2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.renderer;
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.CodingUtils;
25 import jalview.analysis.Rna;
26 import jalview.analysis.StructureFrequency;
27 import jalview.api.AlignViewportI;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.Annotation;
30 import jalview.datamodel.ColumnSelection;
31 import jalview.datamodel.ProfilesI;
32 import jalview.renderer.api.AnnotationRendererFactoryI;
33 import jalview.renderer.api.AnnotationRowRendererI;
34 import jalview.schemes.ColourSchemeI;
35 import jalview.schemes.ResidueProperties;
36 import jalview.util.Platform;
38 import java.awt.BasicStroke;
39 import java.awt.Color;
41 import java.awt.FontMetrics;
42 import java.awt.Graphics;
43 import java.awt.Graphics2D;
44 import java.awt.Image;
45 import java.awt.font.LineMetrics;
46 import java.awt.geom.AffineTransform;
47 import java.awt.image.ImageObserver;
48 import java.util.BitSet;
49 import java.util.Hashtable;
51 public class AnnotationRenderer
53 private static final int UPPER_TO_LOWER = 'a' - 'A'; // 32
55 private static final int CHAR_A = 'A'; // 65
57 private static final int CHAR_Z = 'Z'; // 90
60 * flag indicating if timing and redraw parameter info should be output
62 private final boolean debugRedraw;
64 private int charWidth, endRes, charHeight;
66 private boolean validCharWidth, hasHiddenColumns;
68 private FontMetrics fm;
70 private final boolean MAC = Platform.isAMac();
72 boolean av_renderHistogram = true, av_renderProfile = true,
73 av_normaliseProfile = false;
75 ColourSchemeI profcolour = null;
77 private ColumnSelection columnSelection;
79 private ProfilesI hconsensus;
81 private Hashtable[] complementConsensus;
83 private Hashtable[] hStrucConsensus;
85 private boolean av_ignoreGapsConsensus;
88 * attributes set from AwtRenderPanelI
91 * old image used when data is currently being calculated and cannot be
94 private Image fadedImage;
97 * panel being rendered into
99 private ImageObserver annotationPanel;
102 * width of image to render in panel
104 private int imgWidth;
107 * offset to beginning of visible area
112 * offset to end of visible area
114 private int visHeight;
117 * indicate if the renderer should only render the visible portion of the
118 * annotation given the current view settings
120 private boolean useClip = true;
123 * master flag indicating if renderer should ever try to clip. not enabled for
126 private boolean canClip = false;
128 public AnnotationRenderer()
134 * Create a new annotation Renderer
137 * flag indicating if timing and redraw parameter info should be
140 public AnnotationRenderer(boolean debugRedraw)
142 this.debugRedraw = debugRedraw;
146 * Remove any references and resources when this object is no longer required
148 public void dispose()
151 complementConsensus = null;
152 hStrucConsensus = null;
154 annotationPanel = null;
155 rendererFactoryI = null;
158 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
159 int x, int y, int iconOffset, int startRes, int column,
160 boolean validRes, boolean validEnd)
162 g.setColor(STEM_COLOUR);
163 int sCol = (lastSSX / charWidth) + startRes;
165 int x2 = (x * charWidth);
167 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
168 : row_annotations[column - 1].secondaryStructure;
170 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
171 || dc != row_annotations[sCol - 1].secondaryStructure;
172 boolean diffdownstream = !validRes || !validEnd
173 || row_annotations[column] == null
174 || dc != row_annotations[column].secondaryStructure;
176 if (column > 0 && Rna.isClosingParenthesis(dc))
179 // if (validRes && column>1 && row_annotations[column-2]!=null &&
180 // dc.equals(row_annotations[column-2].displayCharacter))
183 * if new annotation with a closing base pair half of the stem,
184 * display a backward arrow
186 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
187 new int[] { y + iconOffset, y + 14 + iconOffset,
188 y + 8 + iconOffset }, 3);
198 // display a forward arrow
202 * if annotation ending with an opeing base pair half of the stem,
203 * display a forward arrow
205 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
206 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
215 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
218 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
219 Annotation[] row_annotations, int lastSSX, int x, int y,
220 int iconOffset, int startRes, int column, boolean validRes,
223 // System.out.println(nonCanColor);
225 g.setColor(nonCanColor);
226 int sCol = (lastSSX / charWidth) + startRes;
228 int x2 = (x * charWidth);
230 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
231 : row_annotations[column - 1].displayCharacter;
233 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
234 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
235 boolean diffdownstream = !validRes || !validEnd
236 || row_annotations[column] == null
237 || !dc.equals(row_annotations[column].displayCharacter);
238 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
239 // If a closing base pair half of the stem, display a backward arrow
240 if (column > 0 && Rna.isClosingParenthesis(dc))
244 // if (validRes && column>1 && row_annotations[column-2]!=null &&
245 // dc.equals(row_annotations[column-2].displayCharacter))
247 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
248 new int[] { y + iconOffset, y + 14 + iconOffset,
249 y + 8 + iconOffset }, 3);
260 // display a forward arrow
263 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
264 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
273 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
276 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
278 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
281 fm = annotPanel.getFontMetrics();
282 annotationPanel = annotPanel;
283 fadedImage = annotPanel.getFadedImage();
284 imgWidth = annotPanel.getFadedImageWidth();
285 // visible area for rendering
286 int[] bounds = annotPanel.getVisibleVRange();
290 visHeight = bounds[1];
305 rendererFactoryI = AnnotationRendererFactory.getRendererFactory();
306 updateFromAlignViewport(av);
309 public void updateFromAlignViewport(AlignViewportI av)
311 charWidth = av.getCharWidth();
312 endRes = av.getEndRes();
313 charHeight = av.getCharHeight();
314 hasHiddenColumns = av.hasHiddenColumns();
315 validCharWidth = av.isValidCharWidth();
316 av_renderHistogram = av.isShowConsensusHistogram();
317 av_renderProfile = av.isShowSequenceLogo();
318 av_normaliseProfile = av.isNormaliseSequenceLogo();
319 profcolour = av.getGlobalColourScheme();
320 if (profcolour == null)
322 // Set the default colour for sequence logo if the alignnent has no
324 profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
325 : new jalview.schemes.ZappoColourScheme();
327 columnSelection = av.getColumnSelection();
328 hconsensus = av.getSequenceConsensusHash();
329 complementConsensus = av.getComplementConsensusHash();
330 hStrucConsensus = av.getRnaStructureConsensusHash();
331 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
335 * Returns profile data; the first element is the profile type, the second is
336 * the number of distinct values, the third the total count, and the remainder
337 * depend on the profile type.
343 int[] getProfileFor(AlignmentAnnotation aa, int column)
345 // TODO : consider refactoring the global alignment calculation
346 // properties/rendering attributes as a global 'alignment group' which holds
347 // all vis settings for the alignment as a whole rather than a subset
349 if (aa.autoCalculated
350 && (aa.label.startsWith("Consensus") || aa.label
351 .startsWith("cDNA Consensus")))
353 boolean forComplement = aa.label.startsWith("cDNA Consensus");
354 if (aa.groupRef != null && aa.groupRef.consensusData != null
355 && aa.groupRef.isShowSequenceLogo())
357 // TODO? group consensus for cDNA complement
358 return AAFrequency.extractProfile(
359 aa.groupRef.consensusData.get(column),
360 aa.groupRef.getIgnoreGapsConsensus());
362 // TODO extend annotation row to enable dynamic and static profile data to
364 if (aa.groupRef == null && aa.sequenceRef == null)
368 return AAFrequency.extractCdnaProfile(
369 complementConsensus[column], av_ignoreGapsConsensus);
373 return AAFrequency.extractProfile(hconsensus.get(column),
374 av_ignoreGapsConsensus);
380 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
382 // TODO implement group structure consensus
384 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
385 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
386 * group selections return StructureFrequency.extractProfile(
387 * aa.groupRef.consensusData[column], aa.groupRef
388 * .getIgnoreGapsConsensus()); }
390 // TODO extend annotation row to enable dynamic and static profile data
393 if (aa.groupRef == null && aa.sequenceRef == null
394 && hStrucConsensus != null
395 && hStrucConsensus.length > column)
397 return StructureFrequency.extractProfile(hStrucConsensus[column],
398 av_ignoreGapsConsensus);
407 private AnnotationRendererFactoryI rendererFactoryI;
410 * Render the annotation rows associated with an alignment.
415 * data and view settings to render
417 * destination for graphics
419 * row where a mouse event occured (or -1)
421 * first column that will be drawn
423 * last column that will be drawn
424 * @return true if the fadedImage was used for any alignment annotation rows
425 * currently being calculated
427 public boolean drawComponent(AwtRenderPanelI annotPanel,
428 AlignViewportI av, Graphics g, int activeRow, int startRes,
431 long stime = System.currentTimeMillis();
432 boolean usedFaded = false;
434 // AnnotationPanel needs to implement: ImageObserver, access to
436 updateFromAwtRenderPanel(annotPanel, av);
437 fm = g.getFontMetrics();
438 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
449 boolean validRes = false;
450 boolean validEnd = false;
451 boolean labelAllCols = false;
452 boolean centreColLabels;
453 boolean centreColLabelsDef = av.isCentreColumnLabels();
454 boolean scaleColLabel = false;
455 final AlignmentAnnotation consensusAnnot = av
456 .getAlignmentConsensusAnnotation();
457 final AlignmentAnnotation structConsensusAnnot = av
458 .getAlignmentStrucConsensusAnnotation();
459 final AlignmentAnnotation complementConsensusAnnot = av
460 .getComplementConsensusAnnotation();
461 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
463 BitSet graphGroupDrawn = new BitSet();
464 int charOffset = 0; // offset for a label
465 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
467 Font ofont = g.getFont();
470 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
471 boolean clipst = false, clipend = false;
472 for (int i = 0; i < aa.length; i++)
474 AlignmentAnnotation row = aa[i];
477 // check if this is a consensus annotation row and set the display
478 // settings appropriately
479 // TODO: generalise this to have render styles for consensus/profile
481 if (row.groupRef != null && row == row.groupRef.getConsensus())
483 renderHistogram = row.groupRef.isShowConsensusHistogram();
484 renderProfile = row.groupRef.isShowSequenceLogo();
485 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
487 else if (row == consensusAnnot || row == structConsensusAnnot
488 || row == complementConsensusAnnot)
490 renderHistogram = av_renderHistogram;
491 renderProfile = av_renderProfile;
492 normaliseProfile = av_normaliseProfile;
496 renderHistogram = true;
497 // don't need to set render/normaliseProfile since they are not
498 // currently used in any other annotation track renderer
501 Annotation[] row_annotations = row.annotations;
506 centreColLabels = row.centreColLabels || centreColLabelsDef;
507 labelAllCols = row.showAllColLabels;
508 scaleColLabel = row.scaleColLabel;
513 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
514 {// if_in_visible_region
525 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
530 // this is so that we draw the characters below the graph
535 iconOffset = charHeight - fm.getDescent();
539 else if (row.hasText)
541 iconOffset = charHeight - fm.getDescent();
549 if (row.autoCalculated && av.isCalculationInProgress(row))
553 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
554 - row.height, imgWidth, y, annotationPanel);
555 g.setColor(Color.black);
556 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
562 * else if (annotationPanel.av.updatingConservation &&
563 * aa[i].label.equals("Conservation")) {
565 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
566 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
567 * annotationPanel.imgWidth, y, annotationPanel);
569 * g.setColor(Color.black); //
570 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
572 * continue; } else if (annotationPanel.av.updatingConservation &&
573 * aa[i].label.equals("Quality")) {
575 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
576 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
577 * annotationPanel.imgWidth, y, annotationPanel);
578 * g.setColor(Color.black); // /
579 * g.drawString("Calculating Quality....",20, y-row.height/2);
583 // first pass sets up state for drawing continuation from left-hand
586 x = (startRes == 0) ? 0 : -1;
587 while (x < endRes - startRes)
589 if (hasHiddenColumns)
591 column = columnSelection.adjustForHiddenColumns(startRes + x);
592 if (column > row_annotations.length - 1)
599 column = startRes + x;
602 if ((row_annotations == null)
603 || (row_annotations.length <= column)
604 || (row_annotations[column] == null))
612 final String displayChar = validRes ? row_annotations[column].displayCharacter
618 g.setColor(Color.red);
620 if (columnSelection != null)
622 if (columnSelection.contains(column))
624 g.fillRect(x * charWidth, y, charWidth, charHeight);
628 if (row.getInvalidStrucPos() > x)
630 g.setColor(Color.orange);
631 g.fillRect(x * charWidth, y, charWidth, charHeight);
633 else if (row.getInvalidStrucPos() == x)
635 g.setColor(Color.orange.darker());
636 g.fillRect(x * charWidth, y, charWidth, charHeight);
638 if (validCharWidth && validRes && displayChar != null
639 && (displayChar.length() > 0))
642 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
643 displayChar.length());
644 if (/* centreColLabels || */scaleColLabel)
646 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
647 // displayChar.length());
649 // if (scaleColLabel)
651 // justify the label and scale to fit in column
652 if (fmWidth > charWidth)
654 // scale only if the current font isn't already small enough
655 fmScaling = charWidth;
656 fmScaling /= fmWidth;
657 g.setFont(ofont.deriveFont(AffineTransform
658 .getScaleInstance(fmScaling, 1.0)));
659 // and update the label's width to reflect the scaling.
664 // TODO is it ok to use width of / show all characters here?
667 // fmWidth = fm.charWidth(displayChar.charAt(0));
669 charOffset = (int) ((charWidth - fmWidth) / 2f);
671 if (row_annotations[column].colour == null)
673 g.setColor(Color.black);
677 g.setColor(row_annotations[column].colour);
680 if (column == 0 || row.graph > 0)
682 g.drawString(displayChar, (x * charWidth) + charOffset, y
685 else if (row_annotations[column - 1] == null
688 .equals(row_annotations[column - 1].displayCharacter) || (displayChar
689 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
691 g.drawString(displayChar, x * charWidth + charOffset, y
699 char ss = validRes ? row_annotations[column].secondaryStructure
704 // distinguish between forward/backward base-pairing
705 if (displayChar.indexOf(')') > -1)
714 if ((displayChar.indexOf(']') > -1))
722 // distinguish between forward/backward base-pairing
723 if (displayChar.indexOf('}') > -1)
731 // distinguish between forward/backward base-pairing
732 if (displayChar.indexOf('<') > -1)
738 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
740 // distinguish between forward/backward base-pairing
741 int ssLowerCase = ss + UPPER_TO_LOWER;
742 // TODO would .equals() be safer here? or charAt(0)?
743 if (displayChar.indexOf(ssLowerCase) > -1)
745 ss = (char) ssLowerCase;
749 if (!validRes || (ss != lastSS))
755 int nb_annot = x - temp;
756 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
759 case '(': // Stem case for RNA secondary structure
760 case ')': // and opposite direction
761 drawStemAnnot(g, row_annotations, lastSSX, x, y,
762 iconOffset, startRes, column, validRes, validEnd);
769 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
770 iconOffset, startRes, column, validRes,
774 // no break if isRNA - falls through to drawNotCanonicalAnnot!
778 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
779 iconOffset, startRes, column, validRes,
783 // no break if isRNA - fall through to drawNotCanonicalAnnot!
842 Color nonCanColor = getNotCanonicalColor(lastSS);
843 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
844 lastSSX, x, y, iconOffset, startRes, column,
849 g.setColor(Color.gray);
850 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
866 lastSSX = (x * charWidth);
873 if (column >= row_annotations.length)
875 column = row_annotations.length - 1;
882 if ((row_annotations == null) || (row_annotations.length <= column)
883 || (row_annotations[column] == null))
901 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
902 startRes, column, validRes, validEnd);
905 // no break if isRNA - fall through to drawNotCanonicalAnnot!
910 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
911 startRes, column, validRes, validEnd);
914 // no break if isRNA - fall through to drawNotCanonicalAnnot!
917 case ')': // Stem case for RNA secondary structure
919 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
920 startRes, column, validRes, validEnd);
977 // System.out.println(lastSS);
978 Color nonCanColor = getNotCanonicalColor(lastSS);
979 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
980 x, y, iconOffset, startRes, column, validRes, validEnd);
983 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
984 startRes, column, validRes, validEnd);
989 if (row.graph > 0 && row.graphHeight > 0)
991 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
993 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
995 // TODO: JAL-1291 revise rendering model so the graphGroup map is
996 // computed efficiently for all visible labels
997 float groupmax = -999999, groupmin = 9999999;
998 for (int gg = 0; gg < aa.length; gg++)
1000 if (aa[gg].graphGroup != row.graphGroup)
1007 aa[gg].visible = false;
1009 if (aa[gg].graphMax > groupmax)
1011 groupmax = aa[gg].graphMax;
1013 if (aa[gg].graphMin < groupmin)
1015 groupmin = aa[gg].graphMin;
1019 for (int gg = 0; gg < aa.length; gg++)
1021 if (aa[gg].graphGroup == row.graphGroup)
1023 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1024 endRes, y, groupmin, groupmax, row.graphHeight);
1028 graphGroupDrawn.set(row.graphGroup);
1032 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1033 row.graphMin, row.graphMax, row.graphHeight);
1036 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1038 drawBarGraph(g, row, row_annotations, startRes, endRes,
1039 row.graphMin, row.graphMax, y, renderHistogram,
1040 renderProfile, normaliseProfile);
1044 AnnotationRowRendererI renderer = rendererFactoryI
1045 .getRendererFor(row);
1046 if (renderer != null)
1048 renderer.renderRow(g, charWidth, charHeight,
1049 hasHiddenColumns, av, columnSelection, row,
1050 row_annotations, startRes, endRes, row.graphMin,
1052 System.err.println("rendered with "
1053 + renderer.getClass().toString());
1060 if (clipst && !clipend)
1064 }// end if_in_visible_region
1065 if (row.graph > 0 && row.hasText)
1081 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1086 System.err.println("End clip at : " + yto + " (index " + f_to
1091 System.err.println("Annotation Rendering time:"
1092 + (System.currentTimeMillis() - stime));
1099 public static final Color GLYPHLINE_COLOR = Color.gray;
1101 public static final Color SHEET_COLOUR = Color.green;
1103 public static final Color HELIX_COLOUR = Color.red;
1105 public static final Color STEM_COLOUR = Color.blue;
1107 private Color sdNOTCANONICAL_COLOUR;
1109 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1110 int y, int iconOffset, int startRes, int column,
1111 boolean validRes, boolean validEnd)
1113 g.setColor(GLYPHLINE_COLOR);
1114 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1117 void drawSheetAnnot(Graphics g, Annotation[] row,
1119 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1120 boolean validRes, boolean validEnd)
1122 g.setColor(SHEET_COLOUR);
1124 if (!validEnd || !validRes || row == null || row[column] == null
1125 || row[column].secondaryStructure != 'E')
1127 g.fillRect(lastSSX, y + 4 + iconOffset,
1128 (x * charWidth) - lastSSX - 4, 7);
1129 g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
1130 (x * charWidth) }, new int[] { y + iconOffset,
1131 y + 14 + iconOffset, y + 7 + iconOffset }, 3);
1135 g.fillRect(lastSSX, y + 4 + iconOffset,
1136 (x + 1) * charWidth - lastSSX, 7);
1141 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1142 int y, int iconOffset, int startRes, int column,
1143 boolean validRes, boolean validEnd)
1145 g.setColor(HELIX_COLOUR);
1147 int sCol = (lastSSX / charWidth) + startRes;
1149 int x2 = (x * charWidth);
1153 int ofs = charWidth / 2;
1154 // Off by 1 offset when drawing rects and ovals
1155 // to offscreen image on the MAC
1156 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1157 if (sCol == 0 || row[sCol - 1] == null
1158 || row[sCol - 1].secondaryStructure != 'H')
1163 // g.setColor(Color.orange);
1164 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1167 if (!validRes || row[column] == null
1168 || row[column].secondaryStructure != 'H')
1174 // g.setColor(Color.magenta);
1175 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1183 if (sCol == 0 || row[sCol - 1] == null
1184 || row[sCol - 1].secondaryStructure != 'H')
1186 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1187 x1 += charWidth / 2;
1190 if (!validRes || row[column] == null
1191 || row[column].secondaryStructure != 'H')
1193 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1195 x2 -= charWidth / 2;
1198 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1201 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1202 Annotation[] aa_annotations, int sRes, int eRes, int y,
1203 float min, float max, int graphHeight)
1205 if (sRes > aa_annotations.length)
1212 // Adjustment for fastpaint to left
1218 eRes = Math.min(eRes, aa_annotations.length);
1226 float range = max - min;
1231 y2 = y - (int) ((0 - min / range) * graphHeight);
1234 g.setColor(Color.gray);
1235 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1237 eRes = Math.min(eRes, aa_annotations.length);
1240 int aaMax = aa_annotations.length - 1;
1242 while (x < eRes - sRes)
1245 if (hasHiddenColumns)
1247 column = columnSelection.adjustForHiddenColumns(column);
1255 if (aa_annotations[column] == null
1256 || aa_annotations[column - 1] == null)
1262 if (aa_annotations[column].colour == null)
1264 g.setColor(Color.black);
1268 g.setColor(aa_annotations[column].colour);
1272 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1274 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1276 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1277 + charWidth / 2, y2);
1281 if (_aa.threshold != null)
1283 g.setColor(_aa.threshold.colour);
1284 Graphics2D g2 = (Graphics2D) g;
1285 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1286 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1288 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1289 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1290 g2.setStroke(new BasicStroke());
1294 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1295 Annotation[] aa_annotations, int sRes, int eRes, float min,
1296 float max, int y, boolean renderHistogram, boolean renderProfile,
1297 boolean normaliseProfile)
1299 if (sRes > aa_annotations.length)
1303 Font ofont = g.getFont();
1304 eRes = Math.min(eRes, aa_annotations.length);
1306 int x = 0, y1 = y, y2 = y;
1308 float range = max - min;
1312 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1315 g.setColor(Color.gray);
1317 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1320 int aaMax = aa_annotations.length - 1;
1321 while (x < eRes - sRes)
1324 if (hasHiddenColumns)
1326 column = columnSelection.adjustForHiddenColumns(column);
1334 if (aa_annotations[column] == null)
1339 if (aa_annotations[column].colour == null)
1341 g.setColor(Color.black);
1345 g.setColor(aa_annotations[column].colour);
1349 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1351 if (renderHistogram)
1355 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1359 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1362 // draw profile if available
1367 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1369 int profl[] = getProfileFor(_aa, column);
1371 // just try to draw the logo if profl is not null
1372 if (profl != null && profl[2] != 0)
1374 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1375 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1376 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1377 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1384 * Render a single base for a sequence profile, a base pair for
1385 * structure profile, and a triplet for a cdna profile
1387 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1389 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1390 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1391 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1395 * Traverse the character(s)/percentage data in the array
1398 int valuesProcessed = 0;
1399 // profl[1] is the number of values in the profile
1400 while (valuesProcessed < profl[1])
1402 if (isStructureProfile)
1404 // todo can we encode a structure pair as an int, like codons?
1405 dc[0] = (char) profl[c++];
1406 dc[1] = (char) profl[c++];
1408 else if (isCdnaProfile)
1410 dc = CodingUtils.decodeCodon(profl[c++]);
1414 dc[0] = (char) profl[c++];
1418 wdth /= fm.charsWidth(dc, 0, dc.length);
1421 // next profl[] position is profile % for the character(s)
1422 scl = htn * scale * profl[c++];
1423 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1424 .getFontRenderContext());
1425 Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
1426 wdth, scl / lm.getAscent()));
1428 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1430 // Debug - render boxes around characters
1431 // g.setColor(Color.red);
1432 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1434 // g.setColor(profcolour.findColour(dc[0]).darker());
1437 * Set character colour as per alignment colour scheme; use the
1438 * codon translation if a cDNA profile
1440 Color colour = null;
1443 final String codonTranslation = ResidueProperties
1444 .codonTranslate(new String(dc));
1445 colour = profcolour.findColour(codonTranslation.charAt(0),
1450 colour = profcolour.findColour(dc[0], column, null);
1452 g.setColor(colour == Color.white ? Color.lightGray : colour);
1454 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1455 .getBaselineIndex()]));
1457 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1465 if (_aa.threshold != null)
1467 g.setColor(_aa.threshold.colour);
1468 Graphics2D g2 = (Graphics2D) g;
1469 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1470 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1472 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1474 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1475 g2.setStroke(new BasicStroke());
1479 // used by overview window
1480 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1481 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1483 eRes = Math.min(eRes, aa_annotations.length);
1484 g.setColor(Color.white);
1485 g.fillRect(0, 0, width, y);
1486 g.setColor(new Color(0, 0, 180));
1490 for (int j = sRes; j < eRes; j++)
1492 if (aa_annotations[j] != null)
1494 if (aa_annotations[j].colour == null)
1496 g.setColor(Color.black);
1500 g.setColor(aa_annotations[j].colour);
1503 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1509 g.fillRect(x, y - height, charWidth, height);
1515 Color getNotCanonicalColor(char lastss)
1521 return new Color(255, 125, 5);
1525 return new Color(245, 115, 10);
1529 return new Color(235, 135, 15);
1533 return new Color(225, 105, 20);
1537 return new Color(215, 145, 30);
1541 return new Color(205, 95, 35);
1545 return new Color(195, 155, 45);
1549 return new Color(185, 85, 55);
1553 return new Color(175, 165, 65);
1557 return new Color(170, 75, 75);
1561 return new Color(160, 175, 85);
1565 return new Color(150, 65, 95);
1569 return new Color(140, 185, 105);
1573 return new Color(130, 55, 110);
1577 return new Color(120, 195, 120);
1581 return new Color(110, 45, 130);
1585 return new Color(100, 205, 140);
1589 return new Color(90, 35, 150);
1593 return new Color(85, 215, 160);
1597 return new Color(75, 25, 170);
1601 return new Color(65, 225, 180);
1605 return new Color(55, 15, 185);
1609 return new Color(45, 235, 195);
1613 return new Color(35, 5, 205);
1617 return new Color(25, 245, 215);
1621 return new Color(15, 0, 225);
1625 return new Color(10, 255, 235);
1629 return new Color(5, 150, 245);
1633 return new Color(0, 80, 255);
1636 System.out.println("This is not a interaction : " + lastss);