/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SearchResults;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Graphics;
+import java.awt.Insets;
import java.awt.event.AdjustmentEvent;
import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
import java.awt.print.PageFormat;
import java.awt.print.Printable;
import java.awt.print.PrinterException;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
+import java.util.List;
import javax.swing.SwingUtilities;
* @version $Revision: 1.161 $
*/
public class AlignmentPanel extends GAlignmentPanel implements
- AdjustmentListener, Printable, AlignmentViewPanel
+ AdjustmentListener, Printable, AlignmentViewPanel,
+ ViewportListenerI
{
public AlignViewport av;
+ ViewportRanges vpRanges;
+
OverviewPanel overviewPanel;
private SeqPanel seqPanel;
private IdPanel idPanel;
private boolean headless;
+
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
// this value is set false when selection area being dragged
boolean fastPaint = true;
- int hextent = 0;
+ private int hextent = 0;
+
+ private int vextent = 0;
+
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * false, suppresses invoking the same method recursively.
+ */
+ private boolean scrollComplementaryPanel = true;
+
+ private PropertyChangeListener propertyChangeListener;
- int vextent = 0;
+ private CalculationChooser calculationDialog;
/**
* Creates a new AlignmentPanel object.
*
* @param af
- * DOCUMENT ME!
* @param av
- * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
alignFrame = af;
this.av = av;
+ vpRanges = av.getRanges();
setSeqPanel(new SeqPanel(av, this));
setIdPanel(new IdPanel(av, this));
setScrollValues(0, 0);
- setAnnotationVisible(av.isShowAnnotation());
-
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ // 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 = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ });
+
final AlignmentPanel ap = this;
- av.addPropertyChangeListener(new PropertyChangeListener()
+ propertyChangeListener = new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
alignmentChanged();
}
}
- });
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
+
+ av.getRanges().addPropertyChangeListener(this);
fontChanged();
adjustAnnotationHeight();
+ updateLayout();
+ }
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
}
public void alignmentChanged()
{
av.alignmentChanged(this);
+ if (getCalculationDialog() != null)
+ {
+ getCalculationDialog().validateCalcTypes();
+ }
+
alignFrame.updateEditMenuBar();
paintAlignment(true);
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
- + fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+ scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
+ .getCharHeight() + fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
getAnnotationPanel().adjustPanelHeight();
Dimension d = calculateIdWidth();
+
d.setSize(d.width + 4, d.height);
getIdPanel().getIdCanvas().setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(d);
- if (overviewPanel != null)
+ if (this.alignFrame.getSplitViewContainer() != null)
{
- overviewPanel.setBoxPosition();
+ ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
}
repaint();
public Dimension calculateIdWidth()
{
// calculate sensible default width when no preference is available
-
- int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int maxwidth = Math.max(20,
- Math.min(afwidth - 200, 2 * afwidth / 3));
- return calculateIdWidth(maxwidth);
+ Dimension r = null;
+ if (av.getIdWidth() < 0)
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+ r = calculateIdWidth(maxwidth);
+ av.setIdWidth(r.width);
+ }
+ else
+ {
+ r = new Dimension();
+ r.width = av.getIdWidth();
+ r.height = 0;
+ }
+ return r;
}
/**
* Highlight the given results on the alignment.
*
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
scrollToPosition(results);
getSeqPanel().seqCanvas.highlightSearchResults(results);
}
/**
- * scroll the view to show the position of the highlighted region in results
+ * Scroll the view to show the position of the highlighted region in results
* (if any) and redraw the overview
*
* @param results
*/
- public boolean scrollToPosition(SearchResults results)
+ public boolean scrollToPosition(SearchResultsI results)
+ {
+ return scrollToPosition(results, 0, true, false);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param searchResults
+ * @param redrawOverview
+ * @return
+ */
+ public boolean scrollToPosition(SearchResultsI searchResults,
+ boolean redrawOverview)
{
- return scrollToPosition(results, true);
+ return scrollToPosition(searchResults, 0, redrawOverview, false);
}
/**
- * scroll the view to show the position of the highlighted region in results
+ * Scroll the view to show the position of the highlighted region in results
* (if any)
*
* @param results
+ * @param verticalOffset
+ * if greater than zero, allows scrolling to a position below the
+ * first displayed sequence
* @param redrawOverview
* - when set, the overview will be recalculated (takes longer)
+ * @param centre
+ * if true, try to centre the search results horizontally in the view
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results,
- boolean redrawOverview)
+ public boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset, boolean redrawOverview, boolean centre)
{
- int startv, endv, starts, ends, width;
+ int startv, endv, starts, ends;
// TODO: properly locate search results in view when large numbers of hidden
// columns exist before highlighted region
// do we need to scroll the panel?
- // TODO: tons of nullpointereexceptions raised here.
+ // TODO: tons of nullpointerexceptions raised here.
if (results != null && results.getSize() > 0 && av != null
&& av.getAlignment() != null)
{
}
int start = r[0];
int end = r[1];
- // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
- // DEBUG
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+ - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ }
if (start < 0)
{
return false;
}
if (av.hasHiddenColumns())
{
- start = av.getColumnSelection().findColumnPosition(start);
- end = av.getColumnSelection().findColumnPosition(end);
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ start = hidden.findColumnPosition(start);
+ end = hidden.findColumnPosition(end);
if (start == end)
{
- if (!av.getColumnSelection().isVisible(r[0]))
+ if (!hidden.isVisible(r[0]))
{
// don't scroll - position isn't visible
return false;
}
}
}
- if (!av.wrapAlignment)
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+
+ if (!av.getWrapAlignment())
{
- if ((startv = av.getStartRes()) >= start)
+ if ((startv = vpRanges.getStartRes()) >= start)
{
- setScrollValues(start - 1, seqIndex);
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start, seqIndex);
}
- else if ((endv = av.getEndRes()) <= end)
+ else if ((endv = vpRanges.getEndRes()) <= end)
{
- setScrollValues(startv + 1 + end - endv, seqIndex);
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + end - endv, seqIndex);
}
- else if ((starts = av.getStartSeq()) > seqIndex)
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
{
- setScrollValues(av.getStartRes(), seqIndex);
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
}
- else if ((ends = av.getEndSeq()) <= seqIndex)
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
{
- setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ /*
+ * 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);
+ vpRanges.scrollToWrappedVisible(start);
}
}
- if (redrawOverview && overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
+
paintAlignment(redrawOverview);
return true;
}
- void scrollToWrappedVisible(int res)
- {
- int cwidth = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
- {
- vscroll.setValue((res / cwidth));
- av.startRes = vscroll.getValue() * cwidth;
- }
-
- }
-
/**
* DOCUMENT ME!
*
*/
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationScroller.setVisible(b);
* 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
*/
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
- int height = getAnnotationPanel().adjustPanelHeight();
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
- int theight = av.getCharHeight()
- * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
- : av.getAlignment().getHiddenSequences().getSize()));
- float sscaling = (float) (theight / (1.0 * theight + height));
- float ascaling = (float) (height * 1.0 / alignFrame.getHeight());
- int rheight = alignFrame.getHeight() - height - av.getCharHeight();
if (adjustPanelHeight)
{
- // NOTE: this logic is different in the applet. Need a better algorithm to
- // define behaviour
- // try and set height according to alignment
- if (ascaling > 0 && sscaling < 0.5)
- {
- // if the alignment is too big then
- // default is 0.5 split
- height = alignFrame.getHeight() / 2;
- }
- else
+ int rowHeight = av.getCharHeight();
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+ /*
+ * Estimate available height in the AlignFrame for alignment +
+ * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+ * hscroll, status bar (as these are not laid out we can't inspect their
+ * actual heights). Insets gives frame borders.
+ */
+ int stuff = Platform.isAMac() ? 80 : 100;
+ Insets insets = alignFrame.getInsets();
+ int availableHeight = alignFrame.getHeight() - stuff - insets.top
+ - insets.bottom;
+
+ /*
+ * If not enough vertical space, maximize annotation height while keeping
+ * at least two rows of alignment visible
+ */
+ if (annotationHeight + alignmentHeight > availableHeight)
{
- // if space for more than one sequence row left when annotation is fully
- // displayed then set height to annotation height
- // otherwise, leave at least two lines of sequence shown.
- height = (rheight > av.getCharHeight()) ? height
- : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling)));
+ annotationHeight = Math.min(annotationHeight, availableHeight - 2
+ * rowHeight);
}
}
else
{
// maintain same window layout whilst updating sliders
- height = annotationScroller.getSize().height;
+ annotationHeight = annotationScroller.getSize().height;
}
hscroll.addNotify();
annotationScroller.setPreferredSize(new Dimension(annotationScroller
- .getWidth(), height));
+ .getWidth(), annotationHeight));
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(), height));
- annotationScroller.validate();// repaint();
+ annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ annotationScroller.validate();
annotationScroller.addNotify();
}
/**
- * DOCUMENT ME!
+ * update alignment layout for viewport settings
*
* @param wrap
* DOCUMENT ME!
*/
- public void setWrapAlignment(boolean wrap)
+ public void updateLayout()
{
- av.startSeq = 0;
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
+ vpRanges.setStartSeq(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
annotationSpaceFillerHolder.setVisible(true);
}
+ int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+ if (canvasWidth > 0)
+ { // may not yet be laid out
+ if (wrap)
+ {
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(canvasWidth);
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = (canvasWidth / av.getCharWidth()) - 1;
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight() / av
+ .getCharHeight()) - 1;
+
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
+ }
+
idSpaceFillerPanel1.setVisible(!wrap);
repaint();
}
- // return value is true if the scroll is valid
- public boolean scrollUp(boolean up)
+
+ /**
+ * Adjust row/column scrollers to show a visible position in the alignment.
+ *
+ * @param x
+ * visible column to scroll to
+ * @param y
+ * visible row to scroll to
+ *
+ */
+ public void setScrollValues(int xpos, int ypos)
{
- if (up)
+ int x = xpos;
+ int y = ypos;
+
+ if (av == null || av.getAlignment() == null)
{
- if (vscroll.getValue() < 1)
- {
- return false;
- }
+ return;
+ }
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() - 1);
+ if (av.getWrapAlignment())
+ {
+ setScrollingForWrappedPanel(x);
}
else
{
- if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
+
+ if (av.hasHiddenColumns())
{
- return false;
+ // reset the width to exclude hidden columns
+ width = av.getAlignment().getHiddenColumns().findColumnPosition(width);
}
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() + 1);
- }
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
- fastPaint = true;
+ if (hextent > width)
+ {
+ hextent = width;
+ }
- return true;
- }
+ if (vextent > height)
+ {
+ vextent = height;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param right
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean scrollRight(boolean right)
- {
- if (!right)
- {
- if (hscroll.getValue() < 1)
+ if ((hextent + x) > width)
{
- return false;
+ x = width - hextent;
}
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
- }
- else
- {
- if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+ if ((vextent + y) > height)
{
- return false;
+ y = height - vextent;
}
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
- }
+ if (y < 0)
+ {
+ y = 0;
+ }
- fastPaint = true;
+ if (x < 0)
+ {
+ x = 0;
+ }
- return true;
+ // update the scroll values
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
}
/**
- * Adjust row/column scrollers to show a visible position in the alignment.
- *
- * @param x
- * visible column to scroll to DOCUMENT ME!
- * @param y
- * visible row to scroll to
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
*
+ * @param evt
+ * adjustment event encoding whether hscroll or vscroll changed
*/
- public void setScrollValues(int x, int y)
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
{
- // System.err.println("Scroll to "+x+","+y);
- if (av == null || av.getAlignment() == null)
+ if (av.getWrapAlignment())
{
+ adjustScrollingWrapped(evt);
return;
}
- int width = av.getAlignment().getWidth();
- int height = av.getAlignment().getHeight();
-
- if (av.hasHiddenColumns())
- {
- width = av.getColumnSelection().findColumnPosition(width);
- }
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1);
-
- hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth;
- vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight;
-
- if (hextent > width)
- {
- hextent = width;
- }
-
- if (vextent > height)
+ if (evt.getSource() == hscroll)
{
- vextent = height;
- }
+ int oldX = vpRanges.getStartRes();
+ int oldwidth = vpRanges.getViewportWidth();
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
- if ((hextent + x) > width)
- {
- x = width - hextent;
+ // 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))
+ {
+ return;
+ }
+ vpRanges.setViewportStartAndWidth(x, width);
}
-
- if ((vextent + y) > height)
+ else if (evt.getSource() == vscroll)
{
- y = height - vextent;
- }
+ int oldY = vpRanges.getStartSeq();
+ int oldheight = vpRanges.getViewportHeight();
+ int y = vscroll.getValue();
+ int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
- if (y < 0)
- {
- y = 0;
+ // 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))
+ {
+ return;
+ }
+ vpRanges.setViewportStartAndHeight(y, height);
}
-
- if (x < 0)
+ if (!fastPaint)
{
- x = 0;
+ repaint();
}
-
- hscroll.setValues(x, hextent, 0, width);
- vscroll.setValues(y, vextent, 0, height);
}
/**
- * DOCUMENT ME!
+ * Responds to a scroll change by setting the start position of the viewport.
+ * Does
*
* @param evt
- * DOCUMENT ME!
*/
- public void adjustmentValueChanged(AdjustmentEvent evt)
+ protected void adjustScrollingWrapped(AdjustmentEvent evt)
{
-
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
-
if (evt.getSource() == hscroll)
{
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ return; // no horizontal scroll when wrapped
}
-
if (evt.getSource() == vscroll)
{
- int offy = vscroll.getValue();
+ int newY = vscroll.getValue();
- if (av.getWrapAlignment())
+ /*
+ * 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)
{
- if (offy > -1)
- {
- int rowSize = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- av.setStartRes(offy * rowSize);
- av.setEndRes((offy + 1) * rowSize);
- }
- else
- {
- // This is only called if file loaded is a jar file that
- // was wrapped when saved and user has wrap alignment true
- // as preference setting
- SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
- });
- }
+ return;
}
- else
+ if (newY > -1)
{
- av.setStartSeq(offy);
- av.setEndSeq(offy
- + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
+ /*
+ * 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);
}
}
-
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
-
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
-
- if (av.getWrapAlignment() || !fastPaint)
- {
- repaint();
- }
else
{
- // 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)
+ // This is only called if file loaded is a jar file that
+ // was wrapped when saved and user has wrap alignment true
+ // as preference setting
+ SwingUtilities.invokeLater(new Runnable()
{
- scrollX = av.startRes - av.endRes;
- }
-
- if (scrollX != 0 || scrollY != 0)
+ @Override
+ public void run()
{
- getIdPanel().getIdCanvas().fastPaint(scrollY);
- getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
- getScalePanel().repaint();
-
- if (av.isShowAnnotation() && scrollX != 0)
- {
- getAnnotationPanel().fastPaint(scrollX);
+ // When updating scrolling to use ViewportChange events, this code
+ // could not be validated and it is not clear if it is now being
+ // called. Log warning here in case it is called and unforeseen
+ // problems occur
+ Cache.log
+ .warn("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);
}
- }
+ });
}
+ repaint();
}
/**
* Repaint the alignment including the annotations and overview panels (if
* shown).
*/
+ @Override
public void paintAlignment(boolean updateOverview)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment()
- .getAlignmentAnnotation(),
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
av.getSortAnnotationsBy());
repaint();
if (updateOverview)
{
+ // TODO: determine if this paintAlignment changed structure colours
av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
invalidate();
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
validate();
- if (av.getWrapAlignment())
- {
- int maxwidth = av.getAlignment().getWidth();
-
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
+ /*
+ * set scroll bar positions
+ */
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+ }
- int canvasWidth = getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
- if (canvasWidth > 0)
- {
- int max = maxwidth
- / getSeqPanel().seqCanvas
- .getWrappedCanvasWidth(getSeqPanel().seqCanvas
- .getWidth()) + 1;
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
- }
- }
- else
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
+ /**
+ * Set vertical scroll bar position, and number of increments, 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);
}
/**
* @throws PrinterException
* DOCUMENT ME!
*/
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
if (av.getWrapAlignment())
{
- return printWrappedAlignment(pg, pwidth, pheight, pi);
+ return printWrappedAlignment(pwidth, pheight, pi, pg);
}
else
{
- return printUnwrapped(pg, pwidth, pheight, pi);
+ return printUnwrapped(pwidth, pheight, pi, pg, pg);
}
}
* @throws PrinterException
* DOCUMENT ME!
*/
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+ /**
+ * Draws the alignment image, including sequence ids, sequences, and
+ * annotation labels and annotations if shown, on either one or two Graphics
+ * context.
+ *
+ * @param pageWidth
+ * @param pageHeight
+ * @param pi
+ * @param idGraphics
+ * the graphics context for sequence ids and annotation labels
+ * @param alignmentGraphics
+ * the graphics context for sequences and annotations (may or may not
+ * be the same context as idGraphics)
+ * @return
+ * @throws PrinterException
+ */
+ public int printUnwrapped(int pageWidth, int pageHeight, int pi,
+ Graphics idGraphics, Graphics alignmentGraphics)
throws PrinterException
{
- int idWidth = getVisibleIdWidth(false);
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
-
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
+ final int idWidth = getVisibleIdWidth(false);
- // //////////////////////////////////
- // / How many sequences and residues can we fit on a printable page?
- int totalRes = (pwidth - idWidth) / av.getCharWidth();
+ /*
+ * Get the horizontal offset to where we draw the sequences.
+ * This is idWidth if using a single Graphics context, else zero.
+ */
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth;
- int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int charHeight = av.getCharHeight();
+ int scaleHeight = charHeight + fm.getDescent();
- int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
+ idGraphics.setColor(Color.white);
+ idGraphics.fillRect(0, 0, pageWidth, pageHeight);
+ idGraphics.setFont(av.getFont());
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int startRes;
+ /*
+ * How many sequences and residues can we fit on a printable page?
+ */
+ int totalRes = (pageWidth - idWidth) / av.getCharWidth();
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int endRes;
+ int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int startSeq;
+ int alignmentWidth = av.getAlignment().getWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int endSeq;
- startRes = (pi % pagesWide) * totalRes;
- endRes = (startRes + totalRes) - 1;
+ final int startRes = (pi % pagesWide) * totalRes;
+ int endRes = (startRes + totalRes) - 1;
- if (endRes > (av.getAlignment().getWidth() - 1))
+ if (endRes > (alignmentWidth - 1))
{
- endRes = av.getAlignment().getWidth() - 1;
+ endRes = alignmentWidth - 1;
}
- startSeq = (pi / pagesWide) * totalSeq;
- endSeq = startSeq + totalSeq;
+ final int startSeq = (pi / pagesWide) * totalSeq;
+ int endSeq = startSeq + totalSeq;
- if (endSeq > av.getAlignment().getHeight())
+ int alignmentHeight = av.getAlignment().getHeight();
+ if (endSeq > alignmentHeight)
{
- endSeq = av.getAlignment().getHeight();
+ endSeq = alignmentHeight;
}
- int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
- * pheight;
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1)
+ * pageHeight;
if (av.isShowAnnotation())
{
pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
}
- pagesHigh /= pheight;
+ pagesHigh /= pageHeight;
if (pi >= (pagesWide * pagesHigh))
{
return Printable.NO_SUCH_PAGE;
}
-
- // draw Scale
- pg.translate(idWidth, 0);
- getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth,
- scaleHeight);
- pg.translate(-idWidth, scaleHeight);
-
- // //////////////
- // Draw the ids
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight
+ + 3;
+
+ /*
+ * draw the Scale at horizontal offset, then reset to top left (0, 0)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, 0);
+ getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
+ pageWidth - idWidth, scaleHeight);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ /*
+ * Draw the sequence ids, offset for scale height,
+ * then reset to top left (0, 0)
+ */
+ idGraphics.translate(0, scaleHeight);
+ idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont());
Color currentColor = null;
Color currentTextColor = null;
- pg.setFont(getIdPanel().getIdCanvas().getIdfont());
-
SequenceI seq;
for (int i = startSeq; i < endSeq; i++)
{
if ((av.getSelectionGroup() != null)
&& av.getSelectionGroup().getSequences(null).contains(seq))
{
+ /*
+ * gray out ids of sequences in selection group (if any)
+ */
currentColor = Color.gray;
currentTextColor = Color.black;
}
currentTextColor = Color.black;
}
- pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
- av.getCharHeight());
+ idGraphics.setColor(currentColor);
+ idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth,
+ charHeight);
- pg.setColor(currentTextColor);
+ idGraphics.setColor(currentTextColor);
int xPos = 0;
+ String displayId = seq.getDisplayId(av.getShowJVSuffix());
if (av.isRightAlignIds())
{
- fm = pg.getFontMetrics();
+ fm = idGraphics.getFontMetrics();
xPos = idWidth
- - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
+ - fm.stringWidth(displayId)
- 4;
}
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
- (((i - startSeq) * av.charHeight) + av.getCharHeight())
- - (av.getCharHeight() / 5));
+ idGraphics.drawString(displayId, xPos,
+ (((i - startSeq) * charHeight) + charHeight)
+ - (charHeight / 5));
}
-
- pg.setFont(av.getFont());
-
- // draw main sequence panel
- pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
-
- if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
- {
- // draw annotation - need to offset for current scroll position
- int offset = -getAlabels().getScrollOffset();
- pg.translate(0, offset);
- pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
- getAlabels().drawComponent(pg, idWidth);
- pg.translate(idWidth + 3, 0);
+ idGraphics.setFont(av.getFont());
+ idGraphics.translate(0, -scaleHeight);
+
+ /*
+ * draw the sequences, offset for scale height, and id width (if using a
+ * single graphics context), then reset to (0, scale height)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
+ getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes,
+ startSeq, endSeq, 0);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ if (av.isShowAnnotation() && (endSeq == alignmentHeight))
+ {
+ /*
+ * draw annotation labels; drawComponent() translates by
+ * getScrollOffset(), so compensate for that first;
+ * then reset to (0, scale height)
+ */
+ int offset = getAlabels().getScrollOffset();
+ idGraphics.translate(0, -offset);
+ idGraphics.translate(0, alignmentDrawnHeight);
+ getAlabels().drawComponent(idGraphics, idWidth);
+ idGraphics.translate(0, -alignmentDrawnHeight);
+
+ /*
+ * draw the annotations starting at
+ * (idOffset, alignmentHeight) from (0, scaleHeight)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
- pg, -1, startRes, endRes + 1);
- pg.translate(0, -offset);
+ alignmentGraphics, -1, startRes, endRes + 1);
}
return Printable.PAGE_EXISTS;
* @throws PrinterException
* DOCUMENT ME!
*/
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
- int pi) throws PrinterException
+ public int printWrappedAlignment(int pwidth, int pheight, int pi,
+ Graphics pg) throws PrinterException
{
-
int annotationHeight = 0;
AnnotationLabels labels = null;
if (av.isShowAnnotation())
labels = new AnnotationLabels(av);
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int idWidth = getVisibleIdWidth(false);
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
xPos = idWidth - fm.stringWidth(string) - 4;
}
pg.drawString(string, xPos,
- ((i * av.charHeight) + ypos + av.charHeight)
- - (av.charHeight / 5));
+ ((i * av.getCharHeight()) + ypos + av.getCharHeight())
+ - (av.getCharHeight() / 5));
}
if (labels != null)
{
- pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.charHeight));
+ pg.translate(-3,
+ ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(+3, -ypos
- - (av.getAlignment().getHeight() * av.charHeight));
+ pg.translate(
+ +3,
+ -ypos
+ - (av.getAlignment().getHeight() * av
+ .getCharHeight()));
}
ypos += cHeight;
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
- 0);
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ totalHeight, 0);
if ((pi * pheight) < totalHeight)
{
if (onscreen
|| (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
- : calculateIdWidth().width + 4);
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width + 4);
}
return idwidth.intValue() + 4;
}
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
- long progress = System.currentTimeMillis();
+ int boarderBottomOffset = 5;
+ long pSessionId = System.currentTimeMillis();
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file",
- new String[]
- { type.getLabel() }), progress);
+ if (file != null)
+ {
+ alignFrame.setProgressBar(MessageManager.formatMessage(
+ "status.saving_file", new Object[] { type.getLabel() }),
+ pSessionId);
+ }
}
try
{
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight(), file,
- imageTitle);
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file, imageTitle,
+ alignFrame, pSessionId, headless);
+ Graphics graphics = im.getGraphics();
if (av.getWrapAlignment())
{
- if (im.getGraphics() != null)
+ if (graphics != null)
{
- printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ printWrappedAlignment(aDimension.getWidth(),
+ aDimension.getHeight() + boarderBottomOffset, 0,
+ graphics);
im.writeImage();
}
}
else
{
- if (im.getGraphics() != null)
+ if (graphics != null)
{
- printUnwrapped(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
+ 0, graphics, graphics);
im.writeImage();
}
}
+
} catch (OutOfMemoryError err)
{
// Be noisy here.
}
} finally
{
- if (alignFrame != null && !headless)
- {
- alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
- }
+
}
}
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
}
- int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+ int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ getScalePanel().getHeight();
- int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
if (av.getWrapAlignment())
{
{
makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
}
+
public void makePNGImageMap(File imgMapFile, String imageName)
{
- // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
// Gen image map
// ////////////////////////////////
{
int s, sSize = av.getAlignment().getHeight(), res, alwidth = av
.getAlignment().getWidth(), g, gSize, f, fSize, sy;
- StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
out.println("<img src=\"" + imageName
for (s = 0; s < sSize; s++)
{
- sy = s * av.charHeight + scaleHeight;
+ sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
- SequenceFeature[] features = seq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature[] features = seq.getSequenceFeatures();
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
- text = new StringBuffer();
- Object obj = null;
+ StringBuilder text = new StringBuilder();
+ String triplet = null;
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
- + "");
+ triplet = ResidueProperties.nucleotideName.get(seq
+ .getCharAt(res) + "");
}
else
{
- obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ "");
}
- if (obj == null)
+ if (triplet == null)
{
continue;
}
- String triplet = obj.toString();
int alIndex = seq.findPosition(res);
gSize = groups.length;
for (g = 0; g < gSize; g++)
{
if (text.length() < 1)
{
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
}
if (groups[g].getStartRes() < res
&& groups[g].getEndRes() > res)
{
- text.append("<br><em>" + groups[g].getName() + "</em>");
+ text.append("<br><em>").append(groups[g].getName())
+ .append("</em>");
}
}
{
if (text.length() < 1)
{
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + res * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (res + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(alIndex).append(" ").append(triplet);
}
fSize = features.length;
for (f = 0; f < fSize; f++)
if ((features[f].getBegin() <= seq.findPosition(res))
&& (features[f].getEnd() >= seq.findPosition(res)))
{
- if (features[f].getType().equals("disulfide bond"))
+ if (features[f].isContactFeature())
{
if (features[f].getBegin() == seq.findPosition(res)
|| features[f].getEnd() == seq
.findPosition(res))
{
- text.append("<br>disulfide bond "
- + features[f].getBegin() + ":"
- + features[f].getEnd());
+ text.append("<br>").append(features[f].getType())
+ .append(" ").append(features[f].getBegin())
+ .append(":").append(features[f].getEnd());
}
}
else
&& !features[f].getType().equals(
features[f].getDescription()))
{
- text.append(" " + features[f].getDescription());
+ text.append(" ").append(features[f].getDescription());
}
if (features[f].getValue("status") != null)
{
- text.append(" (" + features[f].getValue("status")
- + ")");
+ text.append(" (").append(features[f].getValue("status"))
+ .append(")");
}
}
}
int chunkWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(seqPanelWidth);
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
int annotationHeight = 0;
annotationHeight = getAnnotationPanel().adjustPanelHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
int height = ((maxwidth / chunkWidth) + 1) * cHeight;
PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
+
+ closeChildFrames();
+
+ /*
+ * try to ensure references are nulled
+ */
+ if (annotationPanel != null)
+ {
+ annotationPanel.dispose();
+ }
+
if (av != null)
{
+ av.removePropertyChangeListener(propertyChangeListener);
jalview.structure.StructureSelectionManager ssm = av
.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
- av.setAlignment(null);
+ ssm.removeCommandListener(av);
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
+ av.dispose();
av = null;
}
else
}
/**
+ * Close any open dialogs that would be orphaned when this one is closed
+ */
+ protected void closeChildFrames()
+ {
+ if (calculationDialog != null)
+ {
+ calculationDialog.closeFrame();
+ }
+ }
+
+ /**
* hides or shows dynamic annotation rows based on groups and av state flags
*/
public void updateAnnotation()
@Override
public AlignmentI getAlignment()
{
- return av.getAlignment();
+ return av == null ? null : av.getAlignment();
}
-
@Override
public String getViewName()
{
{
try
{
+ if (alignFrame.getSplitViewContainer() != null)
+ {
+ /*
+ * bring enclosing SplitFrame to front first if there is one
+ */
+ ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
+ }
alignFrame.setSelected(b);
} catch (Exception ex)
{
}
- ;
if (b)
{
return new FeatureRenderer(this);
}
- @Override
+
+ @Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.getFeatureRenderer();
}
- public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
{
fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
}
{
this.idPanel = idPanel;
}
+
+ /**
+ * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+ * The aim is to keep the two alignments 'lined up' on their centre columns.
+ *
+ * @param sr
+ * holds mapped region(s) of this alignment that we are scrolling
+ * 'to'; may be modified for sequence offset by this method
+ * @param verticalOffset
+ * the number of visible sequences to show above the mapped region
+ */
+ public void scrollToCentre(SearchResultsI sr, int verticalOffset)
+ {
+ /*
+ * 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.getResults().get(0).getSequence();
+ List<SequenceI> seqs = av.getAlignment().getSequences();
+
+ /*
+ * This is like AlignmentI.findIndex(seq) but here we are matching the
+ * dataset sequence not the aligned sequence
+ */
+ boolean matched = false;
+ for (SequenceI seq : seqs)
+ {
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ return; // failsafe, shouldn't happen
+ }
+
+ /*
+ * Scroll to position but centring the target residue.
+ */
+ scrollToPosition(sr, verticalOffset, true, true);
+ }
+
+ /**
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setToScrollComplementPanel(boolean b)
+ {
+ 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;
+ }
+
+ /**
+ * Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
+ */
+ protected void refresh(boolean adjustHeight)
+ {
+ validateAnnotationDimensions(adjustHeight);
+ addNotify();
+ if (adjustHeight)
+ {
+ // sort, repaint, update overview
+ paintAlignment(true);
+ }
+ else
+ {
+ // lightweight repaint
+ repaint();
+ }
+ }
+
+ @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)
+ {
+ // 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();
+ setToScrollComplementPanel(true);
+ }
+ }
+
+ /**
+ * Set the reference to the PCA/Tree chooser dialog for this panel. This
+ * reference should be nulled when the dialog is closed.
+ *
+ * @param calculationChooser
+ */
+ public void setCalculationDialog(CalculationChooser calculationChooser)
+ {
+ calculationDialog = calculationChooser;
+ }
+
+ /**
+ * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+ * if none is open)
+ */
+ public CalculationChooser getCalculationDialog()
+ {
+ return calculationDialog;
+ }
}
git://source.jalview.org / jalview.git / blobdiff