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 ? ""
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 if (aa.groupRef != null && aa.groupRef.consensusData != null
167 && aa.groupRef.isShowSequenceLogo())
169 //TODO check what happens for group selections
170 return StructureFrequency.extractProfile(
171 aa.groupRef.consensusData[column], aa.groupRef
172 .getIgnoreGapsConsensus());
174 // TODO extend annotation row to enable dynamic and static profile data
177 if (aa.groupRef == null && aa.sequenceRef == null
180 return StructureFrequency.extractProfile(hStrucConsensus[column],
181 av_ignoreGapsConsensus);
191 * @param annotationPanel TODO
199 public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av, Graphics g, int activeRow, int startRes, int endRes)
202 // AnnotationPanel needs to implement: ImageObserver, access to AlignViewport
203 updateFromAwtRenderPanel(annotPanel, av);
204 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
211 boolean validRes = false;
212 boolean validEnd = false;
213 boolean labelAllCols = false;
214 boolean centreColLabels, centreColLabelsDef = av
215 .getCentreColumnLabels();
216 boolean scaleColLabel = false;
217 boolean[] graphGroupDrawn = new boolean[aa.length];
218 int charOffset = 0; // offset for a label
219 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
221 Font ofont = g.getFont();
223 for (int i = 0; i < aa.length; i++)
225 AlignmentAnnotation row = aa[i];
231 centreColLabels = row.centreColLabels || centreColLabelsDef;
232 labelAllCols = row.showAllColLabels;
233 scaleColLabel = row.scaleColLabel;
238 if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
243 // this is so that we draw the characters below the graph
248 iconOffset = charHeight - fm.getDescent();
252 else if (row.hasText)
254 iconOffset = charHeight - fm.getDescent();
262 if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
266 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
267 - row.height, imgWidth, y, annotationPanel);
268 g.setColor(Color.black);
269 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
274 /* else if (annotationPanel.av.updatingConservation
275 && aa[i].label.equals("Conservation"))
279 g.drawImage(annotationPanel.fadedImage, 0, y - row.height, annotationPanel.imgWidth, y, 0, y
280 - row.height, annotationPanel.imgWidth, y, annotationPanel);
282 g.setColor(Color.black);
283 // g.drawString("Calculating Conservation.....",20, y-row.height/2);
287 else if (annotationPanel.av.updatingConservation && aa[i].label.equals("Quality"))
291 g.drawImage(annotationPanel.fadedImage, 0, y - row.height, annotationPanel.imgWidth, y, 0, y
292 - row.height, annotationPanel.imgWidth, y, annotationPanel);
293 g.setColor(Color.black);
294 // / g.drawString("Calculating Quality....",20, y-row.height/2);
299 // first pass sets up state for drawing continuation from left-hand column
301 x = (startRes == 0) ? 0 : -1;
302 while (x < endRes - startRes)
304 if (hasHiddenColumns)
306 column = columnSelection.adjustForHiddenColumns(
308 if (column > row.annotations.length - 1)
315 column = startRes + x;
318 if ((row.annotations == null) || (row.annotations.length <= column)
319 || (row.annotations[column] == null))
331 g.setColor(Color.red);
333 if (columnSelection != null)
335 for (int n = 0; n < columnSelection.size(); n++)
337 int v = columnSelection.columnAt(n);
341 g.fillRect(x * charWidth, y, charWidth,
350 && row.annotations[column].displayCharacter != null
351 && (row.annotations[column].displayCharacter.length() > 0))
354 if (centreColLabels || scaleColLabel)
356 fmWidth = (float) fm.charsWidth(
357 row.annotations[column].displayCharacter
359 row.annotations[column].displayCharacter.length());
363 // justify the label and scale to fit in column
364 if (fmWidth > charWidth)
366 // scale only if the current font isn't already small enough
367 fmScaling = charWidth;
368 fmScaling /= fmWidth;
369 g.setFont(ofont.deriveFont(AffineTransform
370 .getScaleInstance(fmScaling, 1.0)));
371 // and update the label's width to reflect the scaling.
379 .charWidth(row.annotations[column].displayCharacter
382 charOffset = (int) ((charWidth - fmWidth) / 2f);
384 if (row.annotations[column].colour == null)
385 g.setColor(Color.black);
387 g.setColor(row.annotations[column].colour);
389 if (column == 0 || row.graph > 0)
391 g.drawString(row.annotations[column].displayCharacter,
392 (x * charWidth) + charOffset, y + iconOffset);
394 else if (row.annotations[column - 1] == null
396 || !row.annotations[column].displayCharacter
397 .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
398 .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
400 g.drawString(row.annotations[column].displayCharacter, x
401 * charWidth + charOffset, y + iconOffset);
408 char ss = validRes ? row.annotations[column].secondaryStructure
412 // distinguish between forward/backward base-pairing
413 if (row.annotations[column].displayCharacter.indexOf(')') > -1)
418 if (!validRes || (ss != lastSS))
425 drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
426 column, validRes, validEnd);
430 drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
431 column, validRes, validEnd);
434 case 'S': // Stem case for RNA secondary structure
435 case 's': // and opposite direction
436 drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
437 column, validRes, validEnd);
441 g.setColor(Color.gray);
442 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
458 lastSSX = (x * charWidth);
465 if (column >= row.annotations.length)
467 column = row.annotations.length - 1;
482 drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
483 column, validRes, validEnd);
487 drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
488 column, validRes, validEnd);
491 case 'S': // Stem case for RNA secondary structure
492 drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
493 column, validRes, validEnd);
496 drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
497 column, validRes, validEnd);
502 if (row.graph > 0 && row.graphHeight > 0)
504 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
506 if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
508 float groupmax = -999999, groupmin = 9999999;
509 for (int gg = 0; gg < aa.length; gg++)
511 if (aa[gg].graphGroup != row.graphGroup)
518 aa[gg].visible = false;
521 if (aa[gg].graphMax > groupmax)
523 groupmax = aa[gg].graphMax;
525 if (aa[gg].graphMin < groupmin)
527 groupmin = aa[gg].graphMin;
531 for (int gg = 0; gg < aa.length; gg++)
533 if (aa[gg].graphGroup == row.graphGroup)
535 drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
536 groupmax, row.graphHeight);
540 graphGroupDrawn[row.graphGroup] = true;
544 drawLineGraph( g, row, startRes, endRes, y, row.graphMin,
545 row.graphMax, row.graphHeight);
548 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
550 drawBarGraph(g, row, startRes, endRes, row.graphMin,
555 if (row.graph > 0 && row.hasText)
567 private Color GLYPHLINE_COLOR=Color.gray;
568 private Color SHEET_COLOUR=Color.green;
569 private Color HELIX_COLOUR=Color.red;
570 private Color STEM_COLOUR=Color.blue;
573 public void drawGlyphLine(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
575 g.setColor(GLYPHLINE_COLOR);
577 .fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
581 public void drawSheetAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
583 g.setColor(SHEET_COLOUR);
585 if (!validEnd || !validRes || row.annotations[column] == null
586 || row.annotations[column].secondaryStructure != 'E')
588 g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX
592 { (x * charWidth) - 4, (x * charWidth) - 4,
593 (x * charWidth) }, new int[]
594 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
599 g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth
605 public void drawHelixAnnot(Graphics g, AlignmentAnnotation row, int lastSSX, int x, int y, int iconOffset, int startRes, int column, boolean validRes, boolean validEnd)
607 g.setColor(HELIX_COLOUR);
609 int sCol = (lastSSX / charWidth) + startRes;
611 int x2 = (x * charWidth);
615 int ofs = charWidth / 2;
616 // Off by 1 offset when drawing rects and ovals
617 // to offscreen image on the MAC
618 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
619 if (sCol == 0 || row.annotations[sCol - 1] == null
620 || row.annotations[sCol - 1].secondaryStructure != 'H')
625 // g.setColor(Color.orange);
626 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
629 if (!validRes || row.annotations[column] == null
630 || row.annotations[column].secondaryStructure != 'H')
636 // g.setColor(Color.magenta);
637 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
645 if (sCol == 0 || row.annotations[sCol - 1] == null
646 || row.annotations[sCol - 1].secondaryStructure != 'H')
648 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
652 if (!validRes || row.annotations[column] == null
653 || row.annotations[column].secondaryStructure != 'H')
655 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset,
656 charWidth, 8, 270, 180);
660 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
663 public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int y, float min, float max, int graphHeight)
665 if (sRes > aa.annotations.length)
672 // Adjustment for fastpaint to left
678 eRes = Math.min(eRes, aa.annotations.length);
686 float range = max - min;
691 y2 = y - (int) ((0 - min / range) * graphHeight);
694 g.setColor(Color.gray);
695 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
697 eRes = Math.min(eRes, aa.annotations.length);
700 int aaMax = aa.annotations.length - 1;
702 while (x < eRes - sRes)
705 if (hasHiddenColumns)
707 column = columnSelection.adjustForHiddenColumns(column);
715 if (aa.annotations[column] == null
716 || aa.annotations[column - 1] == null)
722 if (aa.annotations[column].colour == null)
723 g.setColor(Color.black);
725 g.setColor(aa.annotations[column].colour);
728 - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
730 - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
732 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
733 + charWidth / 2, y2);
737 if (aa.threshold != null)
739 g.setColor(aa.threshold.colour);
740 Graphics2D g2 = (Graphics2D) g;
741 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
742 BasicStroke.JOIN_ROUND, 3f, new float[]
745 y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
746 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
747 g2.setStroke(new BasicStroke());
751 public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, float min, float max, int y)
753 if (sRes > aa.annotations.length)
757 Font ofont = g.getFont();
758 eRes = Math.min(eRes, aa.annotations.length);
760 int x = 0, y1 = y, y2 = y;
762 float range = max - min;
766 y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
769 g.setColor(Color.gray);
771 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
774 int aaMax = aa.annotations.length - 1;
775 boolean renderHistogram = true, renderProfile = true, normaliseProfile=false;
776 // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
778 // TODO: generalise this to have render styles for consensus/profile data
779 if (aa.groupRef != null)
781 renderHistogram = aa.groupRef.isShowConsensusHistogram();
782 renderProfile = aa.groupRef.isShowSequenceLogo();
783 normaliseProfile= aa.groupRef.isNormaliseSequenceLogo();
787 renderHistogram = av_renderHistogram;
788 renderProfile = av_renderProfile;
789 normaliseProfile= av_normaliseProfile;
792 while (x < eRes - sRes)
795 if (hasHiddenColumns)
797 column = columnSelection.adjustForHiddenColumns(column);
805 if (aa.annotations[column] == null)
810 if (aa.annotations[column].colour == null)
811 g.setColor(Color.black);
813 g.setColor(aa.annotations[column].colour);
816 - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
822 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
826 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
829 // draw profile if available
830 if (renderProfile && aa.annotations[column].value != 0)
833 int profl[] = getProfileFor(aa, column);
834 // just try to draw the logo if profl is not null
838 float ht = normaliseProfile ? y-aa.graphHeight : y1;
839 double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
845 * profl.length == 52 indicates that the profile of a secondary
846 * structure conservation row was accesed.
847 * Therefore dc gets length 2, to have space for a basepair instead of
848 * just a single nucleotide
850 if (profl.length == 52)
858 LineMetrics lm=g.getFontMetrics(ofont).getLineMetrics("Q", g);
859 double scale = 1f/(normaliseProfile ? profl[1] : 100f);
860 float ofontHeight = 1f/lm.getAscent();// magnify to fill box
862 for (int c = 2; profl != null && c < profl[0];)
864 dc[0] = (char) profl[c++];
866 if (aa.label.startsWith("StrucConsensus"))
868 dc[1] = (char) profl[c++];
872 wdth /= (float) fm.charsWidth(dc, 0, dc.length);
876 // if (aa.annotations[column].value==0) {
877 // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
878 // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
881 scl=((double)htn)*scale* ((double) profl[c++]);
882 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics().getFontRenderContext());
883 g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
884 wdth, scl/lm.getAscent())));
885 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
889 // ? );// try to get a
890 // colourscheme for the
891 // group(aa.groupRef.cs==null)
892 // ? av.textColour2 :
893 // cs.findColour(dc));
894 // System.out.println(dc[0]);
895 // Debug - render boxes around characters
896 // g.setColor(Color.red);
897 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth, (int)(scl));
898 // g.setColor(profcolour.findColour(dc[0]).darker());
899 g.setColor(profcolour.findColour(dc[0]));
900 // (av.globalColourScheme!=null)
901 g.drawChars(dc, 0, dc.length, x * charWidth,
902 (int) (ht + (scl-lm.getDescent()-lm.getBaselineOffsets()[lm.getBaselineIndex()])));
903 // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
911 if (aa.threshold != null)
913 g.setColor(aa.threshold.colour);
914 Graphics2D g2 = (Graphics2D) g;
915 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
916 BasicStroke.JOIN_ROUND, 3f, new float[]
919 y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
920 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
921 g2.setStroke(new BasicStroke());
924 // used by overview window
925 public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
926 int y, int sRes, int eRes)
928 eRes = Math.min(eRes, aa.annotations.length);
929 g.setColor(Color.white);
930 g.fillRect(0, 0, width, y);
931 g.setColor(new Color(0, 0, 180));
935 for (int j = sRes; j < eRes; j++)
937 if (aa.annotations[j] != null)
939 if (aa.annotations[j].colour == null)
940 g.setColor(Color.black);
942 g.setColor(aa.annotations[j].colour);
944 height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
950 g.fillRect(x, y - height, charWidth, height);