/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
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.print.PageFormat;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
+import java.util.List;
import javax.swing.SwingUtilities;
private IdPanel idPanel;
private boolean headless;
+
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
int vextent = 0;
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * true, suppresses invoking the same method recursively.
+ */
+ private boolean dontScrollComplement;
+
+ private PropertyChangeListener propertyChangeListener;
+
/**
* Creates a new AlignmentPanel object.
*
* @param af
- * DOCUMENT ME!
* @param av
- * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
setScrollValues(0, 0);
- setAnnotationVisible(av.isShowAnnotation());
-
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
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);
fontChanged();
adjustAnnotationHeight();
+ updateLayout();
+ }
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
}
public void alignmentChanged()
// 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);
{
overviewPanel.setBoxPosition();
}
+ if (this.alignFrame.getSplitViewContainer() != null)
+ {
+ ((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;
}
/**
}
/**
- * 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)
{
- return scrollToPosition(results, true);
+ 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(SearchResults searchResults,
+ boolean redrawOverview)
+ {
+ 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)
+ 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
+ // System.err.println(this.av.viewName + " Seq : " + seqIndex
+ // + " Scroll to " + start + "," + end);
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ }
if (start < 0)
{
return false;
}
}
}
- if (!av.wrapAlignment)
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+
+ // System.out.println("start=" + start + ", end=" + end + ", startv="
+ // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+ // + av.getStartSeq() + ", ends=" + av.getEndSeq());
+ if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
{
- setScrollValues(start - 1, seqIndex);
+ /*
+ * Scroll left to make start of search results visible
+ */
+ // setScrollValues(start - 1, seqIndex); // plus one residue
+ setScrollValues(start, seqIndex);
}
else if ((endv = av.getEndRes()) <= end)
{
- setScrollValues(startv + 1 + end - endv, seqIndex);
+ /*
+ * Scroll right to make end of search results visible
+ */
+ // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
+ setScrollValues(startv + 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);
}
+ /*
+ * Else results are already visible - no need to scroll
+ */
}
else
{
*/
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 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();
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+
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)
+ 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 the alignment is too big then
- // default is 0.5 split
- height = alignFrame.getHeight() / 2;
- }
- else
- {
- // 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()
{
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
av.startSeq = 0;
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
* Adjust row/column scrollers to show a visible position in the alignment.
*
* @param x
- * visible column to scroll to DOCUMENT ME!
+ * visible column to scroll to
* @param y
* visible row to scroll to
*
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll to "+x+","+y);
+ // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
- hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth;
- vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight;
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
if (hextent > width)
{
x = 0;
}
+ /*
+ * each scroll adjustment triggers adjustmentValueChanged, which resets the
+ * 'do not scroll complement' flag; ensure it is the same for both
+ * operations
+ */
+ boolean flag = isDontScrollComplement();
hscroll.setValues(x, hextent, 0, width);
+ setDontScrollComplement(flag);
vscroll.setValues(y, vextent, 0, height);
}
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
-
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
// as preference setting
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
setScrollValues(av.getStartRes(), av.getStartSeq());
}
}
}
+ /*
+ * If there is one, scroll the (Protein/cDNA) complementary alignment to
+ * match, unless we are ourselves doing that.
+ */
+ if (isDontScrollComplement())
+ {
+ setDontScrollComplement(false);
+ }
+ else
+ {
+ av.scrollComplementaryAlignment();
+ }
}
/**
* 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();
+ /*
+ * set scroll bar positions; first suppress this being 'followed' in any
+ * complementary split pane
+ */
+ setDontScrollComplement(true);
+
if (av.getWrapAlignment())
{
int maxwidth = av.getAlignment().getWidth();
* @throws PrinterException
* DOCUMENT ME!
*/
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
{
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
pg.setColor(Color.white);
pg.fillRect(0, 0, pwidth, pheight);
}
pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
av.getCharHeight());
pg.setColor(currentTextColor);
- 4;
}
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
- (((i - startSeq) * av.charHeight) + av.getCharHeight())
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+ (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
// draw main sequence panel
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 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);
+ pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
+ + 3);
getAlabels().drawComponent(pg, idWidth);
pg.translate(idWidth + 3, 0);
getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
int pi) 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);
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)
{
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);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ aDimension.getHeight() + boarderBottomOffset, 0);
im.writeImage();
}
}
im.writeImage();
}
}
+
} catch (OutOfMemoryError err)
{
// Be noisy here.
}
} finally
{
- if (alignFrame != null && !headless)
- {
- alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
- }
+
}
}
maxwidth = av.getColumnSelection().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
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
// Gen image map
// ////////////////////////////////
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.getSequenceFeatures();
for (res = 0; res < alwidth; res++)
{
text = new StringBuffer();
- Object obj = null;
+ 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) + "\""
+ + (idWidth + res * av.getCharWidth()) + "," + sy
+ + "," + (idWidth + (res + 1) * av.getCharWidth())
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
if (text.length() < 1)
{
text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
+ + (idWidth + res * av.getCharWidth()) + "," + sy
+ + "," + (idWidth + (res + 1) * av.getCharWidth())
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
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();
PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
+
+ /*
+ * 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
@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(SearchResults 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.getResultSequence(0);
+ 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 setDontScrollComplement(boolean b)
+ {
+ this.dontScrollComplement = b;
+ }
+
+ protected boolean isDontScrollComplement()
+ {
+ return this.dontScrollComplement;
+ }
}
git://source.jalview.org / jalview.git / blobdiff