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.appletgui;
23 import jalview.datamodel.SequenceI;
25 import java.awt.Color;
27 import java.awt.Graphics;
28 import java.awt.Image;
29 import awt2swing.Panel;
30 import java.util.List;
32 public class IdCanvas extends Panel
34 protected AlignViewport av;
36 protected boolean showScores = true;
38 protected int maxIdLength = -1;
40 protected String maxIdStr = null;
48 boolean fastPaint = false;
50 List<SequenceI> searchResults;
52 public IdCanvas(AlignViewport av)
56 PaintRefresher.Register(this, av.getSequenceSetId());
59 public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
63 int charHeight = av.getCharHeight();
65 if (searchResults != null && searchResults.contains(s))
67 gg.setColor(Color.black);
68 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
70 gg.setColor(Color.white);
72 else if (av.getSelectionGroup() != null
73 && av.getSelectionGroup().getSequences(null).contains(s))
75 gg.setColor(Color.lightGray);
76 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
78 gg.setColor(Color.white);
82 gg.setColor(av.getSequenceColour(s));
83 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
85 gg.setColor(Color.black);
88 gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
89 ((i - starty) * charHeight) + ypos + charHeight
94 drawMarker(i, starty, ypos);
99 public void fastPaint(int vertical)
107 gg.copyArea(0, 0, getSize().width, imgHeight, 0,
108 -vertical * av.getCharHeight());
110 int ss = av.startSeq, es = av.endSeq, transY = 0;
111 if (vertical > 0) // scroll down
114 if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
120 transY = imgHeight - vertical * av.getCharHeight();
123 else if (vertical < 0)
132 gg.translate(0, transY);
136 gg.translate(0, -transY);
142 public void paintComponent(Graphics g)
144 if (getSize().height < 0 || getSize().width < 0)
151 g.drawImage(image, 0, 0, this);
155 imgHeight = getSize().height;
156 imgHeight -= imgHeight % av.getCharHeight();
163 if (image == null || imgHeight != image.getHeight(this))
165 image = createImage(getSize().width, imgHeight);
166 gg = image.getGraphics();
167 gg.setFont(av.getFont());
170 // Fill in the background
171 gg.setColor(Color.white);
172 Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
173 .getFont().getSize());
176 gg.fillRect(0, 0, getSize().width, getSize().height);
177 drawIds(av.startSeq, av.endSeq);
178 g.drawImage(image, 0, 0, this);
182 * local copy of av.getCharHeight set at top of drawIds
184 private int avcharHeight;
185 void drawIds(int starty, int endy)
187 // hardwired italic IDs in applet currently
188 Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
189 .getFont().getSize());
190 // temp variable for speed
191 avcharHeight = av.getCharHeight();
195 Color currentColor = Color.white;
196 Color currentTextColor = Color.black;
198 final boolean doHiddenCheck = av.isDisplayReferenceSeq()
199 || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
200 && av.getShowHiddenMarkers();
202 if (av.getWrapAlignment())
204 int maxwidth = av.getAlignment().getWidth();
205 int alheight = av.getAlignment().getHeight();
207 if (av.hasHiddenColumns())
209 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
212 int annotationHeight = 0;
213 AnnotationLabels labels = null;
215 if (av.isShowAnnotation())
217 AnnotationPanel ap = new AnnotationPanel(av);
218 annotationHeight = ap.adjustPanelHeight();
219 labels = new AnnotationLabels(av);
221 int hgap = avcharHeight;
222 if (av.getScaleAboveWrapped())
224 hgap += avcharHeight;
227 int cHeight = alheight * avcharHeight + hgap + annotationHeight;
229 int rowSize = av.getEndRes() - av.getStartRes();
230 // Draw the rest of the panels
231 for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
232 && (row < maxwidth); ypos += cHeight, row += rowSize)
234 for (int i = starty; i < alheight; i++)
237 SequenceI s = av.getAlignment().getSequenceAt(i);
243 drawIdString(gg, hiddenRows, s, i, 0, ypos);
248 gg.translate(0, ypos + (alheight * avcharHeight));
249 labels.drawComponent(gg, getSize().width);
250 gg.translate(0, -ypos - (alheight * avcharHeight));
257 // Now draw the id strings
259 for (int i = starty; i < endy; i++)
262 seq = av.getAlignment().getSequenceAt(i);
268 // boolean isrep=false;
275 // Selected sequence colours
276 if ((searchResults != null) && searchResults.contains(seq))
278 currentColor = Color.black;
279 currentTextColor = Color.white;
281 else if ((av.getSelectionGroup() != null)
282 && av.getSelectionGroup().getSequences(null).contains(seq))
284 currentColor = Color.lightGray;
285 currentTextColor = Color.black;
289 currentColor = av.getSequenceColour(seq);
290 currentTextColor = Color.black;
293 gg.setColor(currentColor);
294 // TODO: isrep could be used to highlight the representative in a
296 gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
298 gg.setColor(currentTextColor);
300 gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
301 (((i - starty) * avcharHeight) + avcharHeight)
302 - (avcharHeight / 5));
306 drawMarker(i, starty, 0);
312 public void setHighlighted(List<SequenceI> list)
314 searchResults = list;
318 void drawMarker(int i, int starty, int yoffset)
320 SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
321 // Use this method here instead of calling hiddenSeq adjust
323 int hSize = hseqs.length;
326 int lastIndex = i - 1;
327 int nextIndex = i + 1;
329 for (int j = 0; j < hSize; j++)
331 if (hseqs[j] != null)
333 if (j - 1 < hiddenIndex)
337 if (j - 1 < lastIndex)
341 if (j - 1 < nextIndex)
348 boolean below = (hiddenIndex > lastIndex + 1);
349 boolean above = (nextIndex > hiddenIndex + 1);
351 gg.setColor(Color.blue);
354 gg.fillPolygon(new int[]
355 { getSize().width - avcharHeight, getSize().width - avcharHeight,
356 getSize().width }, new int[]
357 { (i - starty) * avcharHeight + yoffset,
358 (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
359 (i - starty) * avcharHeight + yoffset }, 3);
363 gg.fillPolygon(new int[]
364 { getSize().width - avcharHeight, getSize().width - avcharHeight,
365 getSize().width }, new int[]
366 { (i - starty + 1) * avcharHeight + yoffset,
367 (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
368 (i - starty + 1) * avcharHeight + yoffset }, 3);
373 boolean setHiddenFont(SequenceI seq)
375 Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
378 if (av.isHiddenRepSequence(seq))