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
75 /** DOCUMENT ME!! */
\r
76 public Vector vconsensus;
\r
77 AlignmentAnnotation consensus;
\r
78 AlignmentAnnotation conservation;
\r
79 AlignmentAnnotation quality;
\r
81 /** DOCUMENT ME!! */
\r
82 public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
\r
84 // JBPNote Prolly only need this in the applet version.
\r
85 private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
\r
87 boolean ignoreGapsInConsensusCalculation = false;
\r
89 boolean isDataset = false;
\r
91 boolean antiAlias = false;
\r
94 public AlignViewport(AlignmentI al, boolean dataset)
\r
96 isDataset = dataset;
\r
101 * Creates a new AlignViewport object.
\r
103 * @param al DOCUMENT ME!
\r
105 public AlignViewport(AlignmentI al)
\r
114 this.endRes = alignment.getWidth() - 1;
\r
116 this.endSeq = alignment.getHeight() - 1;
\r
118 antiAlias = Cache.getDefault("ANTI_ALIAS", false);
\r
120 showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
\r
121 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
\r
122 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
\r
124 showQuality = Cache.getDefault("SHOW_QUALITY", true);
\r
125 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
\r
127 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
\r
128 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
\r
129 String fontSize = Cache.getDefault("FONT_SIZE", "10");
\r
133 if (fontStyle.equals("bold"))
\r
137 else if (fontStyle.equals("italic"))
\r
142 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
\r
145 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
\r
148 // We must set conservation and consensus before setting colour,
\r
149 // as Blosum and Clustal require this to be done
\r
150 if(vconsensus==null && !isDataset)
\r
152 updateConservation();
\r
156 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
\r
158 globalColourScheme = ColourSchemeProperty.getColour(alignment,
\r
159 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
\r
161 if (globalColourScheme instanceof UserColourScheme)
\r
163 globalColourScheme = UserDefinedColours.loadDefaultColours();
\r
164 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
\r
167 if (globalColourScheme != null)
\r
169 globalColourScheme.setConsensus(vconsensus);
\r
179 * @param b DOCUMENT ME!
\r
181 public void showSequenceFeatures(boolean b)
\r
183 showSequenceFeatures = b;
\r
189 public void updateConservation()
\r
191 if(alignment.isNucleotide())
\r
195 Conservation cons = new jalview.analysis.Conservation("All",
\r
196 jalview.schemes.ResidueProperties.propHash, 3,
\r
197 alignment.getSequences(), 0, alignment.getWidth() - 1);
\r
199 cons.verdict(false, ConsPercGaps);
\r
200 cons.findQuality();
\r
202 int alWidth = alignment.getWidth();
\r
203 Annotation[] annotations = new Annotation[alWidth];
\r
204 Annotation[] qannotations = new Annotation[alWidth];
\r
205 String sequence = cons.getConsSequence().getSequence();
\r
215 maxR = 1.0f - minR;
\r
216 maxG = 0.9f - minG;
\r
217 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
\r
221 float qmin = cons.qualityRange[0].floatValue();
\r
222 float qmax = cons.qualityRange[1].floatValue();
\r
224 for (int i = 0; i < alWidth; i++)
\r
230 value = Integer.parseInt(sequence.charAt(i) + "");
\r
232 catch (Exception ex)
\r
234 if (sequence.charAt(i) == '*')
\r
239 if (sequence.charAt(i) == '+')
\r
245 float vprop = value - min;
\r
247 annotations[i] = new Annotation(sequence.charAt(i) + "",
\r
248 String.valueOf(value), ' ', value,
\r
249 new Color(minR + (maxR * vprop),
\r
250 minG + (maxG * vprop),
\r
251 minB + (maxB * vprop)));
\r
254 value = ( (Double) cons.quality.get(i)).floatValue();
\r
255 vprop = value - qmin;
\r
257 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
\r
259 new Color(minR + (maxR * vprop),
\r
260 minG + (maxG * vprop),
\r
261 minB + (maxB * vprop)));
\r
264 if (conservation == null)
\r
266 conservation = new AlignmentAnnotation("Conservation",
\r
267 "Conservation of total alignment less than " +
\r
268 ConsPercGaps + "% gaps",
\r
269 annotations, 0f, // cons.qualityRange[0].floatValue(),
\r
270 11f, // cons.qualityRange[1].floatValue()
\r
271 AlignmentAnnotation.BAR_GRAPH);
\r
273 if (showConservation)
\r
275 alignment.addAnnotation(conservation);
\r
278 quality = new AlignmentAnnotation("Quality",
\r
279 "Alignment Quality based on Blosum62 scores",
\r
281 cons.qualityRange[0].floatValue(),
\r
282 cons.qualityRange[1].floatValue(),
\r
283 AlignmentAnnotation.BAR_GRAPH);
\r
287 alignment.addAnnotation(quality);
\r
292 conservation.annotations = annotations;
\r
293 quality.annotations = qannotations;
\r
294 quality.graphMax = cons.qualityRange[1].floatValue();
\r
297 catch (OutOfMemoryError error)
\r
299 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
300 "Out of memory calculating conservation!!"
\r
302 "\nSee help files for increasing Java Virtual Machine memory."
\r
304 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
305 System.out.println("Conservation calculation: " + error);
\r
314 public void updateConsensus()
\r
317 Annotation[] annotations = new Annotation[alignment.getWidth()];
\r
319 // this routine prevents vconsensus becoming a new object each time
\r
320 // consenus is calculated. Important for speed of Blosum62
\r
321 // and PID colouring of alignment
\r
322 if (vconsensus == null)
\r
324 vconsensus = alignment.getAAFrequency();
\r
328 Vector temp = alignment.getAAFrequency();
\r
329 vconsensus.clear();
\r
331 Enumeration e = temp.elements();
\r
333 while (e.hasMoreElements())
\r
335 vconsensus.add(e.nextElement());
\r
339 Hashtable hash = null;
\r
341 for (int i = 0; i < alignment.getWidth(); i++)
\r
343 hash = (Hashtable) vconsensus.elementAt(i);
\r
346 if (ignoreGapsInConsensusCalculation)
\r
347 value = ( (Float) hash.get("pid_nogaps")).floatValue();
\r
349 value = ( (Float) hash.get("pid_gaps")).floatValue();
\r
351 String maxRes = hash.get("maxResidue").toString();
\r
352 String mouseOver = hash.get("maxResidue") + " ";
\r
354 if (maxRes.length() > 1)
\r
356 mouseOver = "[" + maxRes + "] ";
\r
360 mouseOver += ( (int) value + "%");
\r
361 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
\r
364 if (consensus == null)
\r
366 consensus = new AlignmentAnnotation("Consensus", "PID",
\r
367 annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
\r
371 alignment.addAnnotation(consensus);
\r
376 consensus.annotations = annotations;
\r
379 if (globalColourScheme != null)
\r
380 globalColourScheme.setConsensus(vconsensus);
\r
382 }catch(OutOfMemoryError error)
\r
384 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
385 "Out of memory calculating consensus!!"
\r
387 "\nSee help files for increasing Java Virtual Machine memory."
\r
389 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
390 System.out.println("Consensus calculation: " + error);
\r
399 * @return DOCUMENT ME!
\r
401 public SequenceGroup getSelectionGroup()
\r
403 return selectionGroup;
\r
409 * @param sg DOCUMENT ME!
\r
411 public void setSelectionGroup(SequenceGroup sg)
\r
413 selectionGroup = sg;
\r
419 * @return DOCUMENT ME!
\r
421 public boolean getConservationSelected()
\r
423 return conservationColourSelected;
\r
429 * @param b DOCUMENT ME!
\r
431 public void setConservationSelected(boolean b)
\r
433 conservationColourSelected = b;
\r
439 * @return DOCUMENT ME!
\r
441 public boolean getAbovePIDThreshold()
\r
443 return abovePIDThreshold;
\r
449 * @param b DOCUMENT ME!
\r
451 public void setAbovePIDThreshold(boolean b)
\r
453 abovePIDThreshold = b;
\r
459 * @return DOCUMENT ME!
\r
461 public int getStartRes()
\r
469 * @return DOCUMENT ME!
\r
471 public int getEndRes()
\r
479 * @return DOCUMENT ME!
\r
481 public int getStartSeq()
\r
489 * @param cs DOCUMENT ME!
\r
491 public void setGlobalColourScheme(ColourSchemeI cs)
\r
493 globalColourScheme = cs;
\r
499 * @return DOCUMENT ME!
\r
501 public ColourSchemeI getGlobalColourScheme()
\r
503 return globalColourScheme;
\r
509 * @param res DOCUMENT ME!
\r
511 public void setStartRes(int res)
\r
513 this.startRes = res;
\r
519 * @param seq DOCUMENT ME!
\r
521 public void setStartSeq(int seq)
\r
523 this.startSeq = seq;
\r
529 * @param res DOCUMENT ME!
\r
531 public void setEndRes(int res)
\r
533 if (res > (alignment.getWidth() - 1))
\r
535 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
\r
536 res = alignment.getWidth() - 1;
\r
550 * @param seq DOCUMENT ME!
\r
552 public void setEndSeq(int seq)
\r
554 if (seq > alignment.getHeight())
\r
556 seq = alignment.getHeight();
\r
570 * @return DOCUMENT ME!
\r
572 public int getEndSeq()
\r
580 * @param f DOCUMENT ME!
\r
582 public void setFont(Font f)
\r
586 Container c = new Container();
\r
588 java.awt.FontMetrics fm = c.getFontMetrics(font);
\r
589 setCharHeight(fm.getHeight());
\r
590 setCharWidth(fm.charWidth('M'));
\r
596 * @return DOCUMENT ME!
\r
598 public Font getFont()
\r
606 * @param w DOCUMENT ME!
\r
608 public void setCharWidth(int w)
\r
610 this.charWidth = w;
\r
616 * @return DOCUMENT ME!
\r
618 public int getCharWidth()
\r
626 * @param h DOCUMENT ME!
\r
628 public void setCharHeight(int h)
\r
630 this.charHeight = h;
\r
636 * @return DOCUMENT ME!
\r
638 public int getCharHeight()
\r
646 * @param w DOCUMENT ME!
\r
648 public void setWrappedWidth(int w)
\r
650 this.wrappedWidth = w;
\r
656 * @return DOCUMENT ME!
\r
658 public int getWrappedWidth()
\r
660 return wrappedWidth;
\r
667 * @return DOCUMENT ME!
\r
669 public AlignmentI getAlignment()
\r
677 * @param align DOCUMENT ME!
\r
679 public void setAlignment(AlignmentI align)
\r
681 this.alignment = align;
\r
687 * @param state DOCUMENT ME!
\r
689 public void setWrapAlignment(boolean state)
\r
691 wrapAlignment = state;
\r
697 * @param state DOCUMENT ME!
\r
699 public void setShowText(boolean state)
\r
707 * @param state DOCUMENT ME!
\r
709 public void setRenderGaps(boolean state)
\r
711 renderGaps = state;
\r
717 * @return DOCUMENT ME!
\r
719 public boolean getColourText()
\r
721 return showColourText;
\r
727 * @param state DOCUMENT ME!
\r
729 public void setColourText(boolean state)
\r
731 showColourText = state;
\r
737 * @param state DOCUMENT ME!
\r
739 public void setShowBoxes(boolean state)
\r
747 * @return DOCUMENT ME!
\r
749 public boolean getWrapAlignment()
\r
751 return wrapAlignment;
\r
757 * @return DOCUMENT ME!
\r
759 public boolean getShowText()
\r
767 * @return DOCUMENT ME!
\r
769 public boolean getShowBoxes()
\r
777 * @return DOCUMENT ME!
\r
779 public char getGapCharacter()
\r
781 return getAlignment().getGapCharacter();
\r
787 * @param gap DOCUMENT ME!
\r
789 public void setGapCharacter(char gap)
\r
791 if (getAlignment() != null)
\r
793 getAlignment().setGapCharacter(gap);
\r
800 * @param thresh DOCUMENT ME!
\r
802 public void setThreshold(int thresh)
\r
804 threshold = thresh;
\r
810 * @return DOCUMENT ME!
\r
812 public int getThreshold()
\r
820 * @param inc DOCUMENT ME!
\r
822 public void setIncrement(int inc)
\r
830 * @return DOCUMENT ME!
\r
832 public int getIncrement()
\r
840 * @param y DOCUMENT ME!
\r
842 * @return DOCUMENT ME!
\r
844 public int getIndex(int y)
\r
847 int starty = getStartSeq();
\r
848 int endy = getEndSeq();
\r
850 for (int i = starty; i <= endy; i++)
\r
852 if ((i < alignment.getHeight()) &&
\r
853 (alignment.getSequenceAt(i) != null))
\r
855 int y2 = y1 + getCharHeight();
\r
857 if ((y >= y1) && (y <= y2))
\r
876 * @return DOCUMENT ME!
\r
878 public ColumnSelection getColumnSelection()
\r
887 * @param tree DOCUMENT ME!
\r
889 public void setCurrentTree(NJTree tree)
\r
891 currentTree = tree;
\r
897 * @return DOCUMENT ME!
\r
899 public NJTree getCurrentTree()
\r
901 return currentTree;
\r
907 * @param b DOCUMENT ME!
\r
909 public void setColourAppliesToAllGroups(boolean b)
\r
911 colourAppliesToAllGroups = b;
\r
917 * @return DOCUMENT ME!
\r
919 public boolean getColourAppliesToAllGroups()
\r
921 return colourAppliesToAllGroups;
\r
927 * @return DOCUMENT ME!
\r
929 public boolean getShowJVSuffix()
\r
931 return showJVSuffix;
\r
937 * @param b DOCUMENT ME!
\r
939 public void setShowJVSuffix(boolean b)
\r
948 * @return DOCUMENT ME!
\r
950 public boolean getShowAnnotation()
\r
952 return showAnnotation;
\r
958 * @param b DOCUMENT ME!
\r
960 public void setShowAnnotation(boolean b)
\r
962 showAnnotation = b;
\r
968 * @return DOCUMENT ME!
\r
970 public boolean getScaleAboveWrapped()
\r
972 return scaleAboveWrapped;
\r
978 * @return DOCUMENT ME!
\r
980 public boolean getScaleLeftWrapped()
\r
982 return scaleLeftWrapped;
\r
988 * @return DOCUMENT ME!
\r
990 public boolean getScaleRightWrapped()
\r
992 return scaleRightWrapped;
\r
998 * @param b DOCUMENT ME!
\r
1000 public void setScaleAboveWrapped(boolean b)
\r
1002 scaleAboveWrapped = b;
\r
1008 * @param b DOCUMENT ME!
\r
1010 public void setScaleLeftWrapped(boolean b)
\r
1012 scaleLeftWrapped = b;
\r
1018 * @param b DOCUMENT ME!
\r
1020 public void setScaleRightWrapped(boolean b)
\r
1022 scaleRightWrapped = b;
\r
1026 * Property change listener for changes in alignment
\r
1028 * @param listener DOCUMENT ME!
\r
1030 public void addPropertyChangeListener(
\r
1031 java.beans.PropertyChangeListener listener)
\r
1033 changeSupport.addPropertyChangeListener(listener);
\r
1039 * @param listener DOCUMENT ME!
\r
1041 public void removePropertyChangeListener(
\r
1042 java.beans.PropertyChangeListener listener)
\r
1044 changeSupport.removePropertyChangeListener(listener);
\r
1048 * Property change listener for changes in alignment
\r
1050 * @param prop DOCUMENT ME!
\r
1051 * @param oldvalue DOCUMENT ME!
\r
1052 * @param newvalue DOCUMENT ME!
\r
1054 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
\r
1056 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
\r
1059 public void setIgnoreGapsConsensus(boolean b)
\r
1061 ignoreGapsInConsensusCalculation = b;
\r
1062 updateConsensus();
\r
1063 if(globalColourScheme!=null)
\r
1065 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
\r
1070 public boolean getIgnoreGapsConsensus()
\r
1072 return ignoreGapsInConsensusCalculation;
\r
1075 public void setDataset(boolean b)
\r
1080 public boolean isDataset()
\r