import java.util.Hashtable;
import java.util.Vector;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.*;
-public class AlignmentPanel extends Panel implements AdjustmentListener
+public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
{
public AlignViewport av;
idPanel = new IdPanel(av, this);
scalePanel = new ScalePanel(av, this);
idwidthAdjuster = new IdwidthAdjuster(this);
-// annotationScroller = new ScrollPane();
- // annotationScroller.setBackground(Color.white);
annotationPanel = new AnnotationPanel(this);
annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
- // annotationScroller.setPreferredSize(new Dimension(10,80));
-// annotationScroller.add(annotationPanel);
-// annotationScroller.getInsets().set(0,0,0,0);
-
+
sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
alabels = new AnnotationLabels(this);
annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-
+
fontChanged();
setScrollValues(0, 0);
av.updateSequenceIdColours();
annotationPanel.image = null;
int ap = annotationPanel.adjustPanelHeight(false);
- annotationPanel.repaint();
Dimension d = calculateIdWidth();
d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
alabels.setSize(d.width + 4, ap);
idPanel.idCanvas.setSize(d);
hscrollFillerPanel.setSize(d);
-
+
+ validateAnnotationDimensions(false);
+ annotationPanel.repaint();
validate();
repaint();
{
idPanel.idCanvas.setSize(w, h);
idPanelHolder.setSize(w, idPanelHolder.getSize().height);
+ annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height);
alabels.setSize(w, alabels.getSize().height);
validate();
}
return false;
}
SequenceI seq = av.alignment.getSequenceAt(seqIndex);
- int[] r = results.getResults(seq, seq.getStart(), seq.getEnd());
+ int[] r = results.getResults(seq, 0,av.alignment.getWidth());
if (r == null)
{
+ if (av.applet.debug) {// DEBUG
+ System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
+ }
return false;
}
+ if (av.applet.debug) {
+ // DEBUG
+ System.out.println("DEBUG: scroll didn't happen: start=" + r[0]
+ + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
+ + " seq.end=" + seq.getEnd() + " av.getEndRes()="
+ + av.getEndRes() + " hextent=" + hextent);
+ }
int start = r[0];
int end = r[1];
if (start < 0)
{
start = 0;
}
+
}
if (seqIndex > av.alignment.getHeight() - vextent)
{
if (!av.wrapAlignment)
{
annotationSpaceFillerHolder.setVisible(b);
- annotationPanel.setVisible(b);
+ annotationPanelHolder.setVisible(b);
}
validate();
repaint();
}
-
+
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ public void adjustAnnotationHeight()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getSize().height == 0)
+ {
+ System.out.println("NEEDS FIXING");
+ }
+ fontChanged();
+ validateAnnotationDimensions(true);
+ apvscroll.addNotify();
+ hscroll.addNotify();
+ validate();
+ addNotify();
+ repaint();
+ }
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
+ int height = annotationPanel.calcPanelHeight();
+ if (hscroll.isVisible())
+ {
+ height += hscroll.getPreferredSize().height;
+ }
+ int mheight = height;
+ // sets initial preferred height
+ if ((height+40) > getSize().height / 2)
+ {
+ height = getSize().height / 2;
+ }
+ if (!adjustPanelHeight)
+ {
+ // maintain same window layout whilst updating sliders
+ height=seqPanelHolder.getSize().height;
+ }
+ Dimension d=seqPanelHolder.getSize(),e=idPanel.getSize();
+ annotationPanel.setSize(new Dimension(d.width,height));
+ alabels.setSize(e.width,height);
+ annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
+ annotationPanelHolder.setSize(new Dimension(d.width, height));
+ seqPanelHolder.setSize(d.width,d.height-height);
+ int s=apvscroll.getValue();
+ if (s>mheight-height)
+ {
+ s = 0;
+ }
+ apvscroll.setValues(apvscroll.getValue(), height, 0, mheight);
+ annotationPanel.setScrollOffset(apvscroll.getValue());
+ alabels.setScrollOffset(apvscroll.getValue());
+ }
+
public void setWrapAlignment(boolean wrap)
{
av.startSeq = 0;
if (wrap)
{
- annotationPanel.setVisible(false);
+ annotationPanelHolder.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
else if (av.showAnnotation)
{
- annotationPanel.setVisible(true);
+ annotationPanelHolder.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
}
hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
-
+
if (hextent > width)
{
hextent = width;
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
- if (evt == null || evt.getSource()==apvscroll)
+ if (evt == null || evt.getSource() == apvscroll)
{
annotationPanel.setScrollOffset(apvscroll.getValue());
alabels.setScrollOffset(apvscroll.getValue());
- //annotationPanel.image=null;
- //alabels.image=null;
- //alabels.repaint();
- //annotationPanel.repaint();
+ // annotationPanel.image=null;
+ // alabels.image=null;
+ // alabels.repaint();
+ // annotationPanel.repaint();
}
if (evt == null || evt.getSource() == hscroll)
{
invalidate();
Dimension d = idPanel.idCanvas.getSize();
idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
- annotationPanelHolder.setSize(seqPanel.getSize().width, annotationPanel.getSize().height);
- annotationSpaceFillerHolder.setSize(d.width,
- annotationPanel.getSize().height);
-
- alabels.setSize(d.width, annotationPanelHolder.getSize().height);
-
+
if (av.getWrapAlignment())
{
int maxwidth = av.alignment.getWidth();
if (canvasWidth > 0)
{
int max = maxwidth / canvasWidth;
- vscroll.setMaximum(1+max);
+ vscroll.setMaximum(1 + max);
vscroll.setUnitIncrement(1);
vscroll.setVisibleAmount(1);
}
BorderLayout borderLayout2 = new BorderLayout();
Panel annotationPanelHolder = new Panel();
- protected Scrollbar apvscroll=new Scrollbar();
+
+ protected Scrollbar apvscroll = new Scrollbar();
BorderLayout borderLayout12 = new BorderLayout();
// idPanelHolder.setPreferredSize(new Dimension(70, 10));
this.setLayout(borderLayout7);
- // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+ //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
sequenceHolderPanel.setLayout(borderLayout3);
seqPanelHolder.setLayout(borderLayout1);
scalePanelHolder.setBackground(Color.white);
oldrfs.clear();
adjustAnnotationHeight();
}
- /**
- * automatically adjust annotation panel height for new annotation
- * whilst ensuring the alignment is still visible.
- */
- public void adjustAnnotationHeight()
- {
- // TODO: display vertical annotation scrollbar if necessary
- // this is called after loading new annotation onto alignment
- if (alignFrame.getHeight() == 0)
- {
- System.out.println("NEEDS FIXING");
- }
- fontChanged();
- int height = annotationPanel.adjustPanelHeight();
- if (hscroll.isVisible())
- {
- height += hscroll.getPreferredSize().height;
- }
- int mheight=height;
- // sets initial preferred height
- if (height > alignFrame.getHeight() / 2)
- {
- height = alignFrame.getHeight() / 2;
- }
- apvscroll.setValues(apvscroll.getValue(), height, 0, mheight);
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
- apvscroll.addNotify();
- hscroll.addNotify();
-
- annotationPanelHolder.setPreferredSize(new Dimension(annotationPanel
- .getWidth(), height));
- annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(), height));
-
- //annotationScroller.validate();// repaint();
- validate();
- addNotify();
- repaint();
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.alignment;
}
}
git://source.jalview.org / jalview.git / blobdiff