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.api.AlignmentColsCollectionI;
24 import jalview.api.AlignmentRowsCollectionI;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.AllColsCollection;
27 import jalview.datamodel.AllRowsCollection;
28 import jalview.datamodel.HiddenColumns;
29 import jalview.datamodel.HiddenSequences;
31 public class OverviewDimensionsShowHidden extends OverviewDimensions
33 private ViewportRanges ranges;
36 * Create an OverviewDimensions object
39 * positional properties of the viewport
40 * @param showAnnotationPanel
41 * true if the annotation panel is to be shown, false otherwise
43 public OverviewDimensionsShowHidden(ViewportRanges vpranges,
44 boolean showAnnotationPanel)
46 super(vpranges, showAnnotationPanel);
52 * Check box dimensions and scroll positions and correct if necessary
55 * x position in overview panel
57 * y position in overview panel
63 * viewport position properties
66 public void updateViewportFromMouse(int mousex, int mousey,
67 HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
69 int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
70 int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
72 int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
73 yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
74 hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
75 int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
77 updateViewportFromTopLeft(visXAsRes, visYAsSeq, hiddenSeqs, hiddenCols);
81 public void adjustViewportFromMouse(int mousex, int mousey,
82 HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
84 // calculate translation in pixel terms:
85 // get mouse location in viewport coords, add translation in viewport
87 // convert back to pixel coords
88 int vpx = Math.round((float) mousex * alwidth / width);
89 int visXAsRes = hiddenCols.findColumnPosition(vpx) + fixedX;
91 int vpy = Math.round((float) mousey * alheight / sequencesHeight);
92 int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + fixedY;
94 updateViewportFromTopLeft(visXAsRes, visYAsRes,
100 protected void updateViewportFromTopLeft(int visXAsRes, int visYAsSeq,
101 HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
104 resetAlignmentDims();
117 // Convert x value to residue position
120 // need to determine where scrollCol should be, given x
121 // to do this also need to know width of viewport, and some hidden column
124 // convert x to residues - this is an absolute position
125 // int xAsRes = Math.round((float) x * alwidth / width);
127 // get viewport width in residues
128 int vpwidth = ranges.getViewportWidth();
130 // get where x should be when accounting for hidden cols
131 // if x is in a hidden col region, shift to left - but we still need
133 // so convert back after getting visible region position
136 // check in case we went off the edge of the alignment
137 int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
138 if (visXAsRes + vpwidth - 1 > visAlignWidth)
140 // went past the end of the alignment, adjust backwards
142 // if last position was before the end of the alignment, need to update
143 if (ranges.getEndRes() < visAlignWidth)
145 visXAsRes = hiddenCols.findColumnPosition(hiddenCols
146 .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
150 visXAsRes = ranges.getStartRes();
155 // Convert y value to sequence position
158 // convert y to residues
159 // int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
161 // get viewport height in sequences
162 int vpheight = ranges.getViewportHeight();
164 // get where y should be when accounting for hidden rows
165 // if y is in a hidden row region, shift up - but we still need absolute
167 // so convert back after getting visible region position
170 // check in case we went off the edge of the alignment
171 int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
173 if (visYAsSeq + vpheight - 1 > visAlignHeight)
175 // went past the end of the alignment, adjust backwards
176 if (ranges.getEndSeq() < visAlignHeight)
178 visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
179 .subtractVisibleRows(vpheight - 1, alheight - 1));
183 visYAsSeq = ranges.getStartSeq();
188 ranges.setStartRes(visXAsRes);
189 ranges.setStartSeq(visYAsSeq);
194 * Update the overview panel box when the associated alignment panel is
202 * viewport position properties
205 public void setBoxPosition(HiddenSequences hiddenSeqs,
206 HiddenColumns hiddenCols)
209 // work with absolute values of startRes and endRes
210 int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
211 int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
213 // work with absolute values of startSeq and endSeq
214 int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
215 int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
217 System.out.println("Update box: startres: " + startRes);
219 setBoxPosition(startRes, startSeq, endRes - startRes + 1, endSeq
224 public AlignmentColsCollectionI getColumns(AlignmentI al)
226 return new AllColsCollection(0,
227 ranges.getAbsoluteAlignmentWidth() - 1, al);
231 public AlignmentRowsCollectionI getRows(AlignmentI al)
233 return new AllRowsCollection(0,
234 ranges.getAbsoluteAlignmentHeight() - 1,
239 protected void resetAlignmentDims()
241 alwidth = ranges.getAbsoluteAlignmentWidth();
242 alheight = ranges.getAbsoluteAlignmentHeight();
246 protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
248 int vpx = Math.round((float) mousex * alwidth / width);
249 return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
254 protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
256 int vpy = Math.round((float) mousey * alheight / sequencesHeight);
257 return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
261 public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
262 HiddenColumns hiddenCols)
265 // get alignment position of x and box (can get directly from vpranges) and calc difference
266 int vpx = Math.round((float) x * alwidth / width);
267 fixedX = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
269 int vpy = Math.round((float) y * alheight / sequencesHeight);
270 fixedY = ranges.getStartSeq()
271 - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);