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.Annotation;
8 import jalview.datamodel.ColumnSelection;
9 import jalview.schemes.ColourSchemeI;
11 import java.awt.BasicStroke;
12 import java.awt.Color;
14 import java.awt.FontMetrics;
15 import java.awt.Graphics;
16 import java.awt.Graphics2D;
17 import java.awt.Image;
18 import java.awt.font.LineMetrics;
19 import java.awt.geom.AffineTransform;
20 import java.awt.image.ImageObserver;
21 import java.util.Hashtable;
23 import com.stevesoft.pat.Regex;
25 public class AnnotationRenderer
28 public AnnotationRenderer()
30 // TODO Auto-generated constructor stub
33 public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
34 int lastSSX, int x, int y, int iconOffset, int startRes,
35 int column, boolean validRes, boolean validEnd)
37 g.setColor(STEM_COLOUR);
38 int sCol = (lastSSX / charWidth) + startRes;
40 int x2 = (x * charWidth);
41 Regex closeparen = new Regex("(\\))");
43 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
44 : row_annotations[column - 1].displayCharacter;
46 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
47 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
48 boolean diffdownstream = !validRes || !validEnd
49 || row_annotations[column] == null
50 || !dc.equals(row_annotations[column].displayCharacter);
51 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
52 // If a closing base pair half of the stem, display a backward arrow
53 if (column > 0 && closeparen.search(dc))
56 // if (validRes && column>1 && row_annotations[column-2]!=null &&
57 // dc.equals(row_annotations[column-2].displayCharacter))
59 g.fillPolygon(new int[]
60 { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
61 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
71 // display a forward arrow
74 g.fillPolygon(new int[]
75 { x2 - 5, x2 - 5, x2 }, new int[]
76 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
85 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
88 private int charWidth, endRes, charHeight;
90 private boolean validCharWidth, hasHiddenColumns;
92 private FontMetrics fm;
94 private boolean MAC = new jalview.util.Platform().isAMac();
96 boolean av_renderHistogram = true, av_renderProfile = true,
97 av_normaliseProfile = false;
99 ColourSchemeI profcolour = null;
101 private ColumnSelection columnSelection;
103 private Hashtable[] hconsensus;
105 private Hashtable[] hStrucConsensus;
107 private boolean av_ignoreGapsConsensus;
110 * attributes set from AwtRenderPanelI
113 * old image used when data is currently being calculated and cannot be
116 private Image fadedImage;
119 * panel being rendered into
121 private ImageObserver annotationPanel;
124 * width of image to render in panel
126 private int imgWidth;
128 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
130 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
133 fm = annotPanel.getFontMetrics();
134 annotationPanel = annotPanel;
135 fadedImage = annotPanel.getFadedImage();
136 imgWidth = annotPanel.getFadedImageWidth();
137 updateFromAlignViewport(av);
140 public void updateFromAlignViewport(AlignViewportI av)
142 charWidth = av.getCharWidth();
143 endRes = av.getEndRes();
144 charHeight = av.getCharHeight();
145 hasHiddenColumns = av.hasHiddenColumns();
146 validCharWidth = av.isValidCharWidth();
147 av_renderHistogram = av.isShowConsensusHistogram();
148 av_renderProfile = av.isShowSequenceLogo();
149 av_normaliseProfile = av.isNormaliseSequenceLogo();
150 profcolour = av.getGlobalColourScheme();
151 if (profcolour == null)
153 // Set the default colour for sequence logo if the alignnent has no
155 profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
156 : new jalview.schemes.ZappoColourScheme();
158 columnSelection = av.getColumnSelection();
159 hconsensus = av.getSequenceConsensusHash();// hconsensus;
160 hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
161 av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
164 public int[] getProfileFor(AlignmentAnnotation aa, int column)
166 // TODO : consider refactoring the global alignment calculation
167 // properties/rendering attributes as a global 'alignment group' which holds
168 // all vis settings for the alignment as a whole rather than a subset
170 if (aa.autoCalculated && aa.label.startsWith("Consensus"))
172 if (aa.groupRef != null && aa.groupRef.consensusData != null
173 && aa.groupRef.isShowSequenceLogo())
175 return AAFrequency.extractProfile(
176 aa.groupRef.consensusData[column],
177 aa.groupRef.getIgnoreGapsConsensus());
179 // TODO extend annotation row to enable dynamic and static profile data to
181 if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile)
183 return AAFrequency.extractProfile(hconsensus[column],
184 av_ignoreGapsConsensus);
189 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
191 // TODO implement group structure consensus
193 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
194 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
195 * group selections return StructureFrequency.extractProfile(
196 * aa.groupRef.consensusData[column], aa.groupRef
197 * .getIgnoreGapsConsensus()); }
199 // TODO extend annotation row to enable dynamic and static profile data
202 if (aa.groupRef == null && aa.sequenceRef == null
203 && av_renderProfile && hStrucConsensus != null
204 && hStrucConsensus.length > column)
206 return StructureFrequency.extractProfile(hStrucConsensus[column],
207 av_ignoreGapsConsensus);
217 * @param annotationPanel
226 public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av,
227 Graphics g, int activeRow, int startRes, int endRes)
230 // AnnotationPanel needs to implement: ImageObserver, access to
232 updateFromAwtRenderPanel(annotPanel, av);
233 fm = g.getFontMetrics();
234 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
241 boolean validRes = false;
242 boolean validEnd = false;
243 boolean labelAllCols = false;
244 boolean centreColLabels, centreColLabelsDef = av
245 .getCentreColumnLabels();
246 boolean scaleColLabel = false;
247 boolean[] graphGroupDrawn = new boolean[aa.length];
248 int charOffset = 0; // offset for a label
249 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
251 Font ofont = g.getFont();
253 for (int i = 0; i < aa.length; i++)
255 AlignmentAnnotation row = aa[i];
256 Annotation[] row_annotations=row.annotations;
261 centreColLabels = row.centreColLabels || centreColLabelsDef;
262 labelAllCols = row.showAllColLabels;
263 scaleColLabel = row.scaleColLabel;
268 if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
273 // this is so that we draw the characters below the graph
278 iconOffset = charHeight - fm.getDescent();
282 else if (row.hasText)
284 iconOffset = charHeight - fm.getDescent();
292 if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
296 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
297 - row.height, imgWidth, y, annotationPanel);
298 g.setColor(Color.black);
299 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
305 * else if (annotationPanel.av.updatingConservation &&
306 * aa[i].label.equals("Conservation")) {
308 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
309 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
310 * annotationPanel.imgWidth, y, annotationPanel);
312 * g.setColor(Color.black); //
313 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
315 * continue; } else if (annotationPanel.av.updatingConservation &&
316 * aa[i].label.equals("Quality")) {
318 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
319 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
320 * annotationPanel.imgWidth, y, annotationPanel); g.setColor(Color.black);
321 * // / g.drawString("Calculating Quality....",20, y-row.height/2);
325 // first pass sets up state for drawing continuation from left-hand column
327 x = (startRes == 0) ? 0 : -1;
328 while (x < endRes - startRes)
330 if (hasHiddenColumns)
332 column = columnSelection.adjustForHiddenColumns(startRes + x);
333 if (column > row_annotations.length - 1)
340 column = startRes + x;
343 if ((row_annotations == null) || (row_annotations.length <= column)
344 || (row_annotations[column] == null))
356 g.setColor(Color.red);
358 if (columnSelection != null)
360 for (int n = 0; n < columnSelection.size(); n++)
362 int v = columnSelection.columnAt(n);
366 g.fillRect(x * charWidth, y, charWidth, charHeight);
371 if (!row.isValidStruc())
373 g.setColor(Color.orange);
374 g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
375 charWidth, charHeight);
379 && row_annotations[column].displayCharacter != null
380 && (row_annotations[column].displayCharacter.length() > 0))
383 if (centreColLabels || scaleColLabel)
385 fmWidth = fm.charsWidth(
386 row_annotations[column].displayCharacter
388 row_annotations[column].displayCharacter.length());
392 // justify the label and scale to fit in column
393 if (fmWidth > charWidth)
395 // scale only if the current font isn't already small enough
396 fmScaling = charWidth;
397 fmScaling /= fmWidth;
398 g.setFont(ofont.deriveFont(AffineTransform
399 .getScaleInstance(fmScaling, 1.0)));
400 // and update the label's width to reflect the scaling.
408 .charWidth(row_annotations[column].displayCharacter
411 charOffset = (int) ((charWidth - fmWidth) / 2f);
413 if (row_annotations[column].colour == null)
414 g.setColor(Color.black);
416 g.setColor(row_annotations[column].colour);
418 if (column == 0 || row.graph > 0)
420 g.drawString(row_annotations[column].displayCharacter,
421 (x * charWidth) + charOffset, y + iconOffset);
423 else if (row_annotations[column - 1] == null
425 || !row_annotations[column].displayCharacter
426 .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
427 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
429 g.drawString(row_annotations[column].displayCharacter, x
430 * charWidth + charOffset, y + iconOffset);
437 char ss = validRes ? row_annotations[column].secondaryStructure
441 // distinguish between forward/backward base-pairing
442 if (row_annotations[column].displayCharacter.indexOf(')') > -1)
447 if (!validRes || (ss != lastSS))
454 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
455 column, validRes, validEnd);
459 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
460 column, validRes, validEnd);
463 case 'S': // Stem case for RNA secondary structure
464 case 's': // and opposite direction
465 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
466 column, validRes, validEnd);
470 g.setColor(Color.gray);
471 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
487 lastSSX = (x * charWidth);
494 if (column >= row_annotations.length)
496 column = row_annotations.length - 1;
503 if ((row_annotations == null) || (row_annotations.length <= column)
504 || (row_annotations[column] == null))
520 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
521 column, validRes, validEnd);
525 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
526 column, validRes, validEnd);
529 case 'S': // Stem case for RNA secondary structure
530 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
531 column, validRes, validEnd);
534 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
535 column, validRes, validEnd);
540 if (row.graph > 0 && row.graphHeight > 0)
542 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
544 if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
546 float groupmax = -999999, groupmin = 9999999;
547 for (int gg = 0; gg < aa.length; gg++)
549 if (aa[gg].graphGroup != row.graphGroup)
556 aa[gg].visible = false;
559 if (aa[gg].graphMax > groupmax)
561 groupmax = aa[gg].graphMax;
563 if (aa[gg].graphMin < groupmin)
565 groupmin = aa[gg].graphMin;
569 for (int gg = 0; gg < aa.length; gg++)
571 if (aa[gg].graphGroup == row.graphGroup)
573 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin,
574 groupmax, row.graphHeight);
578 graphGroupDrawn[row.graphGroup] = true;
582 drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin,
583 row.graphMax, row.graphHeight);
586 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
588 drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin,
593 if (row.graph > 0 && row.hasText)
605 private Color GLYPHLINE_COLOR = Color.gray;
607 private Color SHEET_COLOUR = Color.green;
609 private Color HELIX_COLOUR = Color.red;
611 private Color STEM_COLOUR = Color.blue;
613 public void drawGlyphLine(Graphics g, Annotation[] row,
614 int lastSSX, int x, int y, int iconOffset, int startRes,
615 int column, boolean validRes, boolean validEnd)
617 g.setColor(GLYPHLINE_COLOR);
618 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
621 public void drawSheetAnnot(Graphics g, Annotation[] row,
622 int lastSSX, int x, int y, int iconOffset, int startRes,
623 int column, boolean validRes, boolean validEnd)
625 g.setColor(SHEET_COLOUR);
627 if (!validEnd || !validRes || row==null || row[column] == null
628 || row[column].secondaryStructure != 'E')
630 g.fillRect(lastSSX, y + 4 + iconOffset,
631 (x * charWidth) - lastSSX - 4, 7);
632 g.fillPolygon(new int[]
633 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
635 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
640 g.fillRect(lastSSX, y + 4 + iconOffset,
641 (x + 1) * charWidth - lastSSX, 7);
646 public void drawHelixAnnot(Graphics g, Annotation[] row,
647 int lastSSX, int x, int y, int iconOffset, int startRes,
648 int column, boolean validRes, boolean validEnd)
650 g.setColor(HELIX_COLOUR);
652 int sCol = (lastSSX / charWidth) + startRes;
654 int x2 = (x * charWidth);
658 int ofs = charWidth / 2;
659 // Off by 1 offset when drawing rects and ovals
660 // to offscreen image on the MAC
661 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
662 if (sCol == 0 || row[sCol - 1] == null
663 || row[sCol - 1].secondaryStructure != 'H')
668 // g.setColor(Color.orange);
669 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
672 if (!validRes || row[column] == null
673 || row[column].secondaryStructure != 'H')
679 // g.setColor(Color.magenta);
680 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
688 if (sCol == 0 || row[sCol - 1] == null
689 || row[sCol - 1].secondaryStructure != 'H')
691 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
695 if (!validRes || row[column] == null
696 || row[column].secondaryStructure != 'H')
698 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
703 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
706 public void drawLineGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
707 int eRes, int y, float min, float max, int graphHeight)
709 if (sRes > aa_annotations.length)
716 // Adjustment for fastpaint to left
722 eRes = Math.min(eRes, aa_annotations.length);
730 float range = max - min;
735 y2 = y - (int) ((0 - min / range) * graphHeight);
738 g.setColor(Color.gray);
739 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
741 eRes = Math.min(eRes, aa_annotations.length);
744 int aaMax = aa_annotations.length - 1;
746 while (x < eRes - sRes)
749 if (hasHiddenColumns)
751 column = columnSelection.adjustForHiddenColumns(column);
759 if (aa_annotations[column] == null
760 || aa_annotations[column - 1] == null)
766 if (aa_annotations[column].colour == null)
767 g.setColor(Color.black);
769 g.setColor(aa_annotations[column].colour);
772 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
774 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
776 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
777 + charWidth / 2, y2);
781 if (_aa.threshold != null)
783 g.setColor(_aa.threshold.colour);
784 Graphics2D g2 = (Graphics2D) g;
785 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
786 BasicStroke.JOIN_ROUND, 3f, new float[]
789 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
790 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
791 g2.setStroke(new BasicStroke());
795 public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
796 int eRes, float min, float max, int y)
798 if (sRes > aa_annotations.length)
802 Font ofont = g.getFont();
803 eRes = Math.min(eRes, aa_annotations.length);
805 int x = 0, y1 = y, y2 = y;
807 float range = max - min;
811 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
814 g.setColor(Color.gray);
816 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
819 int aaMax = aa_annotations.length - 1;
820 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
821 // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
823 // TODO: generalise this to have render styles for consensus/profile data
824 if (_aa.groupRef != null)
826 renderHistogram = _aa.groupRef.isShowConsensusHistogram();
827 renderProfile = _aa.groupRef.isShowSequenceLogo();
828 normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
832 renderHistogram = av_renderHistogram;
833 renderProfile = av_renderProfile;
834 normaliseProfile = av_normaliseProfile;
837 while (x < eRes - sRes)
840 if (hasHiddenColumns)
842 column = columnSelection.adjustForHiddenColumns(column);
850 if (aa_annotations[column] == null)
855 if (aa_annotations[column].colour == null)
856 g.setColor(Color.black);
858 g.setColor(aa_annotations[column].colour);
861 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
867 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
871 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
874 // draw profile if available
878 int profl[] = getProfileFor(_aa, column);
879 // just try to draw the logo if profl is not null
880 if (profl != null && profl[1] != 0)
882 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
883 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
890 * profl.length == 74 indicates that the profile of a secondary
891 * structure conservation row was accesed. Therefore dc gets length 2,
892 * to have space for a basepair instead of just a single nucleotide
894 if (profl.length == 74)
902 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
903 double scale = 1f / (normaliseProfile ? profl[1] : 100f);
904 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
906 for (int c = 2; c < profl[0];)
908 dc[0] = (char) profl[c++];
910 if (_aa.label.startsWith("StrucConsensus"))
912 dc[1] = (char) profl[c++];
916 wdth /= fm.charsWidth(dc, 0, dc.length);
920 scl = htn * scale * profl[c++];
921 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
922 .getFontRenderContext());
923 g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
924 wdth, scl / lm.getAscent())));
925 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
927 // Debug - render boxes around characters
928 // g.setColor(Color.red);
929 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
931 // g.setColor(profcolour.findColour(dc[0]).darker());
932 g.setColor(profcolour.findColour(dc[0], column,null));
934 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
935 .getBaselineIndex()]));
937 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
945 if (_aa.threshold != null)
947 g.setColor(_aa.threshold.colour);
948 Graphics2D g2 = (Graphics2D) g;
949 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
950 BasicStroke.JOIN_ROUND, 3f, new float[]
953 y2 = (int) (y - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
954 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
955 g2.setStroke(new BasicStroke());
959 // used by overview window
960 public void drawGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int width,
961 int y, int sRes, int eRes)
963 eRes = Math.min(eRes, aa_annotations.length);
964 g.setColor(Color.white);
965 g.fillRect(0, 0, width, y);
966 g.setColor(new Color(0, 0, 180));
970 for (int j = sRes; j < eRes; j++)
972 if (aa_annotations[j] != null)
974 if (aa_annotations[j].colour == null)
975 g.setColor(Color.black);
977 g.setColor(aa_annotations[j].colour);
979 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
985 g.fillRect(x, y - height, charWidth, height);