import jalview.analysis.AnnotationSorter;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.SequenceRenderer;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import java.awt.event.AdjustmentListener;
import java.awt.event.ComponentAdapter;
import java.awt.event.ComponentEvent;
+import java.awt.image.BufferedImage;
import java.awt.print.PageFormat;
import java.awt.print.Printable;
import java.awt.print.PrinterException;
import javax.swing.SwingUtilities;
/**
- * DOCUMENT ME!
+ * The main panel of an AlignFrame, containing holders for the IdPanel,
+ * SeqPanel, AnnotationLabels (a JPanel), and AnnotationPanel.
+ *
+ * Additional holders contain an IdPanelWidthAdjuster space above the idPanel,
+ * AnnotationScroller (JScrollPane for AnnotationPanel), and vertical and
+ * horizontal scrollbars.
+ *
+ *
*
* @author $author$
* @version $Revision: 1.161 $
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
-// setBackground(Color.white); // BH 2019
+ setBackground(Color.white); // BH 2019
+ setOpaque(true);
alignFrame = af;
this.av = av;
setSeqPanel(new SeqPanel(av, this));
annotationScroller.setViewportView(getAnnotationPanel());
annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
-
+ if (!av.isShowAnnotation())
+ {
+ annotationScroller.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
*/
public void updateLayout()
{
- fontChanged();
+ fontChanged(); // fires repaint
setAnnotationVisible(av.isShowAnnotation());
boolean wrap = av.getWrapAlignment();
ViewportRanges ranges = av.getRanges();
}
if (updateOverview)
{
-
if (overviewPanel != null)
{
overviewPanel.updateOverviewImage();
@Override
public void paintComponent(Graphics g)
{
+
invalidate(); // needed so that the id width adjuster works correctly
Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
* 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);
}
return calculationDialog;
}
+ @Override
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return seqPanel.seqCanvas.getSequenceRenderer();
+ }
+
+ 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;
+ }
+
+ @Override
+ public void overviewDone(BufferedImage miniMe)
+ {
+ overviewPanel.canvas.finalizeDraw(miniMe);
+ }
+
+
+ private boolean holdRepaint = false;
+
+ /**
+ * Checked by SeqCanvas when painting
+ *
+ * @return
+ */
+ public boolean getHoldRepaint()
+ {
+ return holdRepaint;
+ }
+
+ /**
+ * Called specifically by Jalview2xml when loading a JPV file
+ *
+ * @param b
+ */
+ public void setHoldRepaint(boolean b)
+ {
+ if (holdRepaint == b)
+ {
+ return;
+ }
+ holdRepaint = b;
+ if (!b)
+ {
+ 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.setSelectionGroup(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<SequenceI> 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());
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff