignment = align;
756 * @param state DOCUMENT ME!
758 public void setWrapAlignment(boolean state)
760 wrapAlignment = state;
766 * @param state DOCUMENT ME!
768 public void setShowText(boolean state)
776 * @param state DOCUMENT ME!
778 public void setRenderGaps(boolean state)
786 * @return DOCUMENT ME!
788 public boolean getColourText()
790 return showColourText;
796 * @param state DOCUMENT ME!
798 public void setColourText(boolean state)
800 showColourText = state;
806 * @param state DOCUMENT ME!
808 public void setShowBoxes(boolean state)
816 * @return DOCUMENT ME!
818 public boolean getWrapAlignment()
820 return wrapAlignment;
826 * @return DOCUMENT ME!
828 public boolean getShowText()
836 * @return DOCUMENT ME!
838 public boolean getShowBoxes()
846 * @return DOCUMENT ME!
848 public char getGapCharacter()
850 return getAlignment().getGapCharacter();
856 * @param gap DOCUMENT ME!
858 public void setGapCharacter(char gap)
860 if (getAlignment() != null)
862 getAlignment().setGapCharacter(gap);
869 * @param thresh DOCUMENT ME!
871 public void setThreshold(int thresh)
879 * @return DOCUMENT ME!
881 public int getThreshold()
889 * @param inc DOCUMENT ME!
891 public void setIncrement(int inc)
899 * @return DOCUMENT ME!
901 public int getIncrement()
910 * @return DOCUMENT ME!
912 public ColumnSelection getColumnSelection()
921 * @param tree DOCUMENT ME!
923 public void setCurrentTree(NJTree tree)
931 * @return DOCUMENT ME!
933 public NJTree getCurrentTree()
941 * @param b DOCUMENT ME!
943 public void setColourAppliesToAllGroups(boolean b)
945 colourAppliesToAllGroups = b;
951 * @return DOCUMENT ME!
953 public boolean getColourAppliesToAllGroups()
955 return colourAppliesToAllGroups;
961 * @return DOCUMENT ME!
963 public boolean getShowJVSuffix()
971 * @param b DOCUMENT ME!
973 public void setShowJVSuffix(boolean b)
982 * @return DOCUMENT ME!
984 public boolean getShowAnnotation()
986 return showAnnotation;
992 * @param b DOCUMENT ME!
994 public void setShowAnnotation(boolean b)
1002 * @return DOCUMENT ME!
1004 public boolean getScaleAboveWrapped()
1006 return scaleAboveWrapped;
1012 * @return DOCUMENT ME!
1014 public boolean getScaleLeftWrapped()
1016 return scaleLeftWrapped;
1022 * @return DOCUMENT ME!
1024 public boolean getScaleRightWrapped()
1026 return scaleRightWrapped;
1032 * @param b DOCUMENT ME!
1034 public void setScaleAboveWrapped(boolean b)
1036 scaleAboveWrapped = b;
1042 * @param b DOCUMENT ME!
1044 public void setScaleLeftWrapped(boolean b)
1046 scaleLeftWrapped = b;
1052 * @param b DOCUMENT ME!
1054 public void setScaleRightWrapped(boolean b)
1056 scaleRightWrapped = b;
1060 * Property change listener for changes in alignment
1062 * @param listener DOCUMENT ME!
1064 public void addPropertyChangeListener(
1065 java.beans.PropertyChangeListener listener)
1067 changeSupport.addPropertyChangeListener(listener);
1073 * @param listener DOCUMENT ME!
1075 public void removePropertyChangeListener(
1076 java.beans.PropertyChangeListener listener)
1078 changeSupport.removePropertyChangeListener(listener);
1082 * Property change listener for changes in alignment
1084 * @param prop DOCUMENT ME!
1085 * @param oldvalue DOCUMENT ME!
1086 * @param newvalue DOCUMENT ME!
1088 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
1090 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
1093 public void setIgnoreGapsConsensus(boolean b)
1095 ignoreGapsInConsensusCalculation = b;
1097 if(globalColourScheme!=null)
1099 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
1103 public boolean getIgnoreGapsConsensus()
1105 return ignoreGapsInConsensusCalculation;
1108 public void setDataset(boolean b)
1113 public boolean isDataset()
1119 public void hideSelectedColumns()
1121 if (colSel.size() < 1)
1124 colSel.hideSelectedColumns();
1125 setSelectionGroup(null);
1127 hasHiddenColumns = true;
1131 public void hideColumns(int start, int end)
1134 colSel.hideColumns(start);
1136 colSel.hideColumns(start, end);
1138 hasHiddenColumns = true;
1141 public void hideAllSelectedSeqs()
1143 if (selectionGroup == null)
1146 SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
1150 setSelectionGroup(null);
1153 public void hideSequence(SequenceI [] seq)
1157 for (int i = 0; i < seq.length; i++)
1158 alignment.getHiddenSequences().hideSequence(seq[i]);
1160 hasHiddenRows = true;
1161 firePropertyChange("alignment", null, alignment.getSequences());
1165 public void showSequence(int index)
1167 Vector tmp = alignment.getHiddenSequences().showSequence(index);
1170 if(selectionGroup==null)
1172 selectionGroup = new SequenceGroup();
1173 selectionGroup.setEndRes(alignment.getWidth()-1);
1176 for (int t = 0; t < tmp.size(); t++)
1178 selectionGroup.addSequence(
1179 (SequenceI) tmp.elementAt(t), false
1182 firePropertyChange("alignment", null, alignment.getSequences());
1185 if(alignment.getHiddenSequences().getSize()<1)
1186 hasHiddenRows = false;
1189 public void showColumn(int col)
1191 colSel.revealHiddenColumns(col);
1192 if(colSel.getHiddenColumns()==null)
1193 hasHiddenColumns = false;
1196 public void showAllHiddenColumns()
1198 colSel.revealAllHiddenColumns();
1199 hasHiddenColumns = false;
1202 public void showAllHiddenSeqs()
1204 if(alignment.getHiddenSequences().getSize()>0)
1206 if(selectionGroup==null)
1208 selectionGroup = new SequenceGroup();
1209 selectionGroup.setEndRes(alignment.getWidth()-1);
1211 Vector tmp = alignment.getHiddenSequences().showAll();
1212 for(int t=0; t<tmp.size(); t++)
1214 selectionGroup.addSequence(
1215 (SequenceI)tmp.elementAt(t), false
1218 firePropertyChange("alignment", null, alignment.getSequences());
1219 hasHiddenRows = false;
1223 public void invertColumnSelection()
1226 for(int i=0; i<alignment.getWidth(); i++)
1230 if(colSel.contains(column))
1231 colSel.removeElement(column);
1233 colSel.addElement(column);
1239 public int adjustForHiddenSeqs(int alignmentIndex)
1241 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
1245 * This method returns the a new SequenceI [] with
1246 * the selection sequence and start and end points adjusted
1249 public SequenceI[] getSelectionAsNewSequence()
1251 SequenceI[] sequences;
1253 if (selectionGroup == null)
1254 sequences = alignment.getSequencesArray();
1256 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
1262 * This method returns the visible alignment as text, as
1263 * seen on the GUI, ie if columns are hidden they will not
1264 * be returned in the result.
1265 * Use this for calculating trees, PCA, redundancy etc on views
1266 * which contain hidden columns.
1269 public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
1271 CigarArray selection=null;
1272 SequenceI [] seqs= null;
1274 int start = 0, end = 0;
1275 if(selectedRegionOnly && selectionGroup!=null)
1277 iSize = selectionGroup.getSize(false);
1278 seqs = selectionGroup.getSequencesInOrder(alignment);
1279 start = selectionGroup.getStartRes();
1280 end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
1284 iSize = alignment.getHeight();
1285 seqs = alignment.getSequencesArray();
1286 end = alignment.getWidth()-1;
1288 SeqCigar[] selseqs = new SeqCigar[iSize];
1289 for(i=0; i<iSize; i++)
1291 selseqs[i] = new SeqCigar(seqs[i], start, end);
1293 selection=new CigarArray(selseqs);
1294 // now construct the CigarArray operations
1295 if (hasHiddenColumns) {
1296 Vector regions = colSel.getHiddenColumns();
1298 int hideStart, hideEnd;
1300 for (int j = 0; last<end & j < regions.size(); j++)
1302 region = (int[]) regions.elementAt(j);
1303 hideStart = region[0];
1304 hideEnd = region[1];
1305 // edit hidden regions to selection range
1306 if(hideStart<last) {
1320 if (hideStart>hideEnd)
1323 * form operations...
1326 selection.addOperation(CigarArray.M, hideStart-last);
1327 selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
1330 // Final match if necessary.
1332 selection.addOperation(CigarArray.M, end-last+1);
1334 selection.addOperation(CigarArray.M, end-start+1);
1339 * return a compact representation of the current alignment selection to
1340 * pass to an analysis function
1341 * @param selectedOnly boolean true to just return the selected view
1342 * @return AlignmentView
1344 jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
1346 // this is here because the AlignmentView constructor modifies the CigarArray
1347 // object. Refactoring of Cigar and alignment view representation should
1348 // be done to remove redundancy.
1349 CigarArray aligview = getViewAsCigars(selectedOnly);
1350 if (aligview!=null) {
1351 return new AlignmentView(aligview,
1352 (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
1357 * This method returns the visible alignment as text, as
1358 * seen on the GUI, ie if columns are hidden they will not
1359 * be returned in the result.
1360 * Use this for calculating trees, PCA, redundancy etc on views
1361 * which contain hidden columns.
1364 public String [] getViewAsString(boolean selectedRegionOnly)
1366 String [] selection = null;
1367 SequenceI [] seqs= null;
1369 int start = 0, end = 0;
1370 if(selectedRegionOnly && selectionGroup!=null)
1372 iSize = selectionGroup.getSize(false);
1373 seqs = selectionGroup.getSequencesInOrder(alignment);
1374 start = selectionGroup.getStartRes();
1375 end = selectionGroup.getEndRes()+1;
1379 iSize = alignment.getHeight();
1380 seqs = alignment.getSequencesArray();
1381 end = alignment.getWidth();
1384 selection = new String[iSize];
1385 if (hasHiddenColumns) {
1386 selection = colSel.getVisibleSequenceStrings(start, end, seqs);
1388 for(i=0; i<iSize; i++)
1390 selection[i] = seqs[i].getSequence(start, end);
1397 public boolean getShowHiddenMarkers()
1399 return showHiddenMarkers;
1402 public void setShowHiddenMarkers(boolean show)
1404 showHiddenMarkers = show;
1407 public String getSequenceSetId()
1409 if(sequenceSetID==null)
1410 sequenceSetID = alignment.hashCode()+"";
1412 return sequenceSetID;