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.ProfilesI;
32 import jalview.schemes.ColourSchemeI;
33 import jalview.schemes.NucleotideColourScheme;
34 import jalview.schemes.ResidueProperties;
35 import jalview.schemes.ZappoColourScheme;
36 import jalview.util.Platform;
38 import java.awt.BasicStroke;
39 import java.awt.Color;
41 import java.awt.FontMetrics;
42 import java.awt.Graphics;
43 import java.awt.Graphics2D;
44 import java.awt.Image;
45 import java.awt.font.LineMetrics;
46 import java.awt.geom.AffineTransform;
47 import java.awt.image.ImageObserver;
48 import java.util.BitSet;
49 import java.util.Hashtable;
51 public class AnnotationRenderer
53 private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
55 private static final int CHAR_A = 'A'; // 65
57 private static final int CHAR_Z = 'Z'; // 90
60 * flag indicating if timing and redraw parameter info should be output
62 private final boolean debugRedraw;
64 private int charWidth, endRes, charHeight;
66 private boolean validCharWidth, hasHiddenColumns;
68 private FontMetrics fm;
70 private final boolean MAC = Platform.isAMac();
72 boolean av_renderHistogram = true, av_renderProfile = true,
73 av_normaliseProfile = false;
75 ResidueShaderI profcolour = null;
77 private ColumnSelection columnSelection;
79 private ProfilesI hconsensus;
81 private Hashtable[] complementConsensus;
83 private Hashtable[] hStrucConsensus;
85 private boolean av_ignoreGapsConsensus;
88 * attributes set from AwtRenderPanelI
91 * old image used when data is currently being calculated and cannot be
94 private Image fadedImage;
97 * panel being rendered into
99 private ImageObserver annotationPanel;
102 * width of image to render in panel
104 private int imgWidth;
107 * offset to beginning of visible area
112 * offset to end of visible area
114 private int visHeight;
117 * indicate if the renderer should only render the visible portion of the
118 * annotation given the current view settings
120 private boolean useClip = true;
123 * master flag indicating if renderer should ever try to clip. not enabled for
126 private boolean canClip = false;
128 public AnnotationRenderer()
134 * Create a new annotation Renderer
137 * flag indicating if timing and redraw parameter info should be
140 public AnnotationRenderer(boolean debugRedraw)
142 this.debugRedraw = debugRedraw;
146 * Remove any references and resources when this object is no longer required
148 public void dispose()
151 complementConsensus = null;
152 hStrucConsensus = null;
154 annotationPanel = null;
157 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
158 int x, int y, int iconOffset, int startRes, int column,
159 boolean validRes, boolean validEnd)
161 g.setColor(STEM_COLOUR);
162 int sCol = (lastSSX / charWidth) + startRes;
164 int x2 = (x * charWidth);
166 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
167 : row_annotations[column - 1].secondaryStructure;
169 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
170 || dc != row_annotations[sCol - 1].secondaryStructure;
171 boolean diffdownstream = !validRes || !validEnd
172 || row_annotations[column] == null
173 || dc != row_annotations[column].secondaryStructure;
175 if (column > 0 && Rna.isClosingParenthesis(dc))
178 // if (validRes && column>1 && row_annotations[column-2]!=null &&
179 // dc.equals(row_annotations[column-2].displayCharacter))
182 * if new annotation with a closing base pair half of the stem,
183 * display a backward arrow
185 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
186 new int[] { y + iconOffset, y + 14 + iconOffset,
187 y + 8 + iconOffset }, 3);
197 // display a forward arrow
201 * if annotation ending with an opeing base pair half of the stem,
202 * display a forward arrow
204 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
205 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
214 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
217 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
218 Annotation[] row_annotations, int lastSSX, int x, int y,
219 int iconOffset, int startRes, int column, boolean validRes,
222 // System.out.println(nonCanColor);
224 g.setColor(nonCanColor);
225 int sCol = (lastSSX / charWidth) + startRes;
227 int x2 = (x * charWidth);
229 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
230 : row_annotations[column - 1].displayCharacter;
232 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
233 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
234 boolean diffdownstream = !validRes || !validEnd
235 || row_annotations[column] == null
236 || !dc.equals(row_annotations[column].displayCharacter);
237 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
238 // If a closing base pair half of the stem, display a backward arrow
239 if (column > 0 && Rna.isClosingParenthesis(dc))
243 // if (validRes && column>1 && row_annotations[column-2]!=null &&
244 // dc.equals(row_annotations[column-2].displayCharacter))
246 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
247 new int[] { y + iconOffset, y + 14 + iconOffset,
248 y + 8 + iconOffset }, 3);
259 // display a forward arrow
262 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
263 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
272 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
275 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
277 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
280 fm = annotPanel.getFontMetrics();
281 annotationPanel = annotPanel;
282 fadedImage = annotPanel.getFadedImage();
283 imgWidth = annotPanel.getFadedImageWidth();
284 // visible area for rendering
285 int[] bounds = annotPanel.getVisibleVRange();
289 visHeight = bounds[1];
304 updateFromAlignViewport(av);
307 public void updateFromAlignViewport(AlignViewportI av)
309 charWidth = av.getCharWidth();
310 endRes = av.getRanges().getEndRes();
311 charHeight = av.getCharHeight();
312 hasHiddenColumns = av.hasHiddenColumns();
313 validCharWidth = av.isValidCharWidth();
314 av_renderHistogram = av.isShowConsensusHistogram();
315 av_renderProfile = av.isShowSequenceLogo();
316 av_normaliseProfile = av.isNormaliseSequenceLogo();
317 profcolour = av.getResidueShading();
318 if (profcolour == null || profcolour.getColourScheme() == null)
321 * Use default colour for sequence logo if
322 * the alignment has no colourscheme set
323 * (would like to use user preference but n/a for applet)
325 ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
326 : new ZappoColourScheme();
327 profcolour = new ResidueShader(col);
329 columnSelection = av.getColumnSelection();
330 hconsensus = av.getSequenceConsensusHash();
331 complementConsensus = av.getComplementConsensusHash();
332 hStrucConsensus = av.getRnaStructureConsensusHash();
333 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
337 * Returns profile data; the first element is the profile type, the second is
338 * the number of distinct values, the third the total count, and the remainder
339 * depend on the profile type.
345 int[] getProfileFor(AlignmentAnnotation aa, int column)
347 // TODO : consider refactoring the global alignment calculation
348 // properties/rendering attributes as a global 'alignment group' which holds
349 // all vis settings for the alignment as a whole rather than a subset
351 if (aa.autoCalculated
352 && (aa.label.startsWith("Consensus") || aa.label
353 .startsWith("cDNA Consensus")))
355 boolean forComplement = aa.label.startsWith("cDNA Consensus");
356 if (aa.groupRef != null && aa.groupRef.consensusData != null
357 && aa.groupRef.isShowSequenceLogo())
359 // TODO? group consensus for cDNA complement
360 return AAFrequency.extractProfile(
361 aa.groupRef.consensusData.get(column),
362 aa.groupRef.getIgnoreGapsConsensus());
364 // TODO extend annotation row to enable dynamic and static profile data to
366 if (aa.groupRef == null && aa.sequenceRef == null)
370 return AAFrequency.extractCdnaProfile(
371 complementConsensus[column], av_ignoreGapsConsensus);
375 return AAFrequency.extractProfile(
376 hconsensus.get(column),
377 av_ignoreGapsConsensus);
383 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
385 // TODO implement group structure consensus
387 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
388 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
389 * group selections return StructureFrequency.extractProfile(
390 * aa.groupRef.consensusData[column], aa.groupRef
391 * .getIgnoreGapsConsensus()); }
393 // TODO extend annotation row to enable dynamic and static profile data
396 if (aa.groupRef == null && aa.sequenceRef == null
397 && hStrucConsensus != null
398 && hStrucConsensus.length > column)
400 return StructureFrequency.extractProfile(hStrucConsensus[column],
401 av_ignoreGapsConsensus);
411 * Render the annotation rows associated with an alignment.
416 * data and view settings to render
418 * destination for graphics
420 * row where a mouse event occured (or -1)
422 * first column that will be drawn
424 * last column that will be drawn
425 * @return true if the fadedImage was used for any alignment annotation rows
426 * currently being calculated
428 public boolean drawComponent(AwtRenderPanelI annotPanel,
429 AlignViewportI av, Graphics g, int activeRow, int startRes,
432 long stime = System.currentTimeMillis();
433 boolean usedFaded = false;
435 // AnnotationPanel needs to implement: ImageObserver, access to
437 updateFromAwtRenderPanel(annotPanel, av);
438 fm = g.getFontMetrics();
439 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
450 boolean validRes = false;
451 boolean validEnd = false;
452 boolean labelAllCols = false;
453 boolean centreColLabels;
454 boolean centreColLabelsDef = av.isCentreColumnLabels();
455 boolean scaleColLabel = false;
456 final AlignmentAnnotation consensusAnnot = av
457 .getAlignmentConsensusAnnotation();
458 final AlignmentAnnotation structConsensusAnnot = av
459 .getAlignmentStrucConsensusAnnotation();
460 final AlignmentAnnotation complementConsensusAnnot = av
461 .getComplementConsensusAnnotation();
462 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
464 BitSet graphGroupDrawn = new BitSet();
465 int charOffset = 0; // offset for a label
466 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
468 Font ofont = g.getFont();
471 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
472 boolean clipst = false, clipend = false;
473 for (int i = 0; i < aa.length; i++)
475 AlignmentAnnotation row = aa[i];
478 // check if this is a consensus annotation row and set the display
479 // settings appropriately
480 // TODO: generalise this to have render styles for consensus/profile
482 if (row.groupRef != null && row == row.groupRef.getConsensus())
484 renderHistogram = row.groupRef.isShowConsensusHistogram();
485 renderProfile = row.groupRef.isShowSequenceLogo();
486 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
488 else if (row == consensusAnnot || row == structConsensusAnnot
489 || row == complementConsensusAnnot)
491 renderHistogram = av_renderHistogram;
492 renderProfile = av_renderProfile;
493 normaliseProfile = av_normaliseProfile;
497 renderHistogram = true;
498 // don't need to set render/normaliseProfile since they are not
499 // currently used in any other annotation track renderer
502 Annotation[] row_annotations = row.annotations;
507 centreColLabels = row.centreColLabels || centreColLabelsDef;
508 labelAllCols = row.showAllColLabels;
509 scaleColLabel = row.scaleColLabel;
514 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
515 {// if_in_visible_region
526 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
531 // this is so that we draw the characters below the graph
536 iconOffset = charHeight - fm.getDescent();
540 else if (row.hasText)
542 iconOffset = charHeight - fm.getDescent();
550 if (row.autoCalculated && av.isCalculationInProgress(row))
554 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
555 - row.height, imgWidth, y, annotationPanel);
556 g.setColor(Color.black);
557 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
563 * else if (annotationPanel.av.updatingConservation &&
564 * aa[i].label.equals("Conservation")) {
566 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
567 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
568 * annotationPanel.imgWidth, y, annotationPanel);
570 * g.setColor(Color.black); //
571 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
573 * continue; } else if (annotationPanel.av.updatingConservation &&
574 * aa[i].label.equals("Quality")) {
576 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
577 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
578 * annotationPanel.imgWidth, y, annotationPanel);
579 * g.setColor(Color.black); // /
580 * g.drawString("Calculating Quality....",20, y-row.height/2);
584 // first pass sets up state for drawing continuation from left-hand
587 x = (startRes == 0) ? 0 : -1;
588 while (x < endRes - startRes)
590 if (hasHiddenColumns)
592 column = columnSelection.adjustForHiddenColumns(startRes + x);
593 if (column > row_annotations.length - 1)
600 column = startRes + x;
603 if ((row_annotations == null)
604 || (row_annotations.length <= column)
605 || (row_annotations[column] == null))
613 final String displayChar = validRes ? row_annotations[column].displayCharacter
619 g.setColor(Color.red);
621 if (columnSelection != null)
623 if (columnSelection.contains(column))
625 g.fillRect(x * charWidth, y, charWidth, charHeight);
629 if (row.getInvalidStrucPos() > x)
631 g.setColor(Color.orange);
632 g.fillRect(x * charWidth, y, charWidth, charHeight);
634 else if (row.getInvalidStrucPos() == x)
636 g.setColor(Color.orange.darker());
637 g.fillRect(x * charWidth, y, charWidth, charHeight);
639 if (validCharWidth && validRes && displayChar != null
640 && (displayChar.length() > 0))
643 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
644 displayChar.length());
645 if (/* centreColLabels || */scaleColLabel)
647 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
648 // displayChar.length());
650 // if (scaleColLabel)
652 // justify the label and scale to fit in column
653 if (fmWidth > charWidth)
655 // scale only if the current font isn't already small enough
656 fmScaling = charWidth;
657 fmScaling /= fmWidth;
658 g.setFont(ofont.deriveFont(AffineTransform
659 .getScaleInstance(fmScaling, 1.0)));
660 // and update the label's width to reflect the scaling.
665 // TODO is it ok to use width of / show all characters here?
668 // fmWidth = fm.charWidth(displayChar.charAt(0));
670 charOffset = (int) ((charWidth - fmWidth) / 2f);
672 if (row_annotations[column].colour == null)
674 g.setColor(Color.black);
678 g.setColor(row_annotations[column].colour);
681 if (column == 0 || row.graph > 0)
683 g.drawString(displayChar, (x * charWidth) + charOffset, y
686 else if (row_annotations[column - 1] == null
689 .equals(row_annotations[column - 1].displayCharacter) || (displayChar
690 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
692 g.drawString(displayChar, x * charWidth + charOffset, y
700 char ss = validRes ? row_annotations[column].secondaryStructure
705 // distinguish between forward/backward base-pairing
706 if (displayChar.indexOf(')') > -1)
715 if ((displayChar.indexOf(']') > -1))
723 // distinguish between forward/backward base-pairing
724 if (displayChar.indexOf('}') > -1)
732 // distinguish between forward/backward base-pairing
733 if (displayChar.indexOf('<') > -1)
739 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
741 // distinguish between forward/backward base-pairing
742 int ssLowerCase = ss + UPPER_TO_LOWER;
743 // TODO would .equals() be safer here? or charAt(0)?
744 if (displayChar.indexOf(ssLowerCase) > -1)
746 ss = (char) ssLowerCase;
750 if (!validRes || (ss != lastSS))
756 int nb_annot = x - temp;
757 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
760 case '(': // Stem case for RNA secondary structure
761 case ')': // and opposite direction
762 drawStemAnnot(g, row_annotations, lastSSX, x, y,
763 iconOffset, startRes, column, validRes, validEnd);
770 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
771 iconOffset, startRes, column, validRes,
775 // no break if isRNA - falls through to drawNotCanonicalAnnot!
779 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
780 iconOffset, startRes, column, validRes,
784 // no break if isRNA - fall through to drawNotCanonicalAnnot!
843 Color nonCanColor = getNotCanonicalColor(lastSS);
844 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
845 lastSSX, x, y, iconOffset, startRes, column,
850 g.setColor(Color.gray);
851 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
867 lastSSX = (x * charWidth);
874 if (column >= row_annotations.length)
876 column = row_annotations.length - 1;
883 if ((row_annotations == null) || (row_annotations.length <= column)
884 || (row_annotations[column] == null))
902 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
903 startRes, column, validRes, validEnd);
906 // no break if isRNA - fall through to drawNotCanonicalAnnot!
911 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
912 startRes, column, validRes, validEnd);
915 // no break if isRNA - fall through to drawNotCanonicalAnnot!
918 case ')': // Stem case for RNA secondary structure
920 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
921 startRes, column, validRes, validEnd);
978 // System.out.println(lastSS);
979 Color nonCanColor = getNotCanonicalColor(lastSS);
980 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
981 x, y, iconOffset, startRes, column, validRes, validEnd);
984 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
985 startRes, column, validRes, validEnd);
990 if (row.graph > 0 && row.graphHeight > 0)
992 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
994 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
996 // TODO: JAL-1291 revise rendering model so the graphGroup map is
997 // computed efficiently for all visible labels
998 float groupmax = -999999, groupmin = 9999999;
999 for (int gg = 0; gg < aa.length; gg++)
1001 if (aa[gg].graphGroup != row.graphGroup)
1008 aa[gg].visible = false;
1010 if (aa[gg].graphMax > groupmax)
1012 groupmax = aa[gg].graphMax;
1014 if (aa[gg].graphMin < groupmin)
1016 groupmin = aa[gg].graphMin;
1020 for (int gg = 0; gg < aa.length; gg++)
1022 if (aa[gg].graphGroup == row.graphGroup)
1024 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1025 endRes, y, groupmin, groupmax, row.graphHeight);
1029 graphGroupDrawn.set(row.graphGroup);
1033 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1034 row.graphMin, row.graphMax, row.graphHeight);
1037 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1039 drawBarGraph(g, row, row_annotations, startRes, endRes,
1040 row.graphMin, row.graphMax, y, renderHistogram,
1041 renderProfile, normaliseProfile);
1047 if (clipst && !clipend)
1051 }// end if_in_visible_region
1052 if (row.graph > 0 && row.hasText)
1068 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1073 System.err.println("End clip at : " + yto + " (index " + f_to
1078 System.err.println("Annotation Rendering time:"
1079 + (System.currentTimeMillis() - stime));
1086 public static final Color GLYPHLINE_COLOR = Color.gray;
1088 public static final Color SHEET_COLOUR = Color.green;
1090 public static final Color HELIX_COLOUR = Color.red;
1092 public static final Color STEM_COLOUR = Color.blue;
1094 private Color sdNOTCANONICAL_COLOUR;
1096 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1097 int y, int iconOffset, int startRes, int column,
1098 boolean validRes, boolean validEnd)
1100 g.setColor(GLYPHLINE_COLOR);
1101 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1104 void drawSheetAnnot(Graphics g, Annotation[] row,
1106 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1107 boolean validRes, boolean validEnd)
1109 g.setColor(SHEET_COLOUR);
1111 if (!validEnd || !validRes || row == null || row[column] == null
1112 || row[column].secondaryStructure != 'E')
1114 g.fillRect(lastSSX, y + 4 + iconOffset,
1115 (x * charWidth) - lastSSX - 4, 7);
1116 g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
1117 (x * charWidth) }, new int[] { y + iconOffset,
1118 y + 14 + iconOffset, y + 7 + iconOffset }, 3);
1122 g.fillRect(lastSSX, y + 4 + iconOffset,
1123 (x + 1) * charWidth - lastSSX, 7);
1128 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1129 int y, int iconOffset, int startRes, int column,
1130 boolean validRes, boolean validEnd)
1132 g.setColor(HELIX_COLOUR);
1134 int sCol = (lastSSX / charWidth) + startRes;
1136 int x2 = (x * charWidth);
1140 int ofs = charWidth / 2;
1141 // Off by 1 offset when drawing rects and ovals
1142 // to offscreen image on the MAC
1143 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1144 if (sCol == 0 || row[sCol - 1] == null
1145 || row[sCol - 1].secondaryStructure != 'H')
1150 // g.setColor(Color.orange);
1151 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1154 if (!validRes || row[column] == null
1155 || row[column].secondaryStructure != 'H')
1161 // g.setColor(Color.magenta);
1162 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1170 if (sCol == 0 || row[sCol - 1] == null
1171 || row[sCol - 1].secondaryStructure != 'H')
1173 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1174 x1 += charWidth / 2;
1177 if (!validRes || row[column] == null
1178 || row[column].secondaryStructure != 'H')
1180 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1182 x2 -= charWidth / 2;
1185 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1188 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1189 Annotation[] aa_annotations, int sRes, int eRes, int y,
1190 float min, float max, int graphHeight)
1192 if (sRes > aa_annotations.length)
1199 // Adjustment for fastpaint to left
1205 eRes = Math.min(eRes, aa_annotations.length);
1213 float range = max - min;
1218 y2 = y - (int) ((0 - min / range) * graphHeight);
1221 g.setColor(Color.gray);
1222 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1224 eRes = Math.min(eRes, aa_annotations.length);
1227 int aaMax = aa_annotations.length - 1;
1229 while (x < eRes - sRes)
1232 if (hasHiddenColumns)
1234 column = columnSelection.adjustForHiddenColumns(column);
1242 if (aa_annotations[column] == null
1243 || aa_annotations[column - 1] == null)
1249 if (aa_annotations[column].colour == null)
1251 g.setColor(Color.black);
1255 g.setColor(aa_annotations[column].colour);
1259 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1261 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1263 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1264 + charWidth / 2, y2);
1268 if (_aa.threshold != null)
1270 g.setColor(_aa.threshold.colour);
1271 Graphics2D g2 = (Graphics2D) g;
1272 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1273 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1275 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1276 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1277 g2.setStroke(new BasicStroke());
1281 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1282 Annotation[] aa_annotations, int sRes, int eRes, float min,
1283 float max, int y, boolean renderHistogram, boolean renderProfile,
1284 boolean normaliseProfile)
1286 if (sRes > aa_annotations.length)
1290 Font ofont = g.getFont();
1291 eRes = Math.min(eRes, aa_annotations.length);
1293 int x = 0, y1 = y, y2 = y;
1295 float range = max - min;
1299 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1302 g.setColor(Color.gray);
1304 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1307 int aaMax = aa_annotations.length - 1;
1308 while (x < eRes - sRes)
1311 if (hasHiddenColumns)
1313 column = columnSelection.adjustForHiddenColumns(column);
1321 if (aa_annotations[column] == null)
1326 if (aa_annotations[column].colour == null)
1328 g.setColor(Color.black);
1332 g.setColor(aa_annotations[column].colour);
1336 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1338 if (renderHistogram)
1342 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1346 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1349 // draw profile if available
1354 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1356 int profl[] = getProfileFor(_aa, column);
1358 // just try to draw the logo if profl is not null
1359 if (profl != null && profl[2] != 0)
1361 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1362 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1363 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1364 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1371 * Render a single base for a sequence profile, a base pair for
1372 * structure profile, and a triplet for a cdna profile
1374 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1376 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1377 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1378 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1382 * Traverse the character(s)/percentage data in the array
1385 int valuesProcessed = 0;
1386 // profl[1] is the number of values in the profile
1387 while (valuesProcessed < profl[1])
1389 if (isStructureProfile)
1391 // todo can we encode a structure pair as an int, like codons?
1392 dc[0] = (char) profl[c++];
1393 dc[1] = (char) profl[c++];
1395 else if (isCdnaProfile)
1397 dc = CodingUtils.decodeCodon(profl[c++]);
1401 dc[0] = (char) profl[c++];
1405 wdth /= fm.charsWidth(dc, 0, dc.length);
1408 // next profl[] position is profile % for the character(s)
1409 scl = htn * scale * profl[c++];
1410 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1411 .getFontRenderContext());
1412 Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
1413 wdth, scl / lm.getAscent()));
1415 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1417 // Debug - render boxes around characters
1418 // g.setColor(Color.red);
1419 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1421 // g.setColor(profcolour.findColour(dc[0]).darker());
1424 * Set character colour as per alignment colour scheme; use the
1425 * codon translation if a cDNA profile
1427 Color colour = null;
1430 final String codonTranslation = ResidueProperties
1431 .codonTranslate(new String(dc));
1432 colour = profcolour.findColour(codonTranslation.charAt(0),
1437 colour = profcolour.findColour(dc[0], column, null);
1439 g.setColor(colour == Color.white ? Color.lightGray : colour);
1441 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1442 .getBaselineIndex()]));
1444 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1452 if (_aa.threshold != null)
1454 g.setColor(_aa.threshold.colour);
1455 Graphics2D g2 = (Graphics2D) g;
1456 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1457 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1459 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1461 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1462 g2.setStroke(new BasicStroke());
1466 // used by overview window
1467 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1468 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1470 eRes = Math.min(eRes, aa_annotations.length);
1471 g.setColor(Color.white);
1472 g.fillRect(0, 0, width, y);
1473 g.setColor(new Color(0, 0, 180));
1477 for (int j = sRes; j < eRes; j++)
1479 if (aa_annotations[j] != null)
1481 if (aa_annotations[j].colour == null)
1483 g.setColor(Color.black);
1487 g.setColor(aa_annotations[j].colour);
1490 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1496 g.fillRect(x, y - height, charWidth, height);
1502 Color getNotCanonicalColor(char lastss)
1508 return new Color(255, 125, 5);
1512 return new Color(245, 115, 10);
1516 return new Color(235, 135, 15);
1520 return new Color(225, 105, 20);
1524 return new Color(215, 145, 30);
1528 return new Color(205, 95, 35);
1532 return new Color(195, 155, 45);
1536 return new Color(185, 85, 55);
1540 return new Color(175, 165, 65);
1544 return new Color(170, 75, 75);
1548 return new Color(160, 175, 85);
1552 return new Color(150, 65, 95);
1556 return new Color(140, 185, 105);
1560 return new Color(130, 55, 110);
1564 return new Color(120, 195, 120);
1568 return new Color(110, 45, 130);
1572 return new Color(100, 205, 140);
1576 return new Color(90, 35, 150);
1580 return new Color(85, 215, 160);
1584 return new Color(75, 25, 170);
1588 return new Color(65, 225, 180);
1592 return new Color(55, 15, 185);
1596 return new Color(45, 235, 195);
1600 return new Color(35, 5, 205);
1604 return new Color(25, 245, 215);
1608 return new Color(15, 0, 225);
1612 return new Color(10, 255, 235);
1616 return new Color(5, 150, 245);
1620 return new Color(0, 80, 255);
1623 System.out.println("This is not a interaction : " + lastss);