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;
90 private boolean av_ignoreBelowBackground;
93 * attributes set from AwtRenderPanelI
96 * old image used when data is currently being calculated and cannot be
99 private Image fadedImage;
102 * panel being rendered into
104 private ImageObserver annotationPanel;
107 * width of image to render in panel
109 private int imgWidth;
112 * offset to beginning of visible area
117 * offset to end of visible area
119 private int visHeight;
122 * indicate if the renderer should only render the visible portion of the
123 * annotation given the current view settings
125 private boolean useClip = true;
128 * master flag indicating if renderer should ever try to clip. not enabled for
131 private boolean canClip = false;
133 public AnnotationRenderer()
139 * Create a new annotation Renderer
142 * flag indicating if timing and redraw parameter info should be
145 public AnnotationRenderer(boolean debugRedraw)
147 this.debugRedraw = debugRedraw;
151 * Remove any references and resources when this object is no longer required
153 public void dispose()
156 complementConsensus = null;
157 hStrucConsensus = null;
159 annotationPanel = null;
162 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
163 int x, int y, int iconOffset, int startRes, int column,
164 boolean validRes, boolean validEnd)
166 g.setColor(STEM_COLOUR);
167 int sCol = (lastSSX / charWidth) + startRes;
169 int x2 = (x * charWidth);
171 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
172 : row_annotations[column - 1].secondaryStructure;
174 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
175 || dc != row_annotations[sCol - 1].secondaryStructure;
176 boolean diffdownstream = !validRes || !validEnd
177 || row_annotations[column] == null
178 || dc != row_annotations[column].secondaryStructure;
180 if (column > 0 && Rna.isClosingParenthesis(dc))
183 // if (validRes && column>1 && row_annotations[column-2]!=null &&
184 // dc.equals(row_annotations[column-2].displayCharacter))
187 * if new annotation with a closing base pair half of the stem,
188 * display a backward arrow
190 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
191 new int[] { y + iconOffset, y + 14 + iconOffset,
192 y + 8 + iconOffset }, 3);
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 }, new int[] {
210 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
219 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
222 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
223 Annotation[] row_annotations, int lastSSX, int x, int y,
224 int iconOffset, int startRes, int column, boolean validRes,
227 // System.out.println(nonCanColor);
229 g.setColor(nonCanColor);
230 int sCol = (lastSSX / charWidth) + startRes;
232 int x2 = (x * charWidth);
234 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
235 : row_annotations[column - 1].displayCharacter;
237 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
238 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
239 boolean diffdownstream = !validRes || !validEnd
240 || row_annotations[column] == null
241 || !dc.equals(row_annotations[column].displayCharacter);
242 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
243 // If a closing base pair half of the stem, display a backward arrow
244 if (column > 0 && Rna.isClosingParenthesis(dc))
248 // if (validRes && column>1 && row_annotations[column-2]!=null &&
249 // dc.equals(row_annotations[column-2].displayCharacter))
251 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
252 new int[] { y + iconOffset, y + 14 + iconOffset,
253 y + 8 + iconOffset }, 3);
264 // display a forward arrow
267 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
268 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
277 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
280 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
282 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
285 fm = annotPanel.getFontMetrics();
286 annotationPanel = annotPanel;
287 fadedImage = annotPanel.getFadedImage();
288 imgWidth = annotPanel.getFadedImageWidth();
289 // visible area for rendering
290 int[] bounds = annotPanel.getVisibleVRange();
294 visHeight = bounds[1];
309 updateFromAlignViewport(av);
312 public void updateFromAlignViewport(AlignViewportI av)
314 charWidth = av.getCharWidth();
315 endRes = av.getRanges().getEndRes();
316 charHeight = av.getCharHeight();
317 hasHiddenColumns = av.hasHiddenColumns();
318 validCharWidth = av.isValidCharWidth();
319 av_renderHistogram = av.isShowConsensusHistogram();
320 av_renderProfile = av.isShowSequenceLogo();
321 av_normaliseProfile = av.isNormaliseSequenceLogo();
322 profcolour = av.getResidueShading();
323 if (profcolour == null || profcolour.getColourScheme() == null)
326 * Use default colour for sequence logo if
327 * the alignment has no colourscheme set
328 * (would like to use user preference but n/a for applet)
330 ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
331 : new ZappoColourScheme();
332 profcolour = new ResidueShader(col);
334 columnSelection = av.getColumnSelection();
335 hiddenColumns = av.getAlignment().getHiddenColumns();
336 hconsensus = av.getSequenceConsensusHash();
337 complementConsensus = av.getComplementConsensusHash();
338 hStrucConsensus = av.getRnaStructureConsensusHash();
339 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
340 av_ignoreBelowBackground = av.isIgnoreBelowBackground();
346 * Returns profile data; the first element is the profile type, the second is
347 * the number of distinct values, the third the total count, and the remainder
348 * depend on the profile type.
354 int[] getProfileFor(AlignmentAnnotation aa, int column)
356 // TODO : consider refactoring the global alignment calculation
357 // properties/rendering attributes as a global 'alignment group' which holds
358 // all vis settings for the alignment as a whole rather than a subset
360 if (aa.label.startsWith("Information"))
362 return AAFrequency.getHMMProfileFor(aa, column,
363 av_ignoreBelowBackground); // TODO check if this follows standard
366 if (aa.autoCalculated
367 && (aa.label.startsWith("Consensus") || aa.label
368 .startsWith("cDNA Consensus")))
370 boolean forComplement = aa.label.startsWith("cDNA Consensus");
371 if (aa.groupRef != null && aa.groupRef.consensusData != null
372 && aa.groupRef.isShowSequenceLogo())
374 // TODO? group consensus for cDNA complement
375 return AAFrequency.extractProfile(
376 aa.groupRef.consensusData.get(column),
377 aa.groupRef.getIgnoreGapsConsensus());
379 // TODO extend annotation row to enable dynamic and static profile data to
381 if (aa.groupRef == null && aa.sequenceRef == null)
385 return AAFrequency.extractCdnaProfile(
386 complementConsensus[column], av_ignoreGapsConsensus);
390 return AAFrequency.extractProfile(
391 hconsensus.get(column),
392 av_ignoreGapsConsensus);
398 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
400 // TODO implement group structure consensus
402 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
403 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
404 * group selections return StructureFrequency.extractProfile(
405 * aa.groupRef.consensusData[column], aa.groupRef
406 * .getIgnoreGapsConsensus()); }
408 // TODO extend annotation row to enable dynamic and static profile data
411 if (aa.groupRef == null && aa.sequenceRef == null
412 && hStrucConsensus != null
413 && hStrucConsensus.length > column)
415 return StructureFrequency.extractProfile(hStrucConsensus[column],
416 av_ignoreGapsConsensus);
426 * Render the annotation rows associated with an alignment.
431 * data and view settings to render
433 * destination for graphics
435 * row where a mouse event occured (or -1)
437 * first column that will be drawn
439 * last column that will be drawn
440 * @return true if the fadedImage was used for any alignment annotation rows
441 * currently being calculated
443 public boolean drawComponent(AwtRenderPanelI annotPanel,
444 AlignViewportI av, Graphics g, int activeRow, int startRes,
447 long stime = System.currentTimeMillis();
448 boolean usedFaded = false;
450 // AnnotationPanel needs to implement: ImageObserver, access to
452 updateFromAwtRenderPanel(annotPanel, av);
453 fm = g.getFontMetrics();
454 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
465 boolean validRes = false;
466 boolean validEnd = false;
467 boolean labelAllCols = false;
468 boolean centreColLabels;
469 boolean centreColLabelsDef = av.isCentreColumnLabels();
470 boolean scaleColLabel = false;
471 final AlignmentAnnotation consensusAnnot = av
472 .getAlignmentConsensusAnnotation();
473 final AlignmentAnnotation structConsensusAnnot = av
474 .getAlignmentStrucConsensusAnnotation();
475 final AlignmentAnnotation complementConsensusAnnot = av
476 .getComplementConsensusAnnotation();
477 boolean renderHistogram = true, renderProfile = true, 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;
529 || ((y - charHeight) < visHeight && (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, y
570 - 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.adjustForHiddenColumns(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 ? row_annotations[column].displayCharacter
634 g.setColor(Color.red);
636 if (columnSelection != null)
638 if (columnSelection.contains(column))
640 g.fillRect(x * charWidth, y, charWidth, charHeight);
644 if (row.getInvalidStrucPos() > x)
646 g.setColor(Color.orange);
647 g.fillRect(x * charWidth, y, charWidth, charHeight);
649 else if (row.getInvalidStrucPos() == x)
651 g.setColor(Color.orange.darker());
652 g.fillRect(x * charWidth, y, charWidth, charHeight);
654 if (validCharWidth && validRes && displayChar != null
655 && (displayChar.length() > 0))
658 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
659 displayChar.length());
660 if (/* centreColLabels || */scaleColLabel)
662 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
663 // displayChar.length());
665 // if (scaleColLabel)
667 // justify the label and scale to fit in column
668 if (fmWidth > charWidth)
670 // scale only if the current font isn't already small enough
671 fmScaling = charWidth;
672 fmScaling /= fmWidth;
673 g.setFont(ofont.deriveFont(AffineTransform
674 .getScaleInstance(fmScaling, 1.0)));
675 // and update the label's width to reflect the scaling.
680 // TODO is it ok to use width of / show all characters here?
683 // fmWidth = fm.charWidth(displayChar.charAt(0));
685 charOffset = (int) ((charWidth - fmWidth) / 2f);
687 if (row_annotations[column].colour == null)
689 g.setColor(Color.black);
693 g.setColor(row_annotations[column].colour);
696 if (column == 0 || row.graph > 0)
698 g.drawString(displayChar, (x * charWidth) + charOffset, y
701 else if (row_annotations[column - 1] == null
704 .equals(row_annotations[column - 1].displayCharacter) || (displayChar
705 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
707 g.drawString(displayChar, x * charWidth + charOffset, y
715 char ss = validRes ? row_annotations[column].secondaryStructure
720 // distinguish between forward/backward base-pairing
721 if (displayChar.indexOf(')') > -1)
730 if ((displayChar.indexOf(']') > -1))
738 // distinguish between forward/backward base-pairing
739 if (displayChar.indexOf('}') > -1)
747 // distinguish between forward/backward base-pairing
748 if (displayChar.indexOf('<') > -1)
754 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
756 // distinguish between forward/backward base-pairing
757 int ssLowerCase = ss + UPPER_TO_LOWER;
758 // TODO would .equals() be safer here? or charAt(0)?
759 if (displayChar.indexOf(ssLowerCase) > -1)
761 ss = (char) ssLowerCase;
765 if (!validRes || (ss != lastSS))
771 int nb_annot = x - temp;
772 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
775 case '(': // Stem case for RNA secondary structure
776 case ')': // and opposite direction
777 drawStemAnnot(g, row_annotations, lastSSX, x, y,
778 iconOffset, startRes, column, validRes, validEnd);
785 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
786 iconOffset, startRes, column, validRes,
790 // no break if isRNA - falls through to drawNotCanonicalAnnot!
794 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
795 iconOffset, startRes, column, validRes,
799 // no break if isRNA - fall through to drawNotCanonicalAnnot!
858 Color nonCanColor = getNotCanonicalColor(lastSS);
859 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
860 lastSSX, x, y, iconOffset, startRes, column,
865 g.setColor(Color.gray);
866 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
882 lastSSX = (x * charWidth);
889 if (column >= row_annotations.length)
891 column = row_annotations.length - 1;
898 if ((row_annotations == null) || (row_annotations.length <= column)
899 || (row_annotations[column] == null))
917 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
918 startRes, column, validRes, validEnd);
921 // no break if isRNA - fall through to drawNotCanonicalAnnot!
926 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
927 startRes, column, validRes, validEnd);
930 // no break if isRNA - fall through to drawNotCanonicalAnnot!
933 case ')': // Stem case for RNA secondary structure
935 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
936 startRes, column, validRes, validEnd);
993 // System.out.println(lastSS);
994 Color nonCanColor = getNotCanonicalColor(lastSS);
995 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
996 x, y, iconOffset, startRes, column, validRes, validEnd);
999 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
1000 startRes, column, validRes, validEnd);
1005 if (row.graph > 0 && row.graphHeight > 0)
1007 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
1009 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
1011 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1012 // computed efficiently for all visible labels
1013 float groupmax = -999999, groupmin = 9999999;
1014 for (int gg = 0; gg < aa.length; gg++)
1016 if (aa[gg].graphGroup != row.graphGroup)
1023 aa[gg].visible = false;
1025 if (aa[gg].graphMax > groupmax)
1027 groupmax = aa[gg].graphMax;
1029 if (aa[gg].graphMin < groupmin)
1031 groupmin = aa[gg].graphMin;
1035 for (int gg = 0; gg < aa.length; gg++)
1037 if (aa[gg].graphGroup == row.graphGroup)
1039 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1040 endRes, y, groupmin, groupmax, row.graphHeight);
1044 graphGroupDrawn.set(row.graphGroup);
1048 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1049 row.graphMin, row.graphMax, row.graphHeight);
1052 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1054 drawBarGraph(g, row, row_annotations, startRes, endRes,
1055 row.graphMin, row.graphMax, y, renderHistogram,
1056 renderProfile, normaliseProfile);
1062 if (clipst && !clipend)
1066 }// end if_in_visible_region
1067 if (row.graph > 0 && row.hasText)
1083 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1088 System.err.println("End clip at : " + yto + " (index " + f_to
1093 System.err.println("Annotation Rendering time:"
1094 + (System.currentTimeMillis() - stime));
1101 public static final Color GLYPHLINE_COLOR = Color.gray;
1103 public static final Color SHEET_COLOUR = Color.green;
1105 public static final Color HELIX_COLOUR = Color.red;
1107 public static final Color STEM_COLOUR = Color.blue;
1109 private Color sdNOTCANONICAL_COLOUR;
1111 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1112 int y, int iconOffset, int startRes, int column,
1113 boolean validRes, boolean validEnd)
1115 g.setColor(GLYPHLINE_COLOR);
1116 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1119 void drawSheetAnnot(Graphics g, Annotation[] row,
1121 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1122 boolean validRes, boolean validEnd)
1124 g.setColor(SHEET_COLOUR);
1126 if (!validEnd || !validRes || row == null || row[column] == null
1127 || row[column].secondaryStructure != 'E')
1129 g.fillRect(lastSSX, y + 4 + iconOffset,
1130 (x * charWidth) - lastSSX - 4, 7);
1131 g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
1132 (x * charWidth) }, new int[] { y + iconOffset,
1133 y + 14 + iconOffset, y + 7 + iconOffset }, 3);
1137 g.fillRect(lastSSX, y + 4 + iconOffset,
1138 (x + 1) * charWidth - lastSSX, 7);
1143 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1144 int y, int iconOffset, int startRes, int column,
1145 boolean validRes, boolean validEnd)
1147 g.setColor(HELIX_COLOUR);
1149 int sCol = (lastSSX / charWidth) + startRes;
1151 int x2 = (x * charWidth);
1155 int ofs = charWidth / 2;
1156 // Off by 1 offset when drawing rects and ovals
1157 // to offscreen image on the MAC
1158 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1159 if (sCol == 0 || row[sCol - 1] == null
1160 || row[sCol - 1].secondaryStructure != 'H')
1165 // g.setColor(Color.orange);
1166 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1169 if (!validRes || row[column] == null
1170 || row[column].secondaryStructure != 'H')
1176 // g.setColor(Color.magenta);
1177 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1185 if (sCol == 0 || row[sCol - 1] == null
1186 || row[sCol - 1].secondaryStructure != 'H')
1188 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1189 x1 += charWidth / 2;
1192 if (!validRes || row[column] == null
1193 || row[column].secondaryStructure != 'H')
1195 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1197 x2 -= charWidth / 2;
1200 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1203 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1204 Annotation[] aa_annotations, int sRes, int eRes, int y,
1205 float min, float max, int graphHeight)
1207 if (sRes > aa_annotations.length)
1214 // Adjustment for fastpaint to left
1220 eRes = Math.min(eRes, aa_annotations.length);
1228 float range = max - min;
1233 y2 = y - (int) ((0 - min / range) * graphHeight);
1236 g.setColor(Color.gray);
1237 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1239 eRes = Math.min(eRes, aa_annotations.length);
1242 int aaMax = aa_annotations.length - 1;
1244 while (x < eRes - sRes)
1247 if (hasHiddenColumns)
1249 column = hiddenColumns.adjustForHiddenColumns(column);
1257 if (aa_annotations[column] == null
1258 || aa_annotations[column - 1] == null)
1264 if (aa_annotations[column].colour == null)
1266 g.setColor(Color.black);
1270 g.setColor(aa_annotations[column].colour);
1274 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1276 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1278 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1279 + charWidth / 2, y2);
1283 if (_aa.threshold != null)
1285 g.setColor(_aa.threshold.colour);
1286 Graphics2D g2 = (Graphics2D) g;
1287 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1288 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1290 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1291 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1292 g2.setStroke(new BasicStroke());
1296 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1297 Annotation[] aa_annotations, int sRes, int eRes, float min,
1298 float max, int y, boolean renderHistogram, boolean renderProfile,
1299 boolean normaliseProfile)
1301 if (sRes > aa_annotations.length)
1305 Font ofont = g.getFont();
1306 eRes = Math.min(eRes, aa_annotations.length);
1308 int x = 0, y1 = y, y2 = y;
1310 float range = max - min;
1314 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1317 g.setColor(Color.gray);
1319 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1322 int aaMax = aa_annotations.length - 1;
1323 while (x < eRes - sRes)
1326 if (hasHiddenColumns)
1328 column = hiddenColumns.adjustForHiddenColumns(column);
1336 if (aa_annotations[column] == null)
1341 if (aa_annotations[column].colour == null)
1343 g.setColor(Color.black);
1347 g.setColor(aa_annotations[column].colour);
1351 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1353 if (renderHistogram)
1357 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1361 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1364 // draw profile if available
1369 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1371 int profl[] = getProfileFor(_aa, column);
1373 // just try to draw the logo if profl is not null
1374 if (profl != null && profl[2] != 0)
1376 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1377 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1378 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1379 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1386 * Render a single base for a sequence profile, a base pair for
1387 * structure profile, and a triplet for a cdna profile
1389 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1391 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1392 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1393 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1397 * Traverse the character(s)/percentage data in the array
1400 int valuesProcessed = 0;
1401 // profl[1] is the number of values in the profile
1402 while (valuesProcessed < profl[1])
1404 if (isStructureProfile)
1406 // todo can we encode a structure pair as an int, like codons?
1407 dc[0] = (char) profl[c++];
1408 dc[1] = (char) profl[c++];
1410 else if (isCdnaProfile)
1412 dc = CodingUtils.decodeCodon(profl[c++]);
1416 dc[0] = (char) profl[c++];
1420 wdth /= fm.charsWidth(dc, 0, dc.length);
1423 // next profl[] position is profile % for the character(s)
1424 scl = htn * scale * profl[c++];
1425 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1426 .getFontRenderContext());
1427 Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
1428 wdth, scl / lm.getAscent()));
1430 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1432 // Debug - render boxes around characters
1433 // g.setColor(Color.red);
1434 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1436 // g.setColor(profcolour.findColour(dc[0]).darker());
1439 * Set character colour as per alignment colour scheme; use the
1440 * codon translation if a cDNA profile
1442 Color colour = null;
1445 final String codonTranslation = ResidueProperties
1446 .codonTranslate(new String(dc));
1447 colour = profcolour.findColour(codonTranslation.charAt(0),
1452 colour = profcolour.findColour(dc[0], column, null);
1454 g.setColor(colour == Color.white ? Color.lightGray : colour);
1456 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1457 .getBaselineIndex()]));
1459 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1467 if (_aa.threshold != null)
1469 g.setColor(_aa.threshold.colour);
1470 Graphics2D g2 = (Graphics2D) g;
1471 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1472 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1474 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1476 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1477 g2.setStroke(new BasicStroke());
1481 // used by overview window
1482 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1483 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1485 eRes = Math.min(eRes, aa_annotations.length);
1486 g.setColor(Color.white);
1487 g.fillRect(0, 0, width, y);
1488 g.setColor(new Color(0, 0, 180));
1492 for (int j = sRes; j < eRes; j++)
1494 if (aa_annotations[j] != null)
1496 if (aa_annotations[j].colour == null)
1498 g.setColor(Color.black);
1502 g.setColor(aa_annotations[j].colour);
1505 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1511 g.fillRect(x, y - height, charWidth, height);
1517 Color getNotCanonicalColor(char lastss)
1523 return new Color(255, 125, 5);
1527 return new Color(245, 115, 10);
1531 return new Color(235, 135, 15);
1535 return new Color(225, 105, 20);
1539 return new Color(215, 145, 30);
1543 return new Color(205, 95, 35);
1547 return new Color(195, 155, 45);
1551 return new Color(185, 85, 55);
1555 return new Color(175, 165, 65);
1559 return new Color(170, 75, 75);
1563 return new Color(160, 175, 85);
1567 return new Color(150, 65, 95);
1571 return new Color(140, 185, 105);
1575 return new Color(130, 55, 110);
1579 return new Color(120, 195, 120);
1583 return new Color(110, 45, 130);
1587 return new Color(100, 205, 140);
1591 return new Color(90, 35, 150);
1595 return new Color(85, 215, 160);
1599 return new Color(75, 25, 170);
1603 return new Color(65, 225, 180);
1607 return new Color(55, 15, 185);
1611 return new Color(45, 235, 195);
1615 return new Color(35, 5, 205);
1619 return new Color(25, 245, 215);
1623 return new Color(15, 0, 225);
1627 return new Color(10, 255, 235);
1631 return new Color(5, 150, 245);
1635 return new Color(0, 80, 255);
1638 System.out.println("This is not a interaction : " + lastss);