/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.util.Hashtable;
import java.util.Vector;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.*;
+import jalview.structure.StructureSelectionManager;
-public class AlignmentPanel extends Panel implements AdjustmentListener
+public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
{
public AlignViewport av;
// this value is set false when selection area being dragged
boolean fastPaint = true;
-
+
+ public void finalize() {
+ alignFrame=null;
+ av=null;
+ seqPanel=null;
+ seqPanelHolder=null;
+ sequenceHolderPanel=null;
+ scalePanel=null;
+ scalePanelHolder=null;
+ annotationPanel=null;
+ annotationPanelHolder=null;
+ annotationSpaceFillerHolder=null;
+ }
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
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);
public void componentResized(ComponentEvent evt)
{
setScrollValues(av.getStartRes(), av.getStartSeq());
+ if (getSize().height>0 && annotationPanelHolder.getSize().height>0) {
+ validateAnnotationDimensions(false);
+ }
repaint();
}
+
});
Dimension d = calculateIdWidth();
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();
}
public boolean scrollToPosition(SearchResults results,
boolean redrawOverview)
{
+
// do we need to scroll the panel?
if (results != null && results.getSize() > 0)
{
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: 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)
{
return false;
}
- if (av.hasHiddenColumns)
+ return scrollTo(start, end, seqIndex, false, redrawOverview);
+ }
+ return true;
+ }
+ 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)
+ {
+ start = av.getColumnSelection().findColumnPosition(ostart);
+ end = av.getColumnSelection().findColumnPosition(end);
+ if (start == end)
{
- start = av.getColumnSelection().findColumnPosition(start);
- end = av.getColumnSelection().findColumnPosition(end);
- if (start == end)
+ if (!scrollToNearest && !av.colSel.isVisible(ostart))
{
- if (!av.colSel.isVisible(r[0]))
- {
- // don't scroll - position isn't visible
- return false;
- }
+ // don't scroll - position isn't visible
+ return false;
}
}
- if (!av.wrapAlignment)
- {
+ }
+ else
+ {
+ start = ostart;
+ }
+ if (!av.wrapAlignment)
+ {
+ /*
+ 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);
+ }
+
+ /* */
if ((av.getStartRes() > end)
|| (av.getEndRes() < start)
|| ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
{
start = 0;
}
+
}
if (seqIndex > av.alignment.getHeight() - vextent)
{
seqIndex = 0;
}
}
+ // System.out.println("trying to scroll to: "+start+" "+seqIndex);
setScrollValues(start, seqIndex);
- }
+ }/**/
}
else
{
scrollToWrappedVisible(start);
}
- }
if (redrawOverview && overviewPanel != null)
{
overviewPanel.setBoxPosition();
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();
+ paintAlignment(true);
+ }
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
+ boolean modified=false;
+ int height = annotationPanel.calcPanelHeight();
+ int minsize=0;
+ if (hscroll.isVisible())
+ {
+ height += (minsize=hscroll.getPreferredSize().height);
+ }
+ if (apvscroll.isVisible()) {
+ minsize+=apvscroll.getPreferredSize().height;
+ }
+ int mheight = height;
+ Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize();
+ int seqandannot=d.height-scalePanelHolder.getSize().height;
+ // sets initial preferred height
+ if ((height+40) > seqandannot / 2)
+ {
+ height = seqandannot / 2;
+ }
+ if (!adjustPanelHeight)
+ {
+ // maintain same window layout whilst updating sliders
+ height=annotationPanelHolder.getSize().height;
+ }
+
+ if (seqandannot-height<5)
+ {
+ height = seqandannot;
+ }
+ annotationPanel.setSize(new Dimension(d.width,height));
+ alabels.setSize(new Dimension(e.width,height));
+ annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
+ annotationPanelHolder.setSize(new Dimension(d.width, height));
+ seqPanelHolder.setSize(d.width,seqandannot-height);
+ seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ int s=apvscroll.getValue();
+ if (s>mheight-height)
+ {
+ s = 0;
+ }
+ apvscroll.setValues(s, 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);
}
{
width = av.getColumnSelection().findColumnPosition(width);
}
-
- av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+ if (x<0) { x = 0; };
hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
-
+
if (hextent > width)
{
hextent = width;
if ((hextent + x) > width)
{
+ System.err.println("hextent was "+hextent+" and x was "+x);
+
x = width - hextent;
}
if (x < 0)
{
+ System.err.println("x was "+x);
x = 0;
}
}
av.setEndSeq(endSeq);
+ av.setStartRes(x);
+ av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+
hscroll.setValues(x, hextent, 0, width);
vscroll.setValues(y, vextent, 0, height);
{
overviewPanel.setBoxPosition();
}
+ sendViewPosition();
+
}
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)
{
annotationPanel.fastPaint(av.getStartRes() - oldX);
}
}
+ sendViewPosition();
}
+ private void sendViewPosition()
+ {
+ StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq);
+ }
public void paintAlignment(boolean updateOverview)
{
if (updateOverview)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sequenceColoursChanged(this);
+ .getStructureSelectionManager(av.applet).sequenceColoursChanged(this);
if (overviewPanel != null)
{
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.getSize().height == 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.setSize(new Dimension(annotationPanel
- .getSize().width, height));
-
- annotationSpaceFillerHolder.setSize(new Dimension(
- annotationSpaceFillerHolder.getSize().width
- , height));
-
- //annotationScroller.validate();// repaint();
- validate();
- addNotify();
- repaint();
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.alignment;
+ }
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(av.applet);
}
}
git://source.jalview.org / jalview.git / blobdiff