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.AlignmentI;
24 import jalview.datamodel.HiddenColumns;
27 * Supplies and updates viewport properties relating to position such as: start
28 * and end residues and sequences; ideally will serve hidden columns/rows too.
29 * Intention also to support calculations for positioning, scrolling etc. such
30 * as finding the middle of the viewport, checking for scrolls off screen
32 public class ViewportRanges extends ViewportProperties
34 public static final String STARTRES = "startres";
36 public static final String ENDRES = "endres";
38 public static final String STARTSEQ = "startseq";
40 public static final String ENDSEQ = "endseq";
42 public static final String STARTRESANDSEQ = "startresandseq";
44 public static final String MOVE_VIEWPORT = "move_viewport";
46 private boolean wrappedMode = false;
48 // start residue of viewport
51 // end residue of viewport
54 // start sequence of viewport
57 // end sequence of viewport
61 private AlignmentI al;
67 * the viewport's alignment
69 public ViewportRanges(AlignmentI alignment)
71 // initial values of viewport settings
73 this.endRes = alignment.getWidth() - 1;
75 this.endSeq = alignment.getHeight() - 1;
80 * Get alignment width in cols, including hidden cols
82 public int getAbsoluteAlignmentWidth()
88 * Get alignment height in rows, including hidden rows
90 public int getAbsoluteAlignmentHeight()
92 return al.getHeight() + al.getHiddenSequences().getSize();
96 * Get alignment width in cols, excluding hidden cols
98 public int getVisibleAlignmentWidth()
100 return al.getVisibleWidth();
104 * Get alignment height in rows, excluding hidden rows
106 public int getVisibleAlignmentHeight()
108 return al.getHeight();
112 * Set first residue visible in the viewport, and retain the current width.
113 * Fires a property change event.
118 public void setStartRes(int res)
120 int width = getViewportWidth();
121 setStartEndRes(res, res + width - 1);
125 * Set start and end residues at the same time. This method only fires one
126 * event for the two changes, and should be used in preference to separate
127 * calls to setStartRes and setEndRes.
134 public void setStartEndRes(int start, int end)
136 int[] oldvalues = updateStartEndRes(start, end);
137 int oldstartres = oldvalues[0];
138 int oldendres = oldvalues[1];
140 if (oldstartres == startRes && oldendres == endRes)
142 return; // BH 2019.07.27 standard check for no changes
145 // "STARTRES" is a misnomer here -- really "STARTORENDRES"
146 // note that this could be "no change" if the range is just being expanded
147 changeSupport.firePropertyChange(STARTRES, oldstartres, startRes);
148 if (oldstartres == startRes)
150 // No listener cares about this
151 // "ENDRES" is a misnomer here -- really "ENDONLYRES"
152 // BH 2019.07.27 adds end change check
153 // fire only if only the end is changed
154 changeSupport.firePropertyChange(ENDRES, oldendres, endRes);
159 * Update start and end residue values, adjusting for width constraints if
166 * @return array containing old start and end residue values
168 private int[] updateStartEndRes(int start, int end)
170 int oldstartres = this.startRes;
173 * if not wrapped, don't leave white space at the right margin
175 int lastColumn = getVisibleAlignmentWidth() - 1;
176 if (!wrappedMode && (start > lastColumn))
178 startRes = Math.max(lastColumn, 0);
189 int oldendres = this.endRes;
194 else if (!wrappedMode && (end > lastColumn))
196 endRes = Math.max(lastColumn, 0);
202 return new int[] { oldstartres, oldendres };
206 * Set the first sequence visible in the viewport, maintaining the height. If
207 * the viewport would extend past the last sequence, sets the viewport so it
208 * sits at the bottom of the alignment. Fires a property change event.
213 public void setStartSeq(int seq)
215 int height = getViewportHeight();
216 int startseq = Math.min(seq, getVisibleAlignmentHeight() - height);
217 // BH 2019.07.27 cosmetic only -- was:
218 // if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
220 // startseq = getVisibleAlignmentHeight() - height;
222 setStartEndSeq(startseq, startseq + height - 1);
226 * Set start and end sequences at the same time. The viewport height may
227 * change. This method only fires one event for the two changes, and should be
228 * used in preference to separate calls to setStartSeq and setEndSeq.
235 public void setStartEndSeq(int start, int end)
237 // System.out.println("ViewportRange setStartEndSeq " + start + " " + end);
238 int[] oldvalues = updateStartEndSeq(start, end);
239 int oldstartseq = oldvalues[0];
240 int oldendseq = oldvalues[1];
242 if (oldstartseq == startSeq && oldendseq == endSeq)
244 return; // BH 2019.07.27 standard check for no changes
247 // "STARTSEQ" is a misnomer here -- really "STARTORENDSEQ"
248 changeSupport.firePropertyChange(STARTSEQ, oldstartseq, startSeq);
249 if (oldstartseq == startSeq)
251 // Note that all listeners ignore this - could be removed, or there is a
253 // "ENDSEQ" is a misnomer here -- really "ENDONLYSEQ"
254 // additional fire, only if only the end is changed
255 changeSupport.firePropertyChange(ENDSEQ, oldendseq, endSeq);
260 * Update start and end sequence values, adjusting for height constraints if
267 * @return array containing old start and end sequence values
269 private int[] updateStartEndSeq(int start, int end)
271 int oldstartseq = this.startSeq;
272 int visibleHeight = getVisibleAlignmentHeight();
273 if (start > visibleHeight - 1)
275 startSeq = Math.max(visibleHeight - 1, 0);
286 int oldendseq = this.endSeq;
287 if (end >= visibleHeight)
289 endSeq = Math.max(visibleHeight - 1, 0);
299 return new int[] { oldstartseq, oldendseq };
303 * Set the last sequence visible in the viewport. Fires a property change
307 * sequence position in the range [0, height)
309 public void setEndSeq(int seq)
311 // BH 2018.04.18 added safety for seq < 0; comment about not being >= height
312 setStartEndSeq(Math.max(0, seq + 1 - getViewportHeight()), seq);
316 * Set start residue and start sequence together (fires single event). The
317 * event supplies a pair of old values and a pair of new values: [old start
318 * residue, old start sequence] and [new start residue, new start sequence]
325 public void setStartResAndSeq(int res, int seq)
327 int width = getViewportWidth();
328 int[] oldresvalues = updateStartEndRes(res, res + width - 1);
331 int height = getViewportHeight();
332 if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
334 startseq = getVisibleAlignmentHeight() - height;
336 int[] oldseqvalues = updateStartEndSeq(startseq, startseq + height - 1);
338 int[] oldvalues = new int[] { oldresvalues[0], oldseqvalues[0] };
339 int[] newvalues = new int[] { startRes, startSeq };
340 changeSupport.firePropertyChange(STARTRESANDSEQ, oldvalues, newvalues);
344 * Get start residue of viewport
346 public int getStartRes()
352 * Get end residue of viewport
354 public int getEndRes()
360 * Get start sequence of viewport
362 public int getStartSeq()
368 * Get end sequence of viewport
370 public int getEndSeq()
376 * Set viewport width in residues, without changing startRes. Use in
377 * preference to calculating endRes from the width, to avoid out by one
378 * errors! Fires a property change event.
383 public void setViewportWidth(int w)
385 setStartEndRes(startRes, startRes + w - 1);
389 * Set viewport height in residues, without changing startSeq. Use in
390 * preference to calculating endSeq from the height, to avoid out by one
391 * errors! Fires a property change event.
394 * height in sequences
396 public void setViewportHeight(int h)
398 setStartEndSeq(startSeq, startSeq + h - 1);
402 * Set viewport horizontal start position and width. Use in preference to
403 * calculating endRes from the width, to avoid out by one errors! Fires a
404 * property change event.
411 public void setViewportStartAndWidth(int start, int w)
420 * if not wrapped, don't leave white space at the right margin
424 if ((w <= getVisibleAlignmentWidth())
425 && (vpstart + w - 1 > getVisibleAlignmentWidth() - 1))
427 vpstart = getVisibleAlignmentWidth() - w;
431 setStartEndRes(vpstart, vpstart + w - 1);
435 * Set viewport vertical start position and height. Use in preference to
436 * calculating endSeq from the height, to avoid out by one errors! Fires a
437 * property change event.
442 * height in sequences
444 public void setViewportStartAndHeight(int start, int h)
448 int visHeight = getVisibleAlignmentHeight();
453 else if (h <= visHeight && vpstart + h > visHeight)
454 // viewport height is less than the full alignment and we are running off
457 vpstart = visHeight - h;
460 setStartEndSeq(vpstart, vpstart + h - 1);
464 * Get width of viewport in residues
466 * @return width of viewport
468 public int getViewportWidth()
470 return (endRes - startRes + 1);
474 * Get height of viewport in residues
476 * @return height of viewport
478 public int getViewportHeight()
480 return (endSeq - startSeq + 1);
484 * Scroll the viewport range vertically. Fires a property change event.
487 * true if scrolling up, false if down
489 * @return true if the scroll is valid
491 public boolean scrollUp(boolean up)
494 * if in unwrapped mode, scroll up or down one sequence row;
495 * if in wrapped mode, scroll by one visible width of columns
509 setStartSeq(startSeq - 1);
520 if (endSeq >= getVisibleAlignmentHeight() - 1)
524 setStartSeq(startSeq + 1);
531 * Scroll the viewport range horizontally. Fires a property change event.
534 * true if scrolling right, false if left
536 * @return true if the scroll is valid
538 public boolean scrollRight(boolean right)
547 setStartRes(startRes - 1);
551 if (endRes >= getVisibleAlignmentWidth() - 1)
556 setStartRes(startRes + 1);
563 * Scroll a wrapped alignment so that the specified residue is in the first
564 * repeat of the wrapped view. Fires a property change event. Answers true if
565 * the startRes changed, else false.
568 * residue position to scroll to NB visible position not absolute
572 public boolean scrollToWrappedVisible(int res)
574 int newStartRes = calcWrappedStartResidue(res);
575 if (newStartRes == startRes)
579 setStartRes(newStartRes);
585 * Calculate wrapped start residue from visible start residue
588 * visible start residue
589 * @return left column of panel res will be located in
591 private int calcWrappedStartResidue(int res)
593 int oldStartRes = startRes;
594 int width = getViewportWidth();
596 boolean up = res < oldStartRes;
597 int widthsToScroll = Math.abs((res - oldStartRes) / width);
603 int residuesToScroll = width * widthsToScroll;
604 int newStartRes = up ? oldStartRes - residuesToScroll : oldStartRes
614 * Scroll so that (x,y) is visible. Fires a property change event.
617 * x position in alignment (absolute position)
619 * y position in alignment (absolute position)
621 public void scrollToVisible(int x, int y)
632 HiddenColumns hidden = al.getHiddenColumns();
633 while (x < hidden.visibleToAbsoluteColumn(startRes))
635 if (!scrollRight(false))
640 while (x > hidden.visibleToAbsoluteColumn(endRes))
642 if (!scrollRight(true))
650 * Set the viewport location so that a position is visible
653 * column to be visible: absolute position in alignment
655 * row to be visible: absolute position in alignment
657 public boolean setViewportLocation(int x, int y)
659 boolean changedLocation = false;
661 // convert the x,y location to visible coordinates
662 int visX = al.getHiddenColumns().absoluteToVisibleColumn(x);
663 int visY = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
665 // if (vis_x,vis_y) is already visible don't do anything
666 if (startRes > visX || visX > endRes
667 || startSeq > visY && visY > endSeq)
669 int[] old = new int[] { startRes, startSeq };
673 int newstartres = calcWrappedStartResidue(visX);
674 setStartRes(newstartres);
675 newresseq = new int[] { startRes, startSeq };
679 // set the viewport x location to contain vis_x
680 int newstartres = visX;
681 int width = getViewportWidth();
682 if (newstartres + width - 1 > getVisibleAlignmentWidth() - 1)
684 newstartres = getVisibleAlignmentWidth() - width;
686 updateStartEndRes(newstartres, newstartres + width - 1);
688 // set the viewport y location to contain vis_y
689 int newstartseq = visY;
690 int height = getViewportHeight();
691 if (newstartseq + height - 1 > getVisibleAlignmentHeight() - 1)
693 newstartseq = getVisibleAlignmentHeight() - height;
695 updateStartEndSeq(newstartseq, newstartseq + height - 1);
697 newresseq = new int[] { startRes, startSeq };
699 changedLocation = true;
700 changeSupport.firePropertyChange(MOVE_VIEWPORT, old, newresseq);
702 return changedLocation;
706 * Adjust sequence position for page up. Fires a property change event.
712 setStartRes(Math.max(0, getStartRes() - getViewportWidth()));
716 setViewportStartAndHeight(startSeq - (endSeq - startSeq),
717 getViewportHeight());
722 * Adjust sequence position for page down. Fires a property change event.
724 public void pageDown()
729 * if height is more than width (i.e. not all sequences fit on screen),
730 * increase page down to height
732 int newStart = getStartRes()
733 + Math.max(getViewportHeight(), getViewportWidth());
736 * don't page down beyond end of alignment, or if not all
737 * sequences fit in the visible height
739 if (newStart < getVisibleAlignmentWidth())
741 setStartRes(newStart);
746 setViewportStartAndHeight(endSeq, getViewportHeight());
750 public void setWrappedMode(boolean wrapped)
752 wrappedMode = wrapped;
755 public boolean isWrappedMode()
761 * Answers the vertical scroll position (0..) to set, given the visible column
762 * that is at top left.
766 * viewport width 40 columns (0-39, 40-79, 80-119...)
767 * column 0 returns scroll position 0
768 * columns 1-40 return scroll position 1
769 * columns 41-80 return scroll position 2
773 * @param topLeftColumn
777 public int getWrappedScrollPosition(final int topLeftColumn)
779 int w = getViewportWidth();
782 * visible whole widths
784 int scroll = topLeftColumn / w;
787 * add 1 for a part width if there is one
789 scroll += topLeftColumn % w > 0 ? 1 : 0;
795 * Answers the maximum wrapped vertical scroll value, given the column
796 * position (0..) to show at top left of the visible region.
798 * @param topLeftColumn
801 public int getWrappedMaxScroll(int topLeftColumn)
803 int scrollPosition = getWrappedScrollPosition(topLeftColumn);
806 * how many more widths could be drawn after this one?
808 int columnsRemaining = getVisibleAlignmentWidth() - topLeftColumn;
809 int width = getViewportWidth();
810 int widthsRemaining = columnsRemaining / width
811 + (columnsRemaining % width > 0 ? 1 : 0) - 1;
812 int maxScroll = scrollPosition + widthsRemaining;
818 public String toString()
820 return "[ViewportRange startRes=" + startRes + " endRes=" + endRes
821 + " startSeq=" + startSeq + " endSeq=" + endSeq + "]";