2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 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
19 package jalview.gui;
\r
21 import jalview.analysis.*;
\r
23 import jalview.bin.*;
\r
25 import jalview.datamodel.*;
\r
27 import jalview.schemes.*;
\r
38 * @version $Revision$
\r
40 public class AlignViewport
\r
46 boolean showJVSuffix = true;
\r
47 boolean showText = true;
\r
48 boolean showColourText = false;
\r
49 boolean showBoxes = true;
\r
50 boolean wrapAlignment = false;
\r
51 boolean renderGaps = true;
\r
52 boolean showSequenceFeatures = false;
\r
53 boolean showAnnotation = true;
\r
54 boolean showConservation = true;
\r
55 boolean showQuality = true;
\r
56 boolean showIdentity = true;
\r
57 boolean colourAppliesToAllGroups = true;
\r
58 ColourSchemeI globalColourScheme = null;
\r
59 boolean conservationColourSelected = false;
\r
60 boolean abovePIDThreshold = false;
\r
61 SequenceGroup selectionGroup;
\r
64 boolean validCharWidth;
\r
67 AlignmentI alignment;
\r
68 ColumnSelection colSel = new ColumnSelection();
\r
71 NJTree currentTree = null;
\r
72 boolean scaleAboveWrapped = false;
\r
73 boolean scaleLeftWrapped = true;
\r
74 boolean scaleRightWrapped = true;
\r
75 boolean hasHiddenColumns = false;
\r
76 boolean hasHiddenRows = false;
\r
77 boolean showHiddenMarkers = true;
\r
79 boolean cursorMode = false;
\r
81 // The following vector holds the features which are
\r
82 // currently visible, in the correct order or rendering
\r
83 Hashtable featuresDisplayed = null;
\r
86 /** DOCUMENT ME!! */
\r
87 public Vector vconsensus;
\r
88 AlignmentAnnotation consensus;
\r
89 AlignmentAnnotation conservation;
\r
90 AlignmentAnnotation quality;
\r
91 boolean autoCalculateConsensus = true;
\r
93 /** DOCUMENT ME!! */
\r
94 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
\r
96 // JBPNote Prolly only need this in the applet version.
\r
97 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
\r
99 boolean ignoreGapsInConsensusCalculation = false;
\r
101 boolean isDataset = false;
\r
103 boolean antiAlias = false;
\r
105 boolean padGaps = false;
\r
108 public AlignViewport(AlignmentI al, boolean dataset)
\r
110 isDataset = dataset;
\r
115 * Creates a new AlignViewport object.
\r
117 * @param al DOCUMENT ME!
\r
119 public AlignViewport(AlignmentI al)
\r
128 this.endRes = alignment.getWidth() - 1;
\r
130 this.endSeq = alignment.getHeight() - 1;
\r
132 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
\r
134 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
\r
135 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
\r
136 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
\r
138 showQuality = Cache.getDefault("SHOW_QUALITY", true);
\r
139 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
\r
141 autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
\r
143 padGaps = Cache.getDefault("PAD_GAPS", false);
\r
145 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
\r
146 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
\r
147 String fontSize = Cache.getDefault("FONT_SIZE", "10");
\r
151 if (fontStyle.equals("bold"))
\r
155 else if (fontStyle.equals("italic"))
\r
160 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
\r
163 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
\r
166 // We must set conservation and consensus before setting colour,
\r
167 // as Blosum and Clustal require this to be done
\r
168 if(vconsensus==null && !isDataset)
\r
170 updateConservation();
\r
174 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
\r
176 globalColourScheme = ColourSchemeProperty.getColour(alignment,
\r
177 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
\r
179 if (globalColourScheme instanceof UserColourScheme)
\r
181 globalColourScheme = UserDefinedColours.loadDefaultColours();
\r
182 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
\r
185 if (globalColourScheme != null)
\r
187 globalColourScheme.setConsensus(vconsensus);
\r
197 * @param b DOCUMENT ME!
\r
199 public void setShowSequenceFeatures(boolean b)
\r
201 showSequenceFeatures = b;
\r
204 public boolean getShowSequenceFeatures()
\r
206 return showSequenceFeatures;
\r
212 public void updateConservation()
\r
214 if(alignment.isNucleotide())
\r
218 Conservation cons = new jalview.analysis.Conservation("All",
\r
219 jalview.schemes.ResidueProperties.propHash, 3,
\r
220 alignment.getSequences(), 0, alignment.getWidth() - 1);
\r
222 cons.verdict(false, ConsPercGaps);
\r
223 cons.findQuality();
\r
225 int alWidth = alignment.getWidth();
\r
226 Annotation[] annotations = new Annotation[alWidth];
\r
227 Annotation[] qannotations = new Annotation[alWidth];
\r
228 String sequence = cons.getConsSequence().getSequence();
\r
238 maxR = 1.0f - minR;
\r
239 maxG = 0.9f - minG;
\r
240 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
\r
244 float qmin = cons.qualityRange[0].floatValue();
\r
245 float qmax = cons.qualityRange[1].floatValue();
\r
247 for (int i = 0; i < alWidth; i++)
\r
253 value = Integer.parseInt(sequence.charAt(i) + "");
\r
255 catch (Exception ex)
\r
257 if (sequence.charAt(i) == '*')
\r
262 if (sequence.charAt(i) == '+')
\r
268 float vprop = value - min;
\r
270 annotations[i] = new Annotation(sequence.charAt(i) + "",
\r
271 String.valueOf(value), ' ', value,
\r
272 new Color(minR + (maxR * vprop),
\r
273 minG + (maxG * vprop),
\r
274 minB + (maxB * vprop)));
\r
277 value = ( (Double) cons.quality.get(i)).floatValue();
\r
278 vprop = value - qmin;
\r
280 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
\r
282 new Color(minR + (maxR * vprop),
\r
283 minG + (maxG * vprop),
\r
284 minB + (maxB * vprop)));
\r
287 if (conservation == null)
\r
289 conservation = new AlignmentAnnotation("Conservation",
\r
290 "Conservation of total alignment less than " +
\r
291 ConsPercGaps + "% gaps",
\r
292 annotations, 0f, // cons.qualityRange[0].floatValue(),
\r
293 11f, // cons.qualityRange[1].floatValue()
\r
294 AlignmentAnnotation.BAR_GRAPH);
\r
296 if (showConservation)
\r
298 alignment.addAnnotation(conservation);
\r
301 quality = new AlignmentAnnotation("Quality",
\r
302 "Alignment Quality based on Blosum62 scores",
\r
304 cons.qualityRange[0].floatValue(),
\r
305 cons.qualityRange[1].floatValue(),
\r
306 AlignmentAnnotation.BAR_GRAPH);
\r
310 alignment.addAnnotation(quality);
\r
315 conservation.annotations = annotations;
\r
316 quality.annotations = qannotations;
\r
317 quality.graphMax = cons.qualityRange[1].floatValue();
\r
320 catch (OutOfMemoryError error)
\r
322 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
326 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
327 "Out of memory calculating conservation!!"
\r
329 "\nSee help files for increasing Java Virtual Machine memory."
\r
331 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
335 System.out.println("Conservation calculation: " + error);
\r
344 public void updateConsensus()
\r
347 Annotation[] annotations = new Annotation[alignment.getWidth()];
\r
349 // this routine prevents vconsensus becoming a new object each time
\r
350 // consenus is calculated. Important for speed of Blosum62
\r
351 // and PID colouring of alignment
\r
352 if (vconsensus == null)
\r
354 vconsensus = alignment.getAAFrequency();
\r
358 Vector temp = alignment.getAAFrequency();
\r
359 vconsensus.clear();
\r
361 Enumeration e = temp.elements();
\r
363 while (e.hasMoreElements())
\r
365 vconsensus.add(e.nextElement());
\r
369 Hashtable hash = null;
\r
371 for (int i = 0; i < alignment.getWidth(); i++)
\r
373 hash = (Hashtable) vconsensus.elementAt(i);
\r
376 if (ignoreGapsInConsensusCalculation)
\r
377 value = ( (Float) hash.get("pid_nogaps")).floatValue();
\r
379 value = ( (Float) hash.get("pid_gaps")).floatValue();
\r
381 String maxRes = hash.get("maxResidue").toString();
\r
382 String mouseOver = hash.get("maxResidue") + " ";
\r
384 if (maxRes.length() > 1)
\r
386 mouseOver = "[" + maxRes + "] ";
\r
390 mouseOver += ( (int) value + "%");
\r
391 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
\r
394 if (consensus == null)
\r
396 consensus = new AlignmentAnnotation("Consensus", "PID",
\r
397 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
\r
401 alignment.addAnnotation(consensus);
\r
406 consensus.annotations = annotations;
\r
409 if (globalColourScheme != null)
\r
410 globalColourScheme.setConsensus(vconsensus);
\r
412 }catch(OutOfMemoryError error)
\r
414 javax.swing.SwingUtilities.invokeLater(new Runnable()
\r
418 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
419 "Out of memory calc45ulating consensus!!"
\r
421 "\nSee help files for increasing Java Virtual Machine memory."
\r
423 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
428 System.out.println("Consensus calculation: " + error);
\r
437 * @return DOCUMENT ME!
\r
439 public SequenceGroup getSelectionGroup()
\r
441 return selectionGroup;
\r
447 * @param sg DOCUMENT ME!
\r
449 public void setSelectionGroup(SequenceGroup sg)
\r
451 selectionGroup = sg;
\r
457 * @return DOCUMENT ME!
\r
459 public boolean getConservationSelected()
\r
461 return conservationColourSelected;
\r
467 * @param b DOCUMENT ME!
\r
469 public void setConservationSelected(boolean b)
\r
471 conservationColourSelected = b;
\r
477 * @return DOCUMENT ME!
\r
479 public boolean getAbovePIDThreshold()
\r
481 return abovePIDThreshold;
\r
487 * @param b DOCUMENT ME!
\r
489 public void setAbovePIDThreshold(boolean b)
\r
491 abovePIDThreshold = b;
\r
497 * @return DOCUMENT ME!
\r
499 public int getStartRes()
\r
507 * @return DOCUMENT ME!
\r
509 public int getEndRes()
\r
517 * @return DOCUMENT ME!
\r
519 public int getStartSeq()
\r
527 * @param cs DOCUMENT ME!
\r
529 public void setGlobalColourScheme(ColourSchemeI cs)
\r
531 globalColourScheme = cs;
\r
537 * @return DOCUMENT ME!
\r
539 public ColourSchemeI getGlobalColourScheme()
\r
541 return globalColourScheme;
\r
547 * @param res DOCUMENT ME!
\r
549 public void setStartRes(int res)
\r
551 this.startRes = res;
\r
557 * @param seq DOCUMENT ME!
\r
559 public void setStartSeq(int seq)
\r
561 this.startSeq = seq;
\r
567 * @param res DOCUMENT ME!
\r
569 public void setEndRes(int res)
\r
571 if (res > (alignment.getWidth() - 1))
\r
573 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
\r
574 res = alignment.getWidth() - 1;
\r
588 * @param seq DOCUMENT ME!
\r
590 public void setEndSeq(int seq)
\r
592 if (seq > alignment.getHeight())
\r
594 seq = alignment.getHeight();
\r
608 * @return DOCUMENT ME!
\r
610 public int getEndSeq()
\r
618 * @param f DOCUMENT ME!
\r
620 public void setFont(Font f)
\r
624 Container c = new Container();
\r
626 java.awt.FontMetrics fm = c.getFontMetrics(font);
\r
627 setCharHeight(fm.getHeight());
\r
628 setCharWidth(fm.charWidth('M'));
\r
629 validCharWidth = true;
\r
635 * @return DOCUMENT ME!
\r
637 public Font getFont()
\r
645 * @param w DOCUMENT ME!
\r
647 public void setCharWidth(int w)
\r
649 this.charWidth = w;
\r
655 * @return DOCUMENT ME!
\r
657 public int getCharWidth()
\r
665 * @param h DOCUMENT ME!
\r
667 public void setCharHeight(int h)
\r
669 this.charHeight = h;
\r
675 * @return DOCUMENT ME!
\r
677 public int getCharHeight()
\r
685 * @param w DOCUMENT ME!
\r
687 public void setWrappedWidth(int w)
\r
689 this.wrappedWidth = w;
\r
695 * @return DOCUMENT ME!
\r
697 public int getWrappedWidth()
\r
699 return wrappedWidth;
\r
706 * @return DOCUMENT ME!
\r
708 public AlignmentI getAlignment()
\r
716 * @param align DOCUMENT ME!
\r
718 public void setAlignment(AlignmentI align)
\r
720 this.alignment = align;
\r
726 * @param state DOCUMENT ME!
\r
728 public void setWrapAlignment(boolean state)
\r
730 wrapAlignment = state;
\r
736 * @param state DOCUMENT ME!
\r
738 public void setShowText(boolean state)
\r
746 * @param state DOCUMENT ME!
\r
748 public void setRenderGaps(boolean state)
\r
750 renderGaps = state;
\r
756 * @return DOCUMENT ME!
\r
758 public boolean getColourText()
\r
760 return showColourText;
\r
766 * @param state DOCUMENT ME!
\r
768 public void setColourText(boolean state)
\r
770 showColourText = state;
\r
776 * @param state DOCUMENT ME!
\r
778 public void setShowBoxes(boolean state)
\r
786 * @return DOCUMENT ME!
\r
788 public boolean getWrapAlignment()
\r
790 return wrapAlignment;
\r
796 * @return DOCUMENT ME!
\r
798 public boolean getShowText()
\r
806 * @return DOCUMENT ME!
\r
808 public boolean getShowBoxes()
\r
816 * @return DOCUMENT ME!
\r
818 public char getGapCharacter()
\r
820 return getAlignment().getGapCharacter();
\r
826 * @param gap DOCUMENT ME!
\r
828 public void setGapCharacter(char gap)
\r
830 if (getAlignment() != null)
\r
832 getAlignment().setGapCharacter(gap);
\r
839 * @param thresh DOCUMENT ME!
\r
841 public void setThreshold(int thresh)
\r
843 threshold = thresh;
\r
849 * @return DOCUMENT ME!
\r
851 public int getThreshold()
\r
859 * @param inc DOCUMENT ME!
\r
861 public void setIncrement(int inc)
\r
869 * @return DOCUMENT ME!
\r
871 public int getIncrement()
\r
880 * @return DOCUMENT ME!
\r
882 public ColumnSelection getColumnSelection()
\r
891 * @param tree DOCUMENT ME!
\r
893 public void setCurrentTree(NJTree tree)
\r
895 currentTree = tree;
\r
901 * @return DOCUMENT ME!
\r
903 public NJTree getCurrentTree()
\r
905 return currentTree;
\r
911 * @param b DOCUMENT ME!
\r
913 public void setColourAppliesToAllGroups(boolean b)
\r
915 colourAppliesToAllGroups = b;
\r
921 * @return DOCUMENT ME!
\r
923 public boolean getColourAppliesToAllGroups()
\r
925 return colourAppliesToAllGroups;
\r
931 * @return DOCUMENT ME!
\r
933 public boolean getShowJVSuffix()
\r
935 return showJVSuffix;
\r
941 * @param b DOCUMENT ME!
\r
943 public void setShowJVSuffix(boolean b)
\r
952 * @return DOCUMENT ME!
\r
954 public boolean getShowAnnotation()
\r
956 return showAnnotation;
\r
962 * @param b DOCUMENT ME!
\r
964 public void setShowAnnotation(boolean b)
\r
966 showAnnotation = b;
\r
972 * @return DOCUMENT ME!
\r
974 public boolean getScaleAboveWrapped()
\r
976 return scaleAboveWrapped;
\r
982 * @return DOCUMENT ME!
\r
984 public boolean getScaleLeftWrapped()
\r
986 return scaleLeftWrapped;
\r
992 * @return DOCUMENT ME!
\r
994 public boolean getScaleRightWrapped()
\r
996 return scaleRightWrapped;
\r
1002 * @param b DOCUMENT ME!
\r
1004 public void setScaleAboveWrapped(boolean b)
\r
1006 scaleAboveWrapped = b;
\r
1012 * @param b DOCUMENT ME!
\r
1014 public void setScaleLeftWrapped(boolean b)
\r
1016 scaleLeftWrapped = b;
\r
1022 * @param b DOCUMENT ME!
\r
1024 public void setScaleRightWrapped(boolean b)
\r
1026 scaleRightWrapped = b;
\r
1030 * Property change listener for changes in alignment
\r
1032 * @param listener DOCUMENT ME!
\r
1034 public void addPropertyChangeListener(
\r
1035 java.beans.PropertyChangeListener listener)
\r
1037 changeSupport.addPropertyChangeListener(listener);
\r
1043 * @param listener DOCUMENT ME!
\r
1045 public void removePropertyChangeListener(
\r
1046 java.beans.PropertyChangeListener listener)
\r
1048 changeSupport.removePropertyChangeListener(listener);
\r
1052 * Property change listener for changes in alignment
\r
1054 * @param prop DOCUMENT ME!
\r
1055 * @param oldvalue DOCUMENT ME!
\r
1056 * @param newvalue DOCUMENT ME!
\r
1058 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
\r
1060 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
\r
1063 public void setIgnoreGapsConsensus(boolean b)
\r
1065 ignoreGapsInConsensusCalculation = b;
\r
1066 updateConsensus();
\r
1067 if(globalColourScheme!=null)
\r
1069 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
\r
1073 public boolean getIgnoreGapsConsensus()
\r
1075 return ignoreGapsInConsensusCalculation;
\r
1078 public void setDataset(boolean b)
\r
1083 public boolean isDataset()
\r
1089 public void hideSelectedColumns()
\r
1091 if (colSel.size() < 1)
\r
1094 colSel.hideSelectedColumns();
\r
1095 setSelectionGroup(null);
\r
1097 hasHiddenColumns = true;
\r
1101 public void hideColumns(int start, int end)
\r
1104 colSel.hideColumns(start);
\r
1106 colSel.hideColumns(start, end);
\r
1107 setSelectionGroup(null);
\r
1108 hasHiddenColumns = true;
\r
1111 public void hideSequence(SequenceI seq)
\r
1115 alignment.getHiddenSequences().hideSequence(seq);
\r
1116 hasHiddenRows = true;
\r
1120 public void showSequence(int index)
\r
1122 alignment.getHiddenSequences().showSequence(index);
\r
1124 if(alignment.getHiddenSequences().getSize()<1)
\r
1125 hasHiddenRows = false;
\r
1128 public void showColumn(int col)
\r
1130 colSel.revealHiddenColumns(col);
\r
1131 if(colSel.getHiddenColumns()==null)
\r
1132 hasHiddenColumns = false;
\r
1135 public void showAllHiddenColumns()
\r
1137 colSel.revealAllHiddenColumns();
\r
1138 hasHiddenColumns = false;
\r
1141 public void showAllHiddenSeqs()
\r
1143 if(alignment.getHiddenSequences().getSize()>0)
\r
1145 alignment.getHiddenSequences().showAll();
\r
1146 hasHiddenRows = false;
\r
1150 public int adjustForHiddenSeqs(int alignmentIndex)
\r
1152 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
\r
1156 * This method returns the a new SequenceI [] with
\r
1157 * the selection sequence and start and end points adjusted
\r
1158 * @return String[]
\r
1160 public SequenceI[] getSelectionAsNewSequence()
\r
1162 SequenceI[] sequences;
\r
1164 if (selectionGroup == null)
\r
1165 sequences = alignment.getSequencesArray();
\r
1167 sequences = selectionGroup.getSelectionAsNewSequences(alignment);
\r
1173 * This method returns the visible alignment as text, as
\r
1174 * seen on the GUI, ie if columns are hidden they will not
\r
1175 * be returned in the result.
\r
1176 * Use this for calculating trees, PCA, redundancy etc on views
\r
1177 * which contain hidden columns.
\r
1178 * @return String[]
\r
1180 public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
\r
1182 CigarArray selection=null;
\r
1183 SequenceI [] seqs= null;
\r
1185 int start = 0, end = 0;
\r
1186 if(selectedRegionOnly && selectionGroup!=null)
\r
1188 iSize = selectionGroup.getSize(false);
\r
1189 seqs = selectionGroup.getSequencesInOrder(alignment);
\r
1190 start = selectionGroup.getStartRes();
\r
1191 end = selectionGroup.getEndRes()+1;
\r
1195 iSize = alignment.getHeight();
\r
1196 seqs = alignment.getSequencesArray();
\r
1197 end = alignment.getWidth();
\r
1199 SeqCigar[] selseqs = new SeqCigar[iSize];
\r
1200 for(i=0; i<iSize; i++)
\r
1202 selseqs[i] = new SeqCigar(seqs[i], start, end);
\r
1204 selection=new CigarArray(selseqs);
\r
1206 int[] hiddenregions = null;
\r
1207 char[] hr_ops = null;
\r
1208 if (hasHiddenColumns) {
\r
1209 Vector _hiddenregions = new Vector();
\r
1210 Vector regions = colSel.getHiddenColumns();
\r
1211 int blockStart = start, blockEnd=end;
\r
1213 int hideStart, hideEnd;
\r
1215 for (int j = 0; last<end & j < regions.size(); j++)
\r
1217 region = (int[]) regions.elementAt(j);
\r
1218 hideStart = region[0];
\r
1219 hideEnd = region[1];
\r
1220 // edit hidden regions to selection range
\r
1221 if(hideStart<last) {
\r
1222 if (hideEnd > last)
\r
1229 if (hideStart>end)
\r
1235 if (hideStart>hideEnd)
\r
1238 * form operations...
\r
1240 if (last<hideStart)
\r
1241 selection.addOperation(CigarArray.M, hideStart-last);
\r
1242 selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
\r
1245 // Final match if necessary.
\r
1247 selection.addOperation(CigarArray.M, end-last);
\r
1249 selection.addOperation(CigarArray.M, end-start);
\r
1255 * This method returns the visible alignment as text, as
\r
1256 * seen on the GUI, ie if columns are hidden they will not
\r
1257 * be returned in the result.
\r
1258 * Use this for calculating trees, PCA, redundancy etc on views
\r
1259 * which contain hidden columns.
\r
1260 * @return String[]
\r
1262 public String [] getViewAsString(boolean selectedRegionOnly)
\r
1264 String [] selection = null;
\r
1265 SequenceI [] seqs= null;
\r
1267 int start = 0, end = 0;
\r
1268 if(selectedRegionOnly && selectionGroup!=null)
\r
1270 iSize = selectionGroup.getSize(false);
\r
1271 seqs = selectionGroup.getSequencesInOrder(alignment);
\r
1272 start = selectionGroup.getStartRes();
\r
1273 end = selectionGroup.getEndRes()+1;
\r
1277 iSize = alignment.getHeight();
\r
1278 seqs = alignment.getSequencesArray();
\r
1279 end = alignment.getWidth();
\r
1282 selection = new String[iSize];
\r
1285 for(i=0; i<iSize; i++)
\r
1287 if (hasHiddenColumns)
\r
1289 StringBuffer visibleSeq = new StringBuffer();
\r
1290 Vector regions = colSel.getHiddenColumns();
\r
1292 int blockStart = start, blockEnd=end;
\r
1294 int hideStart, hideEnd;
\r
1296 for (int j = 0; j < regions.size(); j++)
\r
1298 region = (int[]) regions.elementAt(j);
\r
1299 hideStart = region[0];
\r
1300 hideEnd = region[1];
\r
1302 if(hideStart < start)
\r
1307 blockStart = Math.min(blockStart, hideEnd+1);
\r
1308 blockEnd = Math.min(blockEnd, hideStart);
\r
1310 if(blockStart>blockEnd)
\r
1316 visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
\r
1318 blockStart = hideEnd+1;
\r
1322 if(end>blockStart)
\r
1323 visibleSeq.append(seqs[i].getSequence(blockStart, end));
\r
1325 selection[i] = visibleSeq.toString();
\r
1329 selection[i] = seqs[i].getSequence(start, end);
\r
1336 public boolean getShowHiddenMarkers()
\r
1338 return showHiddenMarkers;
\r
1341 public void setShowHiddenMarkers(boolean show)
\r
1343 showHiddenMarkers = show;
\r