X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=365f8865390807ed2be027df0d42b42dfb197f0d;hb=3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a;hp=fd6652bf415b10c88eac234c70912db13996d735;hpb=f6f774a4fa6885275b9d1902a4c8d470607e3447;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index fd6652b..365f886 100644 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -25,9 +25,11 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.JalviewLite; import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceI; import jalview.structure.StructureSelectionManager; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; import java.awt.BorderLayout; import java.awt.Color; @@ -41,10 +43,11 @@ import java.awt.event.AdjustmentEvent; import java.awt.event.AdjustmentListener; import java.awt.event.ComponentAdapter; import java.awt.event.ComponentEvent; +import java.beans.PropertyChangeEvent; import java.util.List; -public class AlignmentPanel extends Panel implements AdjustmentListener, - AlignmentViewPanel +public class AlignmentPanel extends Panel + implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; @@ -65,23 +68,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, AnnotationLabels alabels; + ViewportRanges vpRanges; + // this value is set false when selection area being dragged boolean fastPaint = true; - public void finalize() - { - alignFrame = null; - av = null; - seqPanel = null; - seqPanelHolder = null; - sequenceHolderPanel = null; - scalePanel = null; - scalePanelHolder = null; - annotationPanel = null; - annotationPanelHolder = null; - annotationSpaceFillerHolder = null; - } - public AlignmentPanel(AlignFrame af, final AlignViewport av) { try @@ -94,6 +85,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, alignFrame = af; this.av = av; + vpRanges = av.getRanges(); seqPanel = new SeqPanel(av, this); idPanel = new IdPanel(av, this); scalePanel = new ScalePanel(av, this); @@ -121,9 +113,29 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, addComponentListener(new ComponentAdapter() { + @Override public void componentResized(ComponentEvent evt) { - setScrollValues(av.getStartRes(), av.getStartSeq()); + // reset the viewport ranges when the alignment panel is resized + // in particular, this initialises the end residue value when Jalview + // is initialised + if (av.getWrapAlignment()) + { + int widthInRes = seqPanel.seqCanvas + .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + vpRanges.setViewportWidth(widthInRes); + } + else + { + int widthInRes = seqPanel.seqCanvas.getWidth() + / av.getCharWidth(); + int heightInSeq = seqPanel.seqCanvas.getHeight() + / av.getCharHeight(); + + vpRanges.setViewportWidth(widthInRes); + vpRanges.setViewportHeight(heightInSeq); + } + // setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); if (getSize().height > 0 && annotationPanelHolder.getSize().height > 0) { @@ -146,6 +158,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, final AlignmentPanel ap = this; av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { + @Override public void propertyChange(java.beans.PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -155,6 +168,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } } }); + av.getRanges().addPropertyChangeListener(this); } @Override @@ -162,15 +176,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { return av; } + public SequenceRenderer getSequenceRenderer() { return seqPanel.seqCanvas.sr; } + @Override public jalview.api.FeatureRenderer getFeatureRenderer() { return seqPanel.seqCanvas.fr; } + @Override public jalview.api.FeatureRenderer cloneFeatureRenderer() { @@ -178,6 +195,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, nfr.transferSettings(seqPanel.seqCanvas.fr); return nfr; } + public void alignmentChanged() { av.alignmentChanged(this); @@ -199,10 +217,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, idPanel.idCanvas.image = null; FontMetrics fm = getFontMetrics(av.getFont()); - scalePanel.setSize(new Dimension(10, av.getCharHeight() - + fm.getDescent())); - idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight() - + fm.getDescent())); + scalePanel.setSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idwidthAdjuster.setSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); av.updateSequenceIdColours(); annotationPanel.image = null; int ap = annotationPanel.adjustPanelHeight(false); @@ -217,11 +235,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, annotationPanel.repaint(); validate(); repaint(); - - if (overviewPanel != null) - { - overviewPanel.updateOverviewImage(); - } } public void setIdWidth(int w, int h) @@ -285,7 +298,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * Highlight the given results on the alignment. * */ - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { scrollToPosition(results); seqPanel.seqCanvas.highlightSearchResults(results); @@ -298,7 +311,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * @param results * @return false if results were not found */ - public boolean scrollToPosition(SearchResults results) + public boolean scrollToPosition(SearchResultsI results) { return scrollToPosition(results, true); } @@ -312,10 +325,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * - when set, the overview will be recalculated (takes longer) * @return false if results were not found */ - public boolean scrollToPosition(SearchResults results, + public boolean scrollToPosition(SearchResultsI results, boolean redrawOverview) { - return scrollToPosition(results, redrawOverview, false); + return scrollToPosition(results, 0, redrawOverview, false); } /** @@ -327,11 +340,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * - when set, the overview will be recalculated (takes longer) * @return false if results were not found */ - public boolean scrollToPosition(SearchResults results, - boolean redrawOverview, boolean centre) + public boolean scrollToPosition(SearchResultsI results, + int verticalOffset, boolean redrawOverview, boolean centre) { // do we need to scroll the panel? - if (results != null && results.getSize() > 0) + if (results != null && results.getCount() > 0) { AlignmentI alignment = av.getAlignment(); int seqIndex = alignment.findIndex(results); @@ -339,14 +352,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { return false; } + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + SequenceI seq = alignment.getSequenceAt(seqIndex); int[] r = results.getResults(seq, 0, alignment.getWidth()); if (r == null) { if (JalviewLite.debug) {// DEBUG - System.out - .println("DEBUG: scroll didn't happen - results not within alignment : " + System.out.println( + "DEBUG: scroll didn't happen - results not within alignment : " + seq.getStart() + "," + seq.getEnd()); } return false; @@ -370,9 +387,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, */ if (centre) { - int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1; + int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 + - 1; start = Math.max(start - offset, 0); - end = Math.min(end + offset, seq.getEnd() - 1); + end = end + offset - 1; + // end = Math.min(end + offset, seq.getEnd() - 1); } if (start < 0) @@ -383,6 +402,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { return false; } + + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); return scrollTo(start, end, seqIndex, false, redrawOverview); } return true; @@ -396,11 +420,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, int start = -1; if (av.hasHiddenColumns()) { - start = av.getColumnSelection().findColumnPosition(ostart); - end = av.getColumnSelection().findColumnPosition(end); + AlignmentI al = av.getAlignment(); + start = al.getHiddenColumns().absoluteToVisibleColumn(ostart); + end = al.getHiddenColumns().absoluteToVisibleColumn(end); if (start == end) { - if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart)) + if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart)) { // don't scroll - position isn't visible return false; @@ -411,6 +436,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { start = ostart; } + if (!av.getWrapAlignment()) { /* @@ -449,59 +475,46 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, // setScrollValues(start, seqIndex); // } // logic copied from jalview.gui.AlignmentPanel: - if ((startv = av.getStartRes()) >= start) - { - /* - * Scroll left to make start of search results visible - */ - setScrollValues(start - 1, seqIndex); - } - else if ((endv = av.getEndRes()) <= end) - { - /* - * Scroll right to make end of search results visible - */ - setScrollValues(startv + 1 + end - endv, seqIndex); - } - else if ((starts = av.getStartSeq()) > seqIndex) - { - /* - * Scroll up to make start of search results visible - */ - setScrollValues(av.getStartRes(), seqIndex); - } - else if ((ends = av.getEndSeq()) <= seqIndex) - { - /* - * Scroll down to make end of search results visible - */ - setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); - } + if ((startv = vpRanges.getStartRes()) >= start) + { + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start - 1, seqIndex); + } + else if ((endv = vpRanges.getEndRes()) <= end) + { /* - * Else results are already visible - no need to scroll + * Scroll right to make end of search results visible */ + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = vpRanges.getStartSeq()) > seqIndex) + { + /* + * Scroll up to make start of search results visible + */ + setScrollValues(vpRanges.getStartRes(), seqIndex); + } + else if ((ends = vpRanges.getEndSeq()) <= seqIndex) + { + /* + * Scroll down to make end of search results visible + */ + setScrollValues(vpRanges.getStartRes(), + starts + seqIndex - ends + 1); + } + /* + * Else results are already visible - no need to scroll + */ } else { - scrollToWrappedVisible(start); - } - if (redrawOverview && overviewPanel != null) - { - overviewPanel.setBoxPosition(); + vpRanges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); - return true; - } - void scrollToWrappedVisible(int res) - { - int cwidth = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); - if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth)) - { - vscroll.setValue(res / cwidth); - av.startRes = vscroll.getValue() * cwidth; - } + paintAlignment(redrawOverview, false); + return true; } public OverviewPanel getOverviewPanel() @@ -534,21 +547,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * automatically adjust annotation panel height for new annotation whilst * ensuring the alignment is still visible. */ + @Override public void adjustAnnotationHeight() { // TODO: display vertical annotation scrollbar if necessary // this is called after loading new annotation onto alignment if (alignFrame.getSize().height == 0) { - System.out - .println("adjustAnnotationHeight frame size zero NEEDS FIXING"); + System.out.println( + "adjustAnnotationHeight frame size zero NEEDS FIXING"); } fontChanged(); validateAnnotationDimensions(true); apvscroll.addNotify(); hscroll.addNotify(); validate(); - paintAlignment(true); + paintAlignment(true, false); } /** @@ -574,8 +588,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, */ if (annotationHeight + alignmentHeight > availableHeight) { - annotationHeight = Math.min(annotationHeight, availableHeight - 2 - * rowHeight); + annotationHeight = Math.min(annotationHeight, + availableHeight - 2 * rowHeight); } } else @@ -592,13 +606,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, annotationPanel.setSize(new Dimension(d.width, annotationHeight)); annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight)); // seqPanelHolder.setSize(d.width, seqandannot - height); - seqPanel.seqCanvas - .setSize(d.width, seqPanel.seqCanvas.getSize().height); + seqPanel.seqCanvas.setSize(d.width, + seqPanel.seqCanvas.getSize().height); Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); - annotationSpaceFillerHolder.setSize(new Dimension(e.width, - annotationHeight)); + annotationSpaceFillerHolder + .setSize(new Dimension(e.width, annotationHeight)); int s = apvscroll.getValue(); if (s > mheight - annotationHeight) @@ -612,8 +626,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, public void setWrapAlignment(boolean wrap) { - av.startSeq = 0; - av.startRes = 0; + vpRanges.setStartEndSeq(0, vpRanges.getVisibleAlignmentHeight()); + vpRanges.setStartRes(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); @@ -644,218 +658,173 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, int vextent = 0; - // return value is true if the scroll is valid - public boolean scrollUp(boolean up) + public void setScrollValues(int xpos, int ypos) { - if (up) + int x = xpos; + int y = ypos; + + if (av.getWrapAlignment()) { - if (vscroll.getValue() < 1) - { - return false; - } - setScrollValues(hscroll.getValue(), vscroll.getValue() - 1); + setScrollingForWrappedPanel(x); } else { - if (vextent + vscroll.getValue() >= av.getAlignment().getHeight()) + int width = av.getAlignment().getVisibleWidth(); + int height = av.getAlignment().getHeight(); + + if (x < 0) { - return false; + x = 0; } - setScrollValues(hscroll.getValue(), vscroll.getValue() + 1); - } - repaint(); - return true; - } + hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth(); + vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight(); - public boolean scrollRight(boolean right) - { - if (!right) - { - if (hscroll.getValue() < 1) + if (hextent > width) { - return false; + hextent = width; } - setScrollValues(hscroll.getValue() - 1, vscroll.getValue()); - } - else - { - if (hextent + hscroll.getValue() >= av.getAlignment().getWidth()) + + if (vextent > height) { - return false; + vextent = height; } - setScrollValues(hscroll.getValue() + 1, vscroll.getValue()); - } - - repaint(); - return true; - } - - public void setScrollValues(int x, int y) - { - int width = av.getAlignment().getWidth(); - int height = av.getAlignment().getHeight(); - - if (av.hasHiddenColumns()) - { - width = av.getColumnSelection().findColumnPosition(width); - } - if (x < 0) - { - x = 0; - } - ; - hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth(); - vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight(); - - if (hextent > width) - { - hextent = width; - } - - if (vextent > height) - { - vextent = height; - } - - if ((hextent + x) > width) - { - System.err.println("hextent was " + hextent + " and x was " + x); - - x = width - hextent; - } - - if ((vextent + y) > height) - { - y = height - vextent; - } + if ((hextent + x) > width) + { + System.err.println("hextent was " + hextent + " and x was " + x); - if (y < 0) - { - y = 0; - } + x = width - hextent; + } - if (x < 0) - { - System.err.println("x was " + x); - x = 0; - } + if ((vextent + y) > height) + { + y = height - vextent; + } - av.setStartSeq(y); + if (y < 0) + { + y = 0; + } - int endSeq = y + vextent; - if (endSeq > av.getAlignment().getHeight()) - { - endSeq = av.getAlignment().getHeight(); - } + if (x < 0) + { + System.err.println("x was " + x); + x = 0; + } - av.setEndSeq(endSeq); - av.setStartRes(x); - av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av - .getCharWidth())) - 1); + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); - hscroll.setValues(x, hextent, 0, width); - vscroll.setValues(y, vextent, 0, height); + // AWT scrollbar does not fire adjustmentValueChanged for setValues + // so also call adjustment code! + adjustHorizontal(x); + adjustVertical(y); - if (overviewPanel != null) - { - overviewPanel.setBoxPosition(); + sendViewPosition(); } - sendViewPosition(); - } + /** + * Respond to adjustment event when horizontal or vertical scrollbar is + * changed + * + * @param evt + * adjustment event encoding whether apvscroll, hscroll or vscroll + * changed + */ + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - int oldX = av.getStartRes(); - int oldY = av.getStartSeq(); - + // Note that this event is NOT fired by the AWT scrollbar when setValues is + // called. Instead manually call adjustHorizontal and adjustVertical + // directly. if (evt == null || evt.getSource() == apvscroll) { annotationPanel.setScrollOffset(apvscroll.getValue(), false); alabels.setScrollOffset(apvscroll.getValue(), false); - // annotationPanel.image=null; - // alabels.image=null; - // alabels.repaint(); - // annotationPanel.repaint(); } if (evt == null || evt.getSource() == hscroll) { int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes(x + seqPanel.seqCanvas.getSize().width - / av.getCharWidth() - 1); + adjustHorizontal(x); } if (evt == null || evt.getSource() == vscroll) { int offy = vscroll.getValue(); - if (av.getWrapAlignment()) - { - int rowSize = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); - av.setStartRes(vscroll.getValue() * rowSize); - av.setEndRes((vscroll.getValue() + 1) * rowSize); - } - else - { - av.setStartSeq(offy); - av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height - / av.getCharHeight()); - } + adjustVertical(offy); } - if (overviewPanel != null) + } + + private void adjustHorizontal(int x) + { + int oldX = vpRanges.getStartRes(); + int oldwidth = vpRanges.getViewportWidth(); + int width = seqPanel.seqCanvas.getWidth() / av.getCharWidth(); + + // if we're scrolling to the position we're already at, stop + // this prevents infinite recursion of events when the scroll/viewport + // ranges values are the same + if ((x == oldX) && (width == oldwidth)) { - overviewPanel.setBoxPosition(); + return; } + vpRanges.setViewportStartAndWidth(x, width); - int scrollX = av.startRes - oldX; - int scrollY = av.startSeq - oldY; - - if (av.getWrapAlignment() || !fastPaint || av.MAC) + if (av.getWrapAlignment() || !fastPaint) { repaint(); } - else + sendViewPosition(); + } + + private void adjustVertical(int newY) + { + if (av.getWrapAlignment()) { - // Make sure we're not trying to draw a panel - // larger than the visible window - if (scrollX > av.endRes - av.startRes) - { - scrollX = av.endRes - av.startRes; - } - else if (scrollX < av.startRes - av.endRes) + /* + * if we're scrolling to the position we're already at, stop + * this prevents infinite recursion of events when the scroll/viewport + * ranges values are the same + */ + int oldX = vpRanges.getStartRes(); + int oldY = vpRanges.getWrappedScrollPosition(oldX); + if (oldY == newY) { - scrollX = av.startRes - av.endRes; + return; } - - idPanel.idCanvas.fastPaint(scrollY); - seqPanel.seqCanvas.fastPaint(scrollX, scrollY); - - scalePanel.repaint(); - if (av.isShowAnnotation()) + if (newY > -1) { - annotationPanel.fastPaint(av.getStartRes() - oldX); + /* + * limit page up/down to one width's worth of positions + */ + int rowSize = vpRanges.getViewportWidth(); + int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; + vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } - sendViewPosition(); - - /* - * If there is one, scroll the (Protein/cDNA) complementary alignment to - * match, unless we are ourselves doing that. - */ - if (isFollowingComplementScroll()) + else { - setFollowingComplementScroll(false); + int height = seqPanel.seqCanvas.getHeight() / av.getCharHeight(); + int oldY = vpRanges.getStartSeq(); + int oldheight = vpRanges.getViewportHeight(); + + // if we're scrolling to the position we're already at, stop + // this prevents infinite recursion of events when the scroll/viewport + // ranges values are the same + if ((newY == oldY) && (height == oldheight)) + { + return; + } + vpRanges.setViewportStartAndHeight(newY, height); } - else + if (av.getWrapAlignment() || !fastPaint) { - AlignmentPanel ap = getComplementPanel(); - av.scrollComplementaryAlignment(ap); + repaint(); } - + sendViewPosition(); } /** @@ -892,21 +861,20 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * @param seqOffset * the number of visible sequences to show above the mapped region */ - protected void scrollToCentre(SearchResults sr, int seqOffset) + protected void scrollToCentre(SearchResultsI sr, int seqOffset) { /* * To avoid jumpy vertical scrolling (if some sequences are gapped or not * mapped), we can make the scroll-to location a sequence above the one * actually mapped. */ - SequenceI mappedTo = sr.getResultSequence(0); + SequenceI mappedTo = sr.getResults().get(0).getSequence(); List seqs = av.getAlignment().getSequences(); /* * This is like AlignmentI.findIndex(seq) but here we are matching the * dataset sequence not the aligned sequence */ - int sequenceIndex = 0; boolean matched = false; for (SequenceI seq : seqs) { @@ -915,35 +883,33 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, matched = true; break; } - sequenceIndex++; } if (!matched) { return; // failsafe, shouldn't happen } - sequenceIndex = Math.max(0, sequenceIndex - seqOffset); - sr.getResults().get(0) - .setSequence(av.getAlignment().getSequenceAt(sequenceIndex)); /* * Scroll to position but centring the target residue. Also set a state flag * to prevent adjustmentValueChanged performing this recursively. */ - setFollowingComplementScroll(true); - scrollToPosition(sr, true, true); + scrollToPosition(sr, seqOffset, true, true); } private void sendViewPosition() { StructureSelectionManager.getStructureSelectionManager(av.applet) - .sendViewPosition(this, av.startRes, av.endRes, av.startSeq, - av.endSeq); + .sendViewPosition(this, vpRanges.getStartRes(), + vpRanges.getEndRes(), vpRanges.getStartSeq(), + vpRanges.getEndSeq()); } /** * Repaint the alignment and annotations, and, optionally, any overview window */ - public void paintAlignment(boolean updateOverview) + @Override + public void paintAlignment(boolean updateOverview, + boolean updateStructures) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); @@ -951,13 +917,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, av.getSortAnnotationsBy()); repaint(); - if (updateOverview) + if (updateStructures) { - // TODO: determine if this paintAlignment changed structure colours jalview.structure.StructureSelectionManager .getStructureSelectionManager(av.applet) .sequenceColoursChanged(this); - + } + if (updateOverview) + { if (overviewPanel != null) { overviewPanel.updateOverviewImage(); @@ -965,11 +932,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { invalidate(); @@ -980,30 +949,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, idPanel.idCanvas.setSize(d.width, canvasHeight); } - if (av.getWrapAlignment()) - { - int maxwidth = av.getAlignment().getWidth(); - - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } - - int canvasWidth = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); - - if (canvasWidth > 0) - { - int max = maxwidth / canvasWidth; - vscroll.setMaximum(1 + max); - vscroll.setUnitIncrement(1); - vscroll.setVisibleAmount(1); - } - } - else - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } + setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq()); seqPanel.seqCanvas.repaint(); idPanel.idCanvas.repaint(); @@ -1019,6 +965,25 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } + /** + * Set vertical scroll bar parameters for wrapped panel + * + * @param topLeftColumn + * the column position at top left (0..) + */ + private void setScrollingForWrappedPanel(int topLeftColumn) + { + int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn); + int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn); + + /* + * a scrollbar's value can be set to at most (maximum-extent) + * so we add extent (1) to the maxScroll value + */ + vscroll.setUnitIncrement(1); + vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1); + } + protected Panel sequenceHolderPanel = new Panel(); protected Scrollbar vscroll = new Scrollbar(); @@ -1043,9 +1008,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, /* * Flag set while scrolling to follow complementary cDNA/protein scroll. When - * true, suppresses invoking the same method recursively. + * false, suppresses invoking the same method recursively. */ - private boolean followingComplementScroll; + private boolean scrollComplementaryPanel = true; private void jbInit() throws Exception { @@ -1154,14 +1119,42 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * * @param b */ - protected void setFollowingComplementScroll(boolean b) + protected void setToScrollComplementPanel(boolean b) { - this.followingComplementScroll = b; + this.scrollComplementaryPanel = b; } - protected boolean isFollowingComplementScroll() + /** + * Get whether to scroll complement panel + * + * @return true if cDNA/protein complement panels should be scrolled + */ + protected boolean isSetToScrollComplementPanel() + { + return this.scrollComplementaryPanel; + } + + @Override + /** + * Property change event fired when a change is made to the viewport ranges + * object associated with this alignment panel's viewport + */ + public void propertyChange(PropertyChangeEvent evt) { - return this.followingComplementScroll; + // update this panel's scroll values based on the new viewport ranges values + int x = vpRanges.getStartRes(); + int y = vpRanges.getStartSeq(); + setScrollValues(x, y); + + // now update any complementary alignment (its viewport ranges object + // is different so does not get automatically updated) + if (isSetToScrollComplementPanel()) + { + setToScrollComplementPanel(false); + av.scrollComplementaryAlignment(getComplementPanel()); + setToScrollComplementPanel(true); + } + } }