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.schemes.ColourSchemeI;
32 import jalview.schemes.ResidueProperties;
34 import java.awt.BasicStroke;
35 import java.awt.Color;
37 import java.awt.FontMetrics;
38 import java.awt.Graphics;
39 import java.awt.Graphics2D;
40 import java.awt.Image;
41 import java.awt.font.LineMetrics;
42 import java.awt.geom.AffineTransform;
43 import java.awt.image.ImageObserver;
44 import java.util.BitSet;
45 import java.util.Hashtable;
47 public class AnnotationRenderer
49 private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
51 private static final int CHAR_A = 'A'; // 65
53 private static final int CHAR_Z = 'Z'; // 90
56 * flag indicating if timing and redraw parameter info should be output
58 private final boolean debugRedraw;
60 public AnnotationRenderer()
66 * Create a new annotation Renderer
69 * flag indicating if timing and redraw parameter info should be
72 public AnnotationRenderer(boolean debugRedraw)
74 this.debugRedraw = debugRedraw;
77 void drawStemAnnot(Graphics g, Annotation[] row_annotations,
78 int lastSSX, int x, int y, int iconOffset, int startRes,
79 int column, boolean validRes, boolean validEnd)
81 g.setColor(STEM_COLOUR);
82 int sCol = (lastSSX / charWidth) + startRes;
84 int x2 = (x * charWidth);
86 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
87 : row_annotations[column - 1].secondaryStructure;
89 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
90 || dc != row_annotations[sCol - 1].secondaryStructure;
91 boolean diffdownstream = !validRes || !validEnd
92 || row_annotations[column] == null
93 || dc != row_annotations[column].secondaryStructure;
95 if (column > 0 && Rna.isClosingParenthesis(dc))
98 // if (validRes && column>1 && row_annotations[column-2]!=null &&
99 // dc.equals(row_annotations[column-2].displayCharacter))
102 * if new annotation with a closing base pair half of the stem,
103 * display a backward arrow
105 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
106 new int[] { y + iconOffset, y + 14 + iconOffset,
107 y + 8 + iconOffset }, 3);
117 // display a forward arrow
121 * if annotation ending with an opeing base pair half of the stem,
122 * display a forward arrow
124 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
125 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
134 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
137 private int charWidth, endRes, charHeight;
139 private boolean validCharWidth, hasHiddenColumns;
141 private FontMetrics fm;
143 private final boolean MAC = jalview.util.Platform.isAMac();
145 boolean av_renderHistogram = true, av_renderProfile = true,
146 av_normaliseProfile = false;
148 ColourSchemeI profcolour = null;
150 private ColumnSelection columnSelection;
152 private Hashtable[] hconsensus;
154 private Hashtable[] complementConsensus;
156 private Hashtable[] hStrucConsensus;
158 private boolean av_ignoreGapsConsensus;
161 * attributes set from AwtRenderPanelI
164 * old image used when data is currently being calculated and cannot be
167 private Image fadedImage;
170 * panel being rendered into
172 private ImageObserver annotationPanel;
175 * width of image to render in panel
177 private int imgWidth;
180 * offset to beginning of visible area
185 * offset to end of visible area
187 private int visHeight;
190 * indicate if the renderer should only render the visible portion of the
191 * annotation given the current view settings
193 private boolean useClip = true;
196 * master flag indicating if renderer should ever try to clip. not enabled for
199 private boolean canClip = false;
201 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
202 Annotation[] row_annotations, int lastSSX, int x, int y,
203 int iconOffset, int startRes, int column, boolean validRes,
206 // System.out.println(nonCanColor);
208 g.setColor(nonCanColor);
209 int sCol = (lastSSX / charWidth) + startRes;
211 int x2 = (x * charWidth);
213 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
214 : row_annotations[column - 1].displayCharacter;
216 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
217 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
218 boolean diffdownstream = !validRes || !validEnd
219 || row_annotations[column] == null
220 || !dc.equals(row_annotations[column].displayCharacter);
221 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
222 // If a closing base pair half of the stem, display a backward arrow
223 if (column > 0 && Rna.isClosingParenthesis(dc))
227 // if (validRes && column>1 && row_annotations[column-2]!=null &&
228 // dc.equals(row_annotations[column-2].displayCharacter))
230 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
231 new int[] { y + iconOffset, y + 14 + iconOffset,
232 y + 8 + iconOffset }, 3);
243 // display a forward arrow
246 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
247 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
256 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
259 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
261 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
264 fm = annotPanel.getFontMetrics();
265 annotationPanel = annotPanel;
266 fadedImage = annotPanel.getFadedImage();
267 imgWidth = annotPanel.getFadedImageWidth();
268 // visible area for rendering
269 int[] bounds = annotPanel.getVisibleVRange();
273 visHeight = bounds[1];
288 updateFromAlignViewport(av);
291 public void updateFromAlignViewport(AlignViewportI av)
293 charWidth = av.getCharWidth();
294 endRes = av.getEndRes();
295 charHeight = av.getCharHeight();
296 hasHiddenColumns = av.hasHiddenColumns();
297 validCharWidth = av.isValidCharWidth();
298 av_renderHistogram = av.isShowConsensusHistogram();
299 av_renderProfile = av.isShowSequenceLogo();
300 av_normaliseProfile = av.isNormaliseSequenceLogo();
301 profcolour = av.getGlobalColourScheme();
302 if (profcolour == null)
304 // Set the default colour for sequence logo if the alignnent has no
306 profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
307 : new jalview.schemes.ZappoColourScheme();
309 columnSelection = av.getColumnSelection();
310 hconsensus = av.getSequenceConsensusHash();
311 complementConsensus = av.getComplementConsensusHash();
312 hStrucConsensus = av.getRnaStructureConsensusHash();
313 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
317 * Returns profile data; the first element is the profile type, the second is
318 * the number of distinct values, the third the total count, and the remainder
319 * depend on the profile type.
325 int[] getProfileFor(AlignmentAnnotation aa, int column)
327 // TODO : consider refactoring the global alignment calculation
328 // properties/rendering attributes as a global 'alignment group' which holds
329 // all vis settings for the alignment as a whole rather than a subset
331 if (aa.autoCalculated
332 && (aa.label.startsWith("Consensus") || aa.label
333 .startsWith("cDNA Consensus")))
335 boolean forComplement = aa.label.startsWith("cDNA Consensus");
336 if (aa.groupRef != null && aa.groupRef.consensusData != null
337 && aa.groupRef.isShowSequenceLogo())
339 // TODO? group consensus for cDNA complement
340 return AAFrequency.extractProfile(
341 aa.groupRef.consensusData[column],
342 aa.groupRef.getIgnoreGapsConsensus());
344 // TODO extend annotation row to enable dynamic and static profile data to
346 if (aa.groupRef == null && aa.sequenceRef == null)
350 return AAFrequency.extractCdnaProfile(
351 complementConsensus[column], av_ignoreGapsConsensus);
355 return AAFrequency.extractProfile(hconsensus[column],
356 av_ignoreGapsConsensus);
362 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
364 // TODO implement group structure consensus
366 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
367 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
368 * group selections return StructureFrequency.extractProfile(
369 * aa.groupRef.consensusData[column], aa.groupRef
370 * .getIgnoreGapsConsensus()); }
372 // TODO extend annotation row to enable dynamic and static profile data
375 if (aa.groupRef == null && aa.sequenceRef == null
376 && hStrucConsensus != null
377 && hStrucConsensus.length > column)
379 return StructureFrequency.extractProfile(hStrucConsensus[column],
380 av_ignoreGapsConsensus);
390 * Render the annotation rows associated with an alignment.
395 * data and view settings to render
397 * destination for graphics
399 * row where a mouse event occured (or -1)
401 * first column that will be drawn
403 * last column that will be drawn
404 * @return true if the fadedImage was used for any alignment annotation rows
405 * currently being calculated
407 public boolean drawComponent(AwtRenderPanelI annotPanel,
408 AlignViewportI av, Graphics g, int activeRow, int startRes,
411 long stime = System.currentTimeMillis();
412 boolean usedFaded = false;
414 // AnnotationPanel needs to implement: ImageObserver, access to
416 updateFromAwtRenderPanel(annotPanel, av);
417 fm = g.getFontMetrics();
418 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
429 boolean validRes = false;
430 boolean validEnd = false;
431 boolean labelAllCols = false;
432 boolean centreColLabels;
433 boolean centreColLabelsDef = av.isCentreColumnLabels();
434 boolean scaleColLabel = false;
435 final AlignmentAnnotation consensusAnnot = av
436 .getAlignmentConsensusAnnotation();
437 final AlignmentAnnotation structConsensusAnnot = av
438 .getAlignmentStrucConsensusAnnotation();
439 final AlignmentAnnotation complementConsensusAnnot = av
440 .getComplementConsensusAnnotation();
441 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
443 BitSet graphGroupDrawn = new BitSet();
444 int charOffset = 0; // offset for a label
445 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
447 Font ofont = g.getFont();
450 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
451 boolean clipst = false, clipend = false;
452 for (int i = 0; i < aa.length; i++)
454 AlignmentAnnotation row = aa[i];
457 // check if this is a consensus annotation row and set the display
458 // settings appropriately
459 // TODO: generalise this to have render styles for consensus/profile
461 if (row.groupRef != null && row == row.groupRef.getConsensus())
463 renderHistogram = row.groupRef.isShowConsensusHistogram();
464 renderProfile = row.groupRef.isShowSequenceLogo();
465 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
467 else if (row == consensusAnnot || row == structConsensusAnnot
468 || row == complementConsensusAnnot)
470 renderHistogram = av_renderHistogram;
471 renderProfile = av_renderProfile;
472 normaliseProfile = av_normaliseProfile;
476 renderHistogram = true;
477 // don't need to set render/normaliseProfile since they are not
478 // currently used in any other annotation track renderer
481 Annotation[] row_annotations = row.annotations;
486 centreColLabels = row.centreColLabels || centreColLabelsDef;
487 labelAllCols = row.showAllColLabels;
488 scaleColLabel = row.scaleColLabel;
493 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
494 {// if_in_visible_region
505 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
510 // this is so that we draw the characters below the graph
515 iconOffset = charHeight - fm.getDescent();
519 else if (row.hasText)
521 iconOffset = charHeight - fm.getDescent();
529 if (row.autoCalculated && av.isCalculationInProgress(row))
533 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
534 - row.height, imgWidth, y, annotationPanel);
535 g.setColor(Color.black);
536 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
542 * else if (annotationPanel.av.updatingConservation &&
543 * aa[i].label.equals("Conservation")) {
545 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
546 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
547 * annotationPanel.imgWidth, y, annotationPanel);
549 * g.setColor(Color.black); //
550 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
552 * continue; } else if (annotationPanel.av.updatingConservation &&
553 * aa[i].label.equals("Quality")) {
555 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
556 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
557 * annotationPanel.imgWidth, y, annotationPanel);
558 * g.setColor(Color.black); // /
559 * g.drawString("Calculating Quality....",20, y-row.height/2);
563 // first pass sets up state for drawing continuation from left-hand
566 x = (startRes == 0) ? 0 : -1;
567 while (x < endRes - startRes)
569 if (hasHiddenColumns)
571 column = columnSelection.adjustForHiddenColumns(startRes + x);
572 if (column > row_annotations.length - 1)
579 column = startRes + x;
582 if ((row_annotations == null)
583 || (row_annotations.length <= column)
584 || (row_annotations[column] == null))
592 final String displayChar = validRes ? row_annotations[column].displayCharacter
598 g.setColor(Color.red);
600 if (columnSelection != null)
602 if (columnSelection.contains(column))
604 g.fillRect(x * charWidth, y, charWidth, charHeight);
608 if (row.getInvalidStrucPos() > x)
610 g.setColor(Color.orange);
611 g.fillRect(x * charWidth, y, charWidth, charHeight);
613 else if (row.getInvalidStrucPos() == x)
615 g.setColor(Color.orange.darker());
616 g.fillRect(x * charWidth, y, charWidth, charHeight);
618 if (validCharWidth && validRes && displayChar != null
619 && (displayChar.length() > 0))
622 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
623 displayChar.length());
624 if (/* centreColLabels || */scaleColLabel)
626 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
627 // displayChar.length());
629 // if (scaleColLabel)
631 // justify the label and scale to fit in column
632 if (fmWidth > charWidth)
634 // scale only if the current font isn't already small enough
635 fmScaling = charWidth;
636 fmScaling /= fmWidth;
637 g.setFont(ofont.deriveFont(AffineTransform
638 .getScaleInstance(fmScaling, 1.0)));
639 // and update the label's width to reflect the scaling.
644 // TODO is it ok to use width of / show all characters here?
647 // fmWidth = fm.charWidth(displayChar.charAt(0));
649 charOffset = (int) ((charWidth - fmWidth) / 2f);
651 if (row_annotations[column].colour == null)
653 g.setColor(Color.black);
657 g.setColor(row_annotations[column].colour);
660 if (column == 0 || row.graph > 0)
662 g.drawString(displayChar, (x * charWidth) + charOffset, y
665 else if (row_annotations[column - 1] == null
668 .equals(row_annotations[column - 1].displayCharacter) || (displayChar
669 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
671 g.drawString(displayChar, x * charWidth + charOffset, y
679 char ss = validRes ? row_annotations[column].secondaryStructure
684 // distinguish between forward/backward base-pairing
685 if (displayChar.indexOf(')') > -1)
694 if ((displayChar.indexOf(']') > -1))
702 // distinguish between forward/backward base-pairing
703 if (displayChar.indexOf('}') > -1)
711 // distinguish between forward/backward base-pairing
712 if (displayChar.indexOf('<') > -1)
718 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
720 // distinguish between forward/backward base-pairing
721 int ssLowerCase = ss + UPPER_TO_LOWER;
722 // TODO would .equals() be safer here? or charAt(0)?
723 if (displayChar.indexOf(ssLowerCase) > -1)
725 ss = (char) ssLowerCase;
729 if (!validRes || (ss != lastSS))
735 int nb_annot = x - temp;
736 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
739 case '(': // Stem case for RNA secondary structure
740 case ')': // and opposite direction
741 drawStemAnnot(g, row_annotations, lastSSX, x, y,
742 iconOffset, startRes, column, validRes, validEnd);
749 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
750 iconOffset, startRes, column, validRes,
754 // no break if isRNA - falls through to drawNotCanonicalAnnot!
758 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
759 iconOffset, startRes, column, validRes,
763 // no break if isRNA - fall through to drawNotCanonicalAnnot!
822 Color nonCanColor = getNotCanonicalColor(lastSS);
823 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
824 lastSSX, x, y, iconOffset, startRes, column,
829 g.setColor(Color.gray);
830 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
846 lastSSX = (x * charWidth);
853 if (column >= row_annotations.length)
855 column = row_annotations.length - 1;
862 if ((row_annotations == null) || (row_annotations.length <= column)
863 || (row_annotations[column] == null))
881 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
882 startRes, column, validRes, validEnd);
885 // no break if isRNA - fall through to drawNotCanonicalAnnot!
890 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
891 startRes, column, validRes, validEnd);
894 // no break if isRNA - fall through to drawNotCanonicalAnnot!
897 case ')': // Stem case for RNA secondary structure
899 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
900 startRes, column, validRes, validEnd);
957 // System.out.println(lastSS);
958 Color nonCanColor = getNotCanonicalColor(lastSS);
959 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
960 x, y, iconOffset, startRes, column, validRes, validEnd);
963 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
964 startRes, column, validRes, validEnd);
969 if (row.graph > 0 && row.graphHeight > 0)
971 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
973 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
975 // TODO: JAL-1291 revise rendering model so the graphGroup map is
976 // computed efficiently for all visible labels
977 float groupmax = -999999, groupmin = 9999999;
978 for (int gg = 0; gg < aa.length; gg++)
980 if (aa[gg].graphGroup != row.graphGroup)
987 aa[gg].visible = false;
989 if (aa[gg].graphMax > groupmax)
991 groupmax = aa[gg].graphMax;
993 if (aa[gg].graphMin < groupmin)
995 groupmin = aa[gg].graphMin;
999 for (int gg = 0; gg < aa.length; gg++)
1001 if (aa[gg].graphGroup == row.graphGroup)
1003 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1004 endRes, y, groupmin, groupmax, row.graphHeight);
1008 graphGroupDrawn.set(row.graphGroup);
1012 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1013 row.graphMin, row.graphMax, row.graphHeight);
1016 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1018 drawBarGraph(g, row, row_annotations, startRes, endRes,
1019 row.graphMin, row.graphMax, y, renderHistogram,
1020 renderProfile, normaliseProfile);
1026 if (clipst && !clipend)
1030 }// end if_in_visible_region
1031 if (row.graph > 0 && row.hasText)
1047 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1052 System.err.println("End clip at : " + yto + " (index " + f_to
1057 System.err.println("Annotation Rendering time:"
1058 + (System.currentTimeMillis() - stime));
1065 public static final Color GLYPHLINE_COLOR = Color.gray;
1067 public static final Color SHEET_COLOUR = Color.green;
1069 public static final Color HELIX_COLOUR = Color.red;
1071 public static final Color STEM_COLOUR = Color.blue;
1073 private Color sdNOTCANONICAL_COLOUR;
1075 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
1076 int x, int y, int iconOffset, int startRes, int column,
1077 boolean validRes, boolean validEnd)
1079 g.setColor(GLYPHLINE_COLOR);
1080 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1083 void drawSheetAnnot(Graphics g, Annotation[] row,
1085 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1086 boolean validRes, boolean validEnd)
1088 g.setColor(SHEET_COLOUR);
1090 if (!validEnd || !validRes || row == null || row[column] == null
1091 || row[column].secondaryStructure != 'E')
1093 g.fillRect(lastSSX, y + 4 + iconOffset,
1094 (x * charWidth) - lastSSX - 4, 7);
1095 g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
1096 (x * charWidth) }, new int[] { y + iconOffset,
1097 y + 14 + iconOffset, y + 7 + iconOffset }, 3);
1101 g.fillRect(lastSSX, y + 4 + iconOffset,
1102 (x + 1) * charWidth - lastSSX, 7);
1107 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
1108 int x, int y, int iconOffset, int startRes, int column,
1109 boolean validRes, boolean validEnd)
1111 g.setColor(HELIX_COLOUR);
1113 int sCol = (lastSSX / charWidth) + startRes;
1115 int x2 = (x * charWidth);
1119 int ofs = charWidth / 2;
1120 // Off by 1 offset when drawing rects and ovals
1121 // to offscreen image on the MAC
1122 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1123 if (sCol == 0 || row[sCol - 1] == null
1124 || row[sCol - 1].secondaryStructure != 'H')
1129 // g.setColor(Color.orange);
1130 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1133 if (!validRes || row[column] == null
1134 || row[column].secondaryStructure != 'H')
1140 // g.setColor(Color.magenta);
1141 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1149 if (sCol == 0 || row[sCol - 1] == null
1150 || row[sCol - 1].secondaryStructure != 'H')
1152 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1153 x1 += charWidth / 2;
1156 if (!validRes || row[column] == null
1157 || row[column].secondaryStructure != 'H')
1159 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1161 x2 -= charWidth / 2;
1164 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1167 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1168 Annotation[] aa_annotations, int sRes, int eRes, int y,
1169 float min, float max, int graphHeight)
1171 if (sRes > aa_annotations.length)
1178 // Adjustment for fastpaint to left
1184 eRes = Math.min(eRes, aa_annotations.length);
1192 float range = max - min;
1197 y2 = y - (int) ((0 - min / range) * graphHeight);
1200 g.setColor(Color.gray);
1201 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1203 eRes = Math.min(eRes, aa_annotations.length);
1206 int aaMax = aa_annotations.length - 1;
1208 while (x < eRes - sRes)
1211 if (hasHiddenColumns)
1213 column = columnSelection.adjustForHiddenColumns(column);
1221 if (aa_annotations[column] == null
1222 || aa_annotations[column - 1] == null)
1228 if (aa_annotations[column].colour == null)
1230 g.setColor(Color.black);
1234 g.setColor(aa_annotations[column].colour);
1238 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1240 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1242 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1243 + charWidth / 2, y2);
1247 if (_aa.threshold != null)
1249 g.setColor(_aa.threshold.colour);
1250 Graphics2D g2 = (Graphics2D) g;
1251 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1252 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1254 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1255 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1256 g2.setStroke(new BasicStroke());
1260 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1261 Annotation[] aa_annotations, int sRes, int eRes, float min,
1262 float max, int y, boolean renderHistogram, boolean renderProfile,
1263 boolean normaliseProfile)
1265 if (sRes > aa_annotations.length)
1269 Font ofont = g.getFont();
1270 eRes = Math.min(eRes, aa_annotations.length);
1272 int x = 0, y1 = y, y2 = y;
1274 float range = max - min;
1278 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1281 g.setColor(Color.gray);
1283 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1286 int aaMax = aa_annotations.length - 1;
1287 while (x < eRes - sRes)
1290 if (hasHiddenColumns)
1292 column = columnSelection.adjustForHiddenColumns(column);
1300 if (aa_annotations[column] == null)
1305 if (aa_annotations[column].colour == null)
1307 g.setColor(Color.black);
1311 g.setColor(aa_annotations[column].colour);
1315 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1317 if (renderHistogram)
1321 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1325 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1328 // draw profile if available
1333 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1335 int profl[] = getProfileFor(_aa, column);
1337 // just try to draw the logo if profl is not null
1338 if (profl != null && profl[2] != 0)
1340 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1341 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1342 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1343 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1350 * Render a single base for a sequence profile, a base pair for
1351 * structure profile, and a triplet for a cdna profile
1353 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1355 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1356 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1357 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1361 * Traverse the character(s)/percentage data in the array
1364 int valuesProcessed = 0;
1365 // profl[1] is the number of values in the profile
1366 while (valuesProcessed < profl[1])
1368 if (isStructureProfile)
1370 // todo can we encode a structure pair as an int, like codons?
1371 dc[0] = (char) profl[c++];
1372 dc[1] = (char) profl[c++];
1374 else if (isCdnaProfile)
1376 dc = CodingUtils.decodeCodon(profl[c++]);
1380 dc[0] = (char) profl[c++];
1384 wdth /= fm.charsWidth(dc, 0, dc.length);
1387 // next profl[] position is profile % for the character(s)
1388 scl = htn * scale * profl[c++];
1389 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1390 .getFontRenderContext());
1391 Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
1392 wdth, scl / lm.getAscent()));
1394 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1396 // Debug - render boxes around characters
1397 // g.setColor(Color.red);
1398 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1400 // g.setColor(profcolour.findColour(dc[0]).darker());
1403 * Set character colour as per alignment colour scheme; use the
1404 * codon translation if a cDNA profile
1406 Color colour = null;
1409 final String codonTranslation = ResidueProperties
1410 .codonTranslate(new String(dc));
1411 colour = profcolour.findColour(codonTranslation.charAt(0),
1416 colour = profcolour.findColour(dc[0], column, null);
1418 g.setColor(colour == Color.white ? Color.lightGray : colour);
1420 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1421 .getBaselineIndex()]));
1423 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1431 if (_aa.threshold != null)
1433 g.setColor(_aa.threshold.colour);
1434 Graphics2D g2 = (Graphics2D) g;
1435 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1436 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1438 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1440 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1441 g2.setStroke(new BasicStroke());
1445 // used by overview window
1446 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1447 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1449 eRes = Math.min(eRes, aa_annotations.length);
1450 g.setColor(Color.white);
1451 g.fillRect(0, 0, width, y);
1452 g.setColor(new Color(0, 0, 180));
1456 for (int j = sRes; j < eRes; j++)
1458 if (aa_annotations[j] != null)
1460 if (aa_annotations[j].colour == null)
1462 g.setColor(Color.black);
1466 g.setColor(aa_annotations[j].colour);
1469 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1475 g.fillRect(x, y - height, charWidth, height);
1481 Color getNotCanonicalColor(char lastss)
1487 return new Color(255, 125, 5);
1491 return new Color(245, 115, 10);
1495 return new Color(235, 135, 15);
1499 return new Color(225, 105, 20);
1503 return new Color(215, 145, 30);
1507 return new Color(205, 95, 35);
1511 return new Color(195, 155, 45);
1515 return new Color(185, 85, 55);
1519 return new Color(175, 165, 65);
1523 return new Color(170, 75, 75);
1527 return new Color(160, 175, 85);
1531 return new Color(150, 65, 95);
1535 return new Color(140, 185, 105);
1539 return new Color(130, 55, 110);
1543 return new Color(120, 195, 120);
1547 return new Color(110, 45, 130);
1551 return new Color(100, 205, 140);
1555 return new Color(90, 35, 150);
1559 return new Color(85, 215, 160);
1563 return new Color(75, 25, 170);
1567 return new Color(65, 225, 180);
1571 return new Color(55, 15, 185);
1575 return new Color(45, 235, 195);
1579 return new Color(35, 5, 205);
1583 return new Color(25, 245, 215);
1587 return new Color(15, 0, 225);
1591 return new Color(10, 255, 235);
1595 return new Color(5, 150, 245);
1599 return new Color(0, 80, 255);
1602 System.out.println("This is not a interaction : " + lastss);