1 package jalview.renderer;
3 import jalview.analysis.AAFrequency;
4 import jalview.analysis.StructureFrequency;
5 import jalview.api.AlignViewportI;
6 import jalview.datamodel.AlignmentAnnotation;
7 import jalview.datamodel.ColumnSelection;
8 import jalview.schemes.ColourSchemeI;
10 import java.awt.BasicStroke;
11 import java.awt.Color;
13 import java.awt.FontMetrics;
14 import java.awt.Graphics;
15 import java.awt.Graphics2D;
16 import java.awt.Image;
17 import java.awt.font.LineMetrics;
18 import java.awt.geom.AffineTransform;
19 import java.awt.image.ImageObserver;
20 import java.util.Hashtable;
22 import com.stevesoft.pat.Regex;
24 public class AnnotationRenderer
27 public AnnotationRenderer()
29 // TODO Auto-generated constructor stub
32 public void drawStemAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
34 g.setColor(STEM_COLOUR);
35 int sCol = (lastSSX / charWidth) + startRes;
37 int x2 = (x * charWidth);
38 Regex closeparen = new Regex("(\\))");
40 String dc = (column == 0 || row.annotations[column-1]==null) ? ""
41 : row.annotations[column - 1].displayCharacter;
43 boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null
44 || !dc.equals(row.annotations[sCol - 1].displayCharacter);
45 boolean diffdownstream = !validRes || !validEnd
46 || row.annotations[column] == null
47 || !dc.equals(row.annotations[column].displayCharacter);
48 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
49 // If a closing base pair half of the stem, display a backward arrow
50 if (column > 0 && closeparen.search(dc))
53 // if (validRes && column>1 && row.annotations[column-2]!=null &&
54 // dc.equals(row.annotations[column-2].displayCharacter))
56 g.fillPolygon(new int[]
57 { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
58 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
68 // display a forward arrow
71 g.fillPolygon(new int[]
72 { x2 - 5, x2 - 5, x2 }, new int[]
73 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
82 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
84 private int charWidth,endRes,charHeight;
85 private boolean validCharWidth, hasHiddenColumns;
86 private FontMetrics fm;
87 private boolean MAC=new jalview.util.Platform().isAMac();
88 boolean av_renderHistogram = true, av_renderProfile = true, av_normaliseProfile=false;
89 ColourSchemeI profcolour=null;
90 private ColumnSelection columnSelection;
91 private Hashtable[] hconsensus;
92 private Hashtable[] hStrucConsensus;
93 private boolean av_ignoreGapsConsensus;
96 * attributes set from AwtRenderPanelI
99 * old image used when data is currently being calculated and cannot be rendered
101 private Image fadedImage;
103 * panel being rendered into
105 private ImageObserver annotationPanel;
107 * width of image to render in panel
109 private int imgWidth;
111 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI av)
112 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel, AlignViewportI av)
114 fm = annotPanel.getFontMetrics();
115 annotationPanel = annotPanel;
116 fadedImage=annotPanel.getFadedImage();
117 imgWidth=annotPanel.getFadedImageWidth();
118 updateFromAlignViewport(av);
120 public void updateFromAlignViewport(AlignViewportI av)
122 charWidth = av.getCharWidth();
123 endRes = av.getEndRes();
124 charHeight = av.getCharHeight();
125 hasHiddenColumns = av.hasHiddenColumns();
126 validCharWidth = av.isValidCharWidth();
127 av_renderHistogram = av.isShowConsensusHistogram();
128 av_renderProfile = av.isShowSequenceLogo();
129 av_normaliseProfile= av.isNormaliseSequenceLogo();
130 profcolour = av.getGlobalColourScheme();
131 if (profcolour == null)
133 // Set the default colour for sequence logo if the alignnent has no colourscheme set
134 profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme() : new jalview.schemes.ZappoColourScheme();
136 columnSelection = av.getColumnSelection();
137 hconsensus = av.getSequenceConsensusHash();//hconsensus;
138 hStrucConsensus = av.getRnaStructureConsensusHash(); //hStrucConsensus;
139 av_ignoreGapsConsensus=av.getIgnoreGapsConsensus();
141 public int[] getProfileFor(AlignmentAnnotation aa, int column)
143 // TODO : consider refactoring the global alignment calculation properties/rendering attributes as a global 'alignment group' which holds all vis settings for the alignment as a whole rather than a subset
145 if (aa.autoCalculated && aa.label.startsWith("Consensus"))
147 if (aa.groupRef != null && aa.groupRef.consensusData != null
148 && aa.groupRef.isShowSequenceLogo())
150 return AAFrequency.extractProfile(
151 aa.groupRef.consensusData[column], aa.groupRef
152 .getIgnoreGapsConsensus());
154 // TODO extend annotation row to enable dynamic and static profile data to
156 if (aa.groupRef == null && aa.sequenceRef == null
159 return AAFrequency.extractProfile(hconsensus[column], av_ignoreGapsConsensus);
164 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
166 // TODO implement group structure consensus
167 /* if (aa.groupRef != null && aa.groupRef.consensusData != null
168 && aa.groupRef.isShowSequenceLogo())
170 //TODO check what happens for group selections
171 return StructureFrequency.extractProfile(
172 aa.groupRef.consensusData[column], aa.groupRef
173 .getIgnoreGapsConsensus());
176 // TODO extend annotation row to enable dynamic and static profile data
179 if (aa.groupRef == null && aa.sequenceRef == null
182 return StructureFrequency.extractProfile(hStrucConsensus[column],
183 av_ignoreGapsConsensus);
193 * @param annotationPanel TODO
201 public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av, Graphics g, int activeRow, int startRes, int endRes)
204 // AnnotationPanel needs to implement: ImageObserver, access to AlignViewport
205 updateFromAwtRenderPanel(annotPanel, av);
206 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
213 boolean validRes = false;
214 boolean validEnd = false;
215 boolean labelAllCols = false;
216 boolean centreColLabels, centreColLabelsDef = av
217 .getCentreColumnLabels();
218 boolean scaleColLabel = false;
219 boolean[] graphGroupDrawn = new boolean[aa.length];
220 int charOffset = 0; // offset for a label
221 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
223 Font ofont = g.getFont();
225 for (int i = 0; i < aa.length; i++)
227 AlignmentAnnotation row = aa[i];
233 centreColLabels = row.centreColLabels || centreColLabelsDef;
234 labelAllCols = row.showAllColLabels;
235 scaleColLabel = row.scaleColLabel;
240 if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
245 // this is so that we draw the characters below the graph
250 iconOffset = charHeight - fm.getDescent();
254 else if (row.hasText)
256 iconOffset = charHeight - fm.getDescent();
264 if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
268 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
269 - row.height, imgWidth, y, annotationPanel);
270 g.setColor(Color.black);
271 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
276 /* else if (annotationPanel.av.updatingConservation
277 && aa[i].label.equals("Conservation"))
281 g.drawImage(annotationPanel.fadedImage, 0, y - row.height, annotationPanel.imgWidth, y, 0, y
282 - row.height, annotationPanel.imgWidth, y, annotationPanel);
284 g.setColor(Color.black);
285 // g.drawString("Calculating Conservation.....",20, y-row.height/2);
289 else if (annotationPanel.av.updatingConservation && aa[i].label.equals("Quality"))
293 g.drawImage(annotationPanel.fadedImage, 0, y - row.height, annotationPanel.imgWidth, y, 0, y
294 - row.height, annotationPanel.imgWidth, y, annotationPanel);
295 g.setColor(Color.black);
296 // / g.drawString("Calculating Quality....",20, y-row.height/2);
301 // first pass sets up state for drawing continuation from left-hand column
303 x = (startRes == 0) ? 0 : -1;
304 while (x < endRes - startRes)
306 if (hasHiddenColumns)
308 column = columnSelection.adjustForHiddenColumns(
310 if (column > row.annotations.length - 1)
317 column = startRes + x;
320 if ((row.annotations == null) || (row.annotations.length <= column)
321 || (row.annotations[column] == null))
333 g.setColor(Color.red);
335 if (columnSelection != null)
337 for (int n = 0; n < columnSelection.size(); n++)
339 int v = columnSelection.columnAt(n);
343 g.fillRect(x * charWidth, y, charWidth,
349 if (!row.isValidStruc())
351 g.setColor(Color.orange);
352 g.fillRect((int)row.getInvalidStrucPos()*charWidth, y, charWidth, charHeight);
356 && row.annotations[column].displayCharacter != null
357 && (row.annotations[column].displayCharacter.length() > 0))
360 if (centreColLabels || scaleColLabel)
362 fmWidth = (float) fm.charsWidth(
363 row.annotations[column].displayCharacter
365 row.annotations[column].displayCharacter.length());
369 // justify the label and scale to fit in column
370 if (fmWidth > charWidth)
372 // scale only if the current font isn't already small enough
373 fmScaling = charWidth;
374 fmScaling /= fmWidth;
375 g.setFont(ofont.deriveFont(AffineTransform
376 .getScaleInstance(fmScaling, 1.0)));
377 // and update the label's width to reflect the scaling.
385 .charWidth(row.annotations[column].displayCharacter
388 charOffset = (int) ((charWidth - fmWidth) / 2f);
390 if (row.annotations[column].colour == null)
391 g.setColor(Color.black);
393 g.setColor(row.annotations[column].colour);
395 if (column == 0 || row.graph > 0)
397 g.drawString(row.annotations[column].displayCharacter,
398 (x * charWidth) + charOffset, y + iconOffset);
400 else if (row.annotations[column - 1] == null
402 || !row.annotations[column].displayCharacter
403 .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
404 .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
406 g.drawString(row.annotations[column].displayCharacter, x
407 * charWidth + charOffset, y + iconOffset);
414 char ss = validRes ? row.annotations[column].secondaryStructure
418 // distinguish between forward/backward base-pairing
419 if (row.annotations[column].displayCharacter.indexOf(')') > -1)
424 if (!validRes || (ss != lastSS))
431 drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
432 column, validRes, validEnd);
436 drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
437 column, validRes, validEnd);
440 case 'S': // Stem case for RNA secondary structure
441 case 's': // and opposite direction
442 drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
443 column, validRes, validEnd);
447 g.setColor(Color.gray);
448 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
464 lastSSX = (x * charWidth);
471 if (column >= row.annotations.length)
473 column = row.annotations.length - 1;
480 if ((row.annotations == null) || (row.annotations.length <= column)
481 || (row.annotations[column] == null))
497 drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
498 column, validRes, validEnd);
502 drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
503 column, validRes, validEnd);
506 case 'S': // Stem case for RNA secondary structure
507 drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
508 column, validRes, validEnd);
511 drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
512 column, validRes, validEnd);
517 if (row.graph > 0 && row.graphHeight > 0)
519 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
521 if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
523 float groupmax = -999999, groupmin = 9999999;
524 for (int gg = 0; gg < aa.length; gg++)
526 if (aa[gg].graphGroup != row.graphGroup)
533 aa[gg].visible = false;
536 if (aa[gg].graphMax > groupmax)
538 groupmax = aa[gg].graphMax;
540 if (aa[gg].graphMin < groupmin)
542 groupmin = aa[gg].graphMin;
546 for (int gg = 0; gg < aa.length; gg++)
548 if (aa[gg].graphGroup == row.graphGroup)
550 drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
551 groupmax, row.graphHeight);
555 graphGroupDrawn[row.graphGroup] = true;
559 drawLineGraph( g, row, startRes, endRes, y, row.graphMin,
560 row.graphMax, row.graphHeight);
563 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
565 drawBarGraph(g, row, startRes, endRes, row.graphMin,
570 if (row.graph > 0 && row.hasText)
582 private Color GLYPHLINE_COLOR=Color.gray;
583 private Color SHEET_COLOUR=Color.green;
584 private Color HELIX_COLOUR=Color.red;
585 private Color STEM_COLOUR=Color.blue;
588 public void drawGlyphLine(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
590 g.setColor(GLYPHLINE_COLOR);
592 .fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
596 public void drawSheetAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
598 g.setColor(SHEET_COLOUR);
600 if (!validEnd || !validRes || row.annotations[column] == null
601 || row.annotations[column].secondaryStructure != 'E')
603 g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX
607 { (x * charWidth) - 4, (x * charWidth) - 4,
608 (x * charWidth) }, new int[]
609 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
614 g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth
620 public void drawHelixAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
622 g.setColor(HELIX_COLOUR);
624 int sCol = (lastSSX / charWidth) + startRes;
626 int x2 = (x * charWidth);
630 int ofs = charWidth / 2;
631 // Off by 1 offset when drawing rects and ovals
632 // to offscreen image on the MAC
633 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
634 if (sCol == 0 || row.annotations[sCol - 1] == null
635 || row.annotations[sCol - 1].secondaryStructure != 'H')
640 // g.setColor(Color.orange);
641 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
644 if (!validRes || row.annotations[column] == null
645 || row.annotations[column].secondaryStructure != 'H')
651 // g.setColor(Color.magenta);
652 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
660 if (sCol == 0 || row.annotations[sCol - 1] == null
661 || row.annotations[sCol - 1].secondaryStructure != 'H')
663 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
667 if (!validRes || row.annotations[column] == null
668 || row.annotations[column].secondaryStructure != 'H')
670 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset,
671 charWidth, 8, 270, 180);
675 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
678 public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int y, float min, float max, int graphHeight)
680 if (sRes > aa.annotations.length)
687 // Adjustment for fastpaint to left
693 eRes = Math.min(eRes, aa.annotations.length);
701 float range = max - min;
706 y2 = y - (int) ((0 - min / range) * graphHeight);
709 g.setColor(Color.gray);
710 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
712 eRes = Math.min(eRes, aa.annotations.length);
715 int aaMax = aa.annotations.length - 1;
717 while (x < eRes - sRes)
720 if (hasHiddenColumns)
722 column = columnSelection.adjustForHiddenColumns(column);
730 if (aa.annotations[column] == null
731 || aa.annotations[column - 1] == null)
737 if (aa.annotations[column].colour == null)
738 g.setColor(Color.black);
740 g.setColor(aa.annotations[column].colour);
743 - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
745 - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
747 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
748 + charWidth / 2, y2);
752 if (aa.threshold != null)
754 g.setColor(aa.threshold.colour);
755 Graphics2D g2 = (Graphics2D) g;
756 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
757 BasicStroke.JOIN_ROUND, 3f, new float[]
760 y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
761 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
762 g2.setStroke(new BasicStroke());
766 public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, float min, float max, int y)
768 if (sRes > aa.annotations.length)
772 Font ofont = g.getFont();
773 eRes = Math.min(eRes, aa.annotations.length);
775 int x = 0, y1 = y, y2 = y;
777 float range = max - min;
781 y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
784 g.setColor(Color.gray);
786 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
789 int aaMax = aa.annotations.length - 1;
790 boolean renderHistogram = true, renderProfile = true, normaliseProfile=false;
791 // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
793 // TODO: generalise this to have render styles for consensus/profile data
794 if (aa.groupRef != null)
796 renderHistogram = aa.groupRef.isShowConsensusHistogram();
797 renderProfile = aa.groupRef.isShowSequenceLogo();
798 normaliseProfile= aa.groupRef.isNormaliseSequenceLogo();
802 renderHistogram = av_renderHistogram;
803 renderProfile = av_renderProfile;
804 normaliseProfile= av_normaliseProfile;
807 while (x < eRes - sRes)
810 if (hasHiddenColumns)
812 column = columnSelection.adjustForHiddenColumns(column);
820 if (aa.annotations[column] == null)
825 if (aa.annotations[column].colour == null)
826 g.setColor(Color.black);
828 g.setColor(aa.annotations[column].colour);
831 - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
837 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
841 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
844 // draw profile if available
845 if (renderProfile && aa.annotations[column].value != 0)
848 int profl[] = getProfileFor(aa, column);
849 // just try to draw the logo if profl is not null
853 float ht = normaliseProfile ? y-aa.graphHeight : y1;
854 double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
860 * profl.length == 52 indicates that the profile of a secondary
861 * structure conservation row was accesed.
862 * Therefore dc gets length 2, to have space for a basepair instead of
863 * just a single nucleotide
865 if (profl.length == 52)
873 LineMetrics lm=g.getFontMetrics(ofont).getLineMetrics("Q", g);
874 double scale = 1f/(normaliseProfile ? profl[1] : 100f);
875 float ofontHeight = 1f/lm.getAscent();// magnify to fill box
877 for (int c = 2; profl != null && c < profl[0];)
879 dc[0] = (char) profl[c++];
881 if (aa.label.startsWith("StrucConsensus"))
883 dc[1] = (char) profl[c++];
887 wdth /= (float) fm.charsWidth(dc, 0, dc.length);
891 // if (aa.annotations[column].value==0) {
892 // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
893 // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
896 scl=((double)htn)*scale* ((double) profl[c++]);
897 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics().getFontRenderContext());
898 g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
899 wdth, scl/lm.getAscent())));
900 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
904 // ? );// try to get a
905 // colourscheme for the
906 // group(aa.groupRef.cs==null)
907 // ? av.textColour2 :
908 // cs.findColour(dc));
909 // System.out.println(dc[0]);
910 // Debug - render boxes around characters
911 // g.setColor(Color.red);
912 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, (int)(scl));
913 // g.setColor(profcolour.findColour(dc[0]).darker());
914 g.setColor(profcolour.findColour(dc[0]));
915 // (av.globalColourScheme!=null)
916 g.drawChars(dc, 0, dc.length, x * charWidth,
917 (int) (ht + (scl-lm.getDescent()-lm.getBaselineOffsets()[lm.getBaselineIndex()])));
918 // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
926 if (aa.threshold != null)
928 g.setColor(aa.threshold.colour);
929 Graphics2D g2 = (Graphics2D) g;
930 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
931 BasicStroke.JOIN_ROUND, 3f, new float[]
934 y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
935 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
936 g2.setStroke(new BasicStroke());
939 // used by overview window
940 public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
941 int y, int sRes, int eRes)
943 eRes = Math.min(eRes, aa.annotations.length);
944 g.setColor(Color.white);
945 g.fillRect(0, 0, width, y);
946 g.setColor(new Color(0, 0, 180));
950 for (int j = sRes; j < eRes; j++)
952 if (aa.annotations[j] != null)
954 if (aa.annotations[j].colour == null)
955 g.setColor(Color.black);
957 g.setColor(aa.annotations[j].colour);
959 height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
965 g.fillRect(x, y - height, charWidth, height);