2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.renderer;
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.CodingUtils;
25 import jalview.analysis.Rna;
26 import jalview.analysis.StructureFrequency;
27 import jalview.api.AlignViewportI;
28 import jalview.bin.Jalview;
29 import jalview.datamodel.AlignmentAnnotation;
30 import jalview.datamodel.Annotation;
31 import jalview.datamodel.ColumnSelection;
32 import jalview.datamodel.HiddenColumns;
33 import jalview.datamodel.ProfilesI;
34 import jalview.schemes.ColourSchemeI;
35 import jalview.schemes.NucleotideColourScheme;
36 import jalview.schemes.ResidueProperties;
37 import jalview.schemes.ZappoColourScheme;
38 import jalview.util.Platform;
40 import java.awt.BasicStroke;
41 import java.awt.Color;
43 import java.awt.FontMetrics;
44 import java.awt.Graphics;
45 import java.awt.Graphics2D;
46 import java.awt.Image;
47 import java.awt.geom.AffineTransform;
48 import java.awt.image.ImageObserver;
49 import java.util.BitSet;
50 import java.util.Hashtable;
52 public class AnnotationRenderer
54 private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
56 private static final int CHAR_A = 'A'; // 65
58 private static final int CHAR_Z = 'Z'; // 90
61 * flag indicating if timing and redraw parameter info should be output
63 private final boolean debugRedraw;
65 private int charWidth, endRes, charHeight;
67 private boolean validCharWidth, hasHiddenColumns;
69 private FontMetrics fm;
71 private final boolean MAC = Platform.isAMac();
73 boolean av_renderHistogram = true, av_renderProfile = true,
74 av_normaliseProfile = false;
76 ResidueShaderI profcolour = null;
78 private ColumnSelection columnSelection;
80 private HiddenColumns hiddenColumns;
82 private ProfilesI hconsensus;
84 private Hashtable[] complementConsensus;
86 private Hashtable[] hStrucConsensus;
88 private boolean av_ignoreGapsConsensus;
91 * attributes set from AwtRenderPanelI
94 * old image used when data is currently being calculated and cannot be
97 private Image fadedImage;
100 * panel being rendered into
102 private ImageObserver annotationPanel;
105 * width of image to render in panel
107 private int imgWidth;
110 * offset to beginning of visible area
115 * offset to end of visible area
117 private int visHeight;
120 * indicate if the renderer should only render the visible portion of the
121 * annotation given the current view settings
123 private boolean useClip = true;
126 * master flag indicating if renderer should ever try to clip. not enabled for
129 private boolean canClip = false;
131 public AnnotationRenderer()
137 * Create a new annotation Renderer
140 * flag indicating if timing and redraw parameter info should be
143 public AnnotationRenderer(boolean debugRedraw)
145 this.debugRedraw = debugRedraw;
149 * Remove any references and resources when this object is no longer required
151 public void dispose()
154 complementConsensus = null;
155 hStrucConsensus = null;
157 annotationPanel = null;
160 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
161 int x, int y, int iconOffset, int startRes, int column,
162 boolean validRes, boolean validEnd)
164 g.setColor(STEM_COLOUR);
165 int sCol = (lastSSX / charWidth)
166 + hiddenColumns.visibleToAbsoluteColumn(startRes);
168 int x2 = (x * charWidth);
170 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
171 : row_annotations[column - 1].secondaryStructure;
173 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
174 || dc != row_annotations[sCol - 1].secondaryStructure;
175 boolean diffdownstream = !validRes || !validEnd
176 || row_annotations[column] == null
177 || dc != row_annotations[column].secondaryStructure;
179 if (column > 0 && Rna.isClosingParenthesis(dc))
182 // if (validRes && column>1 && row_annotations[column-2]!=null &&
183 // dc.equals(row_annotations[column-2].displayCharacter))
186 * if new annotation with a closing base pair half of the stem,
187 * display a backward arrow
189 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
191 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
202 // display a forward arrow
206 * if annotation ending with an opeing base pair half of the stem,
207 * display a forward arrow
209 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
211 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
221 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
224 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
225 Annotation[] row_annotations, int lastSSX, int x, int y,
226 int iconOffset, int startRes, int column, boolean validRes,
229 // System.out.println(nonCanColor);
231 g.setColor(nonCanColor);
232 int sCol = (lastSSX / charWidth)
233 + hiddenColumns.visibleToAbsoluteColumn(startRes);
235 int x2 = (x * charWidth);
237 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
238 : row_annotations[column - 1].displayCharacter;
240 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
241 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
242 boolean diffdownstream = !validRes || !validEnd
243 || row_annotations[column] == null
244 || !dc.equals(row_annotations[column].displayCharacter);
245 // System.out.println("Column "+column+" diff up: "+diffupstream+"
246 // down:"+diffdownstream);
247 // If a closing base pair half of the stem, display a backward arrow
248 if (column > 0 && Rna.isClosingParenthesis(dc))
252 // if (validRes && column>1 && row_annotations[column-2]!=null &&
253 // dc.equals(row_annotations[column-2].displayCharacter))
255 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
257 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
269 // display a forward arrow
272 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
274 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
284 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
287 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
289 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
292 fm = annotPanel.getFontMetrics();
293 annotationPanel = annotPanel;
294 fadedImage = annotPanel.getFadedImage();
295 imgWidth = annotPanel.getFadedImageWidth();
296 // visible area for rendering
297 int[] bounds = annotPanel.getVisibleVRange();
301 visHeight = bounds[1];
316 updateFromAlignViewport(av);
319 public void updateFromAlignViewport(AlignViewportI av)
321 charWidth = av.getCharWidth();
322 endRes = av.getRanges().getEndRes();
323 charHeight = av.getCharHeight();
324 hasHiddenColumns = av.hasHiddenColumns();
325 validCharWidth = av.isValidCharWidth();
326 av_renderHistogram = av.isShowConsensusHistogram();
327 av_renderProfile = av.isShowSequenceLogo();
328 av_normaliseProfile = av.isNormaliseSequenceLogo();
329 profcolour = av.getResidueShading();
330 if (profcolour == null || profcolour.getColourScheme() == null)
333 * Use default colour for sequence logo if
334 * the alignment has no colourscheme set
335 * (would like to use user preference but n/a for applet)
337 ColourSchemeI col = av.getAlignment().isNucleotide()
338 ? new NucleotideColourScheme()
339 : new ZappoColourScheme();
340 profcolour = new ResidueShader(col);
342 columnSelection = av.getColumnSelection();
343 hiddenColumns = av.getAlignment().getHiddenColumns();
344 hconsensus = av.getSequenceConsensusHash();
345 complementConsensus = av.getComplementConsensusHash();
346 hStrucConsensus = av.getRnaStructureConsensusHash();
347 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
351 * Returns profile data; the first element is the profile type, the second is
352 * the number of distinct values, the third the total count, and the remainder
353 * depend on the profile type.
359 int[] getProfileFor(AlignmentAnnotation aa, int column)
361 // TODO : consider refactoring the global alignment calculation
362 // properties/rendering attributes as a global 'alignment group' which holds
363 // all vis settings for the alignment as a whole rather than a subset
365 if (aa.autoCalculated && (aa.label.startsWith("Consensus")
366 || aa.label.startsWith("cDNA Consensus")))
368 boolean forComplement = aa.label.startsWith("cDNA Consensus");
369 if (aa.groupRef != null && aa.groupRef.consensusData != null
370 && aa.groupRef.isShowSequenceLogo())
372 // TODO? group consensus for cDNA complement
373 return AAFrequency.extractProfile(
374 aa.groupRef.consensusData.get(column),
375 aa.groupRef.getIgnoreGapsConsensus());
377 // TODO extend annotation row to enable dynamic and static profile data to
379 if (aa.groupRef == null && aa.sequenceRef == null)
383 return AAFrequency.extractCdnaProfile(complementConsensus[column],
384 av_ignoreGapsConsensus);
388 return AAFrequency.extractProfile(hconsensus.get(column),
389 av_ignoreGapsConsensus);
395 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
397 // TODO implement group structure consensus
399 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
400 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
401 * group selections return StructureFrequency.extractProfile(
402 * aa.groupRef.consensusData[column], aa.groupRef
403 * .getIgnoreGapsConsensus()); }
405 // TODO extend annotation row to enable dynamic and static profile data
408 if (aa.groupRef == null && aa.sequenceRef == null
409 && hStrucConsensus != null
410 && hStrucConsensus.length > column)
412 return StructureFrequency.extractProfile(hStrucConsensus[column],
413 av_ignoreGapsConsensus);
423 * Render the annotation rows associated with an alignment.
428 * data and view settings to render
430 * destination for graphics
432 * row where a mouse event occured (or -1)
434 * first column that will be drawn
436 * last column that will be drawn
437 * @return true if the fadedImage was used for any alignment annotation rows
438 * currently being calculated
440 public boolean drawComponent(AwtRenderPanelI annotPanel,
441 AlignViewportI av, Graphics g, int activeRow, int startRes,
444 long stime = System.currentTimeMillis();
445 boolean usedFaded = false;
447 // AnnotationPanel needs to implement: ImageObserver, access to
449 updateFromAwtRenderPanel(annotPanel, av);
450 fm = g.getFontMetrics();
451 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
462 boolean validRes = false;
463 boolean validEnd = false;
464 boolean labelAllCols = false;
465 boolean centreColLabels;
466 boolean centreColLabelsDef = av.isCentreColumnLabels();
467 boolean scaleColLabel = false;
468 final AlignmentAnnotation consensusAnnot = av
469 .getAlignmentConsensusAnnotation();
470 final AlignmentAnnotation structConsensusAnnot = av
471 .getAlignmentStrucConsensusAnnotation();
472 final AlignmentAnnotation complementConsensusAnnot = av
473 .getComplementConsensusAnnotation();
474 boolean renderHistogram = true, renderProfile = true,
475 normaliseProfile = false, isRNA = rna;
477 BitSet graphGroupDrawn = new BitSet();
478 int charOffset = 0; // offset for a label
481 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
482 boolean clipst = false, clipend = false;
483 for (int i = 0; i < aa.length; i++)
485 AlignmentAnnotation row = aa[i];
488 // check if this is a consensus annotation row and set the display
489 // settings appropriately
490 // TODO: generalise this to have render styles for consensus/profile
492 if (row.groupRef != null && row == row.groupRef.getConsensus())
494 renderHistogram = row.groupRef.isShowConsensusHistogram();
495 renderProfile = row.groupRef.isShowSequenceLogo();
496 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
498 else if (row == consensusAnnot || row == structConsensusAnnot
499 || row == complementConsensusAnnot)
501 renderHistogram = av_renderHistogram;
502 renderProfile = av_renderProfile;
503 normaliseProfile = av_normaliseProfile;
507 renderHistogram = true;
508 // don't need to set render/normaliseProfile since they are not
509 // currently used in any other annotation track renderer
512 Annotation[] row_annotations = row.annotations;
517 centreColLabels = row.centreColLabels || centreColLabelsDef;
518 labelAllCols = row.showAllColLabels;
519 scaleColLabel = row.scaleColLabel;
523 if (!useClip || ((y - charHeight) < visHeight
524 && (y + row.height + charHeight * 2) >= sOffset))
525 {// if_in_visible_region
536 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
541 // this is so that we draw the characters below the graph
546 iconOffset = charHeight - fm.getDescent();
550 else if (row.hasText)
552 iconOffset = charHeight - fm.getDescent();
560 if (row.autoCalculated && av.isCalculationInProgress(row))
564 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0,
565 y - row.height, imgWidth, y, annotationPanel);
566 g.setColor(Color.black);
567 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
573 * else if (annotationPanel.av.updatingConservation &&
574 * aa[i].label.equals("Conservation")) {
576 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
577 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
578 * annotationPanel.imgWidth, y, annotationPanel);
580 * g.setColor(Color.black); //
581 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
583 * continue; } else if (annotationPanel.av.updatingConservation &&
584 * aa[i].label.equals("Quality")) {
586 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
587 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
588 * annotationPanel.imgWidth, y, annotationPanel);
589 * g.setColor(Color.black); // /
590 * g.drawString("Calculating Quality....",20, y-row.height/2);
594 // first pass sets up state for drawing continuation from left-hand
597 x = (startRes == 0) ? 0 : -1;
598 while (x < endRes - startRes)
600 if (hasHiddenColumns)
602 column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
603 if (column > row_annotations.length - 1)
610 column = startRes + x;
613 if ((row_annotations == null)
614 || (row_annotations.length <= column)
615 || (row_annotations[column] == null))
623 final String displayChar = validRes
624 ? row_annotations[column].displayCharacter
630 g.setColor(Color.red);
632 if (columnSelection != null)
634 if (columnSelection.contains(column))
636 g.fillRect(x * charWidth, y, charWidth, charHeight);
640 if (row.getInvalidStrucPos() > x)
642 g.setColor(Color.orange);
643 g.fillRect(x * charWidth, y, charWidth, charHeight);
645 else if (row.getInvalidStrucPos() == x)
647 g.setColor(Color.orange.darker());
648 g.fillRect(x * charWidth, y, charWidth, charHeight);
650 if (validCharWidth && validRes && displayChar != null
651 && (displayChar.length() > 0))
653 Graphics2D gg = ((Graphics2D) g);
654 float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
655 displayChar.length());
658 * shrink label width to fit in column, if that is
659 * both configured and necessary
661 boolean scaledToFit = false;
662 float fmScaling = 1f;
663 if (scaleColLabel && fmWidth > charWidth)
666 fmScaling = charWidth;
667 fmScaling /= fmWidth;
668 // and update the label's width to reflect the scaling.
672 charOffset = (int) ((charWidth - fmWidth) / 2f);
674 if (row_annotations[column].colour == null)
676 gg.setColor(Color.black);
680 gg.setColor(row_annotations[column].colour);
684 * draw the label, unless it is the same secondary structure
685 * symbol (excluding RNA Helix) as the previous column
687 final int xPos = (x * charWidth) + charOffset;
688 final int yPos = y + iconOffset;
691 * translate to drawing position _before_ applying any scaling
693 gg.translate(xPos, yPos);
697 * use a scaling transform to make the label narrower
698 * (JalviewJS doesn't have Font.deriveFont(AffineTransform))
701 AffineTransform.getScaleInstance(fmScaling, 1.0));
703 if (column == 0 || row.graph > 0)
705 gg.drawString(displayChar, 0, 0);
707 else if (row_annotations[column - 1] == null || (labelAllCols
708 || !displayChar.equals(
709 row_annotations[column - 1].displayCharacter)
710 || (displayChar.length() < 2
711 && row_annotations[column].secondaryStructure == ' ')))
713 gg.drawString(displayChar, 0, 0);
718 * undo scaling before translating back
719 * (restoring saved transform does NOT work in JS PDFGraphics!)
721 gg.transform(AffineTransform
722 .getScaleInstance(1D / fmScaling, 1.0));
724 gg.translate(-xPos, -yPos);
729 char ss = validRes ? row_annotations[column].secondaryStructure
734 // distinguish between forward/backward base-pairing
735 if (displayChar.indexOf(')') > -1)
744 if ((displayChar.indexOf(']') > -1))
752 // distinguish between forward/backward base-pairing
753 if (displayChar.indexOf('}') > -1)
761 // distinguish between forward/backward base-pairing
762 if (displayChar.indexOf('<') > -1)
768 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
770 // distinguish between forward/backward base-pairing
771 int ssLowerCase = ss + UPPER_TO_LOWER;
772 // TODO would .equals() be safer here? or charAt(0)?
773 if (displayChar.indexOf(ssLowerCase) > -1)
775 ss = (char) ssLowerCase;
779 if (!validRes || (ss != lastSS))
785 int nb_annot = x - temp;
786 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
787 // annot :"+nb_annot);
790 case '(': // Stem case for RNA secondary structure
791 case ')': // and opposite direction
792 drawStemAnnot(g, row_annotations, lastSSX, x, y,
793 iconOffset, startRes, column, validRes, validEnd);
800 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
801 iconOffset, startRes, column, validRes,
805 // no break if isRNA - falls through to drawNotCanonicalAnnot!
809 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
810 iconOffset, startRes, column, validRes,
814 // no break if isRNA - fall through to drawNotCanonicalAnnot!
873 Color nonCanColor = getNotCanonicalColor(lastSS);
874 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
875 lastSSX, x, y, iconOffset, startRes, column,
880 g.setColor(Color.gray);
881 g.fillRect(lastSSX, y + 6 + iconOffset,
882 (x * charWidth) - lastSSX, 2);
897 lastSSX = (x * charWidth);
904 if (column >= row_annotations.length)
906 column = row_annotations.length - 1;
913 if ((row_annotations == null) || (row_annotations.length <= column)
914 || (row_annotations[column] == null))
932 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
933 startRes, column, validRes, validEnd);
936 // no break if isRNA - fall through to drawNotCanonicalAnnot!
941 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
942 startRes, column, validRes, validEnd);
945 // no break if isRNA - fall through to drawNotCanonicalAnnot!
948 case ')': // Stem case for RNA secondary structure
950 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
951 startRes, column, validRes, validEnd);
1008 // System.out.println(lastSS);
1009 Color nonCanColor = getNotCanonicalColor(lastSS);
1010 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
1011 x, y, iconOffset, startRes, column, validRes, validEnd);
1014 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
1015 startRes, column, validRes, validEnd);
1020 if (row.graph > 0 && row.graphHeight > 0)
1022 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
1024 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
1026 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1027 // computed efficiently for all visible labels
1028 float groupmax = -999999, groupmin = 9999999;
1029 for (int gg = 0; gg < aa.length; gg++)
1031 if (aa[gg].graphGroup != row.graphGroup)
1038 aa[gg].visible = false;
1040 if (aa[gg].graphMax > groupmax)
1042 groupmax = aa[gg].graphMax;
1044 if (aa[gg].graphMin < groupmin)
1046 groupmin = aa[gg].graphMin;
1050 for (int gg = 0; gg < aa.length; gg++)
1052 if (aa[gg].graphGroup == row.graphGroup)
1054 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1055 endRes, y, groupmin, groupmax, row.graphHeight);
1059 graphGroupDrawn.set(row.graphGroup);
1063 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1064 row.graphMin, row.graphMax, row.graphHeight);
1067 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1069 drawBarGraph(g, row, row_annotations, startRes, endRes,
1070 row.graphMin, row.graphMax, y, renderHistogram,
1071 renderProfile, normaliseProfile);
1077 if (clipst && !clipend)
1081 } // end if_in_visible_region
1082 if (row.graph > 0 && row.hasText)
1099 "Start clip at : " + yfrom + " (index " + f_i + ")");
1104 "End clip at : " + yto + " (index " + f_to + ")");
1108 System.err.println("Annotation Rendering time:"
1109 + (System.currentTimeMillis() - stime));
1116 public static final Color GLYPHLINE_COLOR = Color.gray;
1118 public static final Color SHEET_COLOUR = Color.green;
1120 public static final Color HELIX_COLOUR = Color.red;
1122 public static final Color STEM_COLOUR = Color.blue;
1124 private Color sdNOTCANONICAL_COLOUR;
1126 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1127 int y, int iconOffset, int startRes, int column, boolean validRes,
1130 g.setColor(GLYPHLINE_COLOR);
1131 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1134 void drawSheetAnnot(Graphics g, Annotation[] row,
1136 int lastSSX, int x, int y, int iconOffset, int startRes,
1137 int column, boolean validRes, boolean validEnd)
1139 g.setColor(SHEET_COLOUR);
1141 if (!validEnd || !validRes || row == null || row[column] == null
1142 || row[column].secondaryStructure != 'E')
1144 g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
1148 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
1150 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
1155 g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
1161 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1162 int y, int iconOffset, int startRes, int column, boolean validRes,
1165 g.setColor(HELIX_COLOUR);
1167 int sCol = (lastSSX / charWidth)
1168 + hiddenColumns.visibleToAbsoluteColumn(startRes);
1170 int x2 = (x * charWidth);
1174 int ofs = charWidth / 2;
1175 // Off by 1 offset when drawing rects and ovals
1176 // to offscreen image on the MAC
1177 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1178 if (sCol == 0 || row[sCol - 1] == null
1179 || row[sCol - 1].secondaryStructure != 'H')
1184 // g.setColor(Color.orange);
1185 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1188 if (!validRes || row[column] == null
1189 || row[column].secondaryStructure != 'H')
1195 // g.setColor(Color.magenta);
1196 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
1197 x2 - x1 - ofs + 1, 8, 0, 0);
1204 if (sCol == 0 || row[sCol - 1] == null
1205 || row[sCol - 1].secondaryStructure != 'H')
1207 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1208 x1 += charWidth / 2;
1211 if (!validRes || row[column] == null
1212 || row[column].secondaryStructure != 'H')
1214 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1216 x2 -= charWidth / 2;
1219 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1222 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1223 Annotation[] aa_annotations, int sRes, int eRes, int y, float min,
1224 float max, int graphHeight)
1226 if (sRes > aa_annotations.length)
1233 // Adjustment for fastpaint to left
1239 eRes = Math.min(eRes, aa_annotations.length);
1247 float range = max - min;
1252 y2 = y - (int) ((0 - min / range) * graphHeight);
1255 g.setColor(Color.gray);
1256 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1258 eRes = Math.min(eRes, aa_annotations.length);
1261 int aaMax = aa_annotations.length - 1;
1263 while (x < eRes - sRes)
1266 if (hasHiddenColumns)
1268 column = hiddenColumns.visibleToAbsoluteColumn(column);
1276 if (aa_annotations[column] == null
1277 || aa_annotations[column - 1] == null)
1283 if (aa_annotations[column].colour == null)
1285 g.setColor(Color.black);
1289 g.setColor(aa_annotations[column].colour);
1292 y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
1294 y2 = y - (int) (((aa_annotations[column].value - min) / range)
1297 g.drawLine(x * charWidth - charWidth / 2, y1,
1298 x * charWidth + charWidth / 2, y2);
1302 if (_aa.threshold != null)
1304 g.setColor(_aa.threshold.colour);
1305 Graphics2D g2 = (Graphics2D) g;
1306 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1307 BasicStroke.JOIN_ROUND, 3f, new float[]
1310 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1311 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1312 g2.setStroke(new BasicStroke());
1316 @SuppressWarnings("unused")
1317 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1318 Annotation[] aa_annotations, int sRes, int eRes, float min,
1319 float max, int y, boolean renderHistogram, boolean renderProfile,
1320 boolean normaliseProfile)
1322 if (sRes > aa_annotations.length)
1326 Font ofont = g.getFont();
1327 eRes = Math.min(eRes, aa_annotations.length);
1329 int x = 0, y1 = y, y2 = y;
1331 float range = max - min;
1335 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1338 g.setColor(Color.gray);
1340 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1343 int aaMax = aa_annotations.length - 1;
1344 while (x < eRes - sRes)
1347 if (hasHiddenColumns)
1349 column = hiddenColumns.visibleToAbsoluteColumn(column);
1357 if (aa_annotations[column] == null)
1362 if (aa_annotations[column].colour == null)
1364 g.setColor(Color.black);
1368 g.setColor(aa_annotations[column].colour);
1371 y1 = y - (int) (((aa_annotations[column].value - min) / (range))
1374 if (renderHistogram)
1378 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1382 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1385 // draw profile if available
1390 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1392 int profl[] = getProfileFor(_aa, column);
1394 // just try to draw the logo if profl is not null
1395 if (profl != null && profl[2] != 0)
1397 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1398 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1399 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1400 final double normaliseFactor = normaliseProfile ? _aa.graphHeight : (y2 - y1);
1403 * Render a single base for a sequence profile, a base pair for
1404 * structure profile, and a triplet for a cdna profile
1406 char[] dc = new char[isStructureProfile ? 2
1407 : (isCdnaProfile ? 3 : 1)];
1409 // lm is not necessary - we can just use fm - could be off by no more
1411 // LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1412 // System.out.println(asc + " " + dec + " " + (asc - lm.getAscent())
1413 // + " " + (dec - lm.getDescent()));
1415 double asc = fm.getAscent();
1416 double dec = fm.getDescent();
1417 double fht = fm.getHeight();
1419 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1420 // float ofontHeight = 1f / fm.getAscent();// magnify to fill box
1423 * Traverse the character(s)/percentage data in the array
1428 // profl[1] is the number of values in the profile
1429 for (int i = 0, c = 3, last = profl[1]; i < last; i++)
1433 if (isStructureProfile)
1435 // todo can we encode a structure pair as an int, like codons?
1436 dc[0] = (char) profl[c++];
1437 dc[1] = (char) profl[c++];
1440 else if (isCdnaProfile)
1442 CodingUtils.decodeCodon2(profl[c++], dc);
1447 dc[0] = (char) profl[c++];
1450 // next profl[] position is profile % for the character(s)
1452 double newHeight = normaliseFactor * scale * profl[c++];
1455 * Set character colour as per alignment colour scheme; use the
1456 * codon translation if a cDNA profile
1458 Color colour = null;
1461 final String codonTranslation = ResidueProperties
1463 colour = profcolour.findColour(codonTranslation.charAt(0),
1468 colour = profcolour.findColour(dc[0], column, null);
1470 g.setColor(colour == Color.white ? Color.lightGray : colour);
1472 // Debug - render boxes around characters
1473 // g.setColor(Color.red);
1474 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1476 // g.setColor(profcolour.findColour(dc[0]).darker());
1478 double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
1479 double sy = newHeight / asc;
1480 double newAsc = asc * sy;
1481 double newDec = dec * sy;
1482 // it is not necessary to recalculate lm for the new font.
1483 // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0
1484 // by definition. Was:
1485 // int hght = (int) (ht + (newAsc - newDec);
1486 // - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
1491 * SwingJS does not implement font.deriveFont()
1492 * so use a scaling transform to draw instead,
1493 * this is off by a very small amount
1495 final int hght = (int) (ht2 + (newAsc - newDec));
1496 Graphics2D gg = (Graphics2D) g;
1497 int xShift = (int) Math.round(x * charWidth / sx);
1498 int yShift = (int) Math.round(hght / sy);
1499 gg.transform(AffineTransform.getScaleInstance(sx, sy));
1500 gg.drawString(s, xShift, yShift);
1502 AffineTransform.getScaleInstance(1D / sx, 1D / sy));
1508 * Java ('normal') method is to scale the font to fit
1510 final int hght = (int) (ht + (newAsc - newDec));
1512 .deriveFont(AffineTransform.getScaleInstance(sx, sy));
1514 g.drawChars(dc, 0, dc.length, x * charWidth, hght);
1522 if (_aa.threshold != null)
1524 g.setColor(_aa.threshold.colour);
1525 Graphics2D g2 = (Graphics2D) g;
1526 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1527 BasicStroke.JOIN_ROUND, 3f, new float[]
1531 - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
1532 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1533 g2.setStroke(new BasicStroke());
1537 // used by overview window
1538 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1539 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1541 eRes = Math.min(eRes, aa_annotations.length);
1542 g.setColor(Color.white);
1543 g.fillRect(0, 0, width, y);
1544 g.setColor(new Color(0, 0, 180));
1548 for (int j = sRes; j < eRes; j++)
1550 if (aa_annotations[j] != null)
1552 if (aa_annotations[j].colour == null)
1554 g.setColor(Color.black);
1558 g.setColor(aa_annotations[j].colour);
1561 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1567 g.fillRect(x, y - height, charWidth, height);
1573 Color getNotCanonicalColor(char lastss)
1579 return new Color(255, 125, 5);
1583 return new Color(245, 115, 10);
1587 return new Color(235, 135, 15);
1591 return new Color(225, 105, 20);
1595 return new Color(215, 145, 30);
1599 return new Color(205, 95, 35);
1603 return new Color(195, 155, 45);
1607 return new Color(185, 85, 55);
1611 return new Color(175, 165, 65);
1615 return new Color(170, 75, 75);
1619 return new Color(160, 175, 85);
1623 return new Color(150, 65, 95);
1627 return new Color(140, 185, 105);
1631 return new Color(130, 55, 110);
1635 return new Color(120, 195, 120);
1639 return new Color(110, 45, 130);
1643 return new Color(100, 205, 140);
1647 return new Color(90, 35, 150);
1651 return new Color(85, 215, 160);
1655 return new Color(75, 25, 170);
1659 return new Color(65, 225, 180);
1663 return new Color(55, 15, 185);
1667 return new Color(45, 235, 195);
1671 return new Color(35, 5, 205);
1675 return new Color(25, 245, 215);
1679 return new Color(15, 0, 225);
1683 return new Color(10, 255, 235);
1687 return new Color(5, 150, 245);
1691 return new Color(0, 80, 255);
1694 System.out.println("This is not a interaction : " + lastss);