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.HiddenMarkovModel;
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.font.LineMetrics;
48 import java.awt.geom.AffineTransform;
49 import java.awt.image.ImageObserver;
50 import java.util.BitSet;
51 import java.util.Hashtable;
53 public class AnnotationRenderer
55 private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
57 private static final int CHAR_A = 'A'; // 65
59 private static final int CHAR_Z = 'Z'; // 90
62 * flag indicating if timing and redraw parameter info should be output
64 private final boolean debugRedraw;
66 private int charWidth, endRes, charHeight;
68 private boolean validCharWidth, hasHiddenColumns;
70 private FontMetrics fm;
72 private final boolean MAC = Platform.isAMac();
74 boolean av_renderHistogram = true, av_renderProfile = true,
75 av_normaliseProfile = false;
77 boolean av_renderInformationHistogram = true, av_renderHMMProfile = true,
78 av_normaliseHMMProfile = false, av_infoHeight = false;
80 ResidueShaderI profcolour = null;
82 private ColumnSelection columnSelection;
84 private HiddenColumns hiddenColumns;
86 private ProfilesI hconsensus;
88 private Hashtable[] complementConsensus;
90 private Hashtable[] hStrucConsensus;
92 private boolean av_ignoreGapsConsensus;
94 private boolean av_ignoreBelowBackground;
97 * attributes set from AwtRenderPanelI
100 * old image used when data is currently being calculated and cannot be
103 private Image fadedImage;
106 * panel being rendered into
108 private ImageObserver annotationPanel;
111 * width of image to render in panel
113 private int imgWidth;
116 * offset to beginning of visible area
121 * offset to end of visible area
123 private int visHeight;
126 * indicate if the renderer should only render the visible portion of the
127 * annotation given the current view settings
129 private boolean useClip = true;
132 * master flag indicating if renderer should ever try to clip. not enabled for
135 private boolean canClip = false;
137 public AnnotationRenderer()
143 * Create a new annotation Renderer
146 * flag indicating if timing and redraw parameter info should be
149 public AnnotationRenderer(boolean debugRedraw)
151 this.debugRedraw = debugRedraw;
155 * Remove any references and resources when this object is no longer required
157 public void dispose()
160 complementConsensus = null;
161 hStrucConsensus = null;
163 annotationPanel = null;
166 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
167 int x, int y, int iconOffset, int startRes, int column,
168 boolean validRes, boolean validEnd)
170 g.setColor(STEM_COLOUR);
171 int sCol = (lastSSX / charWidth)
172 + hiddenColumns.adjustForHiddenColumns(startRes);
174 int x2 = (x * charWidth);
176 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
177 : row_annotations[column - 1].secondaryStructure;
179 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
180 || dc != row_annotations[sCol - 1].secondaryStructure;
181 boolean diffdownstream = !validRes || !validEnd
182 || row_annotations[column] == null
183 || dc != row_annotations[column].secondaryStructure;
185 if (column > 0 && Rna.isClosingParenthesis(dc))
188 // if (validRes && column>1 && row_annotations[column-2]!=null &&
189 // dc.equals(row_annotations[column-2].displayCharacter))
192 * if new annotation with a closing base pair half of the stem,
193 * display a backward arrow
195 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
197 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
208 // display a forward arrow
212 * if annotation ending with an opeing base pair half of the stem,
213 * display a forward arrow
215 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
217 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
227 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
230 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
231 Annotation[] row_annotations, int lastSSX, int x, int y,
232 int iconOffset, int startRes, int column, boolean validRes,
235 // System.out.println(nonCanColor);
237 g.setColor(nonCanColor);
238 int sCol = (lastSSX / charWidth)
239 + hiddenColumns.adjustForHiddenColumns(startRes);
241 int x2 = (x * charWidth);
243 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
244 : row_annotations[column - 1].displayCharacter;
246 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
247 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
248 boolean diffdownstream = !validRes || !validEnd
249 || row_annotations[column] == null
250 || !dc.equals(row_annotations[column].displayCharacter);
251 // System.out.println("Column "+column+" diff up: "+diffupstream+"
252 // down:"+diffdownstream);
253 // If a closing base pair half of the stem, display a backward arrow
254 if (column > 0 && Rna.isClosingParenthesis(dc))
258 // if (validRes && column>1 && row_annotations[column-2]!=null &&
259 // dc.equals(row_annotations[column-2].displayCharacter))
261 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
263 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
275 // display a forward arrow
278 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
280 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
290 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
293 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
295 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
298 fm = annotPanel.getFontMetrics();
299 annotationPanel = annotPanel;
300 fadedImage = annotPanel.getFadedImage();
301 imgWidth = annotPanel.getFadedImageWidth();
302 // visible area for rendering
303 int[] bounds = annotPanel.getVisibleVRange();
307 visHeight = bounds[1];
322 updateFromAlignViewport(av);
325 public void updateFromAlignViewport(AlignViewportI av)
327 charWidth = av.getCharWidth();
328 endRes = av.getRanges().getEndRes();
329 charHeight = av.getCharHeight();
330 hasHiddenColumns = av.hasHiddenColumns();
331 validCharWidth = av.isValidCharWidth();
332 av_renderHistogram = av.isShowConsensusHistogram();
333 av_renderProfile = av.isShowSequenceLogo();
334 av_normaliseProfile = av.isNormaliseSequenceLogo();
335 av_renderInformationHistogram = av.isShowInformationHistogram();
336 av_renderHMMProfile = av.isShowHMMSequenceLogo();
337 av_normaliseHMMProfile = av.isNormaliseHMMSequenceLogo();
338 profcolour = av.getResidueShading();
339 if (profcolour == null || profcolour.getColourScheme() == null)
342 * Use default colour for sequence logo if
343 * the alignment has no colourscheme set
344 * (would like to use user preference but n/a for applet)
346 ColourSchemeI col = av.getAlignment().isNucleotide()
347 ? new NucleotideColourScheme()
348 : new ZappoColourScheme();
349 profcolour = new ResidueShader(col);
351 columnSelection = av.getColumnSelection();
352 hiddenColumns = av.getAlignment().getHiddenColumns();
353 hconsensus = av.getSequenceConsensusHash();
354 complementConsensus = av.getComplementConsensusHash();
355 hStrucConsensus = av.getRnaStructureConsensusHash();
356 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
357 av_ignoreBelowBackground = av.isIgnoreBelowBackground();
358 av_infoHeight = av.isInfoLetterHeight();
364 * Returns profile data; the first element is the profile type, the second is
365 * the number of distinct values, the third the total count, and the remainder
366 * depend on the profile type.
372 int[] getProfileFor(AlignmentAnnotation aa, int column)
374 // TODO : consider refactoring the global alignment calculation
375 // properties/rendering attributes as a global 'alignment group' which holds
376 // all vis settings for the alignment as a whole rather than a subset
378 if ("HMM".equals(aa.getCalcId()))
380 HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
381 return AAFrequency.extractHMMProfile(hmm, column,
382 av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard
385 if (aa.autoCalculated
386 && (aa.label.startsWith("Consensus") || aa.label
387 .startsWith("cDNA Consensus")))
389 boolean forComplement = aa.label.startsWith("cDNA Consensus");
390 if (aa.groupRef != null && aa.groupRef.consensusData != null
391 && aa.groupRef.isShowSequenceLogo())
393 // TODO? group consensus for cDNA complement
394 return AAFrequency.extractProfile(
395 aa.groupRef.consensusData.get(column),
396 aa.groupRef.getIgnoreGapsConsensus());
398 // TODO extend annotation row to enable dynamic and static profile data to
400 if (aa.groupRef == null && aa.sequenceRef == null)
404 return AAFrequency.extractCdnaProfile(complementConsensus[column],
405 av_ignoreGapsConsensus);
409 return AAFrequency.extractProfile(hconsensus.get(column),
410 av_ignoreGapsConsensus);
416 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
418 // TODO implement group structure consensus
420 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
421 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
422 * group selections return StructureFrequency.extractProfile(
423 * aa.groupRef.consensusData[column], aa.groupRef
424 * .getIgnoreGapsConsensus()); }
426 // TODO extend annotation row to enable dynamic and static profile data
429 if (aa.groupRef == null && aa.sequenceRef == null
430 && hStrucConsensus != null
431 && hStrucConsensus.length > column)
433 return StructureFrequency.extractProfile(hStrucConsensus[column],
434 av_ignoreGapsConsensus);
444 * Render the annotation rows associated with an alignment.
449 * data and view settings to render
451 * destination for graphics
453 * row where a mouse event occured (or -1)
455 * first column that will be drawn
457 * last column that will be drawn
458 * @return true if the fadedImage was used for any alignment annotation rows
459 * currently being calculated
461 public boolean drawComponent(AwtRenderPanelI annotPanel,
462 AlignViewportI av, Graphics g, int activeRow, int startRes,
465 long stime = System.currentTimeMillis();
466 boolean usedFaded = false;
468 // AnnotationPanel needs to implement: ImageObserver, access to
470 updateFromAwtRenderPanel(annotPanel, av);
471 fm = g.getFontMetrics();
472 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
483 boolean validRes = false;
484 boolean validEnd = false;
485 boolean labelAllCols = false;
486 boolean centreColLabels;
487 boolean centreColLabelsDef = av.isCentreColumnLabels();
488 boolean scaleColLabel = false;
489 final AlignmentAnnotation consensusAnnot = av
490 .getAlignmentConsensusAnnotation();
491 final AlignmentAnnotation structConsensusAnnot = av
492 .getAlignmentStrucConsensusAnnotation();
493 final AlignmentAnnotation complementConsensusAnnot = av
494 .getComplementConsensusAnnotation();
495 boolean renderHistogram = true, renderProfile = true,
496 normaliseProfile = false, isRNA = rna;
498 BitSet graphGroupDrawn = new BitSet();
499 int charOffset = 0; // offset for a label
500 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
502 Font ofont = g.getFont();
505 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
506 boolean clipst = false, clipend = false;
507 for (int i = 0; i < aa.length; i++)
509 AlignmentAnnotation row = aa[i];
512 // check if this is a consensus annotation row and set the display
513 // settings appropriately
514 // TODO: generalise this to have render styles for consensus/profile
516 if (row.groupRef != null && row == row.groupRef.getConsensus())
518 renderHistogram = row.groupRef.isShowConsensusHistogram();
519 renderProfile = row.groupRef.isShowSequenceLogo();
520 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
522 else if (row == consensusAnnot || row == structConsensusAnnot
523 || row == complementConsensusAnnot)
525 renderHistogram = av_renderHistogram;
526 renderProfile = av_renderProfile;
527 normaliseProfile = av_normaliseProfile;
529 else if ("HMM".equals(row.getCalcId()))
531 renderHistogram = av_renderInformationHistogram;
532 renderProfile = av_renderHMMProfile;
533 normaliseProfile = av_normaliseHMMProfile;
537 renderHistogram = true;
538 // don't need to set render/normaliseProfile since they are not
539 // currently used in any other annotation track renderer
542 Annotation[] row_annotations = row.annotations;
547 centreColLabels = row.centreColLabels || centreColLabelsDef;
548 labelAllCols = row.showAllColLabels;
549 scaleColLabel = row.scaleColLabel;
553 if (!useClip || ((y - charHeight) < visHeight
554 && (y + row.height + charHeight * 2) >= sOffset))
555 {// if_in_visible_region
566 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
571 // this is so that we draw the characters below the graph
576 iconOffset = charHeight - fm.getDescent();
580 else if (row.hasText)
582 iconOffset = charHeight - fm.getDescent();
590 if (row.autoCalculated && av.isCalculationInProgress(row))
594 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0,
595 y - row.height, imgWidth, y, annotationPanel);
596 g.setColor(Color.black);
597 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
603 * else if (annotationPanel.av.updatingConservation &&
604 * aa[i].label.equals("Conservation")) {
606 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
607 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
608 * annotationPanel.imgWidth, y, annotationPanel);
610 * g.setColor(Color.black); //
611 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
613 * continue; } else if (annotationPanel.av.updatingConservation &&
614 * aa[i].label.equals("Quality")) {
616 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
617 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
618 * annotationPanel.imgWidth, y, annotationPanel);
619 * g.setColor(Color.black); // /
620 * g.drawString("Calculating Quality....",20, y-row.height/2);
624 // first pass sets up state for drawing continuation from left-hand
627 x = (startRes == 0) ? 0 : -1;
628 while (x < endRes - startRes)
630 if (hasHiddenColumns)
632 column = hiddenColumns.adjustForHiddenColumns(startRes + x);
633 if (column > row_annotations.length - 1)
640 column = startRes + x;
643 if ((row_annotations == null)
644 || (row_annotations.length <= column)
645 || (row_annotations[column] == null))
653 final String displayChar = validRes
654 ? row_annotations[column].displayCharacter
660 g.setColor(Color.red);
662 if (columnSelection != null)
664 if (columnSelection.contains(column))
666 g.fillRect(x * charWidth, y, charWidth, charHeight);
670 if (row.getInvalidStrucPos() > x)
672 g.setColor(Color.orange);
673 g.fillRect(x * charWidth, y, charWidth, charHeight);
675 else if (row.getInvalidStrucPos() == x)
677 g.setColor(Color.orange.darker());
678 g.fillRect(x * charWidth, y, charWidth, charHeight);
680 if (validCharWidth && validRes && displayChar != null
681 && (displayChar.length() > 0))
684 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
685 displayChar.length());
686 if (/* centreColLabels || */scaleColLabel)
688 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
689 // displayChar.length());
691 // if (scaleColLabel)
693 // justify the label and scale to fit in column
694 if (fmWidth > charWidth)
696 // scale only if the current font isn't already small enough
697 fmScaling = charWidth;
698 fmScaling /= fmWidth;
699 g.setFont(ofont.deriveFont(AffineTransform
700 .getScaleInstance(fmScaling, 1.0)));
701 // and update the label's width to reflect the scaling.
706 // TODO is it ok to use width of / show all characters here?
709 // fmWidth = fm.charWidth(displayChar.charAt(0));
711 charOffset = (int) ((charWidth - fmWidth) / 2f);
713 if (row_annotations[column].colour == null)
715 g.setColor(Color.black);
719 g.setColor(row_annotations[column].colour);
722 if (column == 0 || row.graph > 0)
724 g.drawString(displayChar, (x * charWidth) + charOffset,
727 else if (row_annotations[column - 1] == null || (labelAllCols
728 || !displayChar.equals(
729 row_annotations[column - 1].displayCharacter)
730 || (displayChar.length() < 2
731 && row_annotations[column].secondaryStructure == ' ')))
733 g.drawString(displayChar, x * charWidth + charOffset,
741 char ss = validRes ? row_annotations[column].secondaryStructure
746 // distinguish between forward/backward base-pairing
747 if (displayChar.indexOf(')') > -1)
756 if ((displayChar.indexOf(']') > -1))
764 // distinguish between forward/backward base-pairing
765 if (displayChar.indexOf('}') > -1)
773 // distinguish between forward/backward base-pairing
774 if (displayChar.indexOf('<') > -1)
780 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
782 // distinguish between forward/backward base-pairing
783 int ssLowerCase = ss + UPPER_TO_LOWER;
784 // TODO would .equals() be safer here? or charAt(0)?
785 if (displayChar.indexOf(ssLowerCase) > -1)
787 ss = (char) ssLowerCase;
791 if (!validRes || (ss != lastSS))
797 int nb_annot = x - temp;
798 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
799 // annot :"+nb_annot);
802 case '(': // Stem case for RNA secondary structure
803 case ')': // and opposite direction
804 drawStemAnnot(g, row_annotations, lastSSX, x, y,
805 iconOffset, startRes, column, validRes, validEnd);
812 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
813 iconOffset, startRes, column, validRes,
817 // no break if isRNA - falls through to drawNotCanonicalAnnot!
821 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
822 iconOffset, startRes, column, validRes,
826 // no break if isRNA - fall through to drawNotCanonicalAnnot!
885 Color nonCanColor = getNotCanonicalColor(lastSS);
886 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
887 lastSSX, x, y, iconOffset, startRes, column,
892 g.setColor(Color.gray);
893 g.fillRect(lastSSX, y + 6 + iconOffset,
894 (x * charWidth) - lastSSX, 2);
909 lastSSX = (x * charWidth);
916 if (column >= row_annotations.length)
918 column = row_annotations.length - 1;
925 if ((row_annotations == null) || (row_annotations.length <= column)
926 || (row_annotations[column] == null))
944 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
945 startRes, column, validRes, validEnd);
948 // no break if isRNA - fall through to drawNotCanonicalAnnot!
953 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
954 startRes, column, validRes, validEnd);
957 // no break if isRNA - fall through to drawNotCanonicalAnnot!
960 case ')': // Stem case for RNA secondary structure
962 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
963 startRes, column, validRes, validEnd);
1020 // System.out.println(lastSS);
1021 Color nonCanColor = getNotCanonicalColor(lastSS);
1022 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
1023 x, y, iconOffset, startRes, column, validRes, validEnd);
1026 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
1027 startRes, column, validRes, validEnd);
1032 if (row.graph > 0 && row.graphHeight > 0)
1034 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
1036 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
1038 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1039 // computed efficiently for all visible labels
1040 float groupmax = -999999, groupmin = 9999999;
1041 for (int gg = 0; gg < aa.length; gg++)
1043 if (aa[gg].graphGroup != row.graphGroup)
1050 aa[gg].visible = false;
1052 if (aa[gg].graphMax > groupmax)
1054 groupmax = aa[gg].graphMax;
1056 if (aa[gg].graphMin < groupmin)
1058 groupmin = aa[gg].graphMin;
1062 for (int gg = 0; gg < aa.length; gg++)
1064 if (aa[gg].graphGroup == row.graphGroup)
1066 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1067 endRes, y, groupmin, groupmax, row.graphHeight);
1071 graphGroupDrawn.set(row.graphGroup);
1075 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1076 row.graphMin, row.graphMax, row.graphHeight);
1079 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1081 drawBarGraph(g, row, row_annotations, startRes, endRes,
1082 row.graphMin, row.graphMax, y, renderHistogram,
1083 renderProfile, normaliseProfile);
1089 if (clipst && !clipend)
1093 } // end if_in_visible_region
1094 if (row.graph > 0 && row.hasText)
1111 "Start clip at : " + yfrom + " (index " + f_i + ")");
1116 "End clip at : " + yto + " (index " + f_to + ")");
1120 System.err.println("Annotation Rendering time:"
1121 + (System.currentTimeMillis() - stime));
1128 public static final Color GLYPHLINE_COLOR = Color.gray;
1130 public static final Color SHEET_COLOUR = Color.green;
1132 public static final Color HELIX_COLOUR = Color.red;
1134 public static final Color STEM_COLOUR = Color.blue;
1136 private Color sdNOTCANONICAL_COLOUR;
1138 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1139 int y, int iconOffset, int startRes, int column, boolean validRes,
1142 g.setColor(GLYPHLINE_COLOR);
1143 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1146 void drawSheetAnnot(Graphics g, Annotation[] row,
1148 int lastSSX, int x, int y, int iconOffset, int startRes,
1149 int column, boolean validRes, boolean validEnd)
1151 g.setColor(SHEET_COLOUR);
1153 if (!validEnd || !validRes || row == null || row[column] == null
1154 || row[column].secondaryStructure != 'E')
1156 g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
1160 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
1162 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
1167 g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
1173 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1174 int y, int iconOffset, int startRes, int column, boolean validRes,
1177 g.setColor(HELIX_COLOUR);
1179 int sCol = (lastSSX / charWidth)
1180 + hiddenColumns.adjustForHiddenColumns(startRes);
1182 int x2 = (x * charWidth);
1186 int ofs = charWidth / 2;
1187 // Off by 1 offset when drawing rects and ovals
1188 // to offscreen image on the MAC
1189 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1190 if (sCol == 0 || row[sCol - 1] == null
1191 || row[sCol - 1].secondaryStructure != 'H')
1196 // g.setColor(Color.orange);
1197 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1200 if (!validRes || row[column] == null
1201 || row[column].secondaryStructure != 'H')
1207 // g.setColor(Color.magenta);
1208 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
1209 x2 - x1 - ofs + 1, 8, 0, 0);
1216 if (sCol == 0 || row[sCol - 1] == null
1217 || row[sCol - 1].secondaryStructure != 'H')
1219 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1220 x1 += charWidth / 2;
1223 if (!validRes || row[column] == null
1224 || row[column].secondaryStructure != 'H')
1226 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1228 x2 -= charWidth / 2;
1231 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1234 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1235 Annotation[] aa_annotations, int sRes, int eRes, int y, float min,
1236 float max, int graphHeight)
1238 if (sRes > aa_annotations.length)
1245 // Adjustment for fastpaint to left
1251 eRes = Math.min(eRes, aa_annotations.length);
1259 float range = max - min;
1264 y2 = y - (int) ((0 - min / range) * graphHeight);
1267 g.setColor(Color.gray);
1268 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1270 eRes = Math.min(eRes, aa_annotations.length);
1273 int aaMax = aa_annotations.length - 1;
1275 while (x < eRes - sRes)
1278 if (hasHiddenColumns)
1280 column = hiddenColumns.adjustForHiddenColumns(column);
1288 if (aa_annotations[column] == null
1289 || aa_annotations[column - 1] == null)
1295 if (aa_annotations[column].colour == null)
1297 g.setColor(Color.black);
1301 g.setColor(aa_annotations[column].colour);
1304 y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
1306 y2 = y - (int) (((aa_annotations[column].value - min) / range)
1309 g.drawLine(x * charWidth - charWidth / 2, y1,
1310 x * charWidth + charWidth / 2, y2);
1314 if (_aa.threshold != null)
1316 g.setColor(_aa.threshold.colour);
1317 Graphics2D g2 = (Graphics2D) g;
1318 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1319 BasicStroke.JOIN_ROUND, 3f, new float[]
1322 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1323 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1324 g2.setStroke(new BasicStroke());
1328 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1329 Annotation[] aa_annotations, int sRes, int eRes, float min,
1330 float max, int y, boolean renderHistogram, boolean renderProfile,
1331 boolean normaliseProfile)
1333 if (sRes > aa_annotations.length)
1337 Font ofont = g.getFont();
1338 eRes = Math.min(eRes, aa_annotations.length);
1340 int x = 0, y1 = y, y2 = y;
1342 float range = max - min;
1346 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1349 g.setColor(Color.gray);
1351 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1354 int aaMax = aa_annotations.length - 1;
1355 while (x < eRes - sRes)
1358 if (hasHiddenColumns)
1360 column = hiddenColumns.adjustForHiddenColumns(column);
1368 if (aa_annotations[column] == null)
1373 if (aa_annotations[column].colour == null)
1375 g.setColor(Color.black);
1379 g.setColor(aa_annotations[column].colour);
1382 y1 = y - (int) (((aa_annotations[column].value - min) / (range))
1385 if (renderHistogram)
1389 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1393 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1396 // draw profile if available
1401 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1403 int profl[] = getProfileFor(_aa, column);
1405 // just try to draw the logo if profl is not null
1406 if (profl != null && profl[2] != 0)
1408 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1409 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1410 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1411 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1418 * Render a single base for a sequence profile, a base pair for
1419 * structure profile, and a triplet for a cdna profile
1421 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1423 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1424 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1425 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1429 * Traverse the character(s)/percentage data in the array
1432 int valuesProcessed = 0;
1433 // profl[1] is the number of values in the profile
1434 while (valuesProcessed < profl[1])
1436 if (isStructureProfile)
1438 // todo can we encode a structure pair as an int, like codons?
1439 dc[0] = (char) profl[c++];
1440 dc[1] = (char) profl[c++];
1442 else if (isCdnaProfile)
1444 dc = CodingUtils.decodeCodon(profl[c++]);
1448 dc[0] = (char) profl[c++];
1452 wdth /= fm.charsWidth(dc, 0, dc.length);
1455 // next profl[] position is profile % for the character(s)
1456 scl = htn * scale * profl[c++];
1457 lm = ofont.getLineMetrics(dc, 0, 1,
1458 g.getFontMetrics().getFontRenderContext());
1459 Font font = ofont.deriveFont(AffineTransform
1460 .getScaleInstance(wdth, scl / lm.getAscent()));
1462 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1464 // Debug - render boxes around characters
1465 // g.setColor(Color.red);
1466 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1468 // g.setColor(profcolour.findColour(dc[0]).darker());
1471 * Set character colour as per alignment colour scheme; use the
1472 * codon translation if a cDNA profile
1474 Color colour = null;
1477 final String codonTranslation = ResidueProperties
1478 .codonTranslate(new String(dc));
1479 colour = profcolour.findColour(codonTranslation.charAt(0),
1484 colour = profcolour.findColour(dc[0], column, null);
1486 g.setColor(colour == Color.white ? Color.lightGray : colour);
1488 hght = (ht + (scl - lm.getDescent()
1489 - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
1491 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1499 if (_aa.threshold != null)
1501 g.setColor(_aa.threshold.colour);
1502 Graphics2D g2 = (Graphics2D) g;
1503 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1504 BasicStroke.JOIN_ROUND, 3f, new float[]
1508 - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
1509 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1510 g2.setStroke(new BasicStroke());
1514 // used by overview window
1515 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1516 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1518 eRes = Math.min(eRes, aa_annotations.length);
1519 g.setColor(Color.white);
1520 g.fillRect(0, 0, width, y);
1521 g.setColor(new Color(0, 0, 180));
1525 for (int j = sRes; j < eRes; j++)
1527 if (aa_annotations[j] != null)
1529 if (aa_annotations[j].colour == null)
1531 g.setColor(Color.black);
1535 g.setColor(aa_annotations[j].colour);
1538 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1544 g.fillRect(x, y - height, charWidth, height);
1550 Color getNotCanonicalColor(char lastss)
1556 return new Color(255, 125, 5);
1560 return new Color(245, 115, 10);
1564 return new Color(235, 135, 15);
1568 return new Color(225, 105, 20);
1572 return new Color(215, 145, 30);
1576 return new Color(205, 95, 35);
1580 return new Color(195, 155, 45);
1584 return new Color(185, 85, 55);
1588 return new Color(175, 165, 65);
1592 return new Color(170, 75, 75);
1596 return new Color(160, 175, 85);
1600 return new Color(150, 65, 95);
1604 return new Color(140, 185, 105);
1608 return new Color(130, 55, 110);
1612 return new Color(120, 195, 120);
1616 return new Color(110, 45, 130);
1620 return new Color(100, 205, 140);
1624 return new Color(90, 35, 150);
1628 return new Color(85, 215, 160);
1632 return new Color(75, 25, 170);
1636 return new Color(65, 225, 180);
1640 return new Color(55, 15, 185);
1644 return new Color(45, 235, 195);
1648 return new Color(35, 5, 205);
1652 return new Color(25, 245, 215);
1656 return new Color(15, 0, 225);
1660 return new Color(10, 255, 235);
1664 return new Color(5, 150, 245);
1668 return new Color(0, 80, 255);
1671 System.out.println("This is not a interaction : " + lastss);