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;
35 private int xdiff; // when dragging, difference in alignment units between
36 // start residue and original mouse click position
38 private int ydiff; // when dragging, difference in alignment units between
39 // start sequence and original mouse click position
42 * Create an OverviewDimensions object
45 * positional properties of the viewport
46 * @param showAnnotationPanel
47 * true if the annotation panel is to be shown, false otherwise
49 public OverviewDimensionsShowHidden(ViewportRanges vpranges,
50 boolean showAnnotationPanel)
52 super(vpranges, showAnnotationPanel);
58 * Check box dimensions and scroll positions and correct if necessary
61 * x position in overview panel
63 * y position in overview panel
69 * viewport position properties
72 public void updateViewportFromMouse(int mousex, int mousey,
73 HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
75 // convert mousex and mousey to alignment units as well as
76 // translating to top left corner of viewport - this is an absolute position
77 int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
78 int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
80 // convert to visible positions
81 int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
82 yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
83 hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
84 yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
85 int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
86 visYAsSeq = Math.max(visYAsSeq, 0); // -1 if before first visible sequence
88 // update viewport accordingly
89 updateViewportFromTopLeft(visXAsRes, visYAsSeq, hiddenSeqs, hiddenCols);
93 public void adjustViewportFromMouse(int mousex, int mousey,
94 HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
96 // calculate translation in pixel terms:
97 // get mouse location in viewport coords, add translation in viewport
99 // convert back to pixel coords
100 int vpx = Math.round((float) mousex * alwidth / width);
101 int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
103 int vpy = Math.round((float) mousey * alheight / sequencesHeight);
104 int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
106 // update viewport accordingly
107 updateViewportFromTopLeft(visXAsRes, visYAsRes,
113 protected void updateViewportFromTopLeft(int leftx, int topy,
114 HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
116 int visXAsRes = leftx;
117 int visYAsSeq = topy;
118 resetAlignmentDims();
130 if (ranges.isWrappedMode())
132 visYAsSeq = 0; // sorry, no vertical scroll when wrapped
135 // Determine where scrollCol should be, given visXAsRes
137 // get viewport width in residues
138 int vpwidth = ranges.getViewportWidth();
140 // check in case we went off the edge of the alignment
141 int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
142 if (visXAsRes + vpwidth - 1 > visAlignWidth)
144 // went past the end of the alignment, adjust backwards
146 // if last position was before the end of the alignment, need to update
147 if (ranges.getEndRes() < visAlignWidth)
149 visXAsRes = hiddenCols.findColumnPosition(hiddenCols
150 .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
154 visXAsRes = ranges.getStartRes();
158 // Determine where scrollRow should be, given visYAsSeq
160 // get viewport height in sequences
161 int vpheight = ranges.getViewportHeight();
163 // check in case we went off the edge of the alignment
164 int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
166 if (visYAsSeq + vpheight - 1 > visAlignHeight)
168 // went past the end of the alignment, adjust backwards
169 if (ranges.getEndSeq() < visAlignHeight)
171 visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
172 .subtractVisibleRows(vpheight - 1, alheight - 1));
176 visYAsSeq = ranges.getStartSeq();
181 ranges.setStartRes(visXAsRes);
182 ranges.setStartSeq(visYAsSeq);
186 * Update the overview panel box when the associated alignment panel is
194 * viewport position properties
197 public void setBoxPosition(HiddenSequences hiddenSeqs,
198 HiddenColumns hiddenCols)
200 // work with absolute values of startRes and endRes
201 int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
202 int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
204 // work with absolute values of startSeq and endSeq
205 int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
206 int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
208 setBoxPosition(startRes, startSeq, endRes - startRes + 1, endSeq
213 public AlignmentColsCollectionI getColumns(AlignmentI al)
215 return new AllColsCollection(0,
216 ranges.getAbsoluteAlignmentWidth() - 1, al);
220 public AlignmentRowsCollectionI getRows(AlignmentI al)
222 return new AllRowsCollection(0,
223 ranges.getAbsoluteAlignmentHeight() - 1,
228 protected void resetAlignmentDims()
230 alwidth = ranges.getAbsoluteAlignmentWidth();
231 alheight = ranges.getAbsoluteAlignmentHeight();
235 protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
237 int vpx = Math.round((float) mousex * alwidth / width);
238 return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
243 protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
245 int vpy = Math.round((float) mousey * alheight / sequencesHeight);
246 return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
250 public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
251 HiddenColumns hiddenCols)
253 // get alignment position of x and box (can get directly from vpranges) and
254 // calculate difference between the positions
255 int vpx = Math.round((float) x * alwidth / width);
256 int vpy = Math.round((float) y * alheight / sequencesHeight);
258 xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
259 ydiff = ranges.getStartSeq()
260 - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);