X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=fd53faf9eb74e918ab01f10176010f83c05f7a7c;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=e84aae0758c77af11c5c011c42b814b71fbe18ee;hpb=04c8f7bff663aa469127e9eed4164e02933782f1;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index e84aae0..fd53faf 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -41,6 +41,7 @@ import jalview.structure.StructureSelectionManager; import jalview.util.Comparison; import jalview.util.ImageMaker; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; @@ -123,6 +124,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { + setName("AligmentPanel"); // setBackground(Color.white); // BH 2019 alignFrame = af; this.av = av; @@ -174,6 +176,7 @@ public class AlignmentPanel extends GAlignmentPanel implements ranges.setViewportWidth(widthInRes); ranges.setViewportHeight(heightInSeq); } + repaint(); } }); @@ -184,10 +187,17 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void propertyChange(PropertyChangeEvent evt) { - if (evt.getPropertyName().equals("alignment")) - { + switch (evt.getPropertyName()) { + case AlignmentViewport.PROPERTY_SEQUENCE: + updateScrollBarsFromRanges(); + if (annotationPanel != null) + annotationPanel.paintImmediately(0, 0, getWidth(), getHeight()); + break; + case AlignmentViewport.PROPERTY_ALIGNMENT: + updateScrollBarsFromRanges(); PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true); alignmentChanged(); + break; } } }; @@ -260,32 +270,37 @@ public class AlignmentPanel extends GAlignmentPanel implements int oldWidth = av.getIdWidth(); // calculate sensible default width when no preference is available - Dimension r = null; + Dimension d = null; if (av.getIdWidth() < 0) { - int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3); - int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth); - r = calculateIdWidth(maxwidth); - av.setIdWidth(r.width); + int maxWidth = getMaxWidth(); + d = calculateIdWidth(maxWidth); + av.setIdWidth(d.width); } else { - r = new Dimension(); - r.width = av.getIdWidth(); - r.height = 0; + d = new Dimension(); + d.width = av.getIdWidth(); + d.height = 0; } /* * fudge: if desired width has changed, update layout * (see also paintComponent - updates layout on a repaint) */ - if (r.width != oldWidth) + if (d.width != oldWidth) { - idPanelHolder.setPreferredSize(r); + idPanelHolder.setPreferredSize(d); validate(); } - return r; + return d; + } + + public int getMaxWidth() + { + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3); + return Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth); } /** @@ -297,9 +312,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ - protected Dimension calculateIdWidth(int maxwidth) + public Dimension calculateIdWidth(int maxwidth) { - Container c = new Container(); + Container c = this;// new Container(); FontMetrics fm = c.getFontMetrics( new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); @@ -308,10 +323,11 @@ public class AlignmentPanel extends GAlignmentPanel implements int i = 0; int idWidth = 0; + boolean withSuffix = av.getShowJVSuffix(); while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) { SequenceI s = al.getSequenceAt(i); - String id = s.getDisplayId(av.getShowJVSuffix()); + String id = s.getDisplayId(withSuffix); int stringWidth = fm.stringWidth(id); idWidth = Math.max(idWidth, stringWidth); i++; @@ -554,17 +570,24 @@ public class AlignmentPanel extends GAlignmentPanel implements { // BH 2018.04.18 comment: addNotify() is not appropriate here. We // are not changing ancestors, and keyboard action listeners do - // not need to be reset. addNotify() is a very expensive operation, + // not need to be reset, and most importantly, we can't be sure we are actually + // connected to resources. + + // addNotify() is a very expensive operation, // requiring a full re-layout of all parents and children. + // Note in JComponent: + // This method is called by the toolkit internally and should // not be called directly by programs. + // I note that addNotify() is called in several areas of Jalview. int annotationHeight = getAnnotationPanel().adjustPanelHeight(); annotationHeight = getAnnotationPanel() .adjustForAlignFrame(adjustPanelHeight, annotationHeight); + // BH no!! hscroll.addNotify(); annotationScroller.setPreferredSize( new Dimension(annotationScroller.getWidth(), annotationHeight)); @@ -572,6 +595,7 @@ public class AlignmentPanel extends GAlignmentPanel implements Dimension e = idPanel.getSize(); alabels.setSize(new Dimension(e.width, annotationHeight)); + annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), annotationHeight)); annotationScroller.validate(); @@ -580,16 +604,13 @@ public class AlignmentPanel extends GAlignmentPanel implements /** * update alignment layout for viewport settings - * - * @param wrap - * DOCUMENT ME! */ public void updateLayout() { + ViewportRanges ranges = av.getRanges(); fontChanged(); setAnnotationVisible(av.isShowAnnotation()); boolean wrap = av.getWrapAlignment(); - ViewportRanges ranges = av.getRanges(); ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); @@ -604,6 +625,22 @@ public class AlignmentPanel extends GAlignmentPanel implements { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); + } + + idSpaceFillerPanel1.setVisible(!wrap); + + /* + * defer dimension calculations if panel not yet added to a Window + * BH 2020.06.09 + */ + if (getTopLevelAncestor() == null) + { + repaint(); + return; + } + + if (!wrap && av.isShowAnnotation()) + { validateAnnotationDimensions(false); } @@ -627,7 +664,10 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - idSpaceFillerPanel1.setVisible(!wrap); + // System.out.println("ap dim = " + getSize()); + // these values will go negative if getSize() returns (0,0): + // System.out.println("seqpan dim = " + getSeqPanel().getSize()); + // System.out.println("seqcan dim = " + getSeqPanel().seqCanvas.getSize()); repaint(); } @@ -641,10 +681,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * visible row to scroll to * */ - public void setScrollValues(int xpos, int ypos) + public void setScrollValues(int x, int y) { - int x = xpos; - int y = ypos; if (av == null || av.getAlignment() == null) { @@ -660,45 +698,23 @@ public class AlignmentPanel extends GAlignmentPanel implements int width = av.getAlignment().getVisibleWidth(); int height = av.getAlignment().getHeight(); - hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); - vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - - if (hextent > width) - { - hextent = width; - } - - if (vextent > height) - { - vextent = height; - } - - if ((hextent + x) > width) - { - x = width - hextent; - } - - if ((vextent + y) > height) - { - y = height - vextent; - } - - if (y < 0) - { - y = 0; - } - - if (x < 0) - { - x = 0; - } - - // update the scroll values - hscroll.setValues(x, hextent, 0, width); - vscroll.setValues(y, vextent, 0, height); + + hextent = Math.min(getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(), width); + vextent = Math.min(getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(), height); + + x = Math.max(0, Math.min(x, width - hextent)); + y = Math.max(0, Math.min(y, height - vextent)); + + updateRanges(x, y); + updateScrollBars(x, y, width, height); } } + private void updateScrollBars(int x, int y, int width, int height) + { + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); + } /** * Respond to adjustment event when horizontal or vertical scrollbar is * changed @@ -715,41 +731,55 @@ public class AlignmentPanel extends GAlignmentPanel implements return; } - ViewportRanges ranges = av.getRanges(); if (evt.getSource() == hscroll) { + if (!updateRanges(hscroll.getValue(), Integer.MIN_VALUE)) + return; + } + else if (evt.getSource() == vscroll) + { + if (!updateRanges(Integer.MIN_VALUE, vscroll.getValue())) + return; + } + repaint(); + } + + private boolean updateRanges(int x, int y) + { + ViewportRanges ranges = av.getRanges(); + boolean isChanged = false; + if (x != Integer.MIN_VALUE) + { int oldX = ranges.getStartRes(); int oldwidth = ranges.getViewportWidth(); - int x = hscroll.getValue(); int width = getSeqPanel().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)) + if (width > 0 && (x != oldX || width != oldwidth)) { - return; + ranges.setViewportStartAndWidth(x, width); + isChanged = true; } - ranges.setViewportStartAndWidth(x, width); } - else if (evt.getSource() == vscroll) + if (y != Integer.MIN_VALUE) { int oldY = ranges.getStartSeq(); int oldheight = ranges.getViewportHeight(); - int y = vscroll.getValue(); int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); // 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 ((y == oldY) && (height == oldheight)) + if (height > 0 && (y != oldY || height != oldheight)) { - return; + ranges.setViewportStartAndHeight(y, height); + isChanged = true; } - ranges.setViewportStartAndHeight(y, height); } - repaint(); + return isChanged; } /** @@ -828,7 +858,6 @@ public class AlignmentPanel extends GAlignmentPanel implements av.isShowAutocalculatedAbove()); sorter.sort(getAlignment().getAlignmentAnnotation(), av.getSortAnnotationsBy()); - repaint(); if (updateStructures) { @@ -837,16 +866,21 @@ public class AlignmentPanel extends GAlignmentPanel implements if (updateOverview) { + alignFrame.repaint(); if (overviewPanel != null) { overviewPanel.updateOverviewImage(); } + } else { + invalidate(); // needed so that the id width adjuster works correctly + repaint(); } } @Override public void paintComponent(Graphics g) { + // BH OUCH! invalidate(); // needed so that the id width adjuster works correctly Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); @@ -860,7 +894,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * though I still think this call should be elsewhere. */ ViewportRanges ranges = av.getRanges(); - setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); + // setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); super.paintComponent(g); } @@ -1067,8 +1101,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, Graphics g) throws PrinterException { - getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(), - getHeight()); + getSeqPanel().seqCanvas.calculateWrappedGeometry(); int annotationHeight = 0; if (av.isShowAnnotation()) { @@ -1542,6 +1575,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { } + if (b) { setAlignFrameView(); @@ -1707,10 +1741,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public void propertyChange(PropertyChangeEvent evt) { // update this panel's scroll values based on the new viewport ranges values - ViewportRanges ranges = av.getRanges(); - int x = ranges.getStartRes(); - int y = ranges.getStartSeq(); - setScrollValues(x, y); + updateScrollBarsFromRanges(); // now update any complementary alignment (its viewport ranges object // is different so does not get automatically updated) @@ -1722,6 +1753,11 @@ public class AlignmentPanel extends GAlignmentPanel implements } } + void updateScrollBarsFromRanges() + { + ViewportRanges ranges = av.getRanges(); + setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); + } /** * Set the reference to the PCA/Tree chooser dialog for this panel. This * reference should be nulled when the dialog is closed. @@ -1742,4 +1778,201 @@ public class AlignmentPanel extends GAlignmentPanel implements return calculationDialog; } + /** + * From appletgui, for JalviewJS JavaScript interface + * + * preliminary - untested + * + * @param ostart + * @param end + * @param seqIndex + * @param scrollToNearest + * @param redrawOverview + * @return + */ + public boolean scrollTo(int ostart, int end, int seqIndex, + boolean scrollToNearest, boolean redrawOverview) + { + int startv, endv, starts, ends;// , width; + + int start = -1; + if (av.hasHiddenColumns()) + { + AlignmentI al = av.getAlignment(); + start = al.getHiddenColumns().absoluteToVisibleColumn(ostart); + end = al.getHiddenColumns().absoluteToVisibleColumn(end); + if (start == end) + { + if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart)) + { + // don't scroll - position isn't visible + return false; + } + } + } + else + { + start = ostart; + } + + ViewportRanges ranges = av.getRanges(); + if (!av.getWrapAlignment()) + { + /* + * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv = + * av.getStartRes()) >= start) { spos=start-1; // seqIn // + * setScrollValues(start - 1, seqIndex); } else if ((endv = + * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end - + * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts = + * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), + * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) { + * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } + */ + + // below is scrolling logic up to Jalview 2.8.2 + // if ((av.getStartRes() > end) + // || (av.getEndRes() < start) + // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + // { + // if (start > av.getAlignment().getWidth() - hextent) + // { + // start = av.getAlignment().getWidth() - hextent; + // if (start < 0) + // { + // start = 0; + // } + // + // } + // if (seqIndex > av.getAlignment().getHeight() - vextent) + // { + // seqIndex = av.getAlignment().getHeight() - vextent; + // if (seqIndex < 0) + // { + // seqIndex = 0; + // } + // } + // setScrollValues(start, seqIndex); + // } + // logic copied from jalview.gui.AlignmentPanel: + if ((startv = ranges.getStartRes()) >= start) + { + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start - 1, seqIndex); + } + else if ((endv = ranges.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = ranges.getStartSeq()) > seqIndex) + { + /* + * Scroll up to make start of search results visible + */ + setScrollValues(ranges.getStartRes(), seqIndex); + } + else if ((ends = ranges.getEndSeq()) <= seqIndex) + { + /* + * Scroll down to make end of search results visible + */ + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1); + } + /* + * Else results are already visible - no need to scroll + */ + } + else + { + ranges.scrollToWrappedVisible(start); + } + + paintAlignment(redrawOverview, false); + return true; + } + + private boolean holdRepaint = false; + + /** + * Called by IdCanvas and SeqPanel to defer painting until after JVP loading. + * + * @return true if holding + */ + public boolean getHoldRepaint() + { + return holdRepaint; + } + + /** + * Called by Jalview2xml while loading + * + * @param tf + */ + public void setHoldRepaint(boolean tf) + { + if (holdRepaint == tf) + { + return; + } + holdRepaint = tf; + if (!tf) + { + repaint(); + } + } + + @Override + public void repaint() + { + if (holdRepaint) + { + // System.out.println("AP repaint holding"); + // Platform.stackTrace(); + return; + } + super.repaint(); + } + + public void selectAllSequences() + { + selectSequences(av.getAlignment().getSequences()); + } + + public void deselectAllSequences() + { + if (av.cursorMode) + { + getSeqPanel().keyboardNo1 = null; + getSeqPanel().keyboardNo2 = null; + } + av.setSelectionGroup(null); + av.getColumnSelection().clear(); + av.setSearchResults(null); + getIdPanel().getIdCanvas().searchResults = null; + av.sendSelection(); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + paintAlignment(false, false); + PaintRefresher.Refresh(this, av.getSequenceSetId()); + } + + public void selectSequences(List seqs) + { + SequenceGroup sg = new SequenceGroup(seqs); + sg.setEndRes(av.getAlignment().getWidth() - 1); + av.setSelectionGroup(sg); + av.isSelectionGroupChanged(true); + av.sendSelection(); + // JAL-2034 - should delegate to + // alignPanel to decide if overview needs + // updating. + paintAlignment(false, false); + PaintRefresher.Refresh(this, av.getSequenceSetId()); + } + }