From 0d3cf98a79df1eb920f71b3093afb150b046f9eb Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 12 Sep 2017 10:48:32 +0100 Subject: [PATCH] JAL-2727 ensure ViewportRanges (and gapcounts) are nulled when viewport is closed --- src/jalview/gui/AlignFrame.java | 25 ++++----- src/jalview/gui/AlignmentPanel.java | 77 ++++++++++++++------------ src/jalview/viewmodel/AlignmentViewport.java | 4 +- 3 files changed, 57 insertions(+), 49 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 13b715e..1ae733e 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -163,8 +163,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; - ViewportRanges vpRanges; - public AlignViewControllerI avc; List alignPanels = new ArrayList<>(); @@ -336,7 +334,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } - vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -654,9 +651,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + ViewportRanges ranges = viewport.getRanges(); + alignPanel.getSeqPanel().seqCanvas.cursorX = ranges .getStartRes(); - alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + alignPanel.getSeqPanel().seqCanvas.cursorY = ranges .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); @@ -689,10 +687,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - vpRanges.pageUp(); + viewport.getRanges().pageUp(); break; case KeyEvent.VK_PAGE_DOWN: - vpRanges.pageDown(); + viewport.getRanges().pageDown(); break; } } @@ -2147,7 +2145,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - vpRanges.setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2548,7 +2546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - vpRanges.setStartRes(0); + viewport.getRanges().setStartRes(0); } else { @@ -2613,13 +2611,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + ViewportRanges ranges = viewport.getRanges(); + int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); + ranges.setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -2652,12 +2651,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + int startRes = seq.findPosition(viewport.getRanges().getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); + viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 76368ed..9b74007 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -76,8 +76,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { public AlignViewport av; - ViewportRanges vpRanges; - OverviewPanel overviewPanel; private SeqPanel seqPanel; @@ -124,7 +122,6 @@ public class AlignmentPanel extends GAlignmentPanel implements { alignFrame = af; this.av = av; - vpRanges = av.getRanges(); setSeqPanel(new SeqPanel(av, this)); setIdPanel(new IdPanel(av, this)); @@ -156,11 +153,12 @@ public class AlignmentPanel extends GAlignmentPanel implements // reset the viewport ranges when the alignment panel is resized // in particular, this initialises the end residue value when Jalview // is initialised + ViewportRanges ranges = av.getRanges(); if (av.getWrapAlignment()) { int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( getSeqPanel().seqCanvas.getWidth()); - vpRanges.setViewportWidth(widthInRes); + ranges.setViewportWidth(widthInRes); } else { @@ -169,8 +167,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int heightInSeq = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - vpRanges.setViewportWidth(widthInRes); - vpRanges.setViewportHeight(heightInSeq); + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); } } @@ -384,6 +382,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; + ViewportRanges ranges = av.getRanges(); if (results == null || results.isEmpty() || av == null || av.getAlignment() == null) @@ -411,7 +410,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ if (centre) { - int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1; + int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1; start = Math.max(start - offset, 0); end = end + offset - 1; } @@ -447,33 +446,33 @@ public class AlignmentPanel extends GAlignmentPanel implements if (!av.getWrapAlignment()) { - if ((startv = vpRanges.getStartRes()) >= start) + if ((startv = ranges.getStartRes()) >= start) { /* * Scroll left to make start of search results visible */ setScrollValues(start, seqIndex); } - else if ((endv = vpRanges.getEndRes()) <= end) + else if ((endv = ranges.getEndRes()) <= end) { /* * Scroll right to make end of search results visible */ setScrollValues(startv + end - endv, seqIndex); } - else if ((starts = vpRanges.getStartSeq()) > seqIndex) + else if ((starts = ranges.getStartSeq()) > seqIndex) { /* * Scroll up to make start of search results visible */ - setScrollValues(vpRanges.getStartRes(), seqIndex); + setScrollValues(ranges.getStartRes(), seqIndex); } - else if ((ends = vpRanges.getEndSeq()) <= seqIndex) + else if ((ends = ranges.getEndSeq()) <= seqIndex) { /* * Scroll down to make end of search results visible */ - setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1); } /* @@ -483,7 +482,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - scrollNeeded = vpRanges.scrollToWrappedVisible(start); + scrollNeeded = ranges.scrollToWrappedVisible(start); } paintAlignment(redrawOverview); @@ -610,7 +609,8 @@ public class AlignmentPanel extends GAlignmentPanel implements fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - vpRanges.setStartSeq(0); + ViewportRanges ranges = av.getRanges(); + ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -633,7 +633,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int widthInRes = getSeqPanel().seqCanvas .getWrappedCanvasWidth(canvasWidth); - vpRanges.setViewportWidth(widthInRes); + ranges.setViewportWidth(widthInRes); } else { @@ -641,8 +641,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()) - 1; - vpRanges.setViewportWidth(widthInRes); - vpRanges.setViewportHeight(heightInSeq); + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); } } @@ -741,10 +741,12 @@ public class AlignmentPanel extends GAlignmentPanel implements return; } + ViewportRanges ranges = av.getRanges(); + if (evt.getSource() == hscroll) { - int oldX = vpRanges.getStartRes(); - int oldwidth = vpRanges.getViewportWidth(); + int oldX = ranges.getStartRes(); + int oldwidth = ranges.getViewportWidth(); int x = hscroll.getValue(); int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); @@ -755,12 +757,12 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - vpRanges.setViewportStartAndWidth(x, width); + ranges.setViewportStartAndWidth(x, width); } else if (evt.getSource() == vscroll) { - int oldY = vpRanges.getStartSeq(); - int oldheight = vpRanges.getViewportHeight(); + int oldY = ranges.getStartSeq(); + int oldheight = ranges.getViewportHeight(); int y = vscroll.getValue(); int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); @@ -771,7 +773,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; } - vpRanges.setViewportStartAndHeight(y, height); + ranges.setViewportStartAndHeight(y, height); } if (!fastPaint) { @@ -791,6 +793,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { return; // no horizontal scroll when wrapped } + final ViewportRanges ranges = av.getRanges(); + if (evt.getSource() == vscroll) { int newY = vscroll.getValue(); @@ -800,8 +804,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * this prevents infinite recursion of events when the scroll/viewport * ranges values are the same */ - int oldX = vpRanges.getStartRes(); - int oldY = vpRanges.getWrappedScrollPosition(oldX); + int oldX = ranges.getStartRes(); + int oldY = ranges.getWrappedScrollPosition(oldX); if (oldY == newY) { return; @@ -811,9 +815,9 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * limit page up/down to one width's worth of positions */ - int rowSize = vpRanges.getViewportWidth(); + int rowSize = ranges.getViewportWidth(); int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; - vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize); + ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } else @@ -834,8 +838,8 @@ public class AlignmentPanel extends GAlignmentPanel implements "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); // scroll to start of panel - vpRanges.setStartRes(0); - vpRanges.setStartSeq(0); + ranges.setStartRes(0); + ranges.setStartSeq(0); } }); } @@ -886,7 +890,8 @@ public class AlignmentPanel extends GAlignmentPanel implements /* * set scroll bar positions */ - setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); + ViewportRanges ranges = av.getRanges(); + setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); } /** @@ -898,8 +903,9 @@ public class AlignmentPanel extends GAlignmentPanel implements */ private void setScrollingForWrappedPanel(int topLeftColumn) { - int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn); - int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn); + ViewportRanges ranges = av.getRanges(); + int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn); + int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn); /* * a scrollbar's value can be set to at most (maximum-extent) @@ -1888,8 +1894,9 @@ public class AlignmentPanel extends GAlignmentPanel implements public void propertyChange(PropertyChangeEvent evt) { // update this panel's scroll values based on the new viewport ranges values - int x = vpRanges.getStartRes(); - int y = vpRanges.getStartSeq(); + ViewportRanges ranges = av.getRanges(); + int x = ranges.getStartRes(); + int y = ranges.getStartSeq(); setScrollValues(x, y); // now update any complementary alignment (its viewport ranges object diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 3702cd0..a66855e 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -80,7 +80,7 @@ import java.util.Map; public abstract class AlignmentViewport implements AlignViewportI, CommandListener, VamsasSource { - final protected ViewportRanges ranges; + protected ViewportRanges ranges; protected ViewStyleI viewStyle = new ViewStyle(); @@ -949,10 +949,12 @@ public abstract class AlignmentViewport groupConservation = null; hconsensus = null; hcomplementConsensus = null; + gapcounts = null; // colour scheme may hold reference to consensus residueShading = null; // TODO remove listeners from changeSupport? changeSupport = null; + ranges = null; setAlignment(null); } -- 1.7.10.2