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.schemes.CollectionColourScheme;
33 import jalview.schemes.CollectionColourSchemeI;
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;
40 import java.awt.BasicStroke;
41 import java.awt.Color;
43 import java.awt.FontMetrics;
44 import java.awt.Graphics;
45 import java.awt.Graphics2D;
46 import java.awt.Image;
47 import java.awt.font.LineMetrics;
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 MAC = Platform.isAMac();
74 boolean av_renderHistogram = true, av_renderProfile = true,
75 av_normaliseProfile = false;
77 CollectionColourSchemeI profcolour = null;
79 private ColumnSelection columnSelection;
81 private ProfilesI hconsensus;
83 private Hashtable[] complementConsensus;
85 private Hashtable[] hStrucConsensus;
87 private boolean av_ignoreGapsConsensus;
90 * attributes set from AwtRenderPanelI
93 * old image used when data is currently being calculated and cannot be
96 private Image fadedImage;
99 * panel being rendered into
101 private ImageObserver annotationPanel;
104 * width of image to render in panel
106 private int imgWidth;
109 * offset to beginning of visible area
114 * offset to end of visible area
116 private int visHeight;
119 * indicate if the renderer should only render the visible portion of the
120 * annotation given the current view settings
122 private boolean useClip = true;
125 * master flag indicating if renderer should ever try to clip. not enabled for
128 private boolean canClip = false;
130 public AnnotationRenderer()
136 * Create a new annotation Renderer
139 * flag indicating if timing and redraw parameter info should be
142 public AnnotationRenderer(boolean debugRedraw)
144 this.debugRedraw = debugRedraw;
148 * Remove any references and resources when this object is no longer required
150 public void dispose()
153 complementConsensus = null;
154 hStrucConsensus = null;
156 annotationPanel = null;
159 void drawStemAnnot(Graphics g, Annotation[] row_annotations, int lastSSX,
160 int x, int y, int iconOffset, int startRes, int column,
161 boolean validRes, boolean validEnd)
163 g.setColor(STEM_COLOUR);
164 int sCol = (lastSSX / charWidth) + startRes;
166 int x2 = (x * charWidth);
168 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
169 : row_annotations[column - 1].secondaryStructure;
171 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
172 || dc != row_annotations[sCol - 1].secondaryStructure;
173 boolean diffdownstream = !validRes || !validEnd
174 || row_annotations[column] == null
175 || dc != row_annotations[column].secondaryStructure;
177 if (column > 0 && Rna.isClosingParenthesis(dc))
180 // if (validRes && column>1 && row_annotations[column-2]!=null &&
181 // dc.equals(row_annotations[column-2].displayCharacter))
184 * if new annotation with a closing base pair half of the stem,
185 * display a backward arrow
187 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
188 new int[] { y + iconOffset, y + 14 + iconOffset,
189 y + 8 + iconOffset }, 3);
199 // display a forward arrow
203 * if annotation ending with an opeing base pair half of the stem,
204 * display a forward arrow
206 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
207 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
216 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
219 void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
220 Annotation[] row_annotations, int lastSSX, int x, int y,
221 int iconOffset, int startRes, int column, boolean validRes,
224 // System.out.println(nonCanColor);
226 g.setColor(nonCanColor);
227 int sCol = (lastSSX / charWidth) + startRes;
229 int x2 = (x * charWidth);
231 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
232 : row_annotations[column - 1].displayCharacter;
234 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
235 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
236 boolean diffdownstream = !validRes || !validEnd
237 || row_annotations[column] == null
238 || !dc.equals(row_annotations[column].displayCharacter);
239 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
240 // If a closing base pair half of the stem, display a backward arrow
241 if (column > 0 && Rna.isClosingParenthesis(dc))
245 // if (validRes && column>1 && row_annotations[column-2]!=null &&
246 // dc.equals(row_annotations[column-2].displayCharacter))
248 g.fillPolygon(new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
249 new int[] { y + iconOffset, y + 14 + iconOffset,
250 y + 8 + iconOffset }, 3);
261 // display a forward arrow
264 g.fillPolygon(new int[] { x2 - 5, x2 - 5, x2 }, new int[] {
265 y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
274 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
277 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
279 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
282 fm = annotPanel.getFontMetrics();
283 annotationPanel = annotPanel;
284 fadedImage = annotPanel.getFadedImage();
285 imgWidth = annotPanel.getFadedImageWidth();
286 // visible area for rendering
287 int[] bounds = annotPanel.getVisibleVRange();
291 visHeight = bounds[1];
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.getViewportColourScheme();
320 if (profcolour == null || profcolour.getColourScheme() == null)
323 * Use default colour for sequence logo if
324 * the alignment has no colourscheme set
325 * (would like to use user preference but n/a for applet)
327 ColourSchemeI col = av.getAlignment().isNucleotide() ? new NucleotideColourScheme()
328 : new ZappoColourScheme();
329 profcolour = new CollectionColourScheme(col);
331 columnSelection = av.getColumnSelection();
332 hconsensus = av.getSequenceConsensusHash();
333 complementConsensus = av.getComplementConsensusHash();
334 hStrucConsensus = av.getRnaStructureConsensusHash();
335 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
339 * Returns profile data; the first element is the profile type, the second is
340 * the number of distinct values, the third the total count, and the remainder
341 * depend on the profile type.
347 int[] getProfileFor(AlignmentAnnotation aa, int column)
349 // TODO : consider refactoring the global alignment calculation
350 // properties/rendering attributes as a global 'alignment group' which holds
351 // all vis settings for the alignment as a whole rather than a subset
353 if (aa.autoCalculated
354 && (aa.label.startsWith("Consensus") || aa.label
355 .startsWith("cDNA Consensus")))
357 boolean forComplement = aa.label.startsWith("cDNA Consensus");
358 if (aa.groupRef != null && aa.groupRef.consensusData != null
359 && aa.groupRef.isShowSequenceLogo())
361 // TODO? group consensus for cDNA complement
362 return AAFrequency.extractProfile(
363 aa.groupRef.consensusData.get(column),
364 aa.groupRef.getIgnoreGapsConsensus());
366 // TODO extend annotation row to enable dynamic and static profile data to
368 if (aa.groupRef == null && aa.sequenceRef == null)
372 return AAFrequency.extractCdnaProfile(
373 complementConsensus[column], av_ignoreGapsConsensus);
377 return AAFrequency.extractProfile(
378 hconsensus.get(column),
379 av_ignoreGapsConsensus);
385 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
387 // TODO implement group structure consensus
389 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
390 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
391 * group selections return StructureFrequency.extractProfile(
392 * aa.groupRef.consensusData[column], aa.groupRef
393 * .getIgnoreGapsConsensus()); }
395 // TODO extend annotation row to enable dynamic and static profile data
398 if (aa.groupRef == null && aa.sequenceRef == null
399 && hStrucConsensus != null
400 && hStrucConsensus.length > column)
402 return StructureFrequency.extractProfile(hStrucConsensus[column],
403 av_ignoreGapsConsensus);
413 * Render the annotation rows associated with an alignment.
418 * data and view settings to render
420 * destination for graphics
422 * row where a mouse event occured (or -1)
424 * first column that will be drawn
426 * last column that will be drawn
427 * @return true if the fadedImage was used for any alignment annotation rows
428 * currently being calculated
430 public boolean drawComponent(AwtRenderPanelI annotPanel,
431 AlignViewportI av, Graphics g, int activeRow, int startRes,
434 long stime = System.currentTimeMillis();
435 boolean usedFaded = false;
437 // AnnotationPanel needs to implement: ImageObserver, access to
439 updateFromAwtRenderPanel(annotPanel, av);
440 fm = g.getFontMetrics();
441 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
452 boolean validRes = false;
453 boolean validEnd = false;
454 boolean labelAllCols = false;
455 boolean centreColLabels;
456 boolean centreColLabelsDef = av.isCentreColumnLabels();
457 boolean scaleColLabel = false;
458 final AlignmentAnnotation consensusAnnot = av
459 .getAlignmentConsensusAnnotation();
460 final AlignmentAnnotation structConsensusAnnot = av
461 .getAlignmentStrucConsensusAnnotation();
462 final AlignmentAnnotation complementConsensusAnnot = av
463 .getComplementConsensusAnnotation();
464 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
466 BitSet graphGroupDrawn = new BitSet();
467 int charOffset = 0; // offset for a label
468 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
470 Font ofont = g.getFont();
473 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
474 boolean clipst = false, clipend = false;
475 for (int i = 0; i < aa.length; i++)
477 AlignmentAnnotation row = aa[i];
480 // check if this is a consensus annotation row and set the display
481 // settings appropriately
482 // TODO: generalise this to have render styles for consensus/profile
484 if (row.groupRef != null && row == row.groupRef.getConsensus())
486 renderHistogram = row.groupRef.isShowConsensusHistogram();
487 renderProfile = row.groupRef.isShowSequenceLogo();
488 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
490 else if (row == consensusAnnot || row == structConsensusAnnot
491 || row == complementConsensusAnnot)
493 renderHistogram = av_renderHistogram;
494 renderProfile = av_renderProfile;
495 normaliseProfile = av_normaliseProfile;
499 renderHistogram = true;
500 // don't need to set render/normaliseProfile since they are not
501 // currently used in any other annotation track renderer
504 Annotation[] row_annotations = row.annotations;
509 centreColLabels = row.centreColLabels || centreColLabelsDef;
510 labelAllCols = row.showAllColLabels;
511 scaleColLabel = row.scaleColLabel;
516 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
517 {// if_in_visible_region
528 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
533 // this is so that we draw the characters below the graph
538 iconOffset = charHeight - fm.getDescent();
542 else if (row.hasText)
544 iconOffset = charHeight - fm.getDescent();
552 if (row.autoCalculated && av.isCalculationInProgress(row))
556 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
557 - row.height, imgWidth, y, annotationPanel);
558 g.setColor(Color.black);
559 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
565 * else if (annotationPanel.av.updatingConservation &&
566 * aa[i].label.equals("Conservation")) {
568 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
569 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
570 * annotationPanel.imgWidth, y, annotationPanel);
572 * g.setColor(Color.black); //
573 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
575 * continue; } else if (annotationPanel.av.updatingConservation &&
576 * aa[i].label.equals("Quality")) {
578 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
579 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
580 * annotationPanel.imgWidth, y, annotationPanel);
581 * g.setColor(Color.black); // /
582 * g.drawString("Calculating Quality....",20, y-row.height/2);
586 // first pass sets up state for drawing continuation from left-hand
589 x = (startRes == 0) ? 0 : -1;
590 while (x < endRes - startRes)
592 if (hasHiddenColumns)
594 column = columnSelection.adjustForHiddenColumns(startRes + x);
595 if (column > row_annotations.length - 1)
602 column = startRes + x;
605 if ((row_annotations == null)
606 || (row_annotations.length <= column)
607 || (row_annotations[column] == null))
615 final String displayChar = validRes ? row_annotations[column].displayCharacter
621 g.setColor(Color.red);
623 if (columnSelection != null)
625 if (columnSelection.contains(column))
627 g.fillRect(x * charWidth, y, charWidth, charHeight);
631 if (row.getInvalidStrucPos() > x)
633 g.setColor(Color.orange);
634 g.fillRect(x * charWidth, y, charWidth, charHeight);
636 else if (row.getInvalidStrucPos() == x)
638 g.setColor(Color.orange.darker());
639 g.fillRect(x * charWidth, y, charWidth, charHeight);
641 if (validCharWidth && validRes && displayChar != null
642 && (displayChar.length() > 0))
645 fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
646 displayChar.length());
647 if (/* centreColLabels || */scaleColLabel)
649 // fmWidth = fm.charsWidth(displayChar.toCharArray(), 0,
650 // displayChar.length());
652 // if (scaleColLabel)
654 // justify the label and scale to fit in column
655 if (fmWidth > charWidth)
657 // scale only if the current font isn't already small enough
658 fmScaling = charWidth;
659 fmScaling /= fmWidth;
660 g.setFont(ofont.deriveFont(AffineTransform
661 .getScaleInstance(fmScaling, 1.0)));
662 // and update the label's width to reflect the scaling.
667 // TODO is it ok to use width of / show all characters here?
670 // fmWidth = fm.charWidth(displayChar.charAt(0));
672 charOffset = (int) ((charWidth - fmWidth) / 2f);
674 if (row_annotations[column].colour == null)
676 g.setColor(Color.black);
680 g.setColor(row_annotations[column].colour);
683 if (column == 0 || row.graph > 0)
685 g.drawString(displayChar, (x * charWidth) + charOffset, y
688 else if (row_annotations[column - 1] == null
691 .equals(row_annotations[column - 1].displayCharacter) || (displayChar
692 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
694 g.drawString(displayChar, x * charWidth + charOffset, y
702 char ss = validRes ? row_annotations[column].secondaryStructure
707 // distinguish between forward/backward base-pairing
708 if (displayChar.indexOf(')') > -1)
717 if ((displayChar.indexOf(']') > -1))
725 // distinguish between forward/backward base-pairing
726 if (displayChar.indexOf('}') > -1)
734 // distinguish between forward/backward base-pairing
735 if (displayChar.indexOf('<') > -1)
741 if (isRNA && (ss >= CHAR_A) && (ss <= CHAR_Z))
743 // distinguish between forward/backward base-pairing
744 int ssLowerCase = ss + UPPER_TO_LOWER;
745 // TODO would .equals() be safer here? or charAt(0)?
746 if (displayChar.indexOf(ssLowerCase) > -1)
748 ss = (char) ssLowerCase;
752 if (!validRes || (ss != lastSS))
758 int nb_annot = x - temp;
759 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
762 case '(': // Stem case for RNA secondary structure
763 case ')': // and opposite direction
764 drawStemAnnot(g, row_annotations, lastSSX, x, y,
765 iconOffset, startRes, column, validRes, validEnd);
772 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
773 iconOffset, startRes, column, validRes,
777 // no break if isRNA - falls through to drawNotCanonicalAnnot!
781 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
782 iconOffset, startRes, column, validRes,
786 // no break if isRNA - fall through to drawNotCanonicalAnnot!
845 Color nonCanColor = getNotCanonicalColor(lastSS);
846 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
847 lastSSX, x, y, iconOffset, startRes, column,
852 g.setColor(Color.gray);
853 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
869 lastSSX = (x * charWidth);
876 if (column >= row_annotations.length)
878 column = row_annotations.length - 1;
885 if ((row_annotations == null) || (row_annotations.length <= column)
886 || (row_annotations[column] == null))
904 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
905 startRes, column, validRes, validEnd);
908 // no break if isRNA - fall through to drawNotCanonicalAnnot!
913 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
914 startRes, column, validRes, validEnd);
917 // no break if isRNA - fall through to drawNotCanonicalAnnot!
920 case ')': // Stem case for RNA secondary structure
922 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
923 startRes, column, validRes, validEnd);
980 // System.out.println(lastSS);
981 Color nonCanColor = getNotCanonicalColor(lastSS);
982 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
983 x, y, iconOffset, startRes, column, validRes, validEnd);
986 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
987 startRes, column, validRes, validEnd);
992 if (row.graph > 0 && row.graphHeight > 0)
994 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
996 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
998 // TODO: JAL-1291 revise rendering model so the graphGroup map is
999 // computed efficiently for all visible labels
1000 float groupmax = -999999, groupmin = 9999999;
1001 for (int gg = 0; gg < aa.length; gg++)
1003 if (aa[gg].graphGroup != row.graphGroup)
1010 aa[gg].visible = false;
1012 if (aa[gg].graphMax > groupmax)
1014 groupmax = aa[gg].graphMax;
1016 if (aa[gg].graphMin < groupmin)
1018 groupmin = aa[gg].graphMin;
1022 for (int gg = 0; gg < aa.length; gg++)
1024 if (aa[gg].graphGroup == row.graphGroup)
1026 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
1027 endRes, y, groupmin, groupmax, row.graphHeight);
1031 graphGroupDrawn.set(row.graphGroup);
1035 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
1036 row.graphMin, row.graphMax, row.graphHeight);
1039 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
1041 drawBarGraph(g, row, row_annotations, startRes, endRes,
1042 row.graphMin, row.graphMax, y, renderHistogram,
1043 renderProfile, normaliseProfile);
1049 if (clipst && !clipend)
1053 }// end if_in_visible_region
1054 if (row.graph > 0 && row.hasText)
1070 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1075 System.err.println("End clip at : " + yto + " (index " + f_to
1080 System.err.println("Annotation Rendering time:"
1081 + (System.currentTimeMillis() - stime));
1088 public static final Color GLYPHLINE_COLOR = Color.gray;
1090 public static final Color SHEET_COLOUR = Color.green;
1092 public static final Color HELIX_COLOUR = Color.red;
1094 public static final Color STEM_COLOUR = Color.blue;
1096 private Color sdNOTCANONICAL_COLOUR;
1098 void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX, int x,
1099 int y, int iconOffset, int startRes, int column,
1100 boolean validRes, boolean validEnd)
1102 g.setColor(GLYPHLINE_COLOR);
1103 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1106 void drawSheetAnnot(Graphics g, Annotation[] row,
1108 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1109 boolean validRes, boolean validEnd)
1111 g.setColor(SHEET_COLOUR);
1113 if (!validEnd || !validRes || row == null || row[column] == null
1114 || row[column].secondaryStructure != 'E')
1116 g.fillRect(lastSSX, y + 4 + iconOffset,
1117 (x * charWidth) - lastSSX - 4, 7);
1118 g.fillPolygon(new int[] { (x * charWidth) - 4, (x * charWidth) - 4,
1119 (x * charWidth) }, new int[] { y + iconOffset,
1120 y + 14 + iconOffset, y + 7 + iconOffset }, 3);
1124 g.fillRect(lastSSX, y + 4 + iconOffset,
1125 (x + 1) * charWidth - lastSSX, 7);
1130 void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
1131 int y, int iconOffset, int startRes, int column,
1132 boolean validRes, boolean validEnd)
1134 g.setColor(HELIX_COLOUR);
1136 int sCol = (lastSSX / charWidth) + startRes;
1138 int x2 = (x * charWidth);
1142 int ofs = charWidth / 2;
1143 // Off by 1 offset when drawing rects and ovals
1144 // to offscreen image on the MAC
1145 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1146 if (sCol == 0 || row[sCol - 1] == null
1147 || row[sCol - 1].secondaryStructure != 'H')
1152 // g.setColor(Color.orange);
1153 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1156 if (!validRes || row[column] == null
1157 || row[column].secondaryStructure != 'H')
1163 // g.setColor(Color.magenta);
1164 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1172 if (sCol == 0 || row[sCol - 1] == null
1173 || row[sCol - 1].secondaryStructure != 'H')
1175 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1176 x1 += charWidth / 2;
1179 if (!validRes || row[column] == null
1180 || row[column].secondaryStructure != 'H')
1182 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1184 x2 -= charWidth / 2;
1187 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1190 void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1191 Annotation[] aa_annotations, int sRes, int eRes, int y,
1192 float min, float max, int graphHeight)
1194 if (sRes > aa_annotations.length)
1201 // Adjustment for fastpaint to left
1207 eRes = Math.min(eRes, aa_annotations.length);
1215 float range = max - min;
1220 y2 = y - (int) ((0 - min / range) * graphHeight);
1223 g.setColor(Color.gray);
1224 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1226 eRes = Math.min(eRes, aa_annotations.length);
1229 int aaMax = aa_annotations.length - 1;
1231 while (x < eRes - sRes)
1234 if (hasHiddenColumns)
1236 column = columnSelection.adjustForHiddenColumns(column);
1244 if (aa_annotations[column] == null
1245 || aa_annotations[column - 1] == null)
1251 if (aa_annotations[column].colour == null)
1253 g.setColor(Color.black);
1257 g.setColor(aa_annotations[column].colour);
1261 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1263 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1265 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1266 + charWidth / 2, y2);
1270 if (_aa.threshold != null)
1272 g.setColor(_aa.threshold.colour);
1273 Graphics2D g2 = (Graphics2D) g;
1274 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1275 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1277 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1278 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1279 g2.setStroke(new BasicStroke());
1283 void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1284 Annotation[] aa_annotations, int sRes, int eRes, float min,
1285 float max, int y, boolean renderHistogram, boolean renderProfile,
1286 boolean normaliseProfile)
1288 if (sRes > aa_annotations.length)
1292 Font ofont = g.getFont();
1293 eRes = Math.min(eRes, aa_annotations.length);
1295 int x = 0, y1 = y, y2 = y;
1297 float range = max - min;
1301 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1304 g.setColor(Color.gray);
1306 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1309 int aaMax = aa_annotations.length - 1;
1310 while (x < eRes - sRes)
1313 if (hasHiddenColumns)
1315 column = columnSelection.adjustForHiddenColumns(column);
1323 if (aa_annotations[column] == null)
1328 if (aa_annotations[column].colour == null)
1330 g.setColor(Color.black);
1334 g.setColor(aa_annotations[column].colour);
1338 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1340 if (renderHistogram)
1344 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1348 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1351 // draw profile if available
1356 * {profile type, #values, total count, char1, pct1, char2, pct2...}
1358 int profl[] = getProfileFor(_aa, column);
1360 // just try to draw the logo if profl is not null
1361 if (profl != null && profl[2] != 0)
1363 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
1364 boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
1365 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1366 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1373 * Render a single base for a sequence profile, a base pair for
1374 * structure profile, and a triplet for a cdna profile
1376 dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
1378 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1379 double scale = 1f / (normaliseProfile ? profl[2] : 100f);
1380 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1384 * Traverse the character(s)/percentage data in the array
1387 int valuesProcessed = 0;
1388 // profl[1] is the number of values in the profile
1389 while (valuesProcessed < profl[1])
1391 if (isStructureProfile)
1393 // todo can we encode a structure pair as an int, like codons?
1394 dc[0] = (char) profl[c++];
1395 dc[1] = (char) profl[c++];
1397 else if (isCdnaProfile)
1399 dc = CodingUtils.decodeCodon(profl[c++]);
1403 dc[0] = (char) profl[c++];
1407 wdth /= fm.charsWidth(dc, 0, dc.length);
1410 // next profl[] position is profile % for the character(s)
1411 scl = htn * scale * profl[c++];
1412 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1413 .getFontRenderContext());
1414 Font font = ofont.deriveFont(AffineTransform.getScaleInstance(
1415 wdth, scl / lm.getAscent()));
1417 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1419 // Debug - render boxes around characters
1420 // g.setColor(Color.red);
1421 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1423 // g.setColor(profcolour.findColour(dc[0]).darker());
1426 * Set character colour as per alignment colour scheme; use the
1427 * codon translation if a cDNA profile
1429 Color colour = null;
1432 final String codonTranslation = ResidueProperties
1433 .codonTranslate(new String(dc));
1434 colour = profcolour.findColour(codonTranslation.charAt(0),
1439 colour = profcolour.findColour(dc[0], column, null);
1441 g.setColor(colour == Color.white ? Color.lightGray : colour);
1443 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1444 .getBaselineIndex()]));
1446 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1454 if (_aa.threshold != null)
1456 g.setColor(_aa.threshold.colour);
1457 Graphics2D g2 = (Graphics2D) g;
1458 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1459 BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
1461 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1463 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1464 g2.setStroke(new BasicStroke());
1468 // used by overview window
1469 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1470 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1472 eRes = Math.min(eRes, aa_annotations.length);
1473 g.setColor(Color.white);
1474 g.fillRect(0, 0, width, y);
1475 g.setColor(new Color(0, 0, 180));
1479 for (int j = sRes; j < eRes; j++)
1481 if (aa_annotations[j] != null)
1483 if (aa_annotations[j].colour == null)
1485 g.setColor(Color.black);
1489 g.setColor(aa_annotations[j].colour);
1492 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1498 g.fillRect(x, y - height, charWidth, height);
1504 Color getNotCanonicalColor(char lastss)
1510 return new Color(255, 125, 5);
1514 return new Color(245, 115, 10);
1518 return new Color(235, 135, 15);
1522 return new Color(225, 105, 20);
1526 return new Color(215, 145, 30);
1530 return new Color(205, 95, 35);
1534 return new Color(195, 155, 45);
1538 return new Color(185, 85, 55);
1542 return new Color(175, 165, 65);
1546 return new Color(170, 75, 75);
1550 return new Color(160, 175, 85);
1554 return new Color(150, 65, 95);
1558 return new Color(140, 185, 105);
1562 return new Color(130, 55, 110);
1566 return new Color(120, 195, 120);
1570 return new Color(110, 45, 130);
1574 return new Color(100, 205, 140);
1578 return new Color(90, 35, 150);
1582 return new Color(85, 215, 160);
1586 return new Color(75, 25, 170);
1590 return new Color(65, 225, 180);
1594 return new Color(55, 15, 185);
1598 return new Color(45, 235, 195);
1602 return new Color(35, 5, 205);
1606 return new Color(25, 245, 215);
1610 return new Color(15, 0, 225);
1614 return new Color(10, 255, 235);
1618 return new Color(5, 150, 245);
1622 return new Color(0, 80, 255);
1625 System.out.println("This is not a interaction : " + lastss);