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.viewmodel;
23 import jalview.datamodel.ColumnSelection;
24 import jalview.datamodel.HiddenSequences;
26 import java.awt.Graphics;
28 public class OverviewDimensions
30 // Default width and height values
31 private static final int DEFAULT_GRAPH_HEIGHT = 20;
33 private static final int MAX_WIDTH = 400;
35 private static final int MIN_WIDTH = 120;
37 private static final int MIN_SEQ_HEIGHT = 40;
39 private static final int MAX_SEQ_HEIGHT = 300;
41 // width of the overview panel
44 // height of sequences part of the overview panel
45 private int sequencesHeight;
47 // height of the graphs part of the overview panel
48 private int graphHeight = DEFAULT_GRAPH_HEIGHT;
50 // dimensions of box outlining current extent of view in alignment panel
51 // location of left side of box
52 private int boxX = -1;
54 // location of bottom of box
55 private int boxY = -1;
58 private int boxWidth = -1;
61 private int boxHeight = -1;
64 * Create an OverviewDimensions object
67 * positional properties of the viewport
68 * @param showAnnotationPanel
69 * true if the annotation panel is to be shown, false otherwise
71 public OverviewDimensions(ViewportRanges ranges,
72 boolean showAnnotationPanel)
74 // scale the initial size of overviewpanel to shape of alignment
75 float initialScale = (float) ranges.getAbsoluteAlignmentWidth()
76 / (float) ranges.getAbsoluteAlignmentHeight();
78 if (!showAnnotationPanel)
83 if (ranges.getAbsoluteAlignmentWidth() > ranges
84 .getAbsoluteAlignmentHeight())
88 sequencesHeight = Math.round(MAX_WIDTH / initialScale);
89 if (sequencesHeight < MIN_SEQ_HEIGHT)
91 sequencesHeight = MIN_SEQ_HEIGHT;
97 width = Math.round(MAX_WIDTH * initialScale);
98 sequencesHeight = MAX_SEQ_HEIGHT;
100 if (width < MIN_WIDTH)
108 * Check box dimensions and scroll positions and correct if necessary
111 * x position in overview panel
113 * y position in overview panel
119 * viewport position properties
121 public void updateViewportFromMouse(int mousex, int mousey,
122 HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
123 ViewportRanges ranges)
128 int alwidth = ranges.getAbsoluteAlignmentWidth();
129 int alheight = ranges.getAbsoluteAlignmentHeight();
142 // Convert x value to residue position
145 // need to determine where scrollCol should be, given x
146 // to do this also need to know width of viewport, and some hidden column
149 // convert x to residues - this is an absolute position
150 int xAsRes = Math.round((float) x * alwidth / width);
152 // get viewport width in residues
153 int vpwidth = ranges.getViewportWidth();
155 // get where x should be when accounting for hidden cols
156 // if x is in a hidden col region, shift to left - but we still need
158 // so convert back after getting visible region position
159 int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
161 // check in case we went off the edge of the alignment
162 int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
163 if (visXAsRes + vpwidth - 1 > visAlignWidth)
165 // went past the end of the alignment, adjust backwards
167 // if last position was before the end of the alignment, need to update
168 if ((ranges.getStartRes() + vpwidth - 1) < visAlignWidth)
170 visXAsRes = hiddenCols.findColumnPosition(hiddenCols
171 .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
175 visXAsRes = ranges.getStartRes();
180 // Convert y value to sequence position
183 // convert y to residues
184 int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
186 // get viewport height in sequences
187 int vpheight = ranges.getViewportHeight();
189 // get where y should be when accounting for hidden rows
190 // if y is in a hidden row region, shift up - but we still need absolute
192 // so convert back after getting visible region position
193 yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
194 .findIndexWithoutHiddenSeqs(yAsSeq));
196 // check in case we went off the edge of the alignment
197 int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
198 int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
199 if (visYAsRes + vpheight - 1 > visAlignHeight)
201 // went past the end of the alignment, adjust backwards
202 if ((ranges.getEndRes() + vpheight - 1) < visAlignHeight)
204 visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
205 .subtractVisibleRows(vpheight - 1, alheight - 1));
209 visYAsRes = ranges.getEndRes();
214 ranges.setStartRes(visXAsRes);
215 ranges.setStartSeq(visYAsRes);
219 * Update the overview panel box when the associated alignment panel is
227 * viewport position properties
229 public void setBoxPosition(HiddenSequences hiddenSeqs,
230 ColumnSelection hiddenCols, ViewportRanges ranges)
232 int alwidth = ranges.getAbsoluteAlignmentWidth();
233 int alheight = ranges.getAbsoluteAlignmentHeight();
235 // work with absolute values of startRes and endRes
236 int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
237 int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
239 // work with absolute values of startSeq and endSeq
240 int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
241 int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
243 // boxX, boxY is the x,y location equivalent to startRes, startSeq
244 boxX = Math.round((float) startRes * width / alwidth);
245 boxY = Math.round((float) startSeq * sequencesHeight / alheight);
247 // boxWidth is the width in residues translated to pixels
248 // since the box includes both the start and end residues, add 1 to the
251 .round((float) (endRes - startRes + 1) * width / alwidth);
252 // boxHeight is the height in sequences translated to pixels
253 boxHeight = Math.round((float) (endSeq - startSeq + 1)
259 * Draw the overview panel's viewport box on a graphics object
262 * the graphics object to draw on
264 public void drawBox(Graphics g)
266 System.out.println("Drawbox: " + boxX + " " + boxY + " " + boxWidth
268 g.drawRect(boxX, boxY, boxWidth, boxHeight);
269 g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
272 // TODO should be removed, when unit test has mock Graphics object available
273 // to check boxX/boxY
279 // TODO should be removed, when unit test has mock Graphics object available
280 // to check boxX/boxY
286 // TODO should be removed, when unit test has mock Graphics object available
287 public int getBoxWidth()
292 // TODO should be removed, when unit test has mock Graphics object available
293 public int getBoxHeight()
298 public void setWidth(int w)
303 public void setHeight(int h)
305 sequencesHeight = h - graphHeight;
308 public int getWidth()
313 public int getHeight()
315 return sequencesHeight + graphHeight;
318 public int getSequencesHeight()
320 return sequencesHeight;
323 public int getGraphHeight()