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.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.Annotation;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.ProfilesI;
33 import jalview.schemes.ColourSchemeI;
34 import jalview.schemes.NucleotideColourScheme;
35 import jalview.schemes.ResidueProperties;
36 import jalview.schemes.ZappoColourScheme;
37 import jalview.util.Platform;
39 import java.awt.BasicStroke;
40 import java.awt.Color;
42 import java.awt.FontMetrics;
43 import java.awt.Graphics;
44 import java.awt.Graphics2D;
45 import java.awt.Image;
46 import java.awt.font.LineMetrics;
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);
422 private int lastDrawnHeight;
425 * Render the annotation rows associated with an alignment.
430 * data and view settings to render
432 * destination for graphics
434 * row where a mouse event occured (or -1)
436 * first column that will be drawn
438 * last column that will be drawn
439 * @return true if the fadedImage was used for any alignment annotation rows
440 * currently being calculated
442 public boolean drawComponent(AwtRenderPanelI annotPanel,
443 AlignViewportI av, Graphics g, int activeRow, int startRes,
446 long stime = System.currentTimeMillis();
447 boolean usedFaded = false;
449 // AnnotationPanel needs to implement: ImageObserver, access to
451 updateFromAwtRenderPanel(annotPanel, av);
452 fm = g.getFontMetrics();
453 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
464 boolean validRes = false;
465 boolean validEnd = false;
466 boolean labelAllCols = false;
467 boolean centreColLabels;
468 boolean centreColLabelsDef = av.isCentreColumnLabels();
469 boolean scaleColLabel = false;
470 final AlignmentAnnotation consensusAnnot = av
471 .getAlignmentConsensusAnnotation();
472 final AlignmentAnnotation structConsensusAnnot = av
473 .getAlignmentStrucConsensusAnnotation();
474 final AlignmentAnnotation complementConsensusAnnot = av
475 .getComplementConsensusAnnotation();
476 boolean renderHistogram = true, renderProfile = true,
477 normaliseProfile = false, isRNA = rna;
479 BitSet graphGroupDrawn = new BitSet();
480 int charOffset = 0; // offset for a label
481 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
483 Font ofont = g.getFont();
486 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
487 boolean clipst = false, clipend = false;
488 for (int i = 0; i < aa.length; i++)
490 AlignmentAnnotation row = aa[i];
493 // check if this is a consensus annotation row and set the display
494 // settings appropriately
495 // TODO: generalise this to have render styles for consensus/profile
497 if (row.groupRef != null && row == row.groupRef.getConsensus())
499 renderHistogram = row.groupRef.isShowConsensusHistogram();
500 renderProfile = row.groupRef.isShowSequenceLogo();
501 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
503 else if (row == consensusAnnot || row == structConsensusAnnot
504 || row == complementConsensusAnnot)
506 renderHistogram = av_renderHistogram;
507 renderProfile = av_renderProfile;
508 normaliseProfile = av_normaliseProfile;
512 renderHistogram = true;
513 // don't need to set render/normaliseProfile since they are not
514 // currently used in any other annotation track renderer
517 Annotation[] row_annotations = row.annotations;
522 centreColLabels = row.centreColLabels || centreColLabelsDef;
523 labelAllCols = row.showAllColLabels;
524 scaleColLabel = row.scaleColLabel;
528 if (!useClip || ((y - charHeight) < visHeight
529 && (y + row.height + charHeight * 2) >= sOffset))
530 {// if_in_visible_region
541 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
546 // this is so that we draw the characters below the graph
551 iconOffset = charHeight - fm.getDescent();
555 else if (row.hasText)
557 iconOffset = charHeight - fm.getDescent();
565 if (row.autoCalculated && av.isCalculationInProgress(row))
569 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0,
570 y - row.height, imgWidth, y, annotationPanel);
571 g.setColor(Color.black);
572 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
578 * else if (annotationPanel.av.updatingConservation &&
579 * aa[i].label.equals("Conservation")) {
581 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
582 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
583 * annotationPanel.imgWidth, y, annotationPanel);
585 * g.setColor(Color.black); //
586 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
588 * continue; } else if (annotationPanel.av.updatingConservation &&
589 * aa[i].label.equals("Quality")) {
591 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
592 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
593 * annotationPanel.imgWidth, y, annotationPanel);
594 * g.setColor(Color.black); // /
595 * g.drawString("Calculating Quality....",20, y-row.height/2);
599 // first pass sets up state for drawing continuation from left-hand
602 x = (startRes == 0) ? 0 : -1;
603 while (x < endRes - startRes)
605 if (hasHiddenColumns)
607 column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
608 if (column > row_annotations.length - 1)
615 column = startRes + x;
618 if ((row_annotations == null)
619 || (row_annotations.length <= column)
620 || (row_annotations[column] == null))
628 final String displayChar = validRes
629 ? row_annotations[column].displayCharacter
635 g.setColor(Color.red);
637 if (columnSelection != null)
639 if (columnSelection.contains(column))
641 g.fillRect(x * charWidth, y, charWidth, charHeight);
645 if (row.getInvalidStrucPos() > x)
647 g.setColor(Color.orange);
648 g.fillRect(x * charWidth, y, charWidth, charHeight);
650 else if (row.getInvalidStrucPos() == x)
652 g.setColor(Color.orange.darker());
653 g.fillRect(x * charWidth, y, charWidth, charHeight);
655 if (validCharWidth && validRes && displayChar != null
656 && (displayChar.length() > 0))
659 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
660 displayChar.length());
661 if (/* centreColLabels || */scaleColLabel)
663 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
664 // displayChar.length());
666 // if (scaleColLabel)
668 // justify the label and scale to fit in column
669 if (fmWidth > charWidth)
671 // scale only if the current font isn't already small enough
672 fmScaling = charWidth;
673 fmScaling /= fmWidth;
674 g.setFont(ofont.deriveFont(AffineTransform
675 .getScaleInstance(fmScaling, 1.0)));
676 // and update the label's width to reflect the scaling.
681 // TODO is it ok to use width of / show all characters here?
684 // fmWidth = fm.charWidth(displayChar.charAt(0));
686 charOffset = (int) ((charWidth - fmWidth) / 2f);
688 if (row_annotations[column].colour == null)
690 g.setColor(Color.black);
694 g.setColor(row_annotations[column].colour);
697 if (column == 0 || row.graph > 0)
699 g.drawString(displayChar, (x * charWidth) + charOffset,
702 else if (row_annotations[column - 1] == null || (labelAllCols
703 || !displayChar.equals(
704 row_annotations[column - 1].displayCharacter)
705 || (displayChar.length() < 2
706 && row_annotations[column].secondaryStructure == ' ')))
708 g.drawString(displayChar, x * charWidth + charOffset,
716 char ss = validRes ? row_annotations[column].secondaryStructure
721 // distinguish between forward/backward base-pairing
722 if (displayChar.indexOf(')') > -1)
731 if ((displayChar.indexOf(']') > -1))
739 // distinguish between forward/backward base-pairing
740 if (displayChar.indexOf('}') > -1)
748 // distinguish between forward/backward base-pairing
749 if (displayChar.indexOf('<') > -1)
755 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
757 // distinguish between forward/backward base-pairing
758 int ssLowerCase = ss + UPPER_TO_LOWER;
759 // TODO would .equals() be safer here? or charAt(0)?
760 if (displayChar.indexOf(ssLowerCase) > -1)
762 ss = (char) ssLowerCase;
766 if (!validRes || (ss != lastSS))
772 int nb_annot = x - temp;
773 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
774 // annot :"+nb_annot);
777 case '(': // Stem case for RNA secondary structure
778 case ')': // and opposite direction
779 drawStemAnnot(g, row_annotations, lastSSX, x, y,
780 iconOffset, startRes, column, validRes, validEnd);
787 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
788 iconOffset, startRes, column, validRes,
792 // no break if isRNA - falls through to drawNotCanonicalAnnot!
796 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
797 iconOffset, startRes, column, validRes,
801 // no break if isRNA - fall through to drawNotCanonicalAnnot!
860 Color nonCanColor = getNotCanonicalColor(lastSS);
861 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
862 lastSSX, x, y, iconOffset, startRes, column,
867 g.setColor(Color.gray);
868 g.fillRect(lastSSX, y + 6 + iconOffset,
869 (x * charWidth) - lastSSX, 2);
884 lastSSX = (x * charWidth);
891 if (column >= row_annotations.length)
893 column = row_annotations.length - 1;
900 if ((row_annotations == null) || (row_annotations.length <= column)
901 || (row_annotations[column] == null))
919 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
920 startRes, column, validRes, validEnd);
923 // no break if isRNA - fall through to drawNotCanonicalAnnot!
928 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
929 startRes, column, validRes, validEnd);
932 // no break if isRNA - fall through to drawNotCanonicalAnnot!
935 case ')': // Stem case for RNA secondary structure
937 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
938 startRes, column, validRes, validEnd);
995 // System.out.println(lastSS);
996 Color nonCanColor = getNotCanonicalColor(lastSS);
997 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
998 x, y, iconOffset, startRes, column, validRes, validEnd);
1001 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
1002 startRes, column, validRes, validEnd);
1007 if (row.graph > 0 && row.graphHeight > 0)
1009 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
1011 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
1013 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1014 // computed efficiently for all visible labels
1015 float groupmax = -999999, groupmin = 9999999;
1016 for (int gg = 0; gg < aa.length; gg++)
1018 if (aa[gg].graphGroup != row.graphGroup)
1025 aa[gg].visible = false;
1027 if (aa[gg].graphMax > groupmax)
1029 groupmax = aa[gg].graphMax;
1031 if (aa[gg].graphMin < groupmin)
1033 groupmin = aa[gg].graphMin;
1037 for (int gg = 0; gg < aa.length; gg++)
1039 if (aa[gg].graphGroup == row.graphGroup)
1041 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1042 endRes, y, groupmin, groupmax, row.graphHeight);
1046 graphGroupDrawn.set(row.graphGroup);
1050 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1051 row.graphMin, row.graphMax, row.graphHeight);
1054 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1056 drawBarGraph(g, row, row_annotations, startRes, endRes,
1057 row.graphMin, row.graphMax, y, renderHistogram,
1058 renderProfile, normaliseProfile);
1064 if (clipst && !clipend)
1068 } // end if_in_visible_region
1069 if (row.graph > 0 && row.hasText)
1086 "Start clip at : " + yfrom + " (index " + f_i + ")");
1091 "End clip at : " + yto + " (index " + f_to + ")");
1095 System.err.println("Annotation Rendering time:"
1096 + (System.currentTimeMillis() - stime));
1098 lastDrawnHeight = y;
1104 * Answers the height in pixels of what was drawn on the graphics in the last
1105 * call to {@code drawComponent}
1109 public int getLastDrawnHeight()
1111 return lastDrawnHeight;
1114 public static final Color GLYPHLINE_COLOR = Color.gray;
1116 public static final Color SHEET_COLOUR = Color.green;
1118 public static final Color HELIX_COLOUR = Color.red;
1120 public static final Color STEM_COLOUR = Color.blue;
1122 private Color sdNOTCANONICAL_COLOUR;
1124 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1125 int y, int iconOffset, int startRes, int column, boolean validRes,
1128 g.setColor(GLYPHLINE_COLOR);
1129 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1132 void drawSheetAnnot(Graphics g, Annotation[] row,
1134 int lastSSX, int x, int y, int iconOffset, int startRes,
1135 int column, boolean validRes, boolean validEnd)
1137 g.setColor(SHEET_COLOUR);
1139 if (!validEnd || !validRes || row == null || row[column] == null
1140 || row[column].secondaryStructure != 'E')
1142 g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
1146 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
1148 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
1153 g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
1159 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1160 int y, int iconOffset, int startRes, int column, boolean validRes,
1163 g.setColor(HELIX_COLOUR);
1165 int sCol = (lastSSX / charWidth)
1166 + hiddenColumns.visibleToAbsoluteColumn(startRes);
1168 int x2 = (x * charWidth);
1172 int ofs = charWidth / 2;
1173 // Off by 1 offset when drawing rects and ovals
1174 // to offscreen image on the MAC
1175 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1176 if (sCol == 0 || row[sCol - 1] == null
1177 || row[sCol - 1].secondaryStructure != 'H')
1182 // g.setColor(Color.orange);
1183 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1186 if (!validRes || row[column] == null
1187 || row[column].secondaryStructure != 'H')
1193 // g.setColor(Color.magenta);
1194 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
1195 x2 - x1 - ofs + 1, 8, 0, 0);
1202 if (sCol == 0 || row[sCol - 1] == null
1203 || row[sCol - 1].secondaryStructure != 'H')
1205 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1206 x1 += charWidth / 2;
1209 if (!validRes || row[column] == null
1210 || row[column].secondaryStructure != 'H')
1212 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1214 x2 -= charWidth / 2;
1217 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1220 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1221 Annotation[] aa_annotations, int sRes, int eRes, int y, float min,
1222 float max, int graphHeight)
1224 if (sRes > aa_annotations.length)
1231 // Adjustment for fastpaint to left
1237 eRes = Math.min(eRes, aa_annotations.length);
1245 float range = max - min;
1250 y2 = y - (int) ((0 - min / range) * graphHeight);
1253 g.setColor(Color.gray);
1254 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1256 eRes = Math.min(eRes, aa_annotations.length);
1259 int aaMax = aa_annotations.length - 1;
1261 while (x < eRes - sRes)
1264 if (hasHiddenColumns)
1266 column = hiddenColumns.visibleToAbsoluteColumn(column);
1274 if (aa_annotations[column] == null
1275 || aa_annotations[column - 1] == null)
1281 if (aa_annotations[column].colour == null)
1283 g.setColor(Color.black);
1287 g.setColor(aa_annotations[column].colour);
1290 y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
1292 y2 = y - (int) (((aa_annotations[column].value - min) / range)
1295 g.drawLine(x * charWidth - charWidth / 2, y1,
1296 x * charWidth + charWidth / 2, y2);
1300 if (_aa.threshold != null)
1302 g.setColor(_aa.threshold.colour);
1303 Graphics2D g2 = (Graphics2D) g;
1304 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1305 BasicStroke.JOIN_ROUND, 3f, new float[]
1308 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1309 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1310 g2.setStroke(new BasicStroke());
1314 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1315 Annotation[] aa_annotations, int sRes, int eRes, float min,
1316 float max, int y, boolean renderHistogram, boolean renderProfile,
1317 boolean normaliseProfile)
1319 if (sRes > aa_annotations.length)
1323 Font ofont = g.getFont();
1324 eRes = Math.min(eRes, aa_annotations.length);
1326 int x = 0, y1 = y, y2 = y;
1328 float range = max - min;
1332 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1335 g.setColor(Color.gray);
1337 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1340 int aaMax = aa_annotations.length - 1;
1341 while (x < eRes - sRes)
1344 if (hasHiddenColumns)
1346 column = hiddenColumns.visibleToAbsoluteColumn(column);
1354 if (aa_annotations[column] == null)
1359 if (aa_annotations[column].colour == null)
1361 g.setColor(Color.black);
1365 g.setColor(aa_annotations[column].colour);
1368 y1 = y - (int) (((aa_annotations[column].value - min) / (range))
1371 if (renderHistogram)
1375 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1379 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1382 // draw profile if available
1387 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1389 int profl[] = getProfileFor(_aa, column);
1391 // just try to draw the logo if profl is not null
1392 if (profl != null && profl[2] != 0)
1394 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1395 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1396 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1397 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1404 * Render a single base for a sequence profile, a base pair for
1405 * structure profile, and a triplet for a cdna profile
1407 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1409 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1410 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1411 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1415 * Traverse the character(s)/percentage data in the array
1418 int valuesProcessed = 0;
1419 // profl[1] is the number of values in the profile
1420 while (valuesProcessed < profl[1])
1422 if (isStructureProfile)
1424 // todo can we encode a structure pair as an int, like codons?
1425 dc[0] = (char) profl[c++];
1426 dc[1] = (char) profl[c++];
1428 else if (isCdnaProfile)
1430 dc = CodingUtils.decodeCodon(profl[c++]);
1434 dc[0] = (char) profl[c++];
1438 wdth /= fm.charsWidth(dc, 0, dc.length);
1441 // next profl[] position is profile % for the character(s)
1442 scl = htn * scale * profl[c++];
1443 lm = ofont.getLineMetrics(dc, 0, 1,
1444 g.getFontMetrics().getFontRenderContext());
1445 Font font = ofont.deriveFont(AffineTransform
1446 .getScaleInstance(wdth, scl / lm.getAscent()));
1448 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1450 // Debug - render boxes around characters
1451 // g.setColor(Color.red);
1452 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1454 // g.setColor(profcolour.findColour(dc[0]).darker());
1457 * Set character colour as per alignment colour scheme; use the
1458 * codon translation if a cDNA profile
1460 Color colour = null;
1463 final String codonTranslation = ResidueProperties
1464 .codonTranslate(new String(dc));
1465 colour = profcolour.findColour(codonTranslation.charAt(0),
1470 colour = profcolour.findColour(dc[0], column, null);
1472 g.setColor(colour == Color.white ? Color.lightGray : colour);
1474 hght = (ht + (scl - lm.getDescent()
1475 - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
1477 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1485 if (_aa.threshold != null)
1487 g.setColor(_aa.threshold.colour);
1488 Graphics2D g2 = (Graphics2D) g;
1489 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1490 BasicStroke.JOIN_ROUND, 3f, new float[]
1494 - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
1495 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1496 g2.setStroke(new BasicStroke());
1500 // used by overview window
1501 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1502 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1504 eRes = Math.min(eRes, aa_annotations.length);
1505 g.setColor(Color.white);
1506 g.fillRect(0, 0, width, y);
1507 g.setColor(new Color(0, 0, 180));
1511 for (int j = sRes; j < eRes; j++)
1513 if (aa_annotations[j] != null)
1515 if (aa_annotations[j].colour == null)
1517 g.setColor(Color.black);
1521 g.setColor(aa_annotations[j].colour);
1524 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1530 g.fillRect(x, y - height, charWidth, height);
1536 Color getNotCanonicalColor(char lastss)
1542 return new Color(255, 125, 5);
1546 return new Color(245, 115, 10);
1550 return new Color(235, 135, 15);
1554 return new Color(225, 105, 20);
1558 return new Color(215, 145, 30);
1562 return new Color(205, 95, 35);
1566 return new Color(195, 155, 45);
1570 return new Color(185, 85, 55);
1574 return new Color(175, 165, 65);
1578 return new Color(170, 75, 75);
1582 return new Color(160, 175, 85);
1586 return new Color(150, 65, 95);
1590 return new Color(140, 185, 105);
1594 return new Color(130, 55, 110);
1598 return new Color(120, 195, 120);
1602 return new Color(110, 45, 130);
1606 return new Color(100, 205, 140);
1610 return new Color(90, 35, 150);
1614 return new Color(85, 215, 160);
1618 return new Color(75, 25, 170);
1622 return new Color(65, 225, 180);
1626 return new Color(55, 15, 185);
1630 return new Color(45, 235, 195);
1634 return new Color(35, 5, 205);
1638 return new Color(25, 245, 215);
1642 return new Color(15, 0, 225);
1646 return new Color(10, 255, 235);
1650 return new Color(5, 150, 245);
1654 return new Color(0, 80, 255);
1657 System.out.println("This is not a interaction : " + lastss);