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;
31 import java.awt.BasicStroke;
32 import java.awt.Color;
34 import java.awt.FontMetrics;
35 import java.awt.Graphics;
36 import java.awt.Graphics2D;
37 import java.awt.Image;
38 import java.awt.font.LineMetrics;
39 import java.awt.geom.AffineTransform;
40 import java.awt.image.ImageObserver;
41 import java.util.BitSet;
42 import java.util.Hashtable;
44 import com.stevesoft.pat.Regex;
46 public class AnnotationRenderer
49 * flag indicating if timing and redraw parameter info should be output
51 private final boolean debugRedraw;
53 public AnnotationRenderer()
59 * Create a new annotation Renderer
62 * flag indicating if timing and redraw parameter info should be
65 public AnnotationRenderer(boolean debugRedraw)
67 this.debugRedraw = debugRedraw;
70 public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
71 int lastSSX, int x, int y, int iconOffset, int startRes,
72 int column, boolean validRes, boolean validEnd)
74 g.setColor(STEM_COLOUR);
75 int sCol = (lastSSX / charWidth) + startRes;
77 int x2 = (x * charWidth);
78 Regex closeparen = new Regex("(\\))");
80 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
81 : row_annotations[column - 1].displayCharacter;
83 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
84 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
85 boolean diffdownstream = !validRes || !validEnd
86 || row_annotations[column] == null
87 || !dc.equals(row_annotations[column].displayCharacter);
88 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
89 // If a closing base pair half of the stem, display a backward arrow
90 if (column > 0 && closeparen.search(dc))
94 // if (validRes && column>1 && row_annotations[column-2]!=null &&
95 // dc.equals(row_annotations[column-2].displayCharacter))
97 g.fillPolygon(new int[]
98 { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
99 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
110 // display a forward arrow
113 g.fillPolygon(new int[]
114 { x2 - 5, x2 - 5, x2 }, new int[]
115 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
124 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
127 private int charWidth, endRes, charHeight;
129 private boolean validCharWidth, hasHiddenColumns;
131 private FontMetrics fm;
133 private final boolean MAC = new jalview.util.Platform().isAMac();
135 boolean av_renderHistogram = true, av_renderProfile = true,
136 av_normaliseProfile = false;
138 ColourSchemeI profcolour = null;
140 private ColumnSelection columnSelection;
142 private Hashtable[] hconsensus;
144 private Hashtable[] hStrucConsensus;
146 private boolean av_ignoreGapsConsensus;
149 * attributes set from AwtRenderPanelI
152 * old image used when data is currently being calculated and cannot be
155 private Image fadedImage;
158 * panel being rendered into
160 private ImageObserver annotationPanel;
163 * width of image to render in panel
165 private int imgWidth;
168 * offset to beginning of visible area
173 * offset to end of visible area
175 private int visHeight;
178 * indicate if the renderer should only render the visible portion of the
179 * annotation given the current view settings
181 private boolean useClip = true;
184 * master flag indicating if renderer should ever try to clip. not enabled for
187 private boolean canClip = false;
189 public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
190 Annotation[] row_annotations, int lastSSX, int x, int y,
191 int iconOffset, int startRes, int column, boolean validRes,
194 // System.out.println(nonCanColor);
196 g.setColor(nonCanColor);
197 int sCol = (lastSSX / charWidth) + startRes;
199 int x2 = (x * charWidth);
200 Regex closeparen = new Regex("}|]|<|[a-z]");
202 String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
203 : row_annotations[column - 1].displayCharacter;
205 boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
206 || !dc.equals(row_annotations[sCol - 1].displayCharacter);
207 boolean diffdownstream = !validRes || !validEnd
208 || row_annotations[column] == null
209 || !dc.equals(row_annotations[column].displayCharacter);
210 // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
211 // If a closing base pair half of the stem, display a backward arrow
212 if (column > 0 && closeparen.search(dc))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.search(dc))
217 // if (validRes && column>1 && row_annotations[column-2]!=null &&
218 // dc.equals(row_annotations[column-2].displayCharacter))
220 g.fillPolygon(new int[]
221 { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
222 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
233 // display a forward arrow
236 g.fillPolygon(new int[]
237 { x2 - 5, x2 - 5, x2 }, new int[]
238 { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
247 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
250 // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
252 public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
255 fm = annotPanel.getFontMetrics();
256 annotationPanel = annotPanel;
257 fadedImage = annotPanel.getFadedImage();
258 imgWidth = annotPanel.getFadedImageWidth();
259 // visible area for rendering
260 int[] bounds = annotPanel.getVisibleVRange();
264 visHeight = bounds[1];
279 updateFromAlignViewport(av);
282 public void updateFromAlignViewport(AlignViewportI av)
284 charWidth = av.getCharWidth();
285 endRes = av.getEndRes();
286 charHeight = av.getCharHeight();
287 hasHiddenColumns = av.hasHiddenColumns();
288 validCharWidth = av.isValidCharWidth();
289 av_renderHistogram = av.isShowConsensusHistogram();
290 av_renderProfile = av.isShowSequenceLogo();
291 av_normaliseProfile = av.isNormaliseSequenceLogo();
292 profcolour = av.getGlobalColourScheme();
293 if (profcolour == null)
295 // Set the default colour for sequence logo if the alignnent has no
297 profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
298 : new jalview.schemes.ZappoColourScheme();
300 columnSelection = av.getColumnSelection();
301 hconsensus = av.getSequenceConsensusHash();// hconsensus;
302 hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
303 av_ignoreGapsConsensus = av.getIgnoreGapsConsensus();
306 public int[] getProfileFor(AlignmentAnnotation aa, int column)
308 // TODO : consider refactoring the global alignment calculation
309 // properties/rendering attributes as a global 'alignment group' which holds
310 // all vis settings for the alignment as a whole rather than a subset
312 if (aa.autoCalculated && aa.label.startsWith("Consensus"))
314 if (aa.groupRef != null && aa.groupRef.consensusData != null
315 && aa.groupRef.isShowSequenceLogo())
317 return AAFrequency.extractProfile(
318 aa.groupRef.consensusData[column],
319 aa.groupRef.getIgnoreGapsConsensus());
321 // TODO extend annotation row to enable dynamic and static profile data to
323 if (aa.groupRef == null && aa.sequenceRef == null)
325 return AAFrequency.extractProfile(hconsensus[column],
326 av_ignoreGapsConsensus);
331 if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
333 // TODO implement group structure consensus
335 * if (aa.groupRef != null && aa.groupRef.consensusData != null &&
336 * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for
337 * group selections return StructureFrequency.extractProfile(
338 * aa.groupRef.consensusData[column], aa.groupRef
339 * .getIgnoreGapsConsensus()); }
341 // TODO extend annotation row to enable dynamic and static profile data
344 if (aa.groupRef == null && aa.sequenceRef == null
345 && hStrucConsensus != null
346 && hStrucConsensus.length > column)
348 return StructureFrequency.extractProfile(hStrucConsensus[column],
349 av_ignoreGapsConsensus);
357 * Render the annotation rows associated with an alignment.
362 * data and view settings to render
364 * destination for graphics
366 * row where a mouse event occured (or -1)
368 * first column that will be drawn
370 * last column that will be drawn
371 * @return true if the fadedImage was used for any alignment annotation rows
372 * currently being calculated
374 public boolean drawComponent(AwtRenderPanelI annotPanel,
375 AlignViewportI av, Graphics g, int activeRow, int startRes,
378 long stime = System.currentTimeMillis();
379 boolean usedFaded = false;
381 // AnnotationPanel needs to implement: ImageObserver, access to
383 updateFromAwtRenderPanel(annotPanel, av);
384 fm = g.getFontMetrics();
385 AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
396 boolean validRes = false;
397 boolean validEnd = false;
398 boolean labelAllCols = false;
399 boolean centreColLabels, centreColLabelsDef = av
400 .getCentreColumnLabels();
401 boolean scaleColLabel = false;
402 AlignmentAnnotation consensusAnnot = av
403 .getAlignmentConsensusAnnotation(), structConsensusAnnot = av
404 .getAlignmentStrucConsensusAnnotation();
405 boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
407 BitSet graphGroupDrawn = new BitSet();
408 int charOffset = 0; // offset for a label
409 float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
411 Font ofont = g.getFont();
414 int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
415 boolean clipst = false, clipend = false;
416 for (int i = 0; i < aa.length; i++)
418 AlignmentAnnotation row = aa[i];
420 // check if this is a consensus annotation row and set the display
421 // settings appropriately
422 // TODO: generalise this to have render styles for consensus/profile
424 if (row.groupRef != null && row == row.groupRef.getConsensus())
426 renderHistogram = row.groupRef.isShowConsensusHistogram();
427 renderProfile = row.groupRef.isShowSequenceLogo();
428 normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
430 else if (row == consensusAnnot || row == structConsensusAnnot)
432 renderHistogram = av_renderHistogram;
433 renderProfile = av_renderProfile;
434 normaliseProfile = av_normaliseProfile;
438 renderHistogram = true;
439 // don't need to set render/normaliseProfile since they are not
440 // currently used in any other annotation track renderer
443 Annotation[] row_annotations = row.annotations;
448 centreColLabels = row.centreColLabels || centreColLabelsDef;
449 labelAllCols = row.showAllColLabels;
450 scaleColLabel = row.scaleColLabel;
455 || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
456 {// if_in_visible_region
467 if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
472 // this is so that we draw the characters below the graph
477 iconOffset = charHeight - fm.getDescent();
481 else if (row.hasText)
483 iconOffset = charHeight - fm.getDescent();
491 if (row.autoCalculated && av.isCalculationInProgress(row))
495 g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
496 - row.height, imgWidth, y, annotationPanel);
497 g.setColor(Color.black);
498 // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
504 * else if (annotationPanel.av.updatingConservation &&
505 * aa[i].label.equals("Conservation")) {
507 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
508 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
509 * annotationPanel.imgWidth, y, annotationPanel);
511 * g.setColor(Color.black); //
512 * g.drawString("Calculating Conservation.....",20, y-row.height/2);
514 * continue; } else if (annotationPanel.av.updatingConservation &&
515 * aa[i].label.equals("Quality")) {
517 * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
518 * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
519 * annotationPanel.imgWidth, y, annotationPanel);
520 * g.setColor(Color.black); // /
521 * g.drawString("Calculating Quality....",20, y-row.height/2);
525 // first pass sets up state for drawing continuation from left-hand
528 x = (startRes == 0) ? 0 : -1;
529 while (x < endRes - startRes)
531 if (hasHiddenColumns)
533 column = columnSelection.adjustForHiddenColumns(startRes + x);
534 if (column > row_annotations.length - 1)
541 column = startRes + x;
544 if ((row_annotations == null)
545 || (row_annotations.length <= column)
546 || (row_annotations[column] == null))
558 g.setColor(Color.red);
560 if (columnSelection != null)
562 for (int n = 0; n < columnSelection.size(); n++)
564 int v = columnSelection.columnAt(n);
568 g.fillRect(x * charWidth, y, charWidth, charHeight);
573 if (!row.isValidStruc())
575 g.setColor(Color.orange);
576 g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
577 charWidth, charHeight);
581 && row_annotations[column].displayCharacter != null
582 && (row_annotations[column].displayCharacter.length() > 0))
585 if (centreColLabels || scaleColLabel)
587 fmWidth = fm.charsWidth(
588 row_annotations[column].displayCharacter
590 row_annotations[column].displayCharacter.length());
594 // justify the label and scale to fit in column
595 if (fmWidth > charWidth)
597 // scale only if the current font isn't already small enough
598 fmScaling = charWidth;
599 fmScaling /= fmWidth;
600 g.setFont(ofont.deriveFont(AffineTransform
601 .getScaleInstance(fmScaling, 1.0)));
602 // and update the label's width to reflect the scaling.
610 .charWidth(row_annotations[column].displayCharacter
613 charOffset = (int) ((charWidth - fmWidth) / 2f);
615 if (row_annotations[column].colour == null)
616 g.setColor(Color.black);
618 g.setColor(row_annotations[column].colour);
620 if (column == 0 || row.graph > 0)
622 g.drawString(row_annotations[column].displayCharacter,
623 (x * charWidth) + charOffset, y + iconOffset);
625 else if (row_annotations[column - 1] == null
627 || !row_annotations[column].displayCharacter
628 .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
629 .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
631 g.drawString(row_annotations[column].displayCharacter, x
632 * charWidth + charOffset, y + iconOffset);
639 char ss = validRes ? row_annotations[column].secondaryStructure
644 // distinguish between forward/backward base-pairing
645 if (row_annotations[column].displayCharacter.indexOf(')') > -1)
654 if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
662 // distinguish between forward/backward base-pairing
663 if (row_annotations[column].displayCharacter.indexOf('}') > -1)
671 // distinguish between forward/backward base-pairing
672 if (row_annotations[column].displayCharacter.indexOf('<') > -1)
680 // distinguish between forward/backward base-pairing
681 if (row_annotations[column].displayCharacter.indexOf(ss + 32) > -1)
684 ss = (char) (ss + 32);
689 if (!validRes || (ss != lastSS))
695 int nb_annot = x - temp;
696 // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
701 drawHelixAnnot(g, row_annotations, lastSSX, x, y,
702 iconOffset, startRes, column, validRes, validEnd);
706 drawSheetAnnot(g, row_annotations, lastSSX, x, y,
707 iconOffset, startRes, column, validRes, validEnd);
710 case '(': // Stem case for RNA secondary structure
711 case ')': // and opposite direction
712 drawStemAnnot(g, row_annotations, lastSSX, x, y,
713 iconOffset, startRes, column, validRes, validEnd);
775 Color nonCanColor = getNotCanonicalColor(lastSS);
776 drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
777 lastSSX, x, y, iconOffset, startRes, column,
782 g.setColor(Color.gray);
783 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
799 lastSSX = (x * charWidth);
806 if (column >= row_annotations.length)
808 column = row_annotations.length - 1;
815 if ((row_annotations == null) || (row_annotations.length <= column)
816 || (row_annotations[column] == null))
832 drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
833 startRes, column, validRes, validEnd);
837 drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
838 startRes, column, validRes, validEnd);
841 case 'S': // Stem case for RNA secondary structure
843 drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
844 startRes, column, validRes, validEnd);
903 // System.out.println(lastSS);
904 Color nonCanColor = getNotCanonicalColor(lastSS);
905 drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
906 x, y, iconOffset, startRes, column, validRes, validEnd);
909 drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
910 startRes, column, validRes, validEnd);
915 if (row.graph > 0 && row.graphHeight > 0)
917 if (row.graph == AlignmentAnnotation.LINE_GRAPH)
919 if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
921 // TODO: JAL-1291 revise rendering model so the graphGroup map is
922 // computed efficiently for all visible labels
923 float groupmax = -999999, groupmin = 9999999;
924 for (int gg = 0; gg < aa.length; gg++)
926 if (aa[gg].graphGroup != row.graphGroup)
933 aa[gg].visible = false;
935 if (aa[gg].graphMax > groupmax)
937 groupmax = aa[gg].graphMax;
939 if (aa[gg].graphMin < groupmin)
941 groupmin = aa[gg].graphMin;
945 for (int gg = 0; gg < aa.length; gg++)
947 if (aa[gg].graphGroup == row.graphGroup)
949 drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
950 endRes, y, groupmin, groupmax, row.graphHeight);
954 graphGroupDrawn.set(row.graphGroup);
958 drawLineGraph(g, row, row_annotations, startRes, endRes, y,
959 row.graphMin, row.graphMax, row.graphHeight);
962 else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
964 drawBarGraph(g, row, row_annotations, startRes, endRes,
965 row.graphMin, row.graphMax, y, renderHistogram,
966 renderProfile, normaliseProfile);
972 if (clipst && !clipend)
976 }// end if_in_visible_region
977 if (row.graph > 0 && row.hasText)
993 System.err.println("Start clip at : " + yfrom + " (index " + f_i
998 System.err.println("End clip at : " + yto + " (index " + f_to
1003 System.err.println("Annotation Rendering time:"
1004 + (System.currentTimeMillis() - stime));
1011 private final Color GLYPHLINE_COLOR = Color.gray;
1013 private final Color SHEET_COLOUR = Color.green;
1015 private final Color HELIX_COLOUR = Color.red;
1017 private final Color STEM_COLOUR = Color.blue;
1019 private Color sdNOTCANONICAL_COLOUR;
1021 public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
1022 int x, int y, int iconOffset, int startRes, int column,
1023 boolean validRes, boolean validEnd)
1025 g.setColor(GLYPHLINE_COLOR);
1026 g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
1029 public void drawSheetAnnot(Graphics g, Annotation[] row,
1031 int lastSSX, int x, int y, int iconOffset, int startRes, int column,
1032 boolean validRes, boolean validEnd)
1034 g.setColor(SHEET_COLOUR);
1036 if (!validEnd || !validRes || row == null || row[column] == null
1037 || row[column].secondaryStructure != 'E')
1039 g.fillRect(lastSSX, y + 4 + iconOffset,
1040 (x * charWidth) - lastSSX - 4, 7);
1041 g.fillPolygon(new int[]
1042 { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
1044 { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
1049 g.fillRect(lastSSX, y + 4 + iconOffset,
1050 (x + 1) * charWidth - lastSSX, 7);
1055 public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
1056 int x, int y, int iconOffset, int startRes, int column,
1057 boolean validRes, boolean validEnd)
1059 g.setColor(HELIX_COLOUR);
1061 int sCol = (lastSSX / charWidth) + startRes;
1063 int x2 = (x * charWidth);
1067 int ofs = charWidth / 2;
1068 // Off by 1 offset when drawing rects and ovals
1069 // to offscreen image on the MAC
1070 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
1071 if (sCol == 0 || row[sCol - 1] == null
1072 || row[sCol - 1].secondaryStructure != 'H')
1077 // g.setColor(Color.orange);
1078 g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
1081 if (!validRes || row[column] == null
1082 || row[column].secondaryStructure != 'H')
1088 // g.setColor(Color.magenta);
1089 g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
1097 if (sCol == 0 || row[sCol - 1] == null
1098 || row[sCol - 1].secondaryStructure != 'H')
1100 g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
1101 x1 += charWidth / 2;
1104 if (!validRes || row[column] == null
1105 || row[column].secondaryStructure != 'H')
1107 g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
1109 x2 -= charWidth / 2;
1112 g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
1115 public void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
1116 Annotation[] aa_annotations, int sRes, int eRes, int y,
1117 float min, float max, int graphHeight)
1119 if (sRes > aa_annotations.length)
1126 // Adjustment for fastpaint to left
1132 eRes = Math.min(eRes, aa_annotations.length);
1140 float range = max - min;
1145 y2 = y - (int) ((0 - min / range) * graphHeight);
1148 g.setColor(Color.gray);
1149 g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
1151 eRes = Math.min(eRes, aa_annotations.length);
1154 int aaMax = aa_annotations.length - 1;
1156 while (x < eRes - sRes)
1159 if (hasHiddenColumns)
1161 column = columnSelection.adjustForHiddenColumns(column);
1169 if (aa_annotations[column] == null
1170 || aa_annotations[column - 1] == null)
1176 if (aa_annotations[column].colour == null)
1177 g.setColor(Color.black);
1179 g.setColor(aa_annotations[column].colour);
1182 - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
1184 - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
1186 g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
1187 + charWidth / 2, y2);
1191 if (_aa.threshold != null)
1193 g.setColor(_aa.threshold.colour);
1194 Graphics2D g2 = (Graphics2D) g;
1195 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1196 BasicStroke.JOIN_ROUND, 3f, new float[]
1199 y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
1200 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1201 g2.setStroke(new BasicStroke());
1205 public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
1206 Annotation[] aa_annotations, int sRes, int eRes, float min,
1207 float max, int y, boolean renderHistogram, boolean renderProfile,
1208 boolean normaliseProfile)
1210 if (sRes > aa_annotations.length)
1214 Font ofont = g.getFont();
1215 eRes = Math.min(eRes, aa_annotations.length);
1217 int x = 0, y1 = y, y2 = y;
1219 float range = max - min;
1223 y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
1226 g.setColor(Color.gray);
1228 g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
1231 int aaMax = aa_annotations.length - 1;
1232 while (x < eRes - sRes)
1235 if (hasHiddenColumns)
1237 column = columnSelection.adjustForHiddenColumns(column);
1245 if (aa_annotations[column] == null)
1250 if (aa_annotations[column].colour == null)
1251 g.setColor(Color.black);
1253 g.setColor(aa_annotations[column].colour);
1256 - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
1258 if (renderHistogram)
1262 g.fillRect(x * charWidth, y2, charWidth, y1 - y2);
1266 g.fillRect(x * charWidth, y1, charWidth, y2 - y1);
1269 // draw profile if available
1273 int profl[] = getProfileFor(_aa, column);
1274 // just try to draw the logo if profl is not null
1275 if (profl != null && profl[1] != 0)
1277 float ht = normaliseProfile ? y - _aa.graphHeight : y1;
1278 double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
1285 * profl.length == 74 indicates that the profile of a secondary
1286 * structure conservation row was accesed. Therefore dc gets length 2,
1287 * to have space for a basepair instead of just a single nucleotide
1289 if (profl.length == 74)
1297 LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
1298 double scale = 1f / (normaliseProfile ? profl[1] : 100f);
1299 float ofontHeight = 1f / lm.getAscent();// magnify to fill box
1301 for (int c = 2; c < profl[0];)
1303 dc[0] = (char) profl[c++];
1305 if (_aa.label.startsWith("StrucConsensus"))
1307 dc[1] = (char) profl[c++];
1311 wdth /= fm.charsWidth(dc, 0, dc.length);
1315 scl = htn * scale * profl[c++];
1316 lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
1317 .getFontRenderContext());
1318 g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
1319 wdth, scl / lm.getAscent())));
1320 lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
1322 // Debug - render boxes around characters
1323 // g.setColor(Color.red);
1324 // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
1326 // g.setColor(profcolour.findColour(dc[0]).darker());
1327 g.setColor(profcolour.findColour(dc[0], column, null));
1329 hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
1330 .getBaselineIndex()]));
1332 g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
1340 if (_aa.threshold != null)
1342 g.setColor(_aa.threshold.colour);
1343 Graphics2D g2 = (Graphics2D) g;
1344 g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
1345 BasicStroke.JOIN_ROUND, 3f, new float[]
1348 y2 = (int) (y - ((_aa.threshold.value - min) / range)
1350 g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
1351 g2.setStroke(new BasicStroke());
1355 // used by overview window
1356 public void drawGraph(Graphics g, AlignmentAnnotation _aa,
1357 Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
1359 eRes = Math.min(eRes, aa_annotations.length);
1360 g.setColor(Color.white);
1361 g.fillRect(0, 0, width, y);
1362 g.setColor(new Color(0, 0, 180));
1366 for (int j = sRes; j < eRes; j++)
1368 if (aa_annotations[j] != null)
1370 if (aa_annotations[j].colour == null)
1371 g.setColor(Color.black);
1373 g.setColor(aa_annotations[j].colour);
1375 height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
1381 g.fillRect(x, y - height, charWidth, height);
1387 Color getNotCanonicalColor(char lastss)
1393 return new Color(255, 125, 5);
1397 return new Color(245, 115, 10);
1401 return new Color(235, 135, 15);
1405 return new Color(225, 105, 20);
1409 return new Color(215, 145, 30);
1413 return new Color(205, 95, 35);
1417 return new Color(195, 155, 45);
1421 return new Color(185, 85, 55);
1425 return new Color(175, 165, 65);
1429 return new Color(170, 75, 75);
1433 return new Color(160, 175, 85);
1437 return new Color(150, 65, 95);
1441 return new Color(140, 185, 105);
1445 return new Color(130, 55, 110);
1449 return new Color(120, 195, 120);
1453 return new Color(110, 45, 130);
1457 return new Color(100, 205, 140);
1461 return new Color(90, 35, 150);
1465 return new Color(85, 215, 160);
1469 return new Color(75, 25, 170);
1473 return new Color(65, 225, 180);
1477 return new Color(55, 15, 185);
1481 return new Color(45, 235, 195);
1485 return new Color(35, 5, 205);
1489 return new Color(25, 245, 215);
1493 return new Color(15, 0, 225);
1497 return new Color(10, 255, 235);
1501 return new Color(5, 150, 245);
1505 return new Color(0, 80, 255);
1508 System.out.println("This is not a interaction : " + lastss);