X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=365f8865390807ed2be027df0d42b42dfb197f0d;hb=3d2750d886f1b6015b2fc3f8671a6cf3e32bb07a;hp=308a550d1117470cd29d1327ff51e73a7e52a74b;hpb=1dff9688cc5ebc8f0a409806c911756a4d80ce52;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 308a550..365f886 100644 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -46,8 +46,8 @@ import java.awt.event.ComponentEvent; import java.beans.PropertyChangeEvent; import java.util.List; -public class AlignmentPanel extends Panel implements AdjustmentListener, - AlignmentViewPanel, ViewportListenerI +public class AlignmentPanel extends Panel + implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; @@ -73,23 +73,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, // this value is set false when selection area being dragged boolean fastPaint = true; - @Override - public void finalize() throws Throwable - { - alignFrame = null; - av = null; - vpRanges = null; - seqPanel = null; - seqPanelHolder = null; - sequenceHolderPanel = null; - scalePanel = null; - scalePanelHolder = null; - annotationPanel = null; - annotationPanelHolder = null; - annotationSpaceFillerHolder = null; - super.finalize(); - } - public AlignmentPanel(AlignFrame af, final AlignViewport av) { try @@ -234,10 +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); @@ -358,11 +341,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * @return false if results were not found */ public boolean scrollToPosition(SearchResultsI results, - int verticalOffset, - boolean redrawOverview, boolean centre) + 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); @@ -380,8 +362,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, { 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; @@ -405,9 +387,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, */ if (centre) { - int offset = (vpRanges.getEndRes() - vpRanges.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) @@ -436,11 +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; @@ -516,8 +501,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, /* * Scroll down to make end of search results visible */ - setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends - + 1); + setScrollValues(vpRanges.getStartRes(), + starts + seqIndex - ends + 1); } /* * Else results are already visible - no need to scroll @@ -528,7 +513,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, vpRanges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); + paintAlignment(redrawOverview, false); return true; } @@ -569,15 +554,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, // 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); } /** @@ -603,8 +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 @@ -621,13 +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) @@ -641,7 +626,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, public void setWrapAlignment(boolean wrap) { - vpRanges.setStartSeq(0); + vpRanges.setStartEndSeq(0, vpRanges.getVisibleAlignmentHeight()); vpRanges.setStartRes(0); scalePanelHolder.setVisible(!wrap); @@ -673,22 +658,20 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, int vextent = 0; - public void setScrollValues(int x, int y) + public void setScrollValues(int xpos, int ypos) { + int x = xpos; + int y = ypos; + if (av.getWrapAlignment()) { setScrollingForWrappedPanel(x); } else { - - int width = av.getAlignment().getWidth(); + int width = av.getAlignment().getVisibleWidth(); int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns()) - { - width = av.getColumnSelection().findColumnPosition(width); - } if (x < 0) { x = 0; @@ -742,6 +725,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } } + /** + * 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) { @@ -789,42 +780,45 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, sendViewPosition(); } - private void adjustVertical(int offy) + private void adjustVertical(int newY) { - int oldX = vpRanges.getStartRes(); - int oldwidth = vpRanges.getViewportWidth(); - int oldY = vpRanges.getStartSeq(); - int oldheight = vpRanges.getViewportHeight(); - if (av.getWrapAlignment()) { - int rowSize = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - - // 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 ((offy * rowSize == oldX) && (oldwidth == rowSize)) + /* + * 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) { return; } - else if (offy > -1) + if (newY > -1) { - vpRanges.setViewportStartAndWidth(offy * rowSize, rowSize); + /* + * 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); } } else { 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 ((offy == oldY) && (height == oldheight)) + if ((newY == oldY) && (height == oldheight)) { return; } - vpRanges.setViewportStartAndHeight(offy, height); + vpRanges.setViewportStartAndHeight(newY, height); } if (av.getWrapAlignment() || !fastPaint) { @@ -914,7 +908,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, * Repaint the alignment and annotations, and, optionally, any overview window */ @Override - public void paintAlignment(boolean updateOverview) + public void paintAlignment(boolean updateOverview, + boolean updateStructures) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), av.isShowAutocalculatedAbove()); @@ -922,13 +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(); @@ -969,34 +965,23 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, } - /* + /** * Set vertical scroll bar parameters for wrapped panel - * @param res - * the residue to scroll to + * + * @param topLeftColumn + * the column position at top left (0..) */ - private void setScrollingForWrappedPanel(int res) + private void setScrollingForWrappedPanel(int topLeftColumn) { - // get the width of the alignment in residues - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } + int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn); + int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn); - // get the width of the canvas in residues - int canvasWidth = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); - if (canvasWidth > 0) - { - // position we want to scroll to is number of canvasWidth's to get there - int current = res / canvasWidth; - - // max scroll position: add one because extent is 1 and scrollbar value - // can only be set to at most max - extent - int max = maxwidth / canvasWidth + 1; - vscroll.setUnitIncrement(1); - vscroll.setValues(current, 1, 0, max); - } + /* + * 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(); @@ -1139,6 +1124,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, this.scrollComplementaryPanel = b; } + /** + * Get whether to scroll complement panel + * + * @return true if cDNA/protein complement panels should be scrolled + */ protected boolean isSetToScrollComplementPanel() { return this.scrollComplementaryPanel; @@ -1146,7 +1136,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener, @Override /** - * Property change event fired when a change is made to the viewport ranges + * 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)