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 // listeners include:
147 // jalview.gui.SeqCanvas[,0,0,568x90,layout=java.awt.BorderLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=9,maximumSize=,minimumSize=,preferredSize=]
148 // STARTRES, STARTRESANDSEQ
149 // jalview.gui.IdCanvas[,0,0,112x90,layout=java.awt.BorderLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=9,maximumSize=,minimumSize=,preferredSize=java.awt.Dimension[width=112,height=0]]
150 // jalview.gui.ScalePanel[,0,0,594x17,layout=java.awt.FlowLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=9,maximumSize=,minimumSize=,preferredSize=]
151 // jalview.gui.AnnotationPanel[,0,0,0x162,alignmentX=0.0,alignmentY=0.0,border=,flags=9,maximumSize=,minimumSize=,preferredSize=java.awt.Dimension[width=1,height=162]]
152 // jalview.gui.AlignmentPanel[,0,0,706x133,layout=java.awt.BorderLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=16777225,maximumSize=,minimumSize=,preferredSize=java.awt.Dimension[width=220,height=166]]
153 // jalview.gui.OverviewPanel[,0,0,543x135,layout=java.awt.BorderLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=9,maximumSize=,minimumSize=,preferredSize=java.awt.Dimension[width=543,height=135]]
156 // "STARTRES" is a misnomer here -- really "STARTORENDRES"
157 // note that this could be "no change" if the range is just being expanded
158 changeSupport.firePropertyChange(STARTRES, oldstartres, startRes);
159 if (oldstartres == startRes)
161 // No listener cares about this
162 // "ENDRES" is a misnomer here -- really "ENDONLYRES"
163 // BH 2019.07.27 adds end change check
164 // fire only if only the end is changed
165 changeSupport.firePropertyChange(ENDRES, oldendres, endRes);
170 * Update start and end residue values, adjusting for width constraints if
177 * @return array containing old start and end residue values
179 private int[] updateStartEndRes(int start, int end)
181 int oldstartres = this.startRes;
184 * if not wrapped, don't leave white space at the right margin
186 int lastColumn = getVisibleAlignmentWidth() - 1;
187 if (!wrappedMode && (start > lastColumn))
189 startRes = Math.max(lastColumn, 0);
200 int oldendres = this.endRes;
205 else if (!wrappedMode && (end > lastColumn))
207 endRes = Math.max(lastColumn, 0);
213 return new int[] { oldstartres, oldendres };
217 * Set the first sequence visible in the viewport, maintaining the height. If
218 * the viewport would extend past the last sequence, sets the viewport so it
219 * sits at the bottom of the alignment. Fires a property change event.
224 public void setStartSeq(int seq)
226 int height = getViewportHeight();
227 int startseq = Math.max(seq, getVisibleAlignmentHeight() - height);
228 // BH 2019.07.27 cosmetic only -- was:
229 // if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
231 // startseq = getVisibleAlignmentHeight() - height;
233 setStartEndSeq(startseq, startseq + height - 1);
237 * Set start and end sequences at the same time. The viewport height may
238 * change. This method only fires one event for the two changes, and should be
239 * used in preference to separate calls to setStartSeq and setEndSeq.
246 public void setStartEndSeq(int start, int end)
248 // System.out.println("ViewportRange setStartEndSeq " + start + " " + end);
249 int[] oldvalues = updateStartEndSeq(start, end);
250 int oldstartseq = oldvalues[0];
251 int oldendseq = oldvalues[1];
253 if (oldstartseq == startSeq && oldendseq == endSeq)
255 return; // BH 2019.07.27 standard check for no changes
258 // "STARTSEQ" is a misnomer here -- really "STARTORENDSEQ"
259 changeSupport.firePropertyChange(STARTSEQ, oldstartseq, startSeq);
260 if (oldstartseq == startSeq)
262 // Note that all listeners ignore this - could be removed, or there is a
264 // "ENDSEQ" is a misnomer here -- really "ENDONLYSEQ"
265 // additional fire, only if only the end is changed
266 changeSupport.firePropertyChange(ENDSEQ, oldendseq, endSeq);
271 * Update start and end sequence values, adjusting for height constraints if
278 * @return array containing old start and end sequence values
280 private int[] updateStartEndSeq(int start, int end)
282 int oldstartseq = this.startSeq;
283 int visibleHeight = getVisibleAlignmentHeight();
284 if (start > visibleHeight - 1)
286 startSeq = Math.max(visibleHeight - 1, 0);
297 int oldendseq = this.endSeq;
298 if (end >= visibleHeight)
300 endSeq = Math.max(visibleHeight - 1, 0);
310 return new int[] { oldstartseq, oldendseq };
314 * Set the last sequence visible in the viewport. Fires a property change
318 * sequence position in the range [0, height)
320 public void setEndSeq(int seq)
322 // BH 2018.04.18 added safety for seq < 0; comment about not being >= height
323 setStartEndSeq(Math.max(0, seq + 1 - getViewportHeight()), seq);
327 * Set start residue and start sequence together (fires single event). The
328 * event supplies a pair of old values and a pair of new values: [old start
329 * residue, old start sequence] and [new start residue, new start sequence]
336 public void setStartResAndSeq(int res, int seq)
338 // from Overview only
339 int width = getViewportWidth();
340 int[] oldresvalues = updateStartEndRes(res, res + width - 1);
343 int height = getViewportHeight();
344 if (startseq + height - 1 > getVisibleAlignmentHeight() - 1)
346 startseq = getVisibleAlignmentHeight() - height;
348 int[] oldseqvalues = updateStartEndSeq(startseq, startseq + height - 1);
350 int[] oldvalues = new int[] { oldresvalues[0], oldseqvalues[0] };
351 int[] newvalues = new int[] { startRes, startSeq };
352 changeSupport.firePropertyChange(STARTRESANDSEQ, oldvalues, newvalues);
356 * Get start residue of viewport
358 public int getStartRes()
364 * Get end residue of viewport
366 public int getEndRes()
372 * Get start sequence of viewport
374 public int getStartSeq()
380 * Get end sequence of viewport
382 public int getEndSeq()
388 * Set viewport width in residues, without changing startRes. Use in
389 * preference to calculating endRes from the width, to avoid out by one
390 * errors! Fires a property change event.
395 public void setViewportWidth(int w)
397 setStartEndRes(startRes, startRes + w - 1);
401 * Set viewport height in residues, without changing startSeq. Use in
402 * preference to calculating endSeq from the height, to avoid out by one
403 * errors! Fires a property change event.
406 * height in sequences
408 public void setViewportHeight(int h)
410 setStartEndSeq(startSeq, startSeq + h - 1);
414 * Set viewport horizontal start position and width. Use in preference to
415 * calculating endRes from the width, to avoid out by one errors! Fires a
416 * property change event.
423 public void setViewportStartAndWidth(int start, int w)
432 * if not wrapped, don't leave white space at the right margin
436 if ((w <= getVisibleAlignmentWidth())
437 && (vpstart + w - 1 > getVisibleAlignmentWidth() - 1))
439 vpstart = getVisibleAlignmentWidth() - w;
443 setStartEndRes(vpstart, vpstart + w - 1);
447 * Set viewport vertical start position and height. Use in preference to
448 * calculating endSeq from the height, to avoid out by one errors! Fires a
449 * property change event.
454 * height in sequences
456 public void setViewportStartAndHeight(int start, int h)
460 int visHeight = getVisibleAlignmentHeight();
465 else if (h <= visHeight && vpstart + h > visHeight)
466 // viewport height is less than the full alignment and we are running off
469 vpstart = visHeight - h;
471 // System.out.println("ViewportRanges setviewportStartAndHeight " + vpstart
472 // + " " + start + " " + h + " " + getVisibleAlignmentHeight());
474 setStartEndSeq(vpstart, vpstart + h - 1);
478 * Get width of viewport in residues
480 * @return width of viewport
482 public int getViewportWidth()
484 return (endRes - startRes + 1);
488 * Get height of viewport in residues
490 * @return height of viewport
492 public int getViewportHeight()
494 return (endSeq - startSeq + 1);
498 * Scroll the viewport range vertically. Fires a property change event.
501 * true if scrolling up, false if down
503 * @return true if the scroll is valid
505 public boolean scrollUp(boolean up)
508 * if in unwrapped mode, scroll up or down one sequence row;
509 * if in wrapped mode, scroll by one visible width of columns
523 setStartSeq(startSeq - 1);
534 if (endSeq >= getVisibleAlignmentHeight() - 1)
538 setStartSeq(startSeq + 1);
545 * Scroll the viewport range horizontally. Fires a property change event.
548 * true if scrolling right, false if left
550 * @return true if the scroll is valid
552 public boolean scrollRight(boolean right)
561 setStartRes(startRes - 1);
565 if (endRes >= getVisibleAlignmentWidth() - 1)
570 setStartRes(startRes + 1);
577 * Scroll a wrapped alignment so that the specified residue is in the first
578 * repeat of the wrapped view. Fires a property change event. Answers true if
579 * the startRes changed, else false.
582 * residue position to scroll to NB visible position not absolute
586 public boolean scrollToWrappedVisible(int res)
588 int newStartRes = calcWrappedStartResidue(res);
589 if (newStartRes == startRes)
593 setStartRes(newStartRes);
599 * Calculate wrapped start residue from visible start residue
602 * visible start residue
603 * @return left column of panel res will be located in
605 private int calcWrappedStartResidue(int res)
607 int oldStartRes = startRes;
608 int width = getViewportWidth();
610 boolean up = res < oldStartRes;
611 int widthsToScroll = Math.abs((res - oldStartRes) / width);
617 int residuesToScroll = width * widthsToScroll;
618 int newStartRes = up ? oldStartRes - residuesToScroll : oldStartRes
628 * Scroll so that (x,y) is visible. Fires a property change event.
631 * x position in alignment (absolute position)
633 * y position in alignment (absolute position)
635 public void scrollToVisible(int x, int y)
646 HiddenColumns hidden = al.getHiddenColumns();
647 while (x < hidden.visibleToAbsoluteColumn(startRes))
649 if (!scrollRight(false))
654 while (x > hidden.visibleToAbsoluteColumn(endRes))
656 if (!scrollRight(true))
664 * Set the viewport location so that a position is visible. From
665 * SeqPanel.scrollToVisible(true) only, from AlignFrame keyboard actions
666 * SeqPanel.scrollCursor[Row(VK_S)/Column(VK_C)/RowAndColumn(VK_ENTER,COMMA)/Position(VK_P)]
670 * column to be visible: absolute position in alignment
672 * row to be visible: absolute position in alignment
674 public boolean setViewportLocation(int x, int y)
676 boolean changedLocation = false;
678 // convert the x,y location to visible coordinates
679 int visX = al.getHiddenColumns().absoluteToVisibleColumn(x);
680 int visY = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
682 // if (vis_x,vis_y) is already visible don't do anything
683 if (startRes > visX || visX > endRes
684 || startSeq > visY && visY > endSeq)
686 int[] old = new int[] { startRes, startSeq };
690 int newstartres = calcWrappedStartResidue(visX);
691 setStartRes(newstartres);
692 newresseq = new int[] { startRes, startSeq };
696 // set the viewport x location to contain vis_x
697 int newstartres = visX;
698 int width = getViewportWidth();
699 if (newstartres + width - 1 > getVisibleAlignmentWidth() - 1)
701 newstartres = getVisibleAlignmentWidth() - width;
703 updateStartEndRes(newstartres, newstartres + width - 1);
705 // set the viewport y location to contain vis_y
706 int newstartseq = visY;
707 int height = getViewportHeight();
708 if (newstartseq + height - 1 > getVisibleAlignmentHeight() - 1)
710 newstartseq = getVisibleAlignmentHeight() - height;
712 updateStartEndSeq(newstartseq, newstartseq + height - 1);
714 newresseq = new int[] { startRes, startSeq };
716 changedLocation = true;
717 changeSupport.firePropertyChange(MOVE_VIEWPORT, old, newresseq);
719 return changedLocation;
723 * Adjust sequence position for page up. Fires a property change event.
729 setStartRes(Math.max(0, getStartRes() - getViewportWidth()));
733 setViewportStartAndHeight(startSeq - (endSeq - startSeq),
734 getViewportHeight());
739 * Adjust sequence position for page down. Fires a property change event.
741 public void pageDown()
746 * if height is more than width (i.e. not all sequences fit on screen),
747 * increase page down to height
749 int newStart = getStartRes()
750 + Math.max(getViewportHeight(), getViewportWidth());
753 * don't page down beyond end of alignment, or if not all
754 * sequences fit in the visible height
756 if (newStart < getVisibleAlignmentWidth())
758 setStartRes(newStart);
763 setViewportStartAndHeight(endSeq, getViewportHeight());
767 public void setWrappedMode(boolean wrapped)
769 wrappedMode = wrapped;
772 public boolean isWrappedMode()
778 * Answers the vertical scroll position (0..) to set, given the visible column
779 * that is at top left.
783 * viewport width 40 columns (0-39, 40-79, 80-119...)
784 * column 0 returns scroll position 0
785 * columns 1-40 return scroll position 1
786 * columns 41-80 return scroll position 2
790 * @param topLeftColumn
794 public int getWrappedScrollPosition(final int topLeftColumn)
796 int w = getViewportWidth();
799 * visible whole widths
801 int scroll = topLeftColumn / w;
804 * add 1 for a part width if there is one
806 scroll += topLeftColumn % w > 0 ? 1 : 0;
812 * Answers the maximum wrapped vertical scroll value, given the column
813 * position (0..) to show at top left of the visible region.
815 * @param topLeftColumn
818 public int getWrappedMaxScroll(int topLeftColumn)
820 int scrollPosition = getWrappedScrollPosition(topLeftColumn);
823 * how many more widths could be drawn after this one?
825 int columnsRemaining = getVisibleAlignmentWidth() - topLeftColumn;
826 int width = getViewportWidth();
827 int widthsRemaining = columnsRemaining / width
828 + (columnsRemaining % width > 0 ? 1 : 0) - 1;
829 int maxScroll = scrollPosition + widthsRemaining;