2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.renderer;
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.CodingUtils;
25 import jalview.analysis.Rna;
26 import jalview.analysis.StructureFrequency;
27 import jalview.api.AlignViewportI;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.Annotation;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.HiddenColumns;
32 import jalview.datamodel.HiddenMarkovModel;
33 import jalview.datamodel.ProfilesI;
34 import jalview.schemes.ColourSchemeI;
35 import jalview.schemes.NucleotideColourScheme;
36 import jalview.schemes.ResidueProperties;
37 import jalview.schemes.ZappoColourScheme;
38 import jalview.util.Platform;
39 import jalview.workers.InformationThread;
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.geom.AffineTransform;
49 import java.awt.image.ImageObserver;
50 import java.util.BitSet;
51 import java.util.Hashtable;
53 public class AnnotationRenderer
55 private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
57 private static final int CHAR_A = 'A'; // 65
59 private static final int CHAR_Z = 'Z'; // 90
62 * flag indicating if timing and redraw parameter info should be output
64 private final boolean debugRedraw;
66 private int charWidth, endRes, charHeight;
68 private boolean validCharWidth, hasHiddenColumns;
70 private FontMetrics fm;
72 private final boolean USE_FILL_ROUND_RECT = Platform.isAMacAndNotJS();
74 // todo remove these flags, read from group/viewport where needed
75 boolean av_renderHistogram = true;
77 boolean av_renderProfile = true;
79 boolean av_normaliseProfile = false;
81 boolean av_infoHeight = false;
83 ResidueShaderI profcolour = null;
85 private ColumnSelection columnSelection;
87 private HiddenColumns hiddenColumns;
89 private ProfilesI hconsensus;
91 private Hashtable<String, Object>[] complementConsensus;
93 private Hashtable<String, Object>[] hStrucConsensus;
95 private boolean av_ignoreGapsConsensus;
97 private boolean av_ignoreBelowBackground;
100 * attributes set from AwtRenderPanelI
103 * old image used when data is currently being calculated and cannot be
106 private Image fadedImage;
109 * panel being rendered into
111 private ImageObserver annotationPanel;
114 * width of image to render in panel
116 private int imgWidth;
119 * offset to beginning of visible area
124 * offset to end of visible area
126 private int visHeight;
129 * indicate if the renderer should only render the visible portion of the
130 * annotation given the current view settings
132 private boolean useClip = true;
135 * master flag indicating if renderer should ever try to clip. not enabled for
138 private boolean canClip = false;
140 public AnnotationRenderer()
146 * Create a new annotation Renderer
149 * flag indicating if timing and redraw parameter info should be
152 public AnnotationRenderer(boolean debugRedraw)
154 this.debugRedraw = debugRedraw;
158 * Remove any references and resources when this object is no longer required
160 public void dispose()
163 complementConsensus = null;
164 hStrucConsensus = null;
166 annotationPanel = null;
169 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
170 int x, int y, int iconOffset, int startRes, int column,
171 boolean validRes, boolean validEnd)
173 g.setColor(STEM_COLOUR);
174 int sCol = (lastSSX / charWidth)
175 + hiddenColumns.visibleToAbsoluteColumn(startRes);
177 int x2 = (x * charWidth);
179 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
180 : row_annotations[column - 1].secondaryStructure;
182 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
183 || dc != row_annotations[sCol - 1].secondaryStructure;
184 boolean diffdownstream = !validRes || !validEnd
185 || row_annotations[column] == null
186 || dc != row_annotations[column].secondaryStructure;
188 if (column > 0 && Rna.isClosingParenthesis(dc))
191 // if (validRes && column>1 && row_annotations[column-2]!=null &&
192 // dc.equals(row_annotations[column-2].displayCharacter))
195 * if new annotation with a closing base pair half of the stem,
196 * display a backward arrow
198 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
200 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
211 // display a forward arrow
215 * if annotation ending with an opeing base pair half of the stem,
216 * display a forward arrow
218 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
220 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
230 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
233 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
234 Annotation[] row_annotations, int lastSSX, int x, int y,
235 int iconOffset, int startRes, int column, boolean validRes,
238 // System.out.println(nonCanColor);
240 g.setColor(nonCanColor);
241 int sCol = (lastSSX / charWidth)
242 + hiddenColumns.visibleToAbsoluteColumn(startRes);
244 int x2 = (x * charWidth);
246 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
247 : row_annotations[column - 1].displayCharacter;
249 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
250 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
251 boolean diffdownstream = !validRes || !validEnd
252 || row_annotations[column] == null
253 || !dc.equals(row_annotations[column].displayCharacter);
254 // System.out.println("Column "+column+" diff up: "+diffupstream+"
255 // down:"+diffdownstream);
256 // If a closing base pair half of the stem, display a backward arrow
257 if (column > 0 && Rna.isClosingParenthesis(dc))
261 // if (validRes && column>1 && row_annotations[column-2]!=null &&
262 // dc.equals(row_annotations[column-2].displayCharacter))
264 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
266 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
278 // display a forward arrow
281 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 },
283 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
293 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
296 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
298 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
301 fm = annotPanel.getFontMetrics();
302 annotationPanel = annotPanel;
303 fadedImage = annotPanel.getFadedImage();
304 imgWidth = annotPanel.getFadedImageWidth();
305 // visible area for rendering
306 int[] bounds = annotPanel.getVisibleVRange();
310 visHeight = bounds[1];
325 updateFromAlignViewport(av);
328 public void updateFromAlignViewport(AlignViewportI av)
330 charWidth = av.getCharWidth();
331 endRes = av.getRanges().getEndRes();
332 charHeight = av.getCharHeight();
333 hasHiddenColumns = av.hasHiddenColumns();
334 validCharWidth = av.isValidCharWidth();
335 av_renderHistogram = av.isShowConsensusHistogram();
336 av_renderProfile = av.isShowSequenceLogo();
337 av_normaliseProfile = av.isNormaliseSequenceLogo();
338 profcolour = av.getResidueShading();
339 if (profcolour == null || profcolour.getColourScheme() == null)
342 * Use default colour for sequence logo if
343 * the alignment has no colourscheme set
344 * (would like to use user preference but n/a for applet)
346 ColourSchemeI col = av.getAlignment().isNucleotide()
347 ? new NucleotideColourScheme()
348 : new ZappoColourScheme();
349 profcolour = new ResidueShader(col);
351 columnSelection = av.getColumnSelection();
352 hiddenColumns = av.getAlignment().getHiddenColumns();
353 hconsensus = av.getSequenceConsensusHash();
354 complementConsensus = av.getComplementConsensusHash();
355 hStrucConsensus = av.getRnaStructureConsensusHash();
356 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
357 av_ignoreBelowBackground = av.isIgnoreBelowBackground();
358 av_infoHeight = av.isInfoLetterHeight();
364 * Returns profile data; the first element is the profile type, the second is
365 * the number of distinct values, the third the total count, and the remainder
366 * depend on the profile type.
372 int[] getProfileFor(AlignmentAnnotation aa, int column)
374 // TODO : consider refactoring the global alignment calculation
375 // properties/rendering attributes as a global 'alignment group' which holds
376 // all vis settings for the alignment as a whole rather than a subset
378 if (InformationThread.HMM_CALC_ID.equals(aa.getCalcId()))
380 HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
381 return AAFrequency.extractHMMProfile(hmm, column,
382 av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard
385 if (aa.autoCalculated
386 && (aa.label.startsWith("Consensus") || aa.label
387 .startsWith("cDNA Consensus")))
389 boolean forComplement = aa.label.startsWith("cDNA Consensus");
390 if (aa.groupRef != null && aa.groupRef.getConsensusData() != null
391 && aa.groupRef.isShowSequenceLogo())
393 // TODO? group consensus for cDNA complement
394 return AAFrequency.extractProfile(
395 aa.groupRef.getConsensusData().get(column),
396 aa.groupRef.getIgnoreGapsConsensus());
398 // TODO extend annotation row to enable dynamic and static profile data to
400 if (aa.groupRef == null && aa.sequenceRef == null)
404 return AAFrequency.extractCdnaProfile(complementConsensus[column],
405 av_ignoreGapsConsensus);
409 return AAFrequency.extractProfile(hconsensus.get(column),
410 av_ignoreGapsConsensus);
416 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
418 // TODO implement group structure consensus
420 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
421 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
422 * group selections return StructureFrequency.extractProfile(
423 * aa.groupRef.consensusData[column], aa.groupRef
424 * .getIgnoreGapsConsensus()); }
426 // TODO extend annotation row to enable dynamic and static profile data
429 if (aa.groupRef == null && aa.sequenceRef == null
430 && hStrucConsensus != null
431 && hStrucConsensus.length > column)
433 return StructureFrequency.extractProfile(hStrucConsensus[column],
434 av_ignoreGapsConsensus);
442 * Render the annotation rows associated with an alignment.
447 * data and view settings to render
449 * destination for graphics
451 * row where a mouse event occured (or -1)
453 * first column that will be drawn
455 * last column that will be drawn
456 * @return true if the fadedImage was used for any alignment annotation rows
457 * currently being calculated
459 public boolean drawComponent(AwtRenderPanelI annotPanel,
460 AlignViewportI av, Graphics g, int activeRow, int startRes,
463 long stime = System.currentTimeMillis();
464 boolean usedFaded = false;
466 // AnnotationPanel needs to implement: ImageObserver, access to
468 updateFromAwtRenderPanel(annotPanel, av);
469 fm = g.getFontMetrics();
470 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
481 boolean validRes = false;
482 boolean validEnd = false;
483 boolean labelAllCols = false;
484 // boolean centreColLabels;
485 // boolean centreColLabelsDef = av.isCentreColumnLabels();
486 boolean scaleColLabel = false;
487 final AlignmentAnnotation consensusAnnot = av
488 .getAlignmentConsensusAnnotation();
489 final AlignmentAnnotation structConsensusAnnot = av
490 .getAlignmentStrucConsensusAnnotation();
491 final AlignmentAnnotation complementConsensusAnnot = av
492 .getComplementConsensusAnnotation();
494 BitSet graphGroupDrawn = new BitSet();
495 int charOffset = 0; // offset for a label
498 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
499 boolean clipst = false, clipend = false;
500 for (int i = 0; i < aa.length; i++)
502 AlignmentAnnotation row = aa[i];
503 boolean renderHistogram = true;
504 boolean renderProfile = false;
505 boolean normaliseProfile = false;
506 boolean isRNA = row.isRNA();
508 // check if this is a consensus annotation row and set the display
509 // settings appropriately
510 // TODO: generalise this to have render styles for consensus/profile
512 if (row.groupRef != null && row == row.groupRef.getConsensus())
514 renderHistogram = row.groupRef.isShowConsensusHistogram();
515 renderProfile = row.groupRef.isShowSequenceLogo();
516 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
518 else if (row == consensusAnnot || row == structConsensusAnnot
519 || row == complementConsensusAnnot)
521 renderHistogram = av_renderHistogram;
522 renderProfile = av_renderProfile;
523 normaliseProfile = av_normaliseProfile;
525 else if (InformationThread.HMM_CALC_ID.equals(row.getCalcId()))
527 if (row.groupRef != null)
529 renderHistogram = row.groupRef.isShowInformationHistogram();
530 renderProfile = row.groupRef.isShowHMMSequenceLogo();
531 normaliseProfile = row.groupRef.isNormaliseHMMSequenceLogo();
535 renderHistogram = av.isShowInformationHistogram();
536 renderProfile = av.isShowHMMSequenceLogo();
537 normaliseProfile = av.isNormaliseHMMSequenceLogo();
540 else if (row == consensusAnnot || row == structConsensusAnnot
541 || row == complementConsensusAnnot)
543 renderHistogram = av_renderHistogram;
544 renderProfile = av_renderProfile;
545 normaliseProfile = av_normaliseProfile;
548 Annotation[] row_annotations = row.annotations;
553 // centreColLabels = row.centreColLabels || centreColLabelsDef;
554 labelAllCols = row.showAllColLabels;
555 scaleColLabel = row.scaleColLabel;
559 if (!useClip || ((y - charHeight) < visHeight
560 && (y + row.height + charHeight * 2) >= sOffset))
561 {// if_in_visible_region
572 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
577 // this is so that we draw the characters below the graph
582 iconOffset = charHeight - fm.getDescent();
586 else if (row.hasText)
588 iconOffset = charHeight - fm.getDescent();
596 if (row.autoCalculated && av.isCalculationInProgress(row))
600 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0,
601 y - row.height, imgWidth, y, annotationPanel);
602 g.setColor(Color.black);
603 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
609 * else if (annotationPanel.av.updatingConservation &&
610 * aa[i].label.equals("Conservation")) {
612 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
613 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
614 * annotationPanel.imgWidth, y, annotationPanel);
616 * g.setColor(Color.black); //
617 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
619 * continue; } else if (annotationPanel.av.updatingConservation &&
620 * aa[i].label.equals("Quality")) {
622 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
623 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
624 * annotationPanel.imgWidth, y, annotationPanel);
625 * g.setColor(Color.black); // /
626 * g.drawString("Calculating Quality....",20, y-row.height/2);
630 // first pass sets up state for drawing continuation from left-hand
633 x = (startRes == 0) ? 0 : -1;
634 while (x < endRes - startRes)
636 if (hasHiddenColumns)
638 column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
639 if (column > row_annotations.length - 1)
646 column = startRes + x;
649 if ((row_annotations == null)
650 || (row_annotations.length <= column)
651 || (row_annotations[column] == null))
659 final String displayChar = validRes
660 ? row_annotations[column].displayCharacter
666 g.setColor(Color.red);
668 if (columnSelection != null)
670 if (columnSelection.contains(column))
672 g.fillRect(x * charWidth, y, charWidth, charHeight);
676 if (row.getInvalidStrucPos() > x)
678 g.setColor(Color.orange);
679 g.fillRect(x * charWidth, y, charWidth, charHeight);
681 else if (row.getInvalidStrucPos() == x)
683 g.setColor(Color.orange.darker());
684 g.fillRect(x * charWidth, y, charWidth, charHeight);
686 if (validCharWidth && validRes && displayChar != null
687 && (displayChar.length() > 0))
689 Graphics2D gg = ((Graphics2D) g);
690 float fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
691 displayChar.length());
694 * shrink label width to fit in column, if that is
695 * both configured and necessary
697 boolean scaledToFit = false;
698 float fmScaling = 1f;
699 if (scaleColLabel && fmWidth > charWidth)
702 fmScaling = charWidth;
703 fmScaling /= fmWidth;
704 // and update the label's width to reflect the scaling.
708 charOffset = (int) ((charWidth - fmWidth) / 2f);
710 if (row_annotations[column].colour == null)
712 gg.setColor(Color.black);
716 gg.setColor(row_annotations[column].colour);
720 * draw the label, unless it is the same secondary structure
721 * symbol (excluding RNA Helix) as the previous column
723 final int xPos = (x * charWidth) + charOffset;
724 final int yPos = y + iconOffset;
727 * translate to drawing position _before_ applying any scaling
729 gg.translate(xPos, yPos);
733 * use a scaling transform to make the label narrower
734 * (JalviewJS doesn't have Font.deriveFont(AffineTransform))
737 AffineTransform.getScaleInstance(fmScaling, 1.0));
739 if (column == 0 || row.graph > 0)
741 gg.drawString(displayChar, 0, 0);
743 else if (row_annotations[column - 1] == null || (labelAllCols
744 || !displayChar.equals(
745 row_annotations[column - 1].displayCharacter)
746 || (displayChar.length() < 2
747 && row_annotations[column].secondaryStructure == ' ')))
749 gg.drawString(displayChar, 0, 0);
754 * undo scaling before translating back
755 * (restoring saved transform does NOT work in JS PDFGraphics!)
757 gg.transform(AffineTransform
758 .getScaleInstance(1D / fmScaling, 1.0));
760 gg.translate(-xPos, -yPos);
765 char ss = validRes ? row_annotations[column].secondaryStructure
770 // distinguish between forward/backward base-pairing
771 if (displayChar.indexOf(')') > -1)
780 if ((displayChar.indexOf(']') > -1))
788 // distinguish between forward/backward base-pairing
789 if (displayChar.indexOf('}') > -1)
797 // distinguish between forward/backward base-pairing
798 if (displayChar.indexOf('<') > -1)
804 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
806 // distinguish between forward/backward base-pairing
807 int ssLowerCase = ss + UPPER_TO_LOWER;
808 // TODO would .equals() be safer here? or charAt(0)?
809 if (displayChar.indexOf(ssLowerCase) > -1)
811 ss = (char) ssLowerCase;
815 if (!validRes || (ss != lastSS))
821 // int nb_annot = x - temp;
822 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre
823 // annot :"+nb_annot);
826 case '(': // Stem case for RNA secondary structure
827 case ')': // and opposite direction
828 drawStemAnnot(g, row_annotations, lastSSX, x, y,
829 iconOffset, startRes, column, validRes, validEnd);
836 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
837 iconOffset, startRes, column, validRes,
841 // no break if isRNA - falls through to drawNotCanonicalAnnot!
845 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
846 iconOffset, startRes, column, validRes,
850 // no break if isRNA - fall through to drawNotCanonicalAnnot!
909 Color nonCanColor = getNotCanonicalColor(lastSS);
910 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
911 lastSSX, x, y, iconOffset, startRes, column,
916 g.setColor(Color.gray);
917 g.fillRect(lastSSX, y + 6 + iconOffset,
918 (x * charWidth) - lastSSX, 2);
933 lastSSX = (x * charWidth);
940 if (column >= row_annotations.length)
942 column = row_annotations.length - 1;
949 if ((row_annotations == null) || (row_annotations.length <= column)
950 || (row_annotations[column] == null))
968 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
969 startRes, column, validRes, validEnd);
972 // no break if isRNA - fall through to drawNotCanonicalAnnot!
977 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
978 startRes, column, validRes, validEnd);
981 // no break if isRNA - fall through to drawNotCanonicalAnnot!
984 case ')': // Stem case for RNA secondary structure
986 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
987 startRes, column, validRes, validEnd);
1044 // System.out.println(lastSS);
1045 Color nonCanColor = getNotCanonicalColor(lastSS);
1046 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
1047 x, y, iconOffset, startRes, column, validRes, validEnd);
1050 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
1051 startRes, column, validRes, validEnd);
1056 if (row.graph > 0 && row.graphHeight > 0)
1058 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
1060 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
1062 // TODO: JAL-1291 revise rendering model so the graphGroup map is
1063 // computed efficiently for all visible labels
1064 float groupmax = -999999, groupmin = 9999999;
1065 for (int gg = 0; gg < aa.length; gg++)
1067 if (aa[gg].graphGroup != row.graphGroup)
1074 aa[gg].visible = false;
1076 if (aa[gg].graphMax > groupmax)
1078 groupmax = aa[gg].graphMax;
1080 if (aa[gg].graphMin < groupmin)
1082 groupmin = aa[gg].graphMin;
1086 for (int gg = 0; gg < aa.length; gg++)
1088 if (aa[gg].graphGroup == row.graphGroup)
1090 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1091 endRes, y, groupmin, groupmax, row.graphHeight);
1095 graphGroupDrawn.set(row.graphGroup);
1099 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1100 row.graphMin, row.graphMax, row.graphHeight);
1103 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1105 drawBarGraph(g, row, row_annotations, startRes, endRes,
1106 row.graphMin, row.graphMax, y, renderHistogram,
1107 renderProfile, normaliseProfile);
1113 if (clipst && !clipend)
1117 } // end if_in_visible_region
1118 if (row.graph > 0 && row.hasText)
1135 "Start clip at : " + yfrom + " (index " + f_i + ")");
1140 "End clip at : " + yto + " (index " + f_to + ")");
1144 System.err.println("Annotation Rendering time:"
1145 + (System.currentTimeMillis() - stime));
1152 public static final Color GLYPHLINE_COLOR = Color.gray;
1154 public static final Color SHEET_COLOUR = Color.green;
1156 public static final Color HELIX_COLOUR = Color.red;
1158 public static final Color STEM_COLOUR = Color.blue;
1160 // private Color sdNOTCANONICAL_COLOUR;
1162 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1163 int y, int iconOffset, int startRes, int column, boolean validRes,
1166 g.setColor(GLYPHLINE_COLOR);
1167 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1170 void drawSheetAnnot(Graphics g, Annotation[] row,
1172 int lastSSX, int x, int y, int iconOffset, int startRes,
1173 int column, boolean validRes, boolean validEnd)
1175 g.setColor(SHEET_COLOUR);
1177 if (!validEnd || !validRes || row == null || row[column] == null
1178 || row[column].secondaryStructure != 'E')
1180 g.fillRect(lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX - 4,
1184 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
1186 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
1191 g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * charWidth - lastSSX,
1197 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1198 int y, int iconOffset, int startRes, int column, boolean validRes,
1201 g.setColor(HELIX_COLOUR);
1203 int sCol = (lastSSX / charWidth)
1204 + hiddenColumns.visibleToAbsoluteColumn(startRes);
1206 int x2 = (x * charWidth);
1208 if (USE_FILL_ROUND_RECT)
1210 int ofs = charWidth / 2;
1211 // Off by 1 offset when drawing rects and ovals
1212 // to offscreen image on the MAC
1213 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1214 if (sCol == 0 || row[sCol - 1] == null
1215 || row[sCol - 1].secondaryStructure != 'H')
1220 // g.setColor(Color.orange);
1221 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1224 if (!validRes || row[column] == null
1225 || row[column].secondaryStructure != 'H')
1231 // g.setColor(Color.magenta);
1232 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset,
1233 x2 - x1 - ofs + 1, 8, 0, 0);
1240 if (sCol == 0 || row[sCol - 1] == null
1241 || row[sCol - 1].secondaryStructure != 'H')
1243 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1244 x1 += charWidth / 2;
1247 if (!validRes || row[column] == null
1248 || row[column].secondaryStructure != 'H')
1250 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1252 x2 -= charWidth / 2;
1255 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1258 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1259 Annotation[] aa_annotations, int sRes, int eRes, int y, float min,
1260 float max, int graphHeight)
1262 if (sRes > aa_annotations.length)
1269 // Adjustment for fastpaint to left
1275 eRes = Math.min(eRes, aa_annotations.length);
1283 float range = max - min;
1288 y2 = y - (int) ((0 - min / range) * graphHeight);
1291 g.setColor(Color.gray);
1292 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1294 eRes = Math.min(eRes, aa_annotations.length);
1297 int aaMax = aa_annotations.length - 1;
1299 while (x < eRes - sRes)
1302 if (hasHiddenColumns)
1304 column = hiddenColumns.visibleToAbsoluteColumn(column);
1312 if (aa_annotations[column] == null
1313 || aa_annotations[column - 1] == null)
1319 if (aa_annotations[column].colour == null)
1321 g.setColor(Color.black);
1325 g.setColor(aa_annotations[column].colour);
1328 y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
1330 y2 = y - (int) (((aa_annotations[column].value - min) / range)
1333 g.drawLine(x * charWidth - charWidth / 2, y1,
1334 x * charWidth + charWidth / 2, y2);
1338 if (_aa.threshold != null)
1340 g.setColor(_aa.threshold.colour);
1341 Graphics2D g2 = (Graphics2D) g;
1342 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1343 BasicStroke.JOIN_ROUND, 3f, new float[]
1346 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1347 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1348 g2.setStroke(new BasicStroke());
1352 @SuppressWarnings("unused")
1353 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1354 Annotation[] aa_annotations, int sRes, int eRes, float min,
1355 float max, int y, boolean renderHistogram, boolean renderProfile,
1356 boolean normaliseProfile)
1358 if (sRes > aa_annotations.length)
1362 Font ofont = g.getFont();
1363 eRes = Math.min(eRes, aa_annotations.length);
1365 int x = 0, y1 = y, y2 = y;
1367 float range = max - min;
1371 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1374 g.setColor(Color.gray);
1376 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1379 int aaMax = aa_annotations.length - 1;
1380 while (x < eRes - sRes)
1383 if (hasHiddenColumns)
1385 column = hiddenColumns.visibleToAbsoluteColumn(column);
1393 if (aa_annotations[column] == null)
1398 if (aa_annotations[column].colour == null)
1400 g.setColor(Color.black);
1404 g.setColor(aa_annotations[column].colour);
1407 y1 = y - (int) (((aa_annotations[column].value - min) / (range))
1410 if (renderHistogram)
1414 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1418 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1421 // draw profile if available
1426 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1428 int profl[] = getProfileFor(_aa, column);
1430 // just try to draw the logo if profl is not null
1431 if (profl != null && profl[2] != 0)
1433 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1434 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1435 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1436 final double normaliseFactor = normaliseProfile ? _aa.graphHeight
1440 * Render a single base for a sequence profile, a base pair for
1441 * structure profile, and a triplet for a cdna profile
1443 char[] dc = new char[isStructureProfile ? 2
1444 : (isCdnaProfile ? 3 : 1)];
1446 // lm is not necessary - we can just use fm - could be off by no more
1448 // LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1449 // System.out.println(asc + " " + dec + " " + (asc - lm.getAscent())
1450 // + " " + (dec - lm.getDescent()));
1452 double asc = fm.getAscent();
1453 double dec = fm.getDescent();
1454 double fht = fm.getHeight();
1456 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1457 // float ofontHeight = 1f / fm.getAscent();// magnify to fill box
1460 * Traverse the character(s)/percentage data in the array
1465 // profl[1] is the number of values in the profile
1466 for (int i = 0, c = 3, last = profl[1]; i < last; i++)
1470 if (isStructureProfile)
1472 // todo can we encode a structure pair as an int, like codons?
1473 dc[0] = (char) profl[c++];
1474 dc[1] = (char) profl[c++];
1477 else if (isCdnaProfile)
1479 CodingUtils.decodeCodon2(profl[c++], dc);
1484 dc[0] = (char) profl[c++];
1487 // next profl[] position is profile % for the character(s)
1489 int percent = profl[c++];
1492 // failsafe in case a count rounds down to 0%
1495 double newHeight = normaliseFactor * scale * percent;
1498 * Set character colour as per alignment colour scheme; use the
1499 * codon translation if a cDNA profile
1501 Color colour = null;
1504 final String codonTranslation = ResidueProperties
1506 colour = profcolour.findColour(codonTranslation.charAt(0),
1511 colour = profcolour.findColour(dc[0], column, null);
1513 g.setColor(colour == Color.white ? Color.lightGray : colour);
1515 // Debug - render boxes around characters
1516 // g.setColor(Color.red);
1517 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1519 // g.setColor(profcolour.findColour(dc[0]).darker());
1521 double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
1522 double sy = newHeight / asc;
1523 double newAsc = asc * sy;
1524 double newDec = dec * sy;
1525 // it is not necessary to recalculate lm for the new font.
1526 // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0
1527 // by definition. Was:
1528 // int hght = (int) (ht + (newAsc - newDec);
1529 // - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
1531 if (Platform.isJS())
1534 * SwingJS does not implement font.deriveFont()
1535 * so use a scaling transform to draw instead,
1536 * this is off by a very small amount
1538 final int hght = (int) (ht2 + (newAsc - newDec));
1539 Graphics2D gg = (Graphics2D) g;
1540 int xShift = (int) Math.round(x * charWidth / sx);
1541 int yShift = (int) Math.round(hght / sy);
1542 gg.transform(AffineTransform.getScaleInstance(sx, sy));
1543 gg.drawString(s, xShift, yShift);
1545 AffineTransform.getScaleInstance(1D / sx, 1D / sy));
1555 // Java ('normal') method is to scale the font to fit
1557 final int hght = (int) (ht + (newAsc - newDec));
1559 .deriveFont(AffineTransform.getScaleInstance(sx, sy));
1561 g.drawChars(dc, 0, dc.length, x * charWidth, hght);
1569 if (_aa.threshold != null)
1571 g.setColor(_aa.threshold.colour);
1572 Graphics2D g2 = (Graphics2D) g;
1573 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1574 BasicStroke.JOIN_ROUND, 3f, new float[]
1578 - ((_aa.threshold.value - min) / range) * _aa.graphHeight);
1579 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1580 g2.setStroke(new BasicStroke());
1584 // used by overview window
1585 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1586 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1588 eRes = Math.min(eRes, aa_annotations.length);
1589 g.setColor(Color.white);
1590 g.fillRect(0, 0, width, y);
1591 g.setColor(new Color(0, 0, 180));
1595 for (int j = sRes; j < eRes; j++)
1597 if (aa_annotations[j] != null)
1599 if (aa_annotations[j].colour == null)
1601 g.setColor(Color.black);
1605 g.setColor(aa_annotations[j].colour);
1608 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1614 g.fillRect(x, y - height, charWidth, height);
1620 Color getNotCanonicalColor(char lastss)
1626 return new Color(255, 125, 5);
1630 return new Color(245, 115, 10);
1634 return new Color(235, 135, 15);
1638 return new Color(225, 105, 20);
1642 return new Color(215, 145, 30);
1646 return new Color(205, 95, 35);
1650 return new Color(195, 155, 45);
1654 return new Color(185, 85, 55);
1658 return new Color(175, 165, 65);
1662 return new Color(170, 75, 75);
1666 return new Color(160, 175, 85);
1670 return new Color(150, 65, 95);
1674 return new Color(140, 185, 105);
1678 return new Color(130, 55, 110);
1682 return new Color(120, 195, 120);
1686 return new Color(110, 45, 130);
1690 return new Color(100, 205, 140);
1694 return new Color(90, 35, 150);
1698 return new Color(85, 215, 160);
1702 return new Color(75, 25, 170);
1706 return new Color(65, 225, 180);
1710 return new Color(55, 15, 185);
1714 return new Color(45, 235, 195);
1718 return new Color(35, 5, 205);
1722 return new Color(25, 245, 215);
1726 return new Color(15, 0, 225);
1730 return new Color(10, 255, 235);
1734 return new Color(5, 150, 245);
1738 return new Color(0, 80, 255);
1741 System.out.println("This is not a interaction : " + lastss);