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 showFullId = false;
\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
90 * Creates a new AlignViewport object.
\r
92 * @param al DOCUMENT ME!
\r
94 public AlignViewport(AlignmentI al)
\r
98 this.endRes = al.getWidth() - 1;
\r
100 this.endSeq = al.getHeight() - 1;
\r
102 updateFromPreferences();
\r
108 public void updateFromPreferences()
\r
110 showFullId = Cache.getDefault("SHOW_FULL_ID", true);
\r
111 showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
\r
112 showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
\r
114 showQuality = Cache.getDefault("SHOW_QUALITY", true);
\r
115 showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
\r
117 String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
\r
118 String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
\r
119 String fontSize = Cache.getDefault("FONT_SIZE", "10");
\r
123 if (fontStyle.equals("bold"))
\r
127 else if (fontStyle.equals("italic"))
\r
132 setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
\r
135 alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
\r
138 // We must set conservation and consensus before setting colour,
\r
139 // as Blosum and Clustal require this to be done
\r
140 updateConservation();
\r
143 if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
\r
145 globalColourScheme = ColourSchemeProperty.getColour(alignment,
\r
146 jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
\r
148 if (globalColourScheme instanceof UserColourScheme)
\r
150 globalColourScheme = UserDefinedColours.loadDefaultColours();
\r
151 ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
\r
154 if (globalColourScheme != null)
\r
156 globalColourScheme.setConsensus(vconsensus);
\r
166 * @param b DOCUMENT ME!
\r
168 public void showSequenceFeatures(boolean b)
\r
170 showSequenceFeatures = b;
\r
176 public void updateConservation()
\r
179 Conservation cons = new jalview.analysis.Conservation("All",
\r
180 jalview.schemes.ResidueProperties.propHash, 3,
\r
181 alignment.getSequences(), 0, alignment.getWidth() - 1);
\r
183 cons.verdict(false, ConsPercGaps);
\r
184 cons.findQuality();
\r
186 int alWidth = alignment.getWidth();
\r
187 Annotation[] annotations = new Annotation[alWidth];
\r
188 Annotation[] qannotations = new Annotation[alWidth];
\r
189 String sequence = cons.getConsSequence().getSequence();
\r
199 maxR = 1.0f - minR;
\r
200 maxG = 0.9f - minG;
\r
201 maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
\r
205 float qmin = cons.qualityRange[0].floatValue();
\r
206 float qmax = cons.qualityRange[1].floatValue();
\r
208 for (int i = 0; i < alWidth; i++)
\r
214 value = Integer.parseInt(sequence.charAt(i) + "");
\r
216 catch (Exception ex)
\r
218 if (sequence.charAt(i) == '*')
\r
223 if (sequence.charAt(i) == '+')
\r
229 float vprop = value - min;
\r
231 annotations[i] = new Annotation(sequence.charAt(i) + "",
\r
232 String.valueOf(value), ' ', value,
\r
233 new Color(minR + (maxR * vprop),
\r
234 minG + (maxG * vprop),
\r
235 minB + (maxB * vprop)));
\r
238 value = ( (Double) cons.quality.get(i)).floatValue();
\r
239 vprop = value - qmin;
\r
241 qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
\r
243 new Color(minR + (maxR * vprop),
\r
244 minG + (maxG * vprop),
\r
245 minB + (maxB * vprop)));
\r
248 if (conservation == null)
\r
250 conservation = new AlignmentAnnotation("Conservation",
\r
251 "Conservation of total alignment less than " +
\r
252 ConsPercGaps + "% gaps",
\r
253 annotations, 0f, // cons.qualityRange[0].floatValue(),
\r
254 11f, // cons.qualityRange[1].floatValue()
\r
257 if (showConservation)
\r
259 alignment.addAnnotation(conservation);
\r
262 quality = new AlignmentAnnotation("Quality",
\r
263 "Alignment Quality based on Blosum62 scores",
\r
265 cons.qualityRange[0].floatValue(),
\r
266 cons.qualityRange[1].floatValue(),
\r
271 alignment.addAnnotation(quality);
\r
276 conservation.annotations = annotations;
\r
277 quality.annotations = qannotations;
\r
278 quality.graphMax = cons.qualityRange[1].floatValue();
\r
281 catch (OutOfMemoryError error)
\r
283 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
284 "Out of memory calculating conservation!!"
\r
286 "\nSee help files for increasing Java Virtual Machine memory."
\r
288 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
289 System.out.println("Conservation calculation: " + error);
\r
298 public void updateConsensus()
\r
301 Annotation[] annotations = new Annotation[alignment.getWidth()];
\r
303 // this routine prevents vconsensus becoming a new object each time
\r
304 // consenus is calculated. Important for speed of Blosum62
\r
305 // and PID colouring of alignment
\r
306 if (vconsensus == null)
\r
308 vconsensus = alignment.getAAFrequency();
\r
312 Vector temp = alignment.getAAFrequency();
\r
313 vconsensus.clear();
\r
315 Enumeration e = temp.elements();
\r
317 while (e.hasMoreElements())
\r
319 vconsensus.add(e.nextElement());
\r
323 Hashtable hash = null;
\r
325 for (int i = 0; i < alignment.getWidth(); i++)
\r
327 hash = (Hashtable) vconsensus.elementAt(i);
\r
330 if (ignoreGapsInConsensusCalculation)
\r
331 value = ( (Float) hash.get("pid_nogaps")).floatValue();
\r
333 value = ( (Float) hash.get("pid_gaps")).floatValue();
\r
335 String maxRes = hash.get("maxResidue").toString();
\r
336 String mouseOver = hash.get("maxResidue") + " ";
\r
338 if (maxRes.length() > 1)
\r
340 mouseOver = "[" + maxRes + "] ";
\r
344 mouseOver += ( (int) value + "%");
\r
345 annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
\r
348 if (consensus == null)
\r
350 consensus = new AlignmentAnnotation("Consensus", "PID",
\r
351 annotations, 0f, 100f, 1);
\r
355 alignment.addAnnotation(consensus);
\r
360 consensus.annotations = annotations;
\r
363 if (globalColourScheme != null)
\r
364 globalColourScheme.setConsensus(vconsensus);
\r
366 }catch(OutOfMemoryError error)
\r
368 javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
369 "Out of memory calculating consensus!!"
\r
371 "\nSee help files for increasing Java Virtual Machine memory."
\r
373 javax.swing.JOptionPane.WARNING_MESSAGE);
\r
374 System.out.println("Consensus calculation: " + error);
\r
383 * @return DOCUMENT ME!
\r
385 public SequenceGroup getSelectionGroup()
\r
387 return selectionGroup;
\r
393 * @param sg DOCUMENT ME!
\r
395 public void setSelectionGroup(SequenceGroup sg)
\r
397 selectionGroup = sg;
\r
403 * @return DOCUMENT ME!
\r
405 public boolean getConservationSelected()
\r
407 return conservationColourSelected;
\r
413 * @param b DOCUMENT ME!
\r
415 public void setConservationSelected(boolean b)
\r
417 conservationColourSelected = b;
\r
423 * @return DOCUMENT ME!
\r
425 public boolean getAbovePIDThreshold()
\r
427 return abovePIDThreshold;
\r
433 * @param b DOCUMENT ME!
\r
435 public void setAbovePIDThreshold(boolean b)
\r
437 abovePIDThreshold = b;
\r
443 * @return DOCUMENT ME!
\r
445 public int getStartRes()
\r
453 * @return DOCUMENT ME!
\r
455 public int getEndRes()
\r
463 * @return DOCUMENT ME!
\r
465 public int getStartSeq()
\r
473 * @param cs DOCUMENT ME!
\r
475 public void setGlobalColourScheme(ColourSchemeI cs)
\r
477 globalColourScheme = cs;
\r
483 * @return DOCUMENT ME!
\r
485 public ColourSchemeI getGlobalColourScheme()
\r
487 return globalColourScheme;
\r
493 * @param res DOCUMENT ME!
\r
495 public void setStartRes(int res)
\r
497 this.startRes = res;
\r
503 * @param seq DOCUMENT ME!
\r
505 public void setStartSeq(int seq)
\r
507 this.startSeq = seq;
\r
513 * @param res DOCUMENT ME!
\r
515 public void setEndRes(int res)
\r
517 if (res > (alignment.getWidth() - 1))
\r
519 // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
\r
520 res = alignment.getWidth() - 1;
\r
534 * @param seq DOCUMENT ME!
\r
536 public void setEndSeq(int seq)
\r
538 if (seq > alignment.getHeight())
\r
540 seq = alignment.getHeight();
\r
554 * @return DOCUMENT ME!
\r
556 public int getEndSeq()
\r
564 * @param f DOCUMENT ME!
\r
566 public void setFont(Font f)
\r
570 Container c = new Container();
\r
572 java.awt.FontMetrics fm = c.getFontMetrics(font);
\r
573 setCharHeight(fm.getHeight());
\r
574 setCharWidth(fm.charWidth('M'));
\r
580 * @return DOCUMENT ME!
\r
582 public Font getFont()
\r
590 * @param w DOCUMENT ME!
\r
592 public void setCharWidth(int w)
\r
594 this.charWidth = w;
\r
600 * @return DOCUMENT ME!
\r
602 public int getCharWidth()
\r
610 * @param h DOCUMENT ME!
\r
612 public void setCharHeight(int h)
\r
614 this.charHeight = h;
\r
620 * @return DOCUMENT ME!
\r
622 public int getCharHeight()
\r
630 * @param w DOCUMENT ME!
\r
632 public void setWrappedWidth(int w)
\r
634 this.wrappedWidth = w;
\r
640 * @return DOCUMENT ME!
\r
642 public int getWrappedWidth()
\r
644 return wrappedWidth;
\r
651 * @return DOCUMENT ME!
\r
653 public AlignmentI getAlignment()
\r
661 * @param align DOCUMENT ME!
\r
663 public void setAlignment(AlignmentI align)
\r
665 this.alignment = align;
\r
671 * @param state DOCUMENT ME!
\r
673 public void setWrapAlignment(boolean state)
\r
675 wrapAlignment = state;
\r
681 * @param state DOCUMENT ME!
\r
683 public void setShowText(boolean state)
\r
691 * @param state DOCUMENT ME!
\r
693 public void setRenderGaps(boolean state)
\r
695 renderGaps = state;
\r
701 * @return DOCUMENT ME!
\r
703 public boolean getColourText()
\r
705 return showColourText;
\r
711 * @param state DOCUMENT ME!
\r
713 public void setColourText(boolean state)
\r
715 showColourText = state;
\r
721 * @param state DOCUMENT ME!
\r
723 public void setShowBoxes(boolean state)
\r
731 * @return DOCUMENT ME!
\r
733 public boolean getWrapAlignment()
\r
735 return wrapAlignment;
\r
741 * @return DOCUMENT ME!
\r
743 public boolean getShowText()
\r
751 * @return DOCUMENT ME!
\r
753 public boolean getShowBoxes()
\r
761 * @return DOCUMENT ME!
\r
763 public char getGapCharacter()
\r
765 return getAlignment().getGapCharacter();
\r
771 * @param gap DOCUMENT ME!
\r
773 public void setGapCharacter(char gap)
\r
775 if (getAlignment() != null)
\r
777 getAlignment().setGapCharacter(gap);
\r
784 * @param thresh DOCUMENT ME!
\r
786 public void setThreshold(int thresh)
\r
788 threshold = thresh;
\r
794 * @return DOCUMENT ME!
\r
796 public int getThreshold()
\r
804 * @param inc DOCUMENT ME!
\r
806 public void setIncrement(int inc)
\r
814 * @return DOCUMENT ME!
\r
816 public int getIncrement()
\r
824 * @param y DOCUMENT ME!
\r
826 * @return DOCUMENT ME!
\r
828 public int getIndex(int y)
\r
831 int starty = getStartSeq();
\r
832 int endy = getEndSeq();
\r
834 for (int i = starty; i <= endy; i++)
\r
836 if ((i < alignment.getHeight()) &&
\r
837 (alignment.getSequenceAt(i) != null))
\r
839 int y2 = y1 + getCharHeight();
\r
841 if ((y >= y1) && (y <= y2))
\r
860 * @return DOCUMENT ME!
\r
862 public ColumnSelection getColumnSelection()
\r
871 * @param tree DOCUMENT ME!
\r
873 public void setCurrentTree(NJTree tree)
\r
875 currentTree = tree;
\r
881 * @return DOCUMENT ME!
\r
883 public NJTree getCurrentTree()
\r
885 return currentTree;
\r
891 * @param b DOCUMENT ME!
\r
893 public void setColourAppliesToAllGroups(boolean b)
\r
895 colourAppliesToAllGroups = b;
\r
901 * @return DOCUMENT ME!
\r
903 public boolean getColourAppliesToAllGroups()
\r
905 return colourAppliesToAllGroups;
\r
911 * @return DOCUMENT ME!
\r
913 public boolean getShowFullId()
\r
921 * @param b DOCUMENT ME!
\r
923 public void setShowFullId(boolean b)
\r
931 * @return DOCUMENT ME!
\r
933 public boolean getShowAnnotation()
\r
935 return showAnnotation;
\r
941 * @param b DOCUMENT ME!
\r
943 public void setShowAnnotation(boolean b)
\r
945 showAnnotation = b;
\r
951 * @return DOCUMENT ME!
\r
953 public boolean getScaleAboveWrapped()
\r
955 return scaleAboveWrapped;
\r
961 * @return DOCUMENT ME!
\r
963 public boolean getScaleLeftWrapped()
\r
965 return scaleLeftWrapped;
\r
971 * @return DOCUMENT ME!
\r
973 public boolean getScaleRightWrapped()
\r
975 return scaleRightWrapped;
\r
981 * @param b DOCUMENT ME!
\r
983 public void setScaleAboveWrapped(boolean b)
\r
985 scaleAboveWrapped = b;
\r
991 * @param b DOCUMENT ME!
\r
993 public void setScaleLeftWrapped(boolean b)
\r
995 scaleLeftWrapped = b;
\r
1001 * @param b DOCUMENT ME!
\r
1003 public void setScaleRightWrapped(boolean b)
\r
1005 scaleRightWrapped = b;
\r
1009 * Property change listener for changes in alignment
\r
1011 * @param listener DOCUMENT ME!
\r
1013 public void addPropertyChangeListener(
\r
1014 java.beans.PropertyChangeListener listener)
\r
1016 changeSupport.addPropertyChangeListener(listener);
\r
1022 * @param listener DOCUMENT ME!
\r
1024 public void removePropertyChangeListener(
\r
1025 java.beans.PropertyChangeListener listener)
\r
1027 changeSupport.removePropertyChangeListener(listener);
\r
1031 * Property change listener for changes in alignment
\r
1033 * @param prop DOCUMENT ME!
\r
1034 * @param oldvalue DOCUMENT ME!
\r
1035 * @param newvalue DOCUMENT ME!
\r
1037 public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
\r
1039 changeSupport.firePropertyChange(prop, oldvalue, newvalue);
\r
1042 public void setIgnoreGapsConsensus(boolean b)
\r
1044 ignoreGapsInConsensusCalculation = b;
\r
1045 updateConsensus();
\r
1046 if(globalColourScheme!=null)
\r
1048 globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
\r
1053 public boolean getIgnoreGapsConsensus()
\r
1055 return ignoreGapsInConsensusCalculation;
\r