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.renderer.api.AnnotationRendererFactoryI;
33 import jalview.renderer.api.AnnotationRowRendererI;
34 import jalview.schemes.ColourSchemeI;
35 import jalview.schemes.ResidueProperties;
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 ColourSchemeI 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;
155 rendererFactoryI = null;
158 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
159 int x, int y, int iconOffset, int startRes, int column,
160 boolean validRes, boolean validEnd)
162 g.setColor(STEM_COLOUR);
163 int sCol = (lastSSX / charWidth) + startRes;
165 int x2 = (x * charWidth);
167 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
168 : row_annotations[column - 1].secondaryStructure;
170 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
171 || dc != row_annotations[sCol - 1].secondaryStructure;
172 boolean diffdownstream = !validRes || !validEnd
173 || row_annotations[column] == null
174 || dc != row_annotations[column].secondaryStructure;
176 if (column > 0 && Rna.isClosingParenthesis(dc))
179 // if (validRes && column>1 && row_annotations[column-2]!=null &&
180 // dc.equals(row_annotations[column-2].displayCharacter))
183 * if new annotation with a closing base pair half of the stem,
184 * display a backward arrow
186 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
187 new int[] { y + iconOffset, y + 14 + iconOffset,
188 y + 8 + iconOffset }, 3);
198 // display a forward arrow
202 * if annotation ending with an opeing base pair half of the stem,
203 * display a forward arrow
205 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
206 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
215 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
218 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
219 Annotation[] row_annotations, int lastSSX, int x, int y,
220 int iconOffset, int startRes, int column, boolean validRes,
223 // System.out.println(nonCanColor);
225 g.setColor(nonCanColor);
226 int sCol = (lastSSX / charWidth) + startRes;
228 int x2 = (x * charWidth);
230 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
231 : row_annotations[column - 1].displayCharacter;
233 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
234 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
235 boolean diffdownstream = !validRes || !validEnd
236 || row_annotations[column] == null
237 || !dc.equals(row_annotations[column].displayCharacter);
238 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
239 // If a closing base pair half of the stem, display a backward arrow
240 if (column > 0 && Rna.isClosingParenthesis(dc))
244 // if (validRes && column>1 && row_annotations[column-2]!=null &&
245 // dc.equals(row_annotations[column-2].displayCharacter))
247 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
248 new int[] { y + iconOffset, y + 14 + iconOffset,
249 y + 8 + iconOffset }, 3);
260 // display a forward arrow
263 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
264 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
273 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
276 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
278 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
281 fm = annotPanel.getFontMetrics();
282 annotationPanel = annotPanel;
283 fadedImage = annotPanel.getFadedImage();
284 imgWidth = annotPanel.getFadedImageWidth();
285 // visible area for rendering
286 int[] bounds = annotPanel.getVisibleVRange();
290 visHeight = bounds[1];
305 updateFromAlignViewport(av);
308 public void updateFromAlignViewport(AlignViewportI av)
310 charWidth = av.getCharWidth();
311 endRes = av.getEndRes();
312 charHeight = av.getCharHeight();
313 hasHiddenColumns = av.hasHiddenColumns();
314 validCharWidth = av.isValidCharWidth();
315 av_renderHistogram = av.isShowConsensusHistogram();
316 av_renderProfile = av.isShowSequenceLogo();
317 av_normaliseProfile = av.isNormaliseSequenceLogo();
318 profcolour = av.getGlobalColourScheme();
319 if (profcolour == null)
321 // Set the default colour for sequence logo if the alignnent has no
323 profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
324 : new jalview.schemes.ZappoColourScheme();
326 columnSelection = av.getColumnSelection();
327 hconsensus = av.getSequenceConsensusHash();
328 complementConsensus = av.getComplementConsensusHash();
329 hStrucConsensus = av.getRnaStructureConsensusHash();
330 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
334 * Returns profile data; the first element is the profile type, the second is
335 * the number of distinct values, the third the total count, and the remainder
336 * depend on the profile type.
342 int[] getProfileFor(AlignmentAnnotation aa, int column)
344 // TODO : consider refactoring the global alignment calculation
345 // properties/rendering attributes as a global 'alignment group' which holds
346 // all vis settings for the alignment as a whole rather than a subset
348 if (aa.autoCalculated
349 && (aa.label.startsWith("Consensus") || aa.label
350 .startsWith("cDNA Consensus")))
352 boolean forComplement = aa.label.startsWith("cDNA Consensus");
353 if (aa.groupRef != null && aa.groupRef.consensusData != null
354 && aa.groupRef.isShowSequenceLogo())
356 // TODO? group consensus for cDNA complement
357 return AAFrequency.extractProfile(
358 aa.groupRef.consensusData.get(column),
359 aa.groupRef.getIgnoreGapsConsensus());
361 // TODO extend annotation row to enable dynamic and static profile data to
363 if (aa.groupRef == null && aa.sequenceRef == null)
367 return AAFrequency.extractCdnaProfile(
368 complementConsensus[column], av_ignoreGapsConsensus);
372 return AAFrequency.extractProfile(hconsensus.get(column),
373 av_ignoreGapsConsensus);
379 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
381 // TODO implement group structure consensus
383 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
384 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
385 * group selections return StructureFrequency.extractProfile(
386 * aa.groupRef.consensusData[column], aa.groupRef
387 * .getIgnoreGapsConsensus()); }
389 // TODO extend annotation row to enable dynamic and static profile data
392 if (aa.groupRef == null && aa.sequenceRef == null
393 && hStrucConsensus != null
394 && hStrucConsensus.length > column)
396 return StructureFrequency.extractProfile(hStrucConsensus[column],
397 av_ignoreGapsConsensus);
406 private AnnotationRendererFactoryI rendererFactoryI;
409 * Render the annotation rows associated with an alignment.
414 * data and view settings to render
416 * destination for graphics
418 * row where a mouse event occured (or -1)
420 * first column that will be drawn
422 * last column that will be drawn
423 * @return true if the fadedImage was used for any alignment annotation rows
424 * currently being calculated
426 public boolean drawComponent(AwtRenderPanelI annotPanel,
427 AlignViewportI av, Graphics g, int activeRow, int startRes,
430 long stime = System.currentTimeMillis();
431 boolean usedFaded = false;
433 // AnnotationPanel needs to implement: ImageObserver, access to
435 updateFromAwtRenderPanel(annotPanel, av);
436 fm = g.getFontMetrics();
437 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
448 boolean validRes = false;
449 boolean validEnd = false;
450 boolean labelAllCols = false;
451 boolean centreColLabels;
452 boolean centreColLabelsDef = av.isCentreColumnLabels();
453 boolean scaleColLabel = false;
454 final AlignmentAnnotation consensusAnnot = av
455 .getAlignmentConsensusAnnotation();
456 final AlignmentAnnotation structConsensusAnnot = av
457 .getAlignmentStrucConsensusAnnotation();
458 final AlignmentAnnotation complementConsensusAnnot = av
459 .getComplementConsensusAnnotation();
460 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
462 BitSet graphGroupDrawn = new BitSet();
463 int charOffset = 0; // offset for a label
464 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
466 Font ofont = g.getFont();
469 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
470 boolean clipst = false, clipend = false;
471 for (int i = 0; i < aa.length; i++)
473 AlignmentAnnotation row = aa[i];
476 // check if this is a consensus annotation row and set the display
477 // settings appropriately
478 // TODO: generalise this to have render styles for consensus/profile
480 if (row.groupRef != null && row == row.groupRef.getConsensus())
482 renderHistogram = row.groupRef.isShowConsensusHistogram();
483 renderProfile = row.groupRef.isShowSequenceLogo();
484 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
486 else if (row == consensusAnnot || row == structConsensusAnnot
487 || row == complementConsensusAnnot)
489 renderHistogram = av_renderHistogram;
490 renderProfile = av_renderProfile;
491 normaliseProfile = av_normaliseProfile;
495 renderHistogram = true;
496 // don't need to set render/normaliseProfile since they are not
497 // currently used in any other annotation track renderer
500 Annotation[] row_annotations = row.annotations;
505 centreColLabels = row.centreColLabels || centreColLabelsDef;
506 labelAllCols = row.showAllColLabels;
507 scaleColLabel = row.scaleColLabel;
512 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
513 {// if_in_visible_region
524 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
529 // this is so that we draw the characters below the graph
534 iconOffset = charHeight - fm.getDescent();
538 else if (row.hasText)
540 iconOffset = charHeight - fm.getDescent();
548 if (row.autoCalculated && av.isCalculationInProgress(row))
552 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
553 - row.height, imgWidth, y, annotationPanel);
554 g.setColor(Color.black);
555 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
561 * else if (annotationPanel.av.updatingConservation &&
562 * aa[i].label.equals("Conservation")) {
564 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
565 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
566 * annotationPanel.imgWidth, y, annotationPanel);
568 * g.setColor(Color.black); //
569 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
571 * continue; } else if (annotationPanel.av.updatingConservation &&
572 * aa[i].label.equals("Quality")) {
574 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
575 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
576 * annotationPanel.imgWidth, y, annotationPanel);
577 * g.setColor(Color.black); // /
578 * g.drawString("Calculating Quality....",20, y-row.height/2);
582 // first pass sets up state for drawing continuation from left-hand
585 x = (startRes == 0) ? 0 : -1;
586 while (x < endRes - startRes)
588 if (hasHiddenColumns)
590 column = columnSelection.adjustForHiddenColumns(startRes + x);
591 if (column > row_annotations.length - 1)
598 column = startRes + x;
601 if ((row_annotations == null)
602 || (row_annotations.length <= column)
603 || (row_annotations[column] == null))
611 final String displayChar = validRes ? row_annotations[column].displayCharacter
617 g.setColor(Color.red);
619 if (columnSelection != null)
621 if (columnSelection.contains(column))
623 g.fillRect(x * charWidth, y, charWidth, charHeight);
627 if (row.getInvalidStrucPos() > x)
629 g.setColor(Color.orange);
630 g.fillRect(x * charWidth, y, charWidth, charHeight);
632 else if (row.getInvalidStrucPos() == x)
634 g.setColor(Color.orange.darker());
635 g.fillRect(x * charWidth, y, charWidth, charHeight);
637 if (validCharWidth && validRes && displayChar != null
638 && (displayChar.length() > 0))
641 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
642 displayChar.length());
643 if (/* centreColLabels || */scaleColLabel)
645 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
646 // displayChar.length());
648 // if (scaleColLabel)
650 // justify the label and scale to fit in column
651 if (fmWidth > charWidth)
653 // scale only if the current font isn't already small enough
654 fmScaling = charWidth;
655 fmScaling /= fmWidth;
656 g.setFont(ofont.deriveFont(AffineTransform
657 .getScaleInstance(fmScaling, 1.0)));
658 // and update the label's width to reflect the scaling.
663 // TODO is it ok to use width of / show all characters here?
666 // fmWidth = fm.charWidth(displayChar.charAt(0));
668 charOffset = (int) ((charWidth - fmWidth) / 2f);
670 if (row_annotations[column].colour == null)
672 g.setColor(Color.black);
676 g.setColor(row_annotations[column].colour);
679 if (column == 0 || row.graph > 0)
681 g.drawString(displayChar, (x * charWidth) + charOffset, y
684 else if (row_annotations[column - 1] == null
687 .equals(row_annotations[column - 1].displayCharacter) || (displayChar
688 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
690 g.drawString(displayChar, x * charWidth + charOffset, y
698 char ss = validRes ? row_annotations[column].secondaryStructure
703 // distinguish between forward/backward base-pairing
704 if (displayChar.indexOf(')') > -1)
713 if ((displayChar.indexOf(']') > -1))
721 // distinguish between forward/backward base-pairing
722 if (displayChar.indexOf('}') > -1)
730 // distinguish between forward/backward base-pairing
731 if (displayChar.indexOf('<') > -1)
737 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
739 // distinguish between forward/backward base-pairing
740 int ssLowerCase = ss + UPPER_TO_LOWER;
741 // TODO would .equals() be safer here? or charAt(0)?
742 if (displayChar.indexOf(ssLowerCase) > -1)
744 ss = (char) ssLowerCase;
748 if (!validRes || (ss != lastSS))
754 int nb_annot = x - temp;
755 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
758 case '(': // Stem case for RNA secondary structure
759 case ')': // and opposite direction
760 drawStemAnnot(g, row_annotations, lastSSX, x, y,
761 iconOffset, startRes, column, validRes, validEnd);
768 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
769 iconOffset, startRes, column, validRes,
773 // no break if isRNA - falls through to drawNotCanonicalAnnot!
777 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
778 iconOffset, startRes, column, validRes,
782 // no break if isRNA - fall through to drawNotCanonicalAnnot!
841 Color nonCanColor = getNotCanonicalColor(lastSS);
842 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
843 lastSSX, x, y, iconOffset, startRes, column,
848 g.setColor(Color.gray);
849 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
865 lastSSX = (x * charWidth);
872 if (column >= row_annotations.length)
874 column = row_annotations.length - 1;
881 if ((row_annotations == null) || (row_annotations.length <= column)
882 || (row_annotations[column] == null))
900 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
901 startRes, column, validRes, validEnd);
904 // no break if isRNA - fall through to drawNotCanonicalAnnot!
909 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
910 startRes, column, validRes, validEnd);
913 // no break if isRNA - fall through to drawNotCanonicalAnnot!
916 case ')': // Stem case for RNA secondary structure
918 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
919 startRes, column, validRes, validEnd);
976 // System.out.println(lastSS);
977 Color nonCanColor = getNotCanonicalColor(lastSS);
978 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
979 x, y, iconOffset, startRes, column, validRes, validEnd);
982 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
983 startRes, column, validRes, validEnd);
988 if (row.graph > 0 && row.graphHeight > 0)
990 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
992 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
994 // TODO: JAL-1291 revise rendering model so the graphGroup map is
995 // computed efficiently for all visible labels
996 float groupmax = -999999, groupmin = 9999999;
997 for (int gg = 0; gg < aa.length; gg++)
999 if (aa[gg].graphGroup != row.graphGroup)
1006 aa[gg].visible = false;
1008 if (aa[gg].graphMax > groupmax)
1010 groupmax = aa[gg].graphMax;
1012 if (aa[gg].graphMin < groupmin)
1014 groupmin = aa[gg].graphMin;
1018 for (int gg = 0; gg < aa.length; gg++)
1020 if (aa[gg].graphGroup == row.graphGroup)
1022 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1023 endRes, y, groupmin, groupmax, row.graphHeight);
1027 graphGroupDrawn.set(row.graphGroup);
1031 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1032 row.graphMin, row.graphMax, row.graphHeight);
1035 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1037 drawBarGraph(g, row, row_annotations, startRes, endRes,
1038 row.graphMin, row.graphMax, y, renderHistogram,
1039 renderProfile, normaliseProfile);
1043 AnnotationRowRendererI renderer = rendererFactoryI
1044 .getRendererFor(row);
1045 if (renderer != null)
1047 renderer.renderRow(g, charWidth, charHeight,
1048 hasHiddenColumns, av, columnSelection, row,
1049 row_annotations, startRes, endRes, row.graphMin,
1051 System.err.println("rendered with "
1052 + renderer.getClass().toString());
1059 if (clipst && !clipend)
1063 }// end if_in_visible_region
1064 if (row.graph > 0 && row.hasText)
1080 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1085 System.err.println("End clip at : " + yto + " (index " + f_to
1090 System.err.println("Annotation Rendering time:"
1091 + (System.currentTimeMillis() - stime));
1098 public static final Color GLYPHLINE_COLOR = Color.gray;
1100 public static final Color SHEET_COLOUR = Color.green;
1102 public static final Color HELIX_COLOUR = Color.red;
1104 public static final Color STEM_COLOUR = Color.blue;
1106 private Color sdNOTCANONICAL_COLOUR;
1108 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1109 int y, int iconOffset, int startRes, int column,
1110 boolean validRes, boolean validEnd)
1112 g.setColor(GLYPHLINE_COLOR);
1113 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1116 void drawSheetAnnot(Graphics g, Annotation[] row,
1118 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1119 boolean validRes, boolean validEnd)
1121 g.setColor(SHEET_COLOUR);
1123 if (!validEnd || !validRes || row == null || row[column] == null
1124 || row[column].secondaryStructure != 'E')
1126 g.fillRect(lastSSX, y + 4 + iconOffset,
1127 (x * charWidth) - lastSSX - 4, 7);
1128 g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
1129 (x * charWidth) }, new int[] { y + iconOffset,
1130 y + 14 + iconOffset, y + 7 + iconOffset }, 3);
1134 g.fillRect(lastSSX, y + 4 + iconOffset,
1135 (x + 1) * charWidth - lastSSX, 7);
1140 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1141 int y, int iconOffset, int startRes, int column,
1142 boolean validRes, boolean validEnd)
1144 g.setColor(HELIX_COLOUR);
1146 int sCol = (lastSSX / charWidth) + startRes;
1148 int x2 = (x * charWidth);
1152 int ofs = charWidth / 2;
1153 // Off by 1 offset when drawing rects and ovals
1154 // to offscreen image on the MAC
1155 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1156 if (sCol == 0 || row[sCol - 1] == null
1157 || row[sCol - 1].secondaryStructure != 'H')
1162 // g.setColor(Color.orange);
1163 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1166 if (!validRes || row[column] == null
1167 || row[column].secondaryStructure != 'H')
1173 // g.setColor(Color.magenta);
1174 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1182 if (sCol == 0 || row[sCol - 1] == null
1183 || row[sCol - 1].secondaryStructure != 'H')
1185 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1186 x1 += charWidth / 2;
1189 if (!validRes || row[column] == null
1190 || row[column].secondaryStructure != 'H')
1192 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1194 x2 -= charWidth / 2;
1197 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1200 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1201 Annotation[] aa_annotations, int sRes, int eRes, int y,
1202 float min, float max, int graphHeight)
1204 if (sRes > aa_annotations.length)
1211 // Adjustment for fastpaint to left
1217 eRes = Math.min(eRes, aa_annotations.length);
1225 float range = max - min;
1230 y2 = y - (int) ((0 - min / range) * graphHeight);
1233 g.setColor(Color.gray);
1234 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1236 eRes = Math.min(eRes, aa_annotations.length);
1239 int aaMax = aa_annotations.length - 1;
1241 while (x < eRes - sRes)
1244 if (hasHiddenColumns)
1246 column = columnSelection.adjustForHiddenColumns(column);
1254 if (aa_annotations[column] == null
1255 || aa_annotations[column - 1] == null)
1261 if (aa_annotations[column].colour == null)
1263 g.setColor(Color.black);
1267 g.setColor(aa_annotations[column].colour);
1271 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1273 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1275 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1276 + charWidth / 2, y2);
1280 if (_aa.threshold != null)
1282 g.setColor(_aa.threshold.colour);
1283 Graphics2D g2 = (Graphics2D) g;
1284 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1285 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1287 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1288 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1289 g2.setStroke(new BasicStroke());
1293 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1294 Annotation[] aa_annotations, int sRes, int eRes, float min,
1295 float max, int y, boolean renderHistogram, boolean renderProfile,
1296 boolean normaliseProfile)
1298 if (sRes > aa_annotations.length)
1302 Font ofont = g.getFont();
1303 eRes = Math.min(eRes, aa_annotations.length);
1305 int x = 0, y1 = y, y2 = y;
1307 float range = max - min;
1311 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1314 g.setColor(Color.gray);
1316 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1319 int aaMax = aa_annotations.length - 1;
1320 while (x < eRes - sRes)
1323 if (hasHiddenColumns)
1325 column = columnSelection.adjustForHiddenColumns(column);
1333 if (aa_annotations[column] == null)
1338 if (aa_annotations[column].colour == null)
1340 g.setColor(Color.black);
1344 g.setColor(aa_annotations[column].colour);
1348 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1350 if (renderHistogram)
1354 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1358 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1361 // draw profile if available
1366 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1368 int profl[] = getProfileFor(_aa, column);
1370 // just try to draw the logo if profl is not null
1371 if (profl != null && profl[2] != 0)
1373 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1374 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1375 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1376 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1383 * Render a single base for a sequence profile, a base pair for
1384 * structure profile, and a triplet for a cdna profile
1386 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1388 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1389 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1390 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1394 * Traverse the character(s)/percentage data in the array
1397 int valuesProcessed = 0;
1398 // profl[1] is the number of values in the profile
1399 while (valuesProcessed < profl[1])
1401 if (isStructureProfile)
1403 // todo can we encode a structure pair as an int, like codons?
1404 dc[0] = (char) profl[c++];
1405 dc[1] = (char) profl[c++];
1407 else if (isCdnaProfile)
1409 dc = CodingUtils.decodeCodon(profl[c++]);
1413 dc[0] = (char) profl[c++];
1417 wdth /= fm.charsWidth(dc, 0, dc.length);
1420 // next profl[] position is profile % for the character(s)
1421 scl = htn * scale * profl[c++];
1422 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1423 .getFontRenderContext());
1424 Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
1425 wdth, scl / lm.getAscent()));
1427 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1429 // Debug - render boxes around characters
1430 // g.setColor(Color.red);
1431 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1433 // g.setColor(profcolour.findColour(dc[0]).darker());
1436 * Set character colour as per alignment colour scheme; use the
1437 * codon translation if a cDNA profile
1439 Color colour = null;
1442 final String codonTranslation = ResidueProperties
1443 .codonTranslate(new String(dc));
1444 colour = profcolour.findColour(codonTranslation.charAt(0),
1449 colour = profcolour.findColour(dc[0], column, null);
1451 g.setColor(colour == Color.white ? Color.lightGray : colour);
1453 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1454 .getBaselineIndex()]));
1456 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1464 if (_aa.threshold != null)
1466 g.setColor(_aa.threshold.colour);
1467 Graphics2D g2 = (Graphics2D) g;
1468 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1469 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1471 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1473 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1474 g2.setStroke(new BasicStroke());
1478 // used by overview window
1479 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1480 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1482 eRes = Math.min(eRes, aa_annotations.length);
1483 g.setColor(Color.white);
1484 g.fillRect(0, 0, width, y);
1485 g.setColor(new Color(0, 0, 180));
1489 for (int j = sRes; j < eRes; j++)
1491 if (aa_annotations[j] != null)
1493 if (aa_annotations[j].colour == null)
1495 g.setColor(Color.black);
1499 g.setColor(aa_annotations[j].colour);
1502 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1508 g.fillRect(x, y - height, charWidth, height);
1514 Color getNotCanonicalColor(char lastss)
1520 return new Color(255, 125, 5);
1524 return new Color(245, 115, 10);
1528 return new Color(235, 135, 15);
1532 return new Color(225, 105, 20);
1536 return new Color(215, 145, 30);
1540 return new Color(205, 95, 35);
1544 return new Color(195, 155, 45);
1548 return new Color(185, 85, 55);
1552 return new Color(175, 165, 65);
1556 return new Color(170, 75, 75);
1560 return new Color(160, 175, 85);
1564 return new Color(150, 65, 95);
1568 return new Color(140, 185, 105);
1572 return new Color(130, 55, 110);
1576 return new Color(120, 195, 120);
1580 return new Color(110, 45, 130);
1584 return new Color(100, 205, 140);
1588 return new Color(90, 35, 150);
1592 return new Color(85, 215, 160);
1596 return new Color(75, 25, 170);
1600 return new Color(65, 225, 180);
1604 return new Color(55, 15, 185);
1608 return new Color(45, 235, 195);
1612 return new Color(35, 5, 205);
1616 return new Color(25, 245, 215);
1620 return new Color(15, 0, 225);
1624 return new Color(10, 255, 235);
1628 return new Color(5, 150, 245);
1632 return new Color(0, 80, 255);
1635 System.out.println("This is not a interaction : " + lastss);