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;
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) + startRes;
173 int x2 = (x * charWidth);
175 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
176 : row_annotations[column - 1].secondaryStructure;
178 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
179 || dc != row_annotations[sCol - 1].secondaryStructure;
180 boolean diffdownstream = !validRes || !validEnd
181 || row_annotations[column] == null
182 || dc != row_annotations[column].secondaryStructure;
184 if (column > 0 && Rna.isClosingParenthesis(dc))
187 // if (validRes && column>1 && row_annotations[column-2]!=null &&
188 // dc.equals(row_annotations[column-2].displayCharacter))
191 * if new annotation with a closing base pair half of the stem,
192 * display a backward arrow
194 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
196 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
207 // display a forward arrow
211 * if annotation ending with an opeing base pair half of the stem,
212 * display a forward arrow
214 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
216 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
226 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
229 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
230 Annotation[] row_annotations, int lastSSX, int x, int y,
231 int iconOffset, int startRes, int column, boolean validRes,
234 // System.out.println(nonCanColor);
236 g.setColor(nonCanColor);
237 int sCol = (lastSSX / charWidth) + startRes;
239 int x2 = (x * charWidth);
241 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
242 : row_annotations[column - 1].displayCharacter;
244 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
245 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
246 boolean diffdownstream = !validRes || !validEnd
247 || row_annotations[column] == null
248 || !dc.equals(row_annotations[column].displayCharacter);
249 // System.out.println("Column "+column+" diff up: "+diffupstream+"
250 // down:"+diffdownstream);
251 // If a closing base pair half of the stem, display a backward arrow
252 if (column > 0 && Rna.isClosingParenthesis(dc))
256 // if (validRes && column>1 && row_annotations[column-2]!=null &&
257 // dc.equals(row_annotations[column-2].displayCharacter))
259 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
261 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
273 // display a forward arrow
276 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
278 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
288 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
291 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
293 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
296 fm = annotPanel.getFontMetrics();
297 annotationPanel = annotPanel;
298 fadedImage = annotPanel.getFadedImage();
299 imgWidth = annotPanel.getFadedImageWidth();
300 // visible area for rendering
301 int[] bounds = annotPanel.getVisibleVRange();
305 visHeight = bounds[1];
320 updateFromAlignViewport(av);
323 public void updateFromAlignViewport(AlignViewportI av)
325 charWidth = av.getCharWidth();
326 endRes = av.getRanges().getEndRes();
327 charHeight = av.getCharHeight();
328 hasHiddenColumns = av.hasHiddenColumns();
329 validCharWidth = av.isValidCharWidth();
330 av_renderHistogram = av.isShowConsensusHistogram();
331 av_renderProfile = av.isShowSequenceLogo();
332 av_normaliseProfile = av.isNormaliseSequenceLogo();
333 av_renderInformationHistogram = av.isShowInformationHistogram();
334 av_renderHMMProfile = av.isShowHMMSequenceLogo();
335 av_normaliseHMMProfile = av.isNormaliseHMMSequenceLogo();
336 profcolour = av.getResidueShading();
337 if (profcolour == null || profcolour.getColourScheme() == null)
340 * Use default colour for sequence logo if
341 * the alignment has no colourscheme set
342 * (would like to use user preference but n/a for applet)
344 ColourSchemeI col = av.getAlignment().isNucleotide()
345 ? new NucleotideColourScheme()
346 : new ZappoColourScheme();
347 profcolour = new ResidueShader(col);
349 columnSelection = av.getColumnSelection();
350 hiddenColumns = av.getAlignment().getHiddenColumns();
351 hconsensus = av.getSequenceConsensusHash();
352 complementConsensus = av.getComplementConsensusHash();
353 hStrucConsensus = av.getRnaStructureConsensusHash();
354 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
355 av_ignoreBelowBackground = av.isIgnoreBelowBackground();
361 * Returns profile data; the first element is the profile type, the second is
362 * the number of distinct values, the third the total count, and the remainder
363 * depend on the profile type.
369 int[] getProfileFor(AlignmentAnnotation aa, int column)
371 // TODO : consider refactoring the global alignment calculation
372 // properties/rendering attributes as a global 'alignment group' which holds
373 // all vis settings for the alignment as a whole rather than a subset
375 if (aa.label.contains("_HMM"))
377 HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
378 return AAFrequency.extractHMMProfile(hmm, column,
379 av_ignoreBelowBackground); // TODO check if this follows standard
382 if (aa.autoCalculated
383 && (aa.label.startsWith("Consensus") || aa.label
384 .startsWith("cDNA Consensus")))
386 boolean forComplement = aa.label.startsWith("cDNA Consensus");
387 if (aa.groupRef != null && aa.groupRef.consensusData != null
388 && aa.groupRef.isShowSequenceLogo())
390 // TODO? group consensus for cDNA complement
391 return AAFrequency.extractProfile(
392 aa.groupRef.consensusData.get(column),
393 aa.groupRef.getIgnoreGapsConsensus());
395 // TODO extend annotation row to enable dynamic and static profile data to
397 if (aa.groupRef == null && aa.sequenceRef == null)
401 return AAFrequency.extractCdnaProfile(complementConsensus[column],
402 av_ignoreGapsConsensus);
406 return AAFrequency.extractProfile(hconsensus.get(column),
407 av_ignoreGapsConsensus);
413 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
415 // TODO implement group structure consensus
417 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
418 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
419 * group selections return StructureFrequency.extractProfile(
420 * aa.groupRef.consensusData[column], aa.groupRef
421 * .getIgnoreGapsConsensus()); }
423 // TODO extend annotation row to enable dynamic and static profile data
426 if (aa.groupRef == null && aa.sequenceRef == null
427 && hStrucConsensus != null
428 && hStrucConsensus.length > column)
430 return StructureFrequency.extractProfile(hStrucConsensus[column],
431 av_ignoreGapsConsensus);
441 * Render the annotation rows associated with an alignment.
446 * data and view settings to render
448 * destination for graphics
450 * row where a mouse event occured (or -1)
452 * first column that will be drawn
454 * last column that will be drawn
455 * @return true if the fadedImage was used for any alignment annotation rows
456 * currently being calculated
458 public boolean drawComponent(AwtRenderPanelI annotPanel,
459 AlignViewportI av, Graphics g, int activeRow, int startRes,
462 long stime = System.currentTimeMillis();
463 boolean usedFaded = false;
465 // AnnotationPanel needs to implement: ImageObserver, access to
467 updateFromAwtRenderPanel(annotPanel, av);
468 fm = g.getFontMetrics();
469 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
480 boolean validRes = false;
481 boolean validEnd = false;
482 boolean labelAllCols = false;
483 boolean centreColLabels;
484 boolean centreColLabelsDef = av.isCentreColumnLabels();
485 boolean scaleColLabel = false;
486 final AlignmentAnnotation consensusAnnot = av
487 .getAlignmentConsensusAnnotation();
488 final AlignmentAnnotation structConsensusAnnot = av
489 .getAlignmentStrucConsensusAnnotation();
490 final AlignmentAnnotation complementConsensusAnnot = av
491 .getComplementConsensusAnnotation();
492 boolean renderHistogram = true, renderProfile = true,
493 normaliseProfile = false, isRNA = rna;
495 BitSet graphGroupDrawn = new BitSet();
496 int charOffset = 0; // offset for a label
497 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
499 Font ofont = g.getFont();
502 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
503 boolean clipst = false, clipend = false;
504 for (int i = 0; i < aa.length; i++)
506 AlignmentAnnotation row = aa[i];
509 // check if this is a consensus annotation row and set the display
510 // settings appropriately
511 // TODO: generalise this to have render styles for consensus/profile
513 if (row.groupRef != null && row == row.groupRef.getConsensus())
515 renderHistogram = row.groupRef.isShowConsensusHistogram();
516 renderProfile = row.groupRef.isShowSequenceLogo();
517 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
519 else if (row == consensusAnnot || row == structConsensusAnnot
520 || row == complementConsensusAnnot)
522 renderHistogram = av_renderHistogram;
523 renderProfile = av_renderProfile;
524 normaliseProfile = av_normaliseProfile;
526 else if (row.label.contains("_HMM"))
528 renderHistogram = av_renderInformationHistogram;
529 renderProfile = av_renderHMMProfile;
530 normaliseProfile = av_normaliseHMMProfile;
534 renderHistogram = true;
535 // don't need to set render/normaliseProfile since they are not
536 // currently used in any other annotation track renderer
539 Annotation[] row_annotations = row.annotations;
544 centreColLabels = row.centreColLabels || centreColLabelsDef;
545 labelAllCols = row.showAllColLabels;
546 scaleColLabel = row.scaleColLabel;
550 if (!useClip || ((y - charHeight) < visHeight
551 && (y + row.height + charHeight * 2) >= sOffset))
552 {// if_in_visible_region
563 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
568 // this is so that we draw the characters below the graph
573 iconOffset = charHeight - fm.getDescent();
577 else if (row.hasText)
579 iconOffset = charHeight - fm.getDescent();
587 if (row.autoCalculated && av.isCalculationInProgress(row))
591 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0,
592 y - row.height, imgWidth, y, annotationPanel);
593 g.setColor(Color.black);
594 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
600 * else if (annotationPanel.av.updatingConservation &&
601 * aa[i].label.equals("Conservation")) {
603 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
604 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
605 * annotationPanel.imgWidth, y, annotationPanel);
607 * g.setColor(Color.black); //
608 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
610 * continue; } else if (annotationPanel.av.updatingConservation &&
611 * aa[i].label.equals("Quality")) {
613 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
614 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
615 * annotationPanel.imgWidth, y, annotationPanel);
616 * g.setColor(Color.black); // /
617 * g.drawString("Calculating Quality....",20, y-row.height/2);
621 // first pass sets up state for drawing continuation from left-hand
624 x = (startRes == 0) ? 0 : -1;
625 while (x < endRes - startRes)
627 if (hasHiddenColumns)
629 column = hiddenColumns.adjustForHiddenColumns(startRes + x);
630 if (column > row_annotations.length - 1)
637 column = startRes + x;
640 if ((row_annotations == null)
641 || (row_annotations.length <= column)
642 || (row_annotations[column] == null))
650 final String displayChar = validRes
651 ? row_annotations[column].displayCharacter
657 g.setColor(Color.red);
659 if (columnSelection != null)
661 if (columnSelection.contains(column))
663 g.fillRect(x * charWidth, y, charWidth, charHeight);
667 if (row.getInvalidStrucPos() > x)
669 g.setColor(Color.orange);
670 g.fillRect(x * charWidth, y, charWidth, charHeight);
672 else if (row.getInvalidStrucPos() == x)
674 g.setColor(Color.orange.darker());
675 g.fillRect(x * charWidth, y, charWidth, charHeight);
677 if (validCharWidth && validRes && displayChar != null
678 && (displayChar.length() > 0))
681 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
682 displayChar.length());
683 if (/* centreColLabels || */scaleColLabel)
685 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
686 // displayChar.length());
688 // if (scaleColLabel)
690 // justify the label and scale to fit in column
691 if (fmWidth > charWidth)
693 // scale only if the current font isn't already small enough
694 fmScaling = charWidth;
695 fmScaling /= fmWidth;
696 g.setFont(ofont.deriveFont(AffineTransform
697 .getScaleInstance(fmScaling, 1.0)));
698 // and update the label's width to reflect the scaling.
703 // TODO is it ok to use width of / show all characters here?
706 // fmWidth = fm.charWidth(displayChar.charAt(0));
708 charOffset = (int) ((charWidth - fmWidth) / 2f);
710 if (row_annotations[column].colour == null)
712 g.setColor(Color.black);
716 g.setColor(row_annotations[column].colour);
719 if (column == 0 || row.graph > 0)
721 g.drawString(displayChar, (x * charWidth) + charOffset,
724 else if (row_annotations[column - 1] == null || (labelAllCols
725 || !displayChar.equals(
726 row_annotations[column - 1].displayCharacter)
727 || (displayChar.length() < 2
728 && row_annotations[column].secondaryStructure == ' ')))
730 g.drawString(displayChar, x * charWidth + charOffset,
738 char ss = validRes ? row_annotations[column].secondaryStructure
743 // distinguish between forward/backward base-pairing
744 if (displayChar.indexOf(')') > -1)
753 if ((displayChar.indexOf(']') > -1))
761 // distinguish between forward/backward base-pairing
762 if (displayChar.indexOf('}') > -1)
770 // distinguish between forward/backward base-pairing
771 if (displayChar.indexOf('<') > -1)
777 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
779 // distinguish between forward/backward base-pairing
780 int ssLowerCase = ss + UPPER_TO_LOWER;
781 // TODO would .equals() be safer here? or charAt(0)?
782 if (displayChar.indexOf(ssLowerCase) > -1)
784 ss = (char) ssLowerCase;
788 if (!validRes || (ss != lastSS))
794 int nb_annot = x - temp;
795 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
796 // annot :"+nb_annot);
799 case '(': // Stem case for RNA secondary structure
800 case ')': // and opposite direction
801 drawStemAnnot(g, row_annotations, lastSSX, x, y,
802 iconOffset, startRes, column, validRes, validEnd);
809 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
810 iconOffset, startRes, column, validRes,
814 // no break if isRNA - falls through to drawNotCanonicalAnnot!
818 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
819 iconOffset, startRes, column, validRes,
823 // no break if isRNA - fall through to drawNotCanonicalAnnot!
882 Color nonCanColor = getNotCanonicalColor(lastSS);
883 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
884 lastSSX, x, y, iconOffset, startRes, column,
889 g.setColor(Color.gray);
890 g.fillRect(lastSSX, y + 6 + iconOffset,
891 (x * charWidth) - lastSSX, 2);
906 lastSSX = (x * charWidth);
913 if (column >= row_annotations.length)
915 column = row_annotations.length - 1;
922 if ((row_annotations == null) || (row_annotations.length <= column)
923 || (row_annotations[column] == null))
941 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
942 startRes, column, validRes, validEnd);
945 // no break if isRNA - fall through to drawNotCanonicalAnnot!
950 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
951 startRes, column, validRes, validEnd);
954 // no break if isRNA - fall through to drawNotCanonicalAnnot!
957 case ')': // Stem case for RNA secondary structure
959 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
960 startRes, column, validRes, validEnd);
1017 // System.out.println(lastSS);
1018 Color nonCanColor = getNotCanonicalColor(lastSS);
1019 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
1020 x, y, iconOffset, startRes, column, validRes, validEnd);
1023 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
1024 startRes, column, validRes, validEnd);
1029 if (row.graph > 0 && row.graphHeight > 0)
1031 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
1033 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
1035 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1036 // computed efficiently for all visible labels
1037 float groupmax = -999999, groupmin = 9999999;
1038 for (int gg = 0; gg < aa.length; gg++)
1040 if (aa[gg].graphGroup != row.graphGroup)
1047 aa[gg].visible = false;
1049 if (aa[gg].graphMax > groupmax)
1051 groupmax = aa[gg].graphMax;
1053 if (aa[gg].graphMin < groupmin)
1055 groupmin = aa[gg].graphMin;
1059 for (int gg = 0; gg < aa.length; gg++)
1061 if (aa[gg].graphGroup == row.graphGroup)
1063 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1064 endRes, y, groupmin, groupmax, row.graphHeight);
1068 graphGroupDrawn.set(row.graphGroup);
1072 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1073 row.graphMin, row.graphMax, row.graphHeight);
1076 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1078 drawBarGraph(g, row, row_annotations, startRes, endRes,
1079 row.graphMin, row.graphMax, y, renderHistogram,
1080 renderProfile, normaliseProfile);
1086 if (clipst && !clipend)
1090 } // end if_in_visible_region
1091 if (row.graph > 0 && row.hasText)
1108 "Start clip at : " + yfrom + " (index " + f_i + ")");
1113 "End clip at : " + yto + " (index " + f_to + ")");
1117 System.err.println("Annotation Rendering time:"
1118 + (System.currentTimeMillis() - stime));
1125 public static final Color GLYPHLINE_COLOR = Color.gray;
1127 public static final Color SHEET_COLOUR = Color.green;
1129 public static final Color HELIX_COLOUR = Color.red;
1131 public static final Color STEM_COLOUR = Color.blue;
1133 private Color sdNOTCANONICAL_COLOUR;
1135 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1136 int y, int iconOffset, int startRes, int column, boolean validRes,
1139 g.setColor(GLYPHLINE_COLOR);
1140 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1143 void drawSheetAnnot(Graphics g, Annotation[] row,
1145 int lastSSX, int x, int y, int iconOffset, int startRes,
1146 int column, boolean validRes, boolean validEnd)
1148 g.setColor(SHEET_COLOUR);
1150 if (!validEnd || !validRes || row == null || row[column] == null
1151 || row[column].secondaryStructure != 'E')
1153 g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
1157 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
1159 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
1164 g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
1170 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1171 int y, int iconOffset, int startRes, int column, boolean validRes,
1174 g.setColor(HELIX_COLOUR);
1176 int sCol = (lastSSX / charWidth) + startRes;
1178 int x2 = (x * charWidth);
1182 int ofs = charWidth / 2;
1183 // Off by 1 offset when drawing rects and ovals
1184 // to offscreen image on the MAC
1185 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1186 if (sCol == 0 || row[sCol - 1] == null
1187 || row[sCol - 1].secondaryStructure != 'H')
1192 // g.setColor(Color.orange);
1193 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1196 if (!validRes || row[column] == null
1197 || row[column].secondaryStructure != 'H')
1203 // g.setColor(Color.magenta);
1204 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
1205 x2 - x1 - ofs + 1, 8, 0, 0);
1212 if (sCol == 0 || row[sCol - 1] == null
1213 || row[sCol - 1].secondaryStructure != 'H')
1215 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1216 x1 += charWidth / 2;
1219 if (!validRes || row[column] == null
1220 || row[column].secondaryStructure != 'H')
1222 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1224 x2 -= charWidth / 2;
1227 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1230 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1231 Annotation[] aa_annotations, int sRes, int eRes, int y, float min,
1232 float max, int graphHeight)
1234 if (sRes > aa_annotations.length)
1241 // Adjustment for fastpaint to left
1247 eRes = Math.min(eRes, aa_annotations.length);
1255 float range = max - min;
1260 y2 = y - (int) ((0 - min / range) * graphHeight);
1263 g.setColor(Color.gray);
1264 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1266 eRes = Math.min(eRes, aa_annotations.length);
1269 int aaMax = aa_annotations.length - 1;
1271 while (x < eRes - sRes)
1274 if (hasHiddenColumns)
1276 column = hiddenColumns.adjustForHiddenColumns(column);
1284 if (aa_annotations[column] == null
1285 || aa_annotations[column - 1] == null)
1291 if (aa_annotations[column].colour == null)
1293 g.setColor(Color.black);
1297 g.setColor(aa_annotations[column].colour);
1300 y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
1302 y2 = y - (int) (((aa_annotations[column].value - min) / range)
1305 g.drawLine(x * charWidth - charWidth / 2, y1,
1306 x * charWidth + charWidth / 2, y2);
1310 if (_aa.threshold != null)
1312 g.setColor(_aa.threshold.colour);
1313 Graphics2D g2 = (Graphics2D) g;
1314 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1315 BasicStroke.JOIN_ROUND, 3f, new float[]
1318 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1319 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1320 g2.setStroke(new BasicStroke());
1324 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1325 Annotation[] aa_annotations, int sRes, int eRes, float min,
1326 float max, int y, boolean renderHistogram, boolean renderProfile,
1327 boolean normaliseProfile)
1329 if (sRes > aa_annotations.length)
1333 Font ofont = g.getFont();
1334 eRes = Math.min(eRes, aa_annotations.length);
1336 int x = 0, y1 = y, y2 = y;
1338 float range = max - min;
1342 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1345 g.setColor(Color.gray);
1347 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1350 int aaMax = aa_annotations.length - 1;
1351 while (x < eRes - sRes)
1354 if (hasHiddenColumns)
1356 column = hiddenColumns.adjustForHiddenColumns(column);
1364 if (aa_annotations[column] == null)
1369 if (aa_annotations[column].colour == null)
1371 g.setColor(Color.black);
1375 g.setColor(aa_annotations[column].colour);
1378 y1 = y - (int) (((aa_annotations[column].value - min) / (range))
1381 if (renderHistogram)
1385 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1389 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1392 // draw profile if available
1397 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1399 int profl[] = getProfileFor(_aa, column);
1401 // just try to draw the logo if profl is not null
1402 if (profl != null && profl[2] != 0)
1404 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1405 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1406 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1407 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1414 * Render a single base for a sequence profile, a base pair for
1415 * structure profile, and a triplet for a cdna profile
1417 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1419 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1420 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1421 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1425 * Traverse the character(s)/percentage data in the array
1428 int valuesProcessed = 0;
1429 // profl[1] is the number of values in the profile
1430 while (valuesProcessed < profl[1])
1432 if (isStructureProfile)
1434 // todo can we encode a structure pair as an int, like codons?
1435 dc[0] = (char) profl[c++];
1436 dc[1] = (char) profl[c++];
1438 else if (isCdnaProfile)
1440 dc = CodingUtils.decodeCodon(profl[c++]);
1444 dc[0] = (char) profl[c++];
1448 wdth /= fm.charsWidth(dc, 0, dc.length);
1451 // next profl[] position is profile % for the character(s)
1452 scl = htn * scale * profl[c++];
1453 lm = ofont.getLineMetrics(dc, 0, 1,
1454 g.getFontMetrics().getFontRenderContext());
1455 Font font = ofont.deriveFont(AffineTransform
1456 .getScaleInstance(wdth, scl / lm.getAscent()));
1458 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1460 // Debug - render boxes around characters
1461 // g.setColor(Color.red);
1462 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1464 // g.setColor(profcolour.findColour(dc[0]).darker());
1467 * Set character colour as per alignment colour scheme; use the
1468 * codon translation if a cDNA profile
1470 Color colour = null;
1473 final String codonTranslation = ResidueProperties
1474 .codonTranslate(new String(dc));
1475 colour = profcolour.findColour(codonTranslation.charAt(0),
1480 colour = profcolour.findColour(dc[0], column, null);
1482 g.setColor(colour == Color.white ? Color.lightGray : colour);
1484 hght = (ht + (scl - lm.getDescent()
1485 - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
1487 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1495 if (_aa.threshold != null)
1497 g.setColor(_aa.threshold.colour);
1498 Graphics2D g2 = (Graphics2D) g;
1499 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1500 BasicStroke.JOIN_ROUND, 3f, new float[]
1504 - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
1505 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1506 g2.setStroke(new BasicStroke());
1510 // used by overview window
1511 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1512 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1514 eRes = Math.min(eRes, aa_annotations.length);
1515 g.setColor(Color.white);
1516 g.fillRect(0, 0, width, y);
1517 g.setColor(new Color(0, 0, 180));
1521 for (int j = sRes; j < eRes; j++)
1523 if (aa_annotations[j] != null)
1525 if (aa_annotations[j].colour == null)
1527 g.setColor(Color.black);
1531 g.setColor(aa_annotations[j].colour);
1534 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1540 g.fillRect(x, y - height, charWidth, height);
1546 Color getNotCanonicalColor(char lastss)
1552 return new Color(255, 125, 5);
1556 return new Color(245, 115, 10);
1560 return new Color(235, 135, 15);
1564 return new Color(225, 105, 20);
1568 return new Color(215, 145, 30);
1572 return new Color(205, 95, 35);
1576 return new Color(195, 155, 45);
1580 return new Color(185, 85, 55);
1584 return new Color(175, 165, 65);
1588 return new Color(170, 75, 75);
1592 return new Color(160, 175, 85);
1596 return new Color(150, 65, 95);
1600 return new Color(140, 185, 105);
1604 return new Color(130, 55, 110);
1608 return new Color(120, 195, 120);
1612 return new Color(110, 45, 130);
1616 return new Color(100, 205, 140);
1620 return new Color(90, 35, 150);
1624 return new Color(85, 215, 160);
1628 return new Color(75, 25, 170);
1632 return new Color(65, 225, 180);
1636 return new Color(55, 15, 185);
1640 return new Color(45, 235, 195);
1644 return new Color(35, 5, 205);
1648 return new Color(25, 245, 215);
1652 return new Color(15, 0, 225);
1656 return new Color(10, 255, 235);
1660 return new Color(5, 150, 245);
1664 return new Color(0, 80, 255);
1667 System.out.println("This is not a interaction : " + lastss);