2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.StructureFrequency;
25 import jalview.api.AlignViewportI;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.Annotation;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.schemes.ColourSchemeI;
30 import jalview.schemes.ResidueProperties;
32 import java.awt.BasicStroke;
33 import java.awt.Color;
35 import java.awt.FontMetrics;
36 import java.awt.Graphics;
37 import java.awt.Graphics2D;
38 import java.awt.Image;
39 import java.awt.font.LineMetrics;
40 import java.awt.geom.AffineTransform;
41 import java.awt.image.ImageObserver;
42 import java.util.BitSet;
43 import java.util.Hashtable;
45 import com.stevesoft.pat.Regex;
47 public class AnnotationRenderer
50 * flag indicating if timing and redraw parameter info should be output
52 private final boolean debugRedraw;
54 public AnnotationRenderer()
60 * Create a new annotation Renderer
63 * flag indicating if timing and redraw parameter info should be
66 public AnnotationRenderer(boolean debugRedraw)
68 this.debugRedraw = debugRedraw;
71 public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
72 int lastSSX, int x, int y, int iconOffset, int startRes,
73 int column, boolean validRes, boolean validEnd)
75 g.setColor(STEM_COLOUR);
76 int sCol = (lastSSX / charWidth) + startRes;
78 int x2 = (x * charWidth);
79 Regex closeparen = new Regex("(\\))");
81 char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
82 : row_annotations[column - 1].secondaryStructure;
84 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
85 || dc != row_annotations[sCol - 1].secondaryStructure;
86 boolean diffdownstream = !validRes || !validEnd
87 || row_annotations[column] == null
88 || dc != row_annotations[column].secondaryStructure;
89 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
90 // If a closing base pair half of the stem, display a backward arrow
91 if (column > 0 && ResidueProperties.isCloseParenRNA(dc))
95 // if (validRes && column>1 && row_annotations[column-2]!=null &&
96 // dc.equals(row_annotations[column-2].displayCharacter))
98 g.fillPolygon(new int[]
99 { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
100 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
111 // display a forward arrow
114 g.fillPolygon(new int[]
115 { x2 - 5, x2 - 5, x2 }, new int[]
116 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
125 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
128 private int charWidth, endRes, charHeight;
130 private boolean validCharWidth, hasHiddenColumns;
132 private FontMetrics fm;
134 private final boolean MAC = new jalview.util.Platform().isAMac();
136 boolean av_renderHistogram = true, av_renderProfile = true,
137 av_normaliseProfile = false;
139 ColourSchemeI profcolour = null;
141 private ColumnSelection columnSelection;
143 private Hashtable[] hconsensus;
145 private Hashtable[] hStrucConsensus;
147 private boolean av_ignoreGapsConsensus;
150 * attributes set from AwtRenderPanelI
153 * old image used when data is currently being calculated and cannot be
156 private Image fadedImage;
159 * panel being rendered into
161 private ImageObserver annotationPanel;
164 * width of image to render in panel
166 private int imgWidth;
169 * offset to beginning of visible area
174 * offset to end of visible area
176 private int visHeight;
179 * indicate if the renderer should only render the visible portion of the
180 * annotation given the current view settings
182 private boolean useClip = true;
185 * master flag indicating if renderer should ever try to clip. not enabled for
188 private boolean canClip = false;
190 public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
191 Annotation[] row_annotations, int lastSSX, int x, int y,
192 int iconOffset, int startRes, int column, boolean validRes,
195 // System.out.println(nonCanColor);
197 g.setColor(nonCanColor);
198 int sCol = (lastSSX / charWidth) + startRes;
200 int x2 = (x * charWidth);
201 Regex closeparen = new Regex("}|]|<|[a-z]");
203 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
204 : row_annotations[column - 1].displayCharacter;
206 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
207 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
208 boolean diffdownstream = !validRes || !validEnd
209 || row_annotations[column] == null
210 || !dc.equals(row_annotations[column].displayCharacter);
211 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
212 // If a closing base pair half of the stem, display a backward arrow
213 if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc))
218 // if (validRes && column>1 && row_annotations[column-2]!=null &&
219 // dc.equals(row_annotations[column-2].displayCharacter))
221 g.fillPolygon(new int[]
222 { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
223 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
234 // display a forward arrow
237 g.fillPolygon(new int[]
238 { x2 - 5, x2 - 5, x2 }, new int[]
239 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
248 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
251 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
253 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
256 fm = annotPanel.getFontMetrics();
257 annotationPanel = annotPanel;
258 fadedImage = annotPanel.getFadedImage();
259 imgWidth = annotPanel.getFadedImageWidth();
260 // visible area for rendering
261 int[] bounds = annotPanel.getVisibleVRange();
265 visHeight = bounds[1];
280 updateFromAlignViewport(av);
283 public void updateFromAlignViewport(AlignViewportI av)
285 charWidth = av.getCharWidth();
286 endRes = av.getEndRes();
287 charHeight = av.getCharHeight();
288 hasHiddenColumns = av.hasHiddenColumns();
289 validCharWidth = av.isValidCharWidth();
290 av_renderHistogram = av.isShowConsensusHistogram();
291 av_renderProfile = av.isShowSequenceLogo();
292 av_normaliseProfile = av.isNormaliseSequenceLogo();
293 profcolour = av.getGlobalColourScheme();
294 if (profcolour == null)
296 // Set the default colour for sequence logo if the alignnent has no
298 profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
299 : new jalview.schemes.ZappoColourScheme();
301 boolean rna = av.getAlignment().isNucleotide();
302 columnSelection = av.getColumnSelection();
303 hconsensus = av.getSequenceConsensusHash();// hconsensus;
304 hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
305 av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
308 public int[] getProfileFor(AlignmentAnnotation aa, int column)
310 // TODO : consider refactoring the global alignment calculation
311 // properties/rendering attributes as a global 'alignment group' which holds
312 // all vis settings for the alignment as a whole rather than a subset
314 if (aa.autoCalculated && aa.label.startsWith("Consensus"))
316 if (aa.groupRef != null && aa.groupRef.consensusData != null
317 && aa.groupRef.isShowSequenceLogo())
319 return AAFrequency.extractProfile(
320 aa.groupRef.consensusData[column],
321 aa.groupRef.getIgnoreGapsConsensus());
323 // TODO extend annotation row to enable dynamic and static profile data to
325 if (aa.groupRef == null && aa.sequenceRef == null)
327 return AAFrequency.extractProfile(hconsensus[column],
328 av_ignoreGapsConsensus);
333 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
335 // TODO implement group structure consensus
337 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
338 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
339 * group selections return StructureFrequency.extractProfile(
340 * aa.groupRef.consensusData[column], aa.groupRef
341 * .getIgnoreGapsConsensus()); }
343 // TODO extend annotation row to enable dynamic and static profile data
346 if (aa.groupRef == null && aa.sequenceRef == null
347 && hStrucConsensus != null
348 && hStrucConsensus.length > column)
350 return StructureFrequency.extractProfile(hStrucConsensus[column],
351 av_ignoreGapsConsensus);
361 * Render the annotation rows associated with an alignment.
366 * data and view settings to render
368 * destination for graphics
370 * row where a mouse event occured (or -1)
372 * first column that will be drawn
374 * last column that will be drawn
375 * @return true if the fadedImage was used for any alignment annotation rows
376 * currently being calculated
378 public boolean drawComponent(AwtRenderPanelI annotPanel,
379 AlignViewportI av, Graphics g, int activeRow, int startRes,
382 long stime = System.currentTimeMillis();
383 boolean usedFaded = false;
385 // AnnotationPanel needs to implement: ImageObserver, access to
387 updateFromAwtRenderPanel(annotPanel, av);
388 fm = g.getFontMetrics();
389 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
400 boolean validRes = false;
401 boolean validEnd = false;
402 boolean labelAllCols = false;
403 boolean centreColLabels, centreColLabelsDef = av.isCentreColumnLabels();
404 boolean scaleColLabel = false;
405 AlignmentAnnotation consensusAnnot = av
406 .getAlignmentConsensusAnnotation(), structConsensusAnnot = av
407 .getAlignmentStrucConsensusAnnotation();
408 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
410 BitSet graphGroupDrawn = new BitSet();
411 int charOffset = 0; // offset for a label
412 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
414 Font ofont = g.getFont();
417 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
418 boolean clipst = false, clipend = false;
419 for (int i = 0; i < aa.length; i++)
421 AlignmentAnnotation row = aa[i];
424 // check if this is a consensus annotation row and set the display
425 // settings appropriately
426 // TODO: generalise this to have render styles for consensus/profile
428 if (row.groupRef != null && row == row.groupRef.getConsensus())
430 renderHistogram = row.groupRef.isShowConsensusHistogram();
431 renderProfile = row.groupRef.isShowSequenceLogo();
432 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
434 else if (row == consensusAnnot || row == structConsensusAnnot)
436 renderHistogram = av_renderHistogram;
437 renderProfile = av_renderProfile;
438 normaliseProfile = av_normaliseProfile;
442 renderHistogram = true;
443 // don't need to set render/normaliseProfile since they are not
444 // currently used in any other annotation track renderer
447 Annotation[] row_annotations = row.annotations;
452 centreColLabels = row.centreColLabels || centreColLabelsDef;
453 labelAllCols = row.showAllColLabels;
454 scaleColLabel = row.scaleColLabel;
459 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
460 {// if_in_visible_region
471 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
476 // this is so that we draw the characters below the graph
481 iconOffset = charHeight - fm.getDescent();
485 else if (row.hasText)
487 iconOffset = charHeight - fm.getDescent();
495 if (row.autoCalculated && av.isCalculationInProgress(row))
499 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
500 - row.height, imgWidth, y, annotationPanel);
501 g.setColor(Color.black);
502 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
508 * else if (annotationPanel.av.updatingConservation &&
509 * aa[i].label.equals("Conservation")) {
511 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
512 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
513 * annotationPanel.imgWidth, y, annotationPanel);
515 * g.setColor(Color.black); //
516 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
518 * continue; } else if (annotationPanel.av.updatingConservation &&
519 * aa[i].label.equals("Quality")) {
521 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
522 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
523 * annotationPanel.imgWidth, y, annotationPanel);
524 * g.setColor(Color.black); // /
525 * g.drawString("Calculating Quality....",20, y-row.height/2);
529 // first pass sets up state for drawing continuation from left-hand
532 x = (startRes == 0) ? 0 : -1;
533 while (x < endRes - startRes)
535 if (hasHiddenColumns)
537 column = columnSelection.adjustForHiddenColumns(startRes + x);
538 if (column > row_annotations.length - 1)
545 column = startRes + x;
548 if ((row_annotations == null)
549 || (row_annotations.length <= column)
550 || (row_annotations[column] == null))
562 g.setColor(Color.red);
564 if (columnSelection != null)
566 for (int n = 0; n < columnSelection.size(); n++)
568 int v = columnSelection.columnAt(n);
572 g.fillRect(x * charWidth, y, charWidth, charHeight);
577 if (row.getInvalidStrucPos() > x)
579 g.setColor(Color.orange);
580 g.fillRect(x * charWidth, y, charWidth, charHeight);
582 else if (row.getInvalidStrucPos() == x)
584 g.setColor(Color.orange.darker());
585 g.fillRect(x * charWidth, y, charWidth, charHeight);
589 && row_annotations[column].displayCharacter != null
590 && (row_annotations[column].displayCharacter.length() > 0))
593 if (centreColLabels || scaleColLabel)
595 fmWidth = fm.charsWidth(
596 row_annotations[column].displayCharacter
598 row_annotations[column].displayCharacter.length());
602 // justify the label and scale to fit in column
603 if (fmWidth > charWidth)
605 // scale only if the current font isn't already small enough
606 fmScaling = charWidth;
607 fmScaling /= fmWidth;
608 g.setFont(ofont.deriveFont(AffineTransform
609 .getScaleInstance(fmScaling, 1.0)));
610 // and update the label's width to reflect the scaling.
618 .charWidth(row_annotations[column].displayCharacter
621 charOffset = (int) ((charWidth - fmWidth) / 2f);
623 if (row_annotations[column].colour == null)
625 g.setColor(Color.black);
629 g.setColor(row_annotations[column].colour);
632 if (column == 0 || row.graph > 0)
634 g.drawString(row_annotations[column].displayCharacter,
635 (x * charWidth) + charOffset, y + iconOffset);
637 else if (row_annotations[column - 1] == null
639 || !row_annotations[column].displayCharacter
640 .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
641 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
643 g.drawString(row_annotations[column].displayCharacter, x
644 * charWidth + charOffset, y + iconOffset);
651 char ss = validRes ? row_annotations[column].secondaryStructure
656 // distinguish between forward/backward base-pairing
657 if (row_annotations[column].displayCharacter.indexOf(')') > -1)
666 if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
674 // distinguish between forward/backward base-pairing
675 if (row_annotations[column].displayCharacter.indexOf('}') > -1)
683 // distinguish between forward/backward base-pairing
684 if (row_annotations[column].displayCharacter.indexOf('<') > -1)
692 // distinguish between forward/backward base-pairing
693 if (row_annotations[column].displayCharacter.indexOf(ss + 32) > -1)
696 ss = (char) (ss + 32);
701 if (!validRes || (ss != lastSS))
707 int nb_annot = x - temp;
708 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
711 case '(': // Stem case for RNA secondary structure
712 case ')': // and opposite direction
713 drawStemAnnot(g, row_annotations, lastSSX, x, y,
714 iconOffset, startRes, column, validRes, validEnd);
721 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
722 iconOffset, startRes, column, validRes,
730 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
731 iconOffset, startRes, column, validRes,
793 Color nonCanColor = getNotCanonicalColor(lastSS);
794 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
795 lastSSX, x, y, iconOffset, startRes, column,
800 g.setColor(Color.gray);
801 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
817 lastSSX = (x * charWidth);
824 if (column >= row_annotations.length)
826 column = row_annotations.length - 1;
833 if ((row_annotations == null) || (row_annotations.length <= column)
834 || (row_annotations[column] == null))
853 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
854 startRes, column, validRes, validEnd);
861 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
862 startRes, column, validRes, validEnd);
867 case ')': // Stem case for RNA secondary structure
869 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
870 startRes, column, validRes, validEnd);
927 // System.out.println(lastSS);
928 Color nonCanColor = getNotCanonicalColor(lastSS);
929 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
930 x, y, iconOffset, startRes, column, validRes, validEnd);
933 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
934 startRes, column, validRes, validEnd);
939 if (row.graph > 0 && row.graphHeight > 0)
941 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
943 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
945 // TODO: JAL-1291 revise rendering model so the graphGroup map is
946 // computed efficiently for all visible labels
947 float groupmax = -999999, groupmin = 9999999;
948 for (int gg = 0; gg < aa.length; gg++)
950 if (aa[gg].graphGroup != row.graphGroup)
957 aa[gg].visible = false;
959 if (aa[gg].graphMax > groupmax)
961 groupmax = aa[gg].graphMax;
963 if (aa[gg].graphMin < groupmin)
965 groupmin = aa[gg].graphMin;
969 for (int gg = 0; gg < aa.length; gg++)
971 if (aa[gg].graphGroup == row.graphGroup)
973 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
974 endRes, y, groupmin, groupmax, row.graphHeight);
978 graphGroupDrawn.set(row.graphGroup);
982 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
983 row.graphMin, row.graphMax, row.graphHeight);
986 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
988 drawBarGraph(g, row, row_annotations, startRes, endRes,
989 row.graphMin, row.graphMax, y, renderHistogram,
990 renderProfile, normaliseProfile);
996 if (clipst && !clipend)
1000 }// end if_in_visible_region
1001 if (row.graph > 0 && row.hasText)
1017 System.err.println("Start clip at : " + yfrom + " (index " + f_i
1022 System.err.println("End clip at : " + yto + " (index " + f_to
1027 System.err.println("Annotation Rendering time:"
1028 + (System.currentTimeMillis() - stime));
1035 public static final Color GLYPHLINE_COLOR = Color.gray;
1037 public static final Color SHEET_COLOUR = Color.green;
1039 public static final Color HELIX_COLOUR = Color.red;
1041 public static final Color STEM_COLOUR = Color.blue;
1043 private Color sdNOTCANONICAL_COLOUR;
1045 public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
1046 int x, int y, int iconOffset, int startRes, int column,
1047 boolean validRes, boolean validEnd)
1049 g.setColor(GLYPHLINE_COLOR);
1050 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1053 public void drawSheetAnnot(Graphics g, Annotation[] row,
1055 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1056 boolean validRes, boolean validEnd)
1058 g.setColor(SHEET_COLOUR);
1060 if (!validEnd || !validRes || row == null || row[column] == null
1061 || row[column].secondaryStructure != 'E')
1063 g.fillRect(lastSSX, y + 4 + iconOffset,
1064 (x * charWidth) - lastSSX - 4, 7);
1065 g.fillPolygon(new int[]
1066 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
1068 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
1073 g.fillRect(lastSSX, y + 4 + iconOffset,
1074 (x + 1) * charWidth - lastSSX, 7);
1079 public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
1080 int x, int y, int iconOffset, int startRes, int column,
1081 boolean validRes, boolean validEnd)
1083 g.setColor(HELIX_COLOUR);
1085 int sCol = (lastSSX / charWidth) + startRes;
1087 int x2 = (x * charWidth);
1091 int ofs = charWidth / 2;
1092 // Off by 1 offset when drawing rects and ovals
1093 // to offscreen image on the MAC
1094 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1095 if (sCol == 0 || row[sCol - 1] == null
1096 || row[sCol - 1].secondaryStructure != 'H')
1101 // g.setColor(Color.orange);
1102 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1105 if (!validRes || row[column] == null
1106 || row[column].secondaryStructure != 'H')
1112 // g.setColor(Color.magenta);
1113 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1121 if (sCol == 0 || row[sCol - 1] == null
1122 || row[sCol - 1].secondaryStructure != 'H')
1124 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1125 x1 += charWidth / 2;
1128 if (!validRes || row[column] == null
1129 || row[column].secondaryStructure != 'H')
1131 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1133 x2 -= charWidth / 2;
1136 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1139 public void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1140 Annotation[] aa_annotations, int sRes, int eRes, int y,
1141 float min, float max, int graphHeight)
1143 if (sRes > aa_annotations.length)
1150 // Adjustment for fastpaint to left
1156 eRes = Math.min(eRes, aa_annotations.length);
1164 float range = max - min;
1169 y2 = y - (int) ((0 - min / range) * graphHeight);
1172 g.setColor(Color.gray);
1173 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1175 eRes = Math.min(eRes, aa_annotations.length);
1178 int aaMax = aa_annotations.length - 1;
1180 while (x < eRes - sRes)
1183 if (hasHiddenColumns)
1185 column = columnSelection.adjustForHiddenColumns(column);
1193 if (aa_annotations[column] == null
1194 || aa_annotations[column - 1] == null)
1200 if (aa_annotations[column].colour == null)
1202 g.setColor(Color.black);
1206 g.setColor(aa_annotations[column].colour);
1210 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1212 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1214 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1215 + charWidth / 2, y2);
1219 if (_aa.threshold != null)
1221 g.setColor(_aa.threshold.colour);
1222 Graphics2D g2 = (Graphics2D) g;
1223 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1224 BasicStroke.JOIN_ROUND, 3f, new float[]
1227 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1228 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1229 g2.setStroke(new BasicStroke());
1233 public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1234 Annotation[] aa_annotations, int sRes, int eRes, float min,
1235 float max, int y, boolean renderHistogram, boolean renderProfile,
1236 boolean normaliseProfile)
1238 if (sRes > aa_annotations.length)
1242 Font ofont = g.getFont();
1243 eRes = Math.min(eRes, aa_annotations.length);
1245 int x = 0, y1 = y, y2 = y;
1247 float range = max - min;
1251 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1254 g.setColor(Color.gray);
1256 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1259 int aaMax = aa_annotations.length - 1;
1260 while (x < eRes - sRes)
1263 if (hasHiddenColumns)
1265 column = columnSelection.adjustForHiddenColumns(column);
1273 if (aa_annotations[column] == null)
1278 if (aa_annotations[column].colour == null)
1280 g.setColor(Color.black);
1284 g.setColor(aa_annotations[column].colour);
1288 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1290 if (renderHistogram)
1294 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1298 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1301 // draw profile if available
1305 int profl[] = getProfileFor(_aa, column);
1306 // just try to draw the logo if profl is not null
1307 if (profl != null && profl[1] != 0)
1309 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1310 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1317 * profl.length == 74 indicates that the profile of a secondary
1318 * structure conservation row was accesed. Therefore dc gets length 2,
1319 * to have space for a basepair instead of just a single nucleotide
1321 if (profl.length == 74)
1329 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1330 double scale = 1f / (normaliseProfile ? profl[1] : 100f);
1331 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1333 for (int c = 2; c < profl[0];)
1335 dc[0] = (char) profl[c++];
1337 if (_aa.label.startsWith("StrucConsensus"))
1339 dc[1] = (char) profl[c++];
1343 wdth /= fm.charsWidth(dc, 0, dc.length);
1347 scl = htn * scale * profl[c++];
1348 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1349 .getFontRenderContext());
1350 g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
1351 wdth, scl / lm.getAscent())));
1352 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1354 // Debug - render boxes around characters
1355 // g.setColor(Color.red);
1356 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1358 // g.setColor(profcolour.findColour(dc[0]).darker());
1359 g.setColor(profcolour.findColour(dc[0], column, null));
1361 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1362 .getBaselineIndex()]));
1364 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1372 if (_aa.threshold != null)
1374 g.setColor(_aa.threshold.colour);
1375 Graphics2D g2 = (Graphics2D) g;
1376 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1377 BasicStroke.JOIN_ROUND, 3f, new float[]
1380 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1382 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1383 g2.setStroke(new BasicStroke());
1387 // used by overview window
1388 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1389 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1391 eRes = Math.min(eRes, aa_annotations.length);
1392 g.setColor(Color.white);
1393 g.fillRect(0, 0, width, y);
1394 g.setColor(new Color(0, 0, 180));
1398 for (int j = sRes; j < eRes; j++)
1400 if (aa_annotations[j] != null)
1402 if (aa_annotations[j].colour == null)
1404 g.setColor(Color.black);
1408 g.setColor(aa_annotations[j].colour);
1411 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1417 g.fillRect(x, y - height, charWidth, height);
1423 Color getNotCanonicalColor(char lastss)
1429 return new Color(255, 125, 5);
1433 return new Color(245, 115, 10);
1437 return new Color(235, 135, 15);
1441 return new Color(225, 105, 20);
1445 return new Color(215, 145, 30);
1449 return new Color(205, 95, 35);
1453 return new Color(195, 155, 45);
1457 return new Color(185, 85, 55);
1461 return new Color(175, 165, 65);
1465 return new Color(170, 75, 75);
1469 return new Color(160, 175, 85);
1473 return new Color(150, 65, 95);
1477 return new Color(140, 185, 105);
1481 return new Color(130, 55, 110);
1485 return new Color(120, 195, 120);
1489 return new Color(110, 45, 130);
1493 return new Color(100, 205, 140);
1497 return new Color(90, 35, 150);
1501 return new Color(85, 215, 160);
1505 return new Color(75, 25, 170);
1509 return new Color(65, 225, 180);
1513 return new Color(55, 15, 185);
1517 return new Color(45, 235, 195);
1521 return new Color(35, 5, 205);
1525 return new Color(25, 245, 215);
1529 return new Color(15, 0, 225);
1533 return new Color(10, 255, 235);
1537 return new Color(5, 150, 245);
1541 return new Color(0, 80, 255);
1544 System.out.println("This is not a interaction : " + lastss);