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)
85 // Convert x value to residue position
88 // need to determine where scrollCol should be, given x
89 // to do this also need to know width of viewport, and some hidden column
92 // convert x to residues - this is an absolute position
93 int xAsRes = Math.round((float) x * alwidth / width);
95 // get viewport width in residues
96 int vpwidth = ranges.getViewportWidth();
98 // get where x should be when accounting for hidden cols
99 // if x is in a hidden col region, shift to left - but we still need
101 // so convert back after getting visible region position
102 int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
104 // check in case we went off the edge of the alignment
105 int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
106 if (visXAsRes + vpwidth - 1 > visAlignWidth)
108 // went past the end of the alignment, adjust backwards
110 // if last position was before the end of the alignment, need to update
111 if (ranges.getEndRes() < visAlignWidth)
113 visXAsRes = hiddenCols.findColumnPosition(hiddenCols
114 .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
118 visXAsRes = ranges.getStartRes();
123 // Convert y value to sequence position
126 // convert y to residues
127 int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
129 // get viewport height in sequences
130 int vpheight = ranges.getViewportHeight();
132 // get where y should be when accounting for hidden rows
133 // if y is in a hidden row region, shift up - but we still need absolute
135 // so convert back after getting visible region position
136 yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
137 .findIndexWithoutHiddenSeqs(yAsSeq));
139 // check in case we went off the edge of the alignment
140 int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
141 int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
142 if (visYAsSeq + vpheight - 1 > visAlignHeight)
144 // went past the end of the alignment, adjust backwards
145 if (ranges.getEndSeq() < visAlignHeight)
147 visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
148 .subtractVisibleRows(vpheight - 1, alheight - 1));
152 visYAsSeq = ranges.getStartSeq();
157 ranges.setStartRes(visXAsRes);
158 ranges.setStartSeq(visYAsSeq);
163 * Update the overview panel box when the associated alignment panel is
171 * viewport position properties
174 public void setBoxPosition(HiddenSequences hiddenSeqs,
175 HiddenColumns hiddenCols)
177 // work with absolute values of startRes and endRes
178 int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
179 int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
181 // work with absolute values of startSeq and endSeq
182 int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
183 int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
185 setBoxPosition(startRes, startSeq, endRes - startRes + 1, endSeq
190 public AlignmentColsCollectionI getColumns(AlignmentI al)
192 return new AllColsCollection(0,
193 ranges.getAbsoluteAlignmentWidth() - 1, al);
197 public AlignmentRowsCollectionI getRows(AlignmentI al)
199 return new AllRowsCollection(0,
200 ranges.getAbsoluteAlignmentHeight() - 1,
205 protected void resetAlignmentDims()
207 alwidth = ranges.getAbsoluteAlignmentWidth();
208 alheight = ranges.getAbsoluteAlignmentHeight();