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.renderer.api.AnnotationRendererFactoryI;
34 import jalview.renderer.api.AnnotationRowRendererI;
35 import jalview.schemes.ColourSchemeI;
36 import jalview.schemes.NucleotideColourScheme;
37 import jalview.schemes.ResidueProperties;
38 import jalview.schemes.ZappoColourScheme;
39 import jalview.util.Platform;
41 import java.awt.BasicStroke;
42 import java.awt.Color;
44 import java.awt.FontMetrics;
45 import java.awt.Graphics;
46 import java.awt.Graphics2D;
47 import java.awt.Image;
48 import java.awt.font.LineMetrics;
49 import java.awt.geom.AffineTransform;
50 import java.awt.image.ImageObserver;
51 import java.util.BitSet;
52 import java.util.Hashtable;
54 public class AnnotationRenderer
56 private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
58 private static final int CHAR_A = 'A'; // 65
60 private static final int CHAR_Z = 'Z'; // 90
63 * flag indicating if timing and redraw parameter info should be output
65 private final boolean debugRedraw;
67 private int charWidth, endRes, charHeight;
69 private boolean validCharWidth, hasHiddenColumns;
71 private FontMetrics fm;
73 private final boolean MAC = Platform.isAMac();
75 boolean av_renderHistogram = true, av_renderProfile = true,
76 av_normaliseProfile = false;
78 ResidueShaderI profcolour = null;
80 private ColumnSelection columnSelection;
82 private HiddenColumns hiddenColumns;
84 private ProfilesI hconsensus;
86 private Hashtable[] complementConsensus;
88 private Hashtable[] hStrucConsensus;
90 private boolean av_ignoreGapsConsensus;
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;
160 rendererFactoryI = null;
163 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
164 int x, int y, int iconOffset, int startRes, int column,
165 boolean validRes, boolean validEnd)
167 g.setColor(STEM_COLOUR);
168 int sCol = (lastSSX / charWidth) + startRes;
170 int x2 = (x * charWidth);
172 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
173 : row_annotations[column - 1].secondaryStructure;
175 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
176 || dc != row_annotations[sCol - 1].secondaryStructure;
177 boolean diffdownstream = !validRes || !validEnd
178 || row_annotations[column] == null
179 || dc != row_annotations[column].secondaryStructure;
181 if (column > 0 && Rna.isClosingParenthesis(dc))
184 // if (validRes && column>1 && row_annotations[column-2]!=null &&
185 // dc.equals(row_annotations[column-2].displayCharacter))
188 * if new annotation with a closing base pair half of the stem,
189 * display a backward arrow
191 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
192 new int[] { y + iconOffset, y + 14 + iconOffset,
193 y + 8 + iconOffset }, 3);
203 // display a forward arrow
207 * if annotation ending with an opeing base pair half of the stem,
208 * display a forward arrow
210 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
211 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
220 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
223 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
224 Annotation[] row_annotations, int lastSSX, int x, int y,
225 int iconOffset, int startRes, int column, boolean validRes,
228 // System.out.println(nonCanColor);
230 g.setColor(nonCanColor);
231 int sCol = (lastSSX / charWidth) + startRes;
233 int x2 = (x * charWidth);
235 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
236 : row_annotations[column - 1].displayCharacter;
238 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
239 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
240 boolean diffdownstream = !validRes || !validEnd
241 || row_annotations[column] == null
242 || !dc.equals(row_annotations[column].displayCharacter);
243 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
244 // If a closing base pair half of the stem, display a backward arrow
245 if (column > 0 && Rna.isClosingParenthesis(dc))
249 // if (validRes && column>1 && row_annotations[column-2]!=null &&
250 // dc.equals(row_annotations[column-2].displayCharacter))
252 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
253 new int[] { y + iconOffset, y + 14 + iconOffset,
254 y + 8 + iconOffset }, 3);
265 // display a forward arrow
268 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
269 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
278 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
281 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
283 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
286 fm = annotPanel.getFontMetrics();
287 annotationPanel = annotPanel;
288 fadedImage = annotPanel.getFadedImage();
289 imgWidth = annotPanel.getFadedImageWidth();
290 // visible area for rendering
291 int[] bounds = annotPanel.getVisibleVRange();
295 visHeight = bounds[1];
310 rendererFactoryI = AnnotationRendererFactory.getRendererFactory();
311 updateFromAlignViewport(av);
314 public void updateFromAlignViewport(AlignViewportI av)
316 charWidth = av.getCharWidth();
317 endRes = av.getRanges().getEndRes();
318 charHeight = av.getCharHeight();
319 hasHiddenColumns = av.hasHiddenColumns();
320 validCharWidth = av.isValidCharWidth();
321 av_renderHistogram = av.isShowConsensusHistogram();
322 av_renderProfile = av.isShowSequenceLogo();
323 av_normaliseProfile = av.isNormaliseSequenceLogo();
324 profcolour = av.getResidueShading();
325 if (profcolour == null || profcolour.getColourScheme() == null)
328 * Use default colour for sequence logo if
329 * the alignment has no colourscheme set
330 * (would like to use user preference but n/a for applet)
332 ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
333 : new ZappoColourScheme();
334 profcolour = new ResidueShader(col);
336 columnSelection = av.getColumnSelection();
337 hiddenColumns = av.getAlignment().getHiddenColumns();
338 hconsensus = av.getSequenceConsensusHash();
339 complementConsensus = av.getComplementConsensusHash();
340 hStrucConsensus = av.getRnaStructureConsensusHash();
341 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
345 * Returns profile data; the first element is the profile type, the second is
346 * the number of distinct values, the third the total count, and the remainder
347 * depend on the profile type.
353 int[] getProfileFor(AlignmentAnnotation aa, int column)
355 // TODO : consider refactoring the global alignment calculation
356 // properties/rendering attributes as a global 'alignment group' which holds
357 // all vis settings for the alignment as a whole rather than a subset
359 if (aa.autoCalculated
360 && (aa.label.startsWith("Consensus") || aa.label
361 .startsWith("cDNA Consensus")))
363 boolean forComplement = aa.label.startsWith("cDNA Consensus");
364 if (aa.groupRef != null && aa.groupRef.consensusData != null
365 && aa.groupRef.isShowSequenceLogo())
367 // TODO? group consensus for cDNA complement
368 return AAFrequency.extractProfile(
369 aa.groupRef.consensusData.get(column),
370 aa.groupRef.getIgnoreGapsConsensus());
372 // TODO extend annotation row to enable dynamic and static profile data to
374 if (aa.groupRef == null && aa.sequenceRef == null)
378 return AAFrequency.extractCdnaProfile(
379 complementConsensus[column], av_ignoreGapsConsensus);
383 return AAFrequency.extractProfile(hconsensus.get(column),
384 av_ignoreGapsConsensus);
390 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
392 // TODO implement group structure consensus
394 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
395 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
396 * group selections return StructureFrequency.extractProfile(
397 * aa.groupRef.consensusData[column], aa.groupRef
398 * .getIgnoreGapsConsensus()); }
400 // TODO extend annotation row to enable dynamic and static profile data
403 if (aa.groupRef == null && aa.sequenceRef == null
404 && hStrucConsensus != null
405 && hStrucConsensus.length > column)
407 return StructureFrequency.extractProfile(hStrucConsensus[column],
408 av_ignoreGapsConsensus);
417 private AnnotationRendererFactoryI rendererFactoryI;
420 * Render the annotation rows associated with an alignment.
425 * data and view settings to render
427 * destination for graphics
429 * row where a mouse event occured (or -1)
431 * first column that will be drawn
433 * last column that will be drawn
434 * @return true if the fadedImage was used for any alignment annotation rows
435 * currently being calculated
437 public boolean drawComponent(AwtRenderPanelI annotPanel,
438 AlignViewportI av, Graphics g, int activeRow, int startRes,
441 long stime = System.currentTimeMillis();
442 boolean usedFaded = false;
444 // AnnotationPanel needs to implement: ImageObserver, access to
446 updateFromAwtRenderPanel(annotPanel, av);
447 fm = g.getFontMetrics();
448 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
459 boolean validRes = false;
460 boolean validEnd = false;
461 boolean labelAllCols = false;
462 boolean centreColLabels;
463 boolean centreColLabelsDef = av.isCentreColumnLabels();
464 boolean scaleColLabel = false;
465 final AlignmentAnnotation consensusAnnot = av
466 .getAlignmentConsensusAnnotation();
467 final AlignmentAnnotation structConsensusAnnot = av
468 .getAlignmentStrucConsensusAnnotation();
469 final AlignmentAnnotation complementConsensusAnnot = av
470 .getComplementConsensusAnnotation();
471 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
473 BitSet graphGroupDrawn = new BitSet();
474 int charOffset = 0; // offset for a label
475 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
477 Font ofont = g.getFont();
480 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
481 boolean clipst = false, clipend = false;
482 for (int i = 0; i < aa.length; i++)
484 AlignmentAnnotation row = aa[i];
487 // check if this is a consensus annotation row and set the display
488 // settings appropriately
489 // TODO: generalise this to have render styles for consensus/profile
491 if (row.groupRef != null && row == row.groupRef.getConsensus())
493 renderHistogram = row.groupRef.isShowConsensusHistogram();
494 renderProfile = row.groupRef.isShowSequenceLogo();
495 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
497 else if (row == consensusAnnot || row == structConsensusAnnot
498 || row == complementConsensusAnnot)
500 renderHistogram = av_renderHistogram;
501 renderProfile = av_renderProfile;
502 normaliseProfile = av_normaliseProfile;
506 renderHistogram = true;
507 // don't need to set render/normaliseProfile since they are not
508 // currently used in any other annotation track renderer
511 Annotation[] row_annotations = row.annotations;
516 centreColLabels = row.centreColLabels || centreColLabelsDef;
517 labelAllCols = row.showAllColLabels;
518 scaleColLabel = row.scaleColLabel;
523 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
524 {// if_in_visible_region
535 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
540 // this is so that we draw the characters below the graph
545 iconOffset = charHeight - fm.getDescent();
549 else if (row.hasText)
551 iconOffset = charHeight - fm.getDescent();
559 if (row.autoCalculated && av.isCalculationInProgress(row))
563 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
564 - row.height, imgWidth, y, annotationPanel);
565 g.setColor(Color.black);
566 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
572 * else if (annotationPanel.av.updatingConservation &&
573 * aa[i].label.equals("Conservation")) {
575 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
576 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
577 * annotationPanel.imgWidth, y, annotationPanel);
579 * g.setColor(Color.black); //
580 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
582 * continue; } else if (annotationPanel.av.updatingConservation &&
583 * aa[i].label.equals("Quality")) {
585 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
586 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
587 * annotationPanel.imgWidth, y, annotationPanel);
588 * g.setColor(Color.black); // /
589 * g.drawString("Calculating Quality....",20, y-row.height/2);
593 // first pass sets up state for drawing continuation from left-hand
596 x = (startRes == 0) ? 0 : -1;
597 while (x < endRes - startRes)
599 if (hasHiddenColumns)
601 column = hiddenColumns.adjustForHiddenColumns(startRes + x);
602 if (column > row_annotations.length - 1)
609 column = startRes + x;
612 if ((row_annotations == null)
613 || (row_annotations.length <= column)
614 || (row_annotations[column] == null))
622 final String displayChar = validRes ? row_annotations[column].displayCharacter
628 g.setColor(Color.red);
630 if (columnSelection != null)
632 if (columnSelection.contains(column))
634 g.fillRect(x * charWidth, y, charWidth, charHeight);
638 if (row.getInvalidStrucPos() > x)
640 g.setColor(Color.orange);
641 g.fillRect(x * charWidth, y, charWidth, charHeight);
643 else if (row.getInvalidStrucPos() == x)
645 g.setColor(Color.orange.darker());
646 g.fillRect(x * charWidth, y, charWidth, charHeight);
648 if (validCharWidth && validRes && displayChar != null
649 && (displayChar.length() > 0))
652 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
653 displayChar.length());
654 if (/* centreColLabels || */scaleColLabel)
656 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
657 // displayChar.length());
659 // if (scaleColLabel)
661 // justify the label and scale to fit in column
662 if (fmWidth > charWidth)
664 // scale only if the current font isn't already small enough
665 fmScaling = charWidth;
666 fmScaling /= fmWidth;
667 g.setFont(ofont.deriveFont(AffineTransform
668 .getScaleInstance(fmScaling, 1.0)));
669 // and update the label's width to reflect the scaling.
674 // TODO is it ok to use width of / show all characters here?
677 // fmWidth = fm.charWidth(displayChar.charAt(0));
679 charOffset = (int) ((charWidth - fmWidth) / 2f);
681 if (row_annotations[column].colour == null)
683 g.setColor(Color.black);
687 g.setColor(row_annotations[column].colour);
690 if (column == 0 || row.graph > 0)
692 g.drawString(displayChar, (x * charWidth) + charOffset, y
695 else if (row_annotations[column - 1] == null
698 .equals(row_annotations[column - 1].displayCharacter) || (displayChar
699 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
701 g.drawString(displayChar, x * charWidth + charOffset, y
709 char ss = validRes ? row_annotations[column].secondaryStructure
714 // distinguish between forward/backward base-pairing
715 if (displayChar.indexOf(')') > -1)
724 if ((displayChar.indexOf(']') > -1))
732 // distinguish between forward/backward base-pairing
733 if (displayChar.indexOf('}') > -1)
741 // distinguish between forward/backward base-pairing
742 if (displayChar.indexOf('<') > -1)
748 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
750 // distinguish between forward/backward base-pairing
751 int ssLowerCase = ss + UPPER_TO_LOWER;
752 // TODO would .equals() be safer here? or charAt(0)?
753 if (displayChar.indexOf(ssLowerCase) > -1)
755 ss = (char) ssLowerCase;
759 if (!validRes || (ss != lastSS))
765 int nb_annot = x - temp;
766 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
769 case '(': // Stem case for RNA secondary structure
770 case ')': // and opposite direction
771 drawStemAnnot(g, row_annotations, lastSSX, x, y,
772 iconOffset, startRes, column, validRes, validEnd);
779 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
780 iconOffset, startRes, column, validRes,
784 // no break if isRNA - falls through to drawNotCanonicalAnnot!
788 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
789 iconOffset, startRes, column, validRes,
793 // no break if isRNA - fall through to drawNotCanonicalAnnot!
852 Color nonCanColor = getNotCanonicalColor(lastSS);
853 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
854 lastSSX, x, y, iconOffset, startRes, column,
859 g.setColor(Color.gray);
860 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
876 lastSSX = (x * charWidth);
883 if (column >= row_annotations.length)
885 column = row_annotations.length - 1;
892 if ((row_annotations == null) || (row_annotations.length <= column)
893 || (row_annotations[column] == null))
911 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
912 startRes, column, validRes, validEnd);
915 // no break if isRNA - fall through to drawNotCanonicalAnnot!
920 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
921 startRes, column, validRes, validEnd);
924 // no break if isRNA - fall through to drawNotCanonicalAnnot!
927 case ')': // Stem case for RNA secondary structure
929 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
930 startRes, column, validRes, validEnd);
987 // System.out.println(lastSS);
988 Color nonCanColor = getNotCanonicalColor(lastSS);
989 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
990 x, y, iconOffset, startRes, column, validRes, validEnd);
993 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
994 startRes, column, validRes, validEnd);
999 if (row.graph > 0 && row.graphHeight > 0)
1001 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
1003 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
1005 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1006 // computed efficiently for all visible labels
1007 float groupmax = -999999, groupmin = 9999999;
1008 for (int gg = 0; gg < aa.length; gg++)
1010 if (aa[gg].graphGroup != row.graphGroup)
1017 aa[gg].visible = false;
1019 if (aa[gg].graphMax > groupmax)
1021 groupmax = aa[gg].graphMax;
1023 if (aa[gg].graphMin < groupmin)
1025 groupmin = aa[gg].graphMin;
1029 for (int gg = 0; gg < aa.length; gg++)
1031 if (aa[gg].graphGroup == row.graphGroup)
1033 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1034 endRes, y, groupmin, groupmax, row.graphHeight);
1038 graphGroupDrawn.set(row.graphGroup);
1042 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1043 row.graphMin, row.graphMax, row.graphHeight);
1046 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1048 drawBarGraph(g, row, row_annotations, startRes, endRes,
1049 row.graphMin, row.graphMax, y, renderHistogram,
1050 renderProfile, normaliseProfile);
1054 AnnotationRowRendererI renderer = rendererFactoryI
1055 .getRendererFor(row);
1056 if (renderer != null)
1058 renderer.renderRow(g, charWidth, charHeight,
1059 hasHiddenColumns, av, hiddenColumns, columnSelection,
1060 row, row_annotations, startRes, endRes, row.graphMin,
1065 if (renderer == null)
1067 System.err.println("No renderer found for "
1072 System.err.println("rendered with "
1073 + renderer.getClass().toString());
1082 if (clipst && !clipend)
1086 }// end if_in_visible_region
1087 if (row.graph > 0 && row.hasText)
1103 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1108 System.err.println("End clip at : " + yto + " (index " + f_to
1113 System.err.println("Annotation Rendering time:"
1114 + (System.currentTimeMillis() - stime));
1121 public static final Color GLYPHLINE_COLOR = Color.gray;
1123 public static final Color SHEET_COLOUR = Color.green;
1125 public static final Color HELIX_COLOUR = Color.red;
1127 public static final Color STEM_COLOUR = Color.blue;
1129 private Color sdNOTCANONICAL_COLOUR;
1131 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1132 int y, int iconOffset, int startRes, int column,
1133 boolean validRes, boolean validEnd)
1135 g.setColor(GLYPHLINE_COLOR);
1136 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1139 void drawSheetAnnot(Graphics g, Annotation[] row,
1141 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1142 boolean validRes, boolean validEnd)
1144 g.setColor(SHEET_COLOUR);
1146 if (!validEnd || !validRes || row == null || row[column] == null
1147 || row[column].secondaryStructure != 'E')
1149 g.fillRect(lastSSX, y + 4 + iconOffset,
1150 (x * charWidth) - lastSSX - 4, 7);
1151 g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
1152 (x * charWidth) }, new int[] { y + iconOffset,
1153 y + 14 + iconOffset, y + 7 + iconOffset }, 3);
1157 g.fillRect(lastSSX, y + 4 + iconOffset,
1158 (x + 1) * charWidth - lastSSX, 7);
1163 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1164 int y, int iconOffset, int startRes, int column,
1165 boolean validRes, boolean validEnd)
1167 g.setColor(HELIX_COLOUR);
1169 int sCol = (lastSSX / charWidth) + startRes;
1171 int x2 = (x * charWidth);
1175 int ofs = charWidth / 2;
1176 // Off by 1 offset when drawing rects and ovals
1177 // to offscreen image on the MAC
1178 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1179 if (sCol == 0 || row[sCol - 1] == null
1180 || row[sCol - 1].secondaryStructure != 'H')
1185 // g.setColor(Color.orange);
1186 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1189 if (!validRes || row[column] == null
1190 || row[column].secondaryStructure != 'H')
1196 // g.setColor(Color.magenta);
1197 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1205 if (sCol == 0 || row[sCol - 1] == null
1206 || row[sCol - 1].secondaryStructure != 'H')
1208 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1209 x1 += charWidth / 2;
1212 if (!validRes || row[column] == null
1213 || row[column].secondaryStructure != 'H')
1215 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1217 x2 -= charWidth / 2;
1220 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1223 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1224 Annotation[] aa_annotations, int sRes, int eRes, int y,
1225 float min, float max, int graphHeight)
1227 if (sRes > aa_annotations.length)
1234 // Adjustment for fastpaint to left
1240 eRes = Math.min(eRes, aa_annotations.length);
1248 float range = max - min;
1253 y2 = y - (int) ((0 - min / range) * graphHeight);
1256 g.setColor(Color.gray);
1257 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1259 eRes = Math.min(eRes, aa_annotations.length);
1262 int aaMax = aa_annotations.length - 1;
1264 while (x < eRes - sRes)
1267 if (hasHiddenColumns)
1269 column = hiddenColumns.adjustForHiddenColumns(column);
1277 if (aa_annotations[column] == null
1278 || aa_annotations[column - 1] == null)
1284 if (aa_annotations[column].colour == null)
1286 g.setColor(Color.black);
1290 g.setColor(aa_annotations[column].colour);
1294 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1296 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1298 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1299 + charWidth / 2, y2);
1303 if (_aa.threshold != null)
1305 g.setColor(_aa.threshold.colour);
1306 Graphics2D g2 = (Graphics2D) g;
1307 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1308 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1310 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1311 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1312 g2.setStroke(new BasicStroke());
1316 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1317 Annotation[] aa_annotations, int sRes, int eRes, float min,
1318 float max, int y, boolean renderHistogram, boolean renderProfile,
1319 boolean normaliseProfile)
1321 if (sRes > aa_annotations.length)
1325 Font ofont = g.getFont();
1326 eRes = Math.min(eRes, aa_annotations.length);
1328 int x = 0, y1 = y, y2 = y;
1330 float range = max - min;
1334 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1337 g.setColor(Color.gray);
1339 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1342 int aaMax = aa_annotations.length - 1;
1343 while (x < eRes - sRes)
1346 if (hasHiddenColumns)
1348 column = hiddenColumns.adjustForHiddenColumns(column);
1356 if (aa_annotations[column] == null)
1361 if (aa_annotations[column].colour == null)
1363 g.setColor(Color.black);
1367 g.setColor(aa_annotations[column].colour);
1371 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1373 if (renderHistogram)
1377 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1381 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1384 // draw profile if available
1389 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1391 int profl[] = getProfileFor(_aa, column);
1393 // just try to draw the logo if profl is not null
1394 if (profl != null && profl[2] != 0)
1396 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1397 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1398 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1399 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1406 * Render a single base for a sequence profile, a base pair for
1407 * structure profile, and a triplet for a cdna profile
1409 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1411 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1412 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1413 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1417 * Traverse the character(s)/percentage data in the array
1420 int valuesProcessed = 0;
1421 // profl[1] is the number of values in the profile
1422 while (valuesProcessed < profl[1])
1424 if (isStructureProfile)
1426 // todo can we encode a structure pair as an int, like codons?
1427 dc[0] = (char) profl[c++];
1428 dc[1] = (char) profl[c++];
1430 else if (isCdnaProfile)
1432 dc = CodingUtils.decodeCodon(profl[c++]);
1436 dc[0] = (char) profl[c++];
1440 wdth /= fm.charsWidth(dc, 0, dc.length);
1443 // next profl[] position is profile % for the character(s)
1444 scl = htn * scale * profl[c++];
1445 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1446 .getFontRenderContext());
1447 Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
1448 wdth, scl / lm.getAscent()));
1450 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1452 // Debug - render boxes around characters
1453 // g.setColor(Color.red);
1454 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1456 // g.setColor(profcolour.findColour(dc[0]).darker());
1459 * Set character colour as per alignment colour scheme; use the
1460 * codon translation if a cDNA profile
1462 Color colour = null;
1465 final String codonTranslation = ResidueProperties
1466 .codonTranslate(new String(dc));
1467 colour = profcolour.findColour(codonTranslation.charAt(0),
1472 colour = profcolour.findColour(dc[0], column, null);
1474 g.setColor(colour == Color.white ? Color.lightGray : colour);
1476 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1477 .getBaselineIndex()]));
1479 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1487 if (_aa.threshold != null)
1489 g.setColor(_aa.threshold.colour);
1490 Graphics2D g2 = (Graphics2D) g;
1491 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1492 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1494 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1496 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1497 g2.setStroke(new BasicStroke());
1501 // used by overview window
1502 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1503 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1505 eRes = Math.min(eRes, aa_annotations.length);
1506 g.setColor(Color.white);
1507 g.fillRect(0, 0, width, y);
1508 g.setColor(new Color(0, 0, 180));
1512 for (int j = sRes; j < eRes; j++)
1514 if (aa_annotations[j] != null)
1516 if (aa_annotations[j].colour == null)
1518 g.setColor(Color.black);
1522 g.setColor(aa_annotations[j].colour);
1525 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1531 g.fillRect(x, y - height, charWidth, height);
1537 Color getNotCanonicalColor(char lastss)
1543 return new Color(255, 125, 5);
1547 return new Color(245, 115, 10);
1551 return new Color(235, 135, 15);
1555 return new Color(225, 105, 20);
1559 return new Color(215, 145, 30);
1563 return new Color(205, 95, 35);
1567 return new Color(195, 155, 45);
1571 return new Color(185, 85, 55);
1575 return new Color(175, 165, 65);
1579 return new Color(170, 75, 75);
1583 return new Color(160, 175, 85);
1587 return new Color(150, 65, 95);
1591 return new Color(140, 185, 105);
1595 return new Color(130, 55, 110);
1599 return new Color(120, 195, 120);
1603 return new Color(110, 45, 130);
1607 return new Color(100, 205, 140);
1611 return new Color(90, 35, 150);
1615 return new Color(85, 215, 160);
1619 return new Color(75, 25, 170);
1623 return new Color(65, 225, 180);
1627 return new Color(55, 15, 185);
1631 return new Color(45, 235, 195);
1635 return new Color(35, 5, 205);
1639 return new Color(25, 245, 215);
1643 return new Color(15, 0, 225);
1647 return new Color(10, 255, 235);
1651 return new Color(5, 150, 245);
1655 return new Color(0, 80, 255);
1658 System.out.println("This is not a interaction : " + lastss);