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
65 Font font = new Font("SansSerif", Font.PLAIN, 10);
\r
66 AlignmentI alignment;
\r
67 ColumnSelection colSel = new ColumnSelection();
\r
70 NJTree currentTree = null;
\r
71 boolean scaleAboveWrapped = false;
\r
72 boolean scaleLeftWrapped = true;
\r
73 boolean scaleRightWrapped = true;
\r
74 boolean hasHiddenColumns = false;
\r
75 boolean hasHiddenRows = false;
\r
77 boolean cursorMode = false;
\r
79 // The following vector holds the features which are
\r
80 // currently visible, in the correct order or rendering
\r
81 Hashtable featuresDisplayed = null;
\r
84 /** DOCUMENT ME!! */
\r
85 public Vector vconsensus;
\r
86 AlignmentAnnotation consensus;
\r
87 AlignmentAnnotation conservation;
\r
88 AlignmentAnnotation quality;
\r
89 boolean autoCalculateConsensus = true;
\r
91 /** DOCUMENT ME!! */
\r
92 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
\r
94 // JBPNote Prolly only need this in the applet version.
\r
95 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
\r
97 boolean ignoreGapsInConsensusCalculation = false;
\r
99 boolean isDataset = false;
\r
101 boolean antiAlias = false;
\r
103 boolean padGaps = false;
\r
106 public AlignViewport(AlignmentI al, boolean dataset)
\r
108 isDataset = dataset;
\r
113 * Creates a new AlignViewport object.
\r
115 * @param al DOCUMENT ME!
\r
117 public AlignViewport(AlignmentI al)
\r
126 this.endRes = alignment.getWidth() - 1;
\r
128 this.endSeq = alignment.getHeight() - 1;
\r
130 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
\r
132 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
\r
133 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
\r
134 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
\r
136 showQuality = Cache.getDefault("SHOW_QUALITY", true);
\r
137 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
\r
139 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
\r
140 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
\r
141 String fontSize = Cache.getDefault("FONT_SIZE", "10");
\r
145 if (fontStyle.equals("bold"))
\r
149 else if (fontStyle.equals("italic"))
\r
154 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
\r
157 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
\r
160 // We must set conservation and consensus before setting colour,
\r
161 // as Blosum and Clustal require this to be done
\r
162 if(vconsensus==null && !isDataset)
\r
164 updateConservation();
\r
168 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
\r
170 globalColourScheme = ColourSchemeProperty.getColour(alignment,
\r
171 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
\r
173 if (globalColourScheme instanceof UserColourScheme)
\r
175 globalColourScheme = UserDefinedColours.loadDefaultColours();
\r
176 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
\r
179 if (globalColourScheme != null)
\r
181 globalColourScheme.setConsensus(vconsensus);
\r
191 * @param b DOCUMENT ME!
\r
193 public void setShowSequenceFeatures(boolean b)
\r
195 showSequenceFeatures = b;
\r
198 public boolean getShowSequenceFeatures()
\r
200 return showSequenceFeatures;
\r
206 public void updateConservation()
\r
208 if(alignment.isNucleotide())
\r
212 Conservation cons = new jalview.analysis.Conservation("All",
\r
213 jalview.schemes.ResidueProperties.propHash, 3,
\r
214 alignment.getSequences(), 0, alignment.getWidth() - 1);
\r
216 cons.verdict(false, ConsPercGaps);
\r
217 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
232 maxR = 1.0f - minR;
\r
233 maxG = 0.9f - minG;
\r
234 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
\r
238 float qmin = cons.qualityRange[0].floatValue();
\r
239 float qmax = cons.qualityRange[1].floatValue();
\r
241 for (int i = 0; i < alWidth; i++)
\r
247 value = Integer.parseInt(sequence.charAt(i) + "");
\r
249 catch (Exception ex)
\r
251 if (sequence.charAt(i) == '*')
\r
256 if (sequence.charAt(i) == '+')
\r
262 float vprop = value - min;
\r
264 annotations[i] = new Annotation(sequence.charAt(i) + "",
\r
265 String.valueOf(value), ' ', value,
\r
266 new Color(minR + (maxR * vprop),
\r
267 minG + (maxG * vprop),
\r
268 minB + (maxB * vprop)));
\r
271 value = ( (Double) cons.quality.get(i)).floatValue();
\r
272 vprop = value - qmin;
\r
274 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
\r
276 new Color(minR + (maxR * vprop),
\r
277 minG + (maxG * vprop),
\r
278 minB + (maxB * vprop)));
\r
281 if (conservation == null)
\r
283 conservation = new AlignmentAnnotation("Conservation",
\r
284 "Conservation of total alignment less than " +
\r
285 ConsPercGaps + "% gaps",
\r
286 annotations, 0f, // cons.qualityRange[0].floatValue(),
\r
287 11f, // cons.qualityRange[1].floatValue()
\r
288 AlignmentAnnotation.BAR_GRAPH);
\r
290 if (showConservation)
\r
292 alignment.addAnnotation(conservation);
\r
295 quality = new AlignmentAnnotation("Quality",
\r
296 "Alignment Quality based on Blosum62 scores",
\r
298 cons.qualityRange[0].floatValue(),
\r
299 cons.qualityRange[1].floatValue(),
\r
300 AlignmentAnnotation.BAR_GRAPH);
\r
304 alignment.addAnnotation(quality);
\r
309 conservation.annotations = annotations;
\r
310 quality.annotations = qannotations;
\r
311 quality.graphMax = cons.qualityRange[1].floatValue();
\r
314 catch (OutOfMemoryError error)
\r
316 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
317 "Out of memory calculating conservation!!"
\r
319 "\nSee help files for increasing Java Virtual Machine memory."
\r
321 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
322 System.out.println("Conservation calculation: " + error);
\r
331 public void updateConsensus()
\r
334 Annotation[] annotations = new Annotation[alignment.getWidth()];
\r
336 // this routine prevents vconsensus becoming a new object each time
\r
337 // consenus is calculated. Important for speed of Blosum62
\r
338 // and PID colouring of alignment
\r
339 if (vconsensus == null)
\r
341 vconsensus = alignment.getAAFrequency();
\r
345 Vector temp = alignment.getAAFrequency();
\r
346 vconsensus.clear();
\r
348 Enumeration e = temp.elements();
\r
350 while (e.hasMoreElements())
\r
352 vconsensus.add(e.nextElement());
\r
356 Hashtable hash = null;
\r
358 for (int i = 0; i < alignment.getWidth(); i++)
\r
360 hash = (Hashtable) vconsensus.elementAt(i);
\r
363 if (ignoreGapsInConsensusCalculation)
\r
364 value = ( (Float) hash.get("pid_nogaps")).floatValue();
\r
366 value = ( (Float) hash.get("pid_gaps")).floatValue();
\r
368 String maxRes = hash.get("maxResidue").toString();
\r
369 String mouseOver = hash.get("maxResidue") + " ";
\r
371 if (maxRes.length() > 1)
\r
373 mouseOver = "[" + maxRes + "] ";
\r
377 mouseOver += ( (int) value + "%");
\r
378 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
\r
381 if (consensus == null)
\r
383 consensus = new AlignmentAnnotation("Consensus", "PID",
\r
384 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
\r
388 alignment.addAnnotation(consensus);
\r
393 consensus.annotations = annotations;
\r
396 if (globalColourScheme != null)
\r
397 globalColourScheme.setConsensus(vconsensus);
\r
399 }catch(OutOfMemoryError error)
\r
401 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
402 "Out of memory calculating consensus!!"
\r
404 "\nSee help files for increasing Java Virtual Machine memory."
\r
406 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
407 System.out.println("Consensus calculation: " + error);
\r
416 * @return DOCUMENT ME!
\r
418 public SequenceGroup getSelectionGroup()
\r
420 return selectionGroup;
\r
426 * @param sg DOCUMENT ME!
\r
428 public void setSelectionGroup(SequenceGroup sg)
\r
430 selectionGroup = sg;
\r
436 * @return DOCUMENT ME!
\r
438 public boolean getConservationSelected()
\r
440 return conservationColourSelected;
\r
446 * @param b DOCUMENT ME!
\r
448 public void setConservationSelected(boolean b)
\r
450 conservationColourSelected = b;
\r
456 * @return DOCUMENT ME!
\r
458 public boolean getAbovePIDThreshold()
\r
460 return abovePIDThreshold;
\r
466 * @param b DOCUMENT ME!
\r
468 public void setAbovePIDThreshold(boolean b)
\r
470 abovePIDThreshold = b;
\r
476 * @return DOCUMENT ME!
\r
478 public int getStartRes()
\r
486 * @return DOCUMENT ME!
\r
488 public int getEndRes()
\r
496 * @return DOCUMENT ME!
\r
498 public int getStartSeq()
\r
506 * @param cs DOCUMENT ME!
\r
508 public void setGlobalColourScheme(ColourSchemeI cs)
\r
510 globalColourScheme = cs;
\r
516 * @return DOCUMENT ME!
\r
518 public ColourSchemeI getGlobalColourScheme()
\r
520 return globalColourScheme;
\r
526 * @param res DOCUMENT ME!
\r
528 public void setStartRes(int res)
\r
530 this.startRes = res;
\r
536 * @param seq DOCUMENT ME!
\r
538 public void setStartSeq(int seq)
\r
540 this.startSeq = seq;
\r
546 * @param res DOCUMENT ME!
\r
548 public void setEndRes(int res)
\r
550 if (res > (alignment.getWidth() - 1))
\r
552 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
\r
553 res = alignment.getWidth() - 1;
\r
567 * @param seq DOCUMENT ME!
\r
569 public void setEndSeq(int seq)
\r
571 if (seq > alignment.getHeight())
\r
573 seq = alignment.getHeight();
\r
587 * @return DOCUMENT ME!
\r
589 public int getEndSeq()
\r
597 * @param f DOCUMENT ME!
\r
599 public void setFont(Font f)
\r
603 Container c = new Container();
\r
605 java.awt.FontMetrics fm = c.getFontMetrics(font);
\r
606 setCharHeight(fm.getHeight());
\r
607 setCharWidth(fm.charWidth('M'));
\r
613 * @return DOCUMENT ME!
\r
615 public Font getFont()
\r
623 * @param w DOCUMENT ME!
\r
625 public void setCharWidth(int w)
\r
627 this.charWidth = w;
\r
633 * @return DOCUMENT ME!
\r
635 public int getCharWidth()
\r
643 * @param h DOCUMENT ME!
\r
645 public void setCharHeight(int h)
\r
647 this.charHeight = h;
\r
653 * @return DOCUMENT ME!
\r
655 public int getCharHeight()
\r
663 * @param w DOCUMENT ME!
\r
665 public void setWrappedWidth(int w)
\r
667 this.wrappedWidth = w;
\r
673 * @return DOCUMENT ME!
\r
675 public int getWrappedWidth()
\r
677 return wrappedWidth;
\r
684 * @return DOCUMENT ME!
\r
686 public AlignmentI getAlignment()
\r
694 * @param align DOCUMENT ME!
\r
696 public void setAlignment(AlignmentI align)
\r
698 this.alignment = align;
\r
704 * @param state DOCUMENT ME!
\r
706 public void setWrapAlignment(boolean state)
\r
708 wrapAlignment = state;
\r
714 * @param state DOCUMENT ME!
\r
716 public void setShowText(boolean state)
\r
724 * @param state DOCUMENT ME!
\r
726 public void setRenderGaps(boolean state)
\r
728 renderGaps = state;
\r
734 * @return DOCUMENT ME!
\r
736 public boolean getColourText()
\r
738 return showColourText;
\r
744 * @param state DOCUMENT ME!
\r
746 public void setColourText(boolean state)
\r
748 showColourText = state;
\r
754 * @param state DOCUMENT ME!
\r
756 public void setShowBoxes(boolean state)
\r
764 * @return DOCUMENT ME!
\r
766 public boolean getWrapAlignment()
\r
768 return wrapAlignment;
\r
774 * @return DOCUMENT ME!
\r
776 public boolean getShowText()
\r
784 * @return DOCUMENT ME!
\r
786 public boolean getShowBoxes()
\r
794 * @return DOCUMENT ME!
\r
796 public char getGapCharacter()
\r
798 return getAlignment().getGapCharacter();
\r
804 * @param gap DOCUMENT ME!
\r
806 public void setGapCharacter(char gap)
\r
808 if (getAlignment() != null)
\r
810 getAlignment().setGapCharacter(gap);
\r
817 * @param thresh DOCUMENT ME!
\r
819 public void setThreshold(int thresh)
\r
821 threshold = thresh;
\r
827 * @return DOCUMENT ME!
\r
829 public int getThreshold()
\r
837 * @param inc DOCUMENT ME!
\r
839 public void setIncrement(int inc)
\r
847 * @return DOCUMENT ME!
\r
849 public int getIncrement()
\r
857 * @param y DOCUMENT ME!
\r
859 * @return DOCUMENT ME!
\r
861 public int getIndex(int y)
\r
864 int starty = getStartSeq();
\r
865 int endy = getEndSeq();
\r
867 for (int i = starty; i <= endy; i++)
\r
869 if ((i < alignment.getHeight()) &&
\r
870 (alignment.getSequenceAt(i) != null))
\r
872 int y2 = y1 + getCharHeight();
\r
874 if ((y >= y1) && (y <= y2))
\r
893 * @return DOCUMENT ME!
\r
895 public ColumnSelection getColumnSelection()
\r
904 * @param tree DOCUMENT ME!
\r
906 public void setCurrentTree(NJTree tree)
\r
908 currentTree = tree;
\r
914 * @return DOCUMENT ME!
\r
916 public NJTree getCurrentTree()
\r
918 return currentTree;
\r
924 * @param b DOCUMENT ME!
\r
926 public void setColourAppliesToAllGroups(boolean b)
\r
928 colourAppliesToAllGroups = b;
\r
934 * @return DOCUMENT ME!
\r
936 public boolean getColourAppliesToAllGroups()
\r
938 return colourAppliesToAllGroups;
\r
944 * @return DOCUMENT ME!
\r
946 public boolean getShowJVSuffix()
\r
948 return showJVSuffix;
\r
954 * @param b DOCUMENT ME!
\r
956 public void setShowJVSuffix(boolean b)
\r
965 * @return DOCUMENT ME!
\r
967 public boolean getShowAnnotation()
\r
969 return showAnnotation;
\r
975 * @param b DOCUMENT ME!
\r
977 public void setShowAnnotation(boolean b)
\r
979 showAnnotation = b;
\r
985 * @return DOCUMENT ME!
\r
987 public boolean getScaleAboveWrapped()
\r
989 return scaleAboveWrapped;
\r
995 * @return DOCUMENT ME!
\r
997 public boolean getScaleLeftWrapped()
\r
999 return scaleLeftWrapped;
\r
1005 * @return DOCUMENT ME!
\r
1007 public boolean getScaleRightWrapped()
\r
1009 return scaleRightWrapped;
\r
1015 * @param b DOCUMENT ME!
\r
1017 public void setScaleAboveWrapped(boolean b)
\r
1019 scaleAboveWrapped = b;
\r
1025 * @param b DOCUMENT ME!
\r
1027 public void setScaleLeftWrapped(boolean b)
\r
1029 scaleLeftWrapped = b;
\r
1035 * @param b DOCUMENT ME!
\r
1037 public void setScaleRightWrapped(boolean b)
\r
1039 scaleRightWrapped = b;
\r
1043 * Property change listener for changes in alignment
\r
1045 * @param listener DOCUMENT ME!
\r
1047 public void addPropertyChangeListener(
\r
1048 java.beans.PropertyChangeListener listener)
\r
1050 changeSupport.addPropertyChangeListener(listener);
\r
1056 * @param listener DOCUMENT ME!
\r
1058 public void removePropertyChangeListener(
\r
1059 java.beans.PropertyChangeListener listener)
\r
1061 changeSupport.removePropertyChangeListener(listener);
\r
1065 * Property change listener for changes in alignment
\r
1067 * @param prop DOCUMENT ME!
\r
1068 * @param oldvalue DOCUMENT ME!
\r
1069 * @param newvalue DOCUMENT ME!
\r
1071 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
\r
1073 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
\r
1076 public void setIgnoreGapsConsensus(boolean b)
\r
1078 ignoreGapsInConsensusCalculation = b;
\r
1079 updateConsensus();
\r
1080 if(globalColourScheme!=null)
\r
1082 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
\r
1086 public boolean getIgnoreGapsConsensus()
\r
1088 return ignoreGapsInConsensusCalculation;
\r
1091 public void setDataset(boolean b)
\r
1096 public boolean isDataset()
\r
1101 public void hideSequence(SequenceI seq)
\r
1103 alignment.getHiddenSequences().hideSequence(seq);
\r
1104 hasHiddenRows = true;
\r
1107 public void showSequence(int index)
\r
1109 alignment.getHiddenSequences().showSequence(index);
\r
1111 if(alignment.getHiddenSequences().getSize()<1)
\r
1112 hasHiddenRows = false;
\r
1115 public int adjustForHiddenSeqs(int alignmentIndex)
\r
1117 return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
\r