fr = new FeatureRenderer(ap);
// scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.alignment.getWidth()
- / (float) av.alignment.getHeight();
+ float initialScale = (float) av.getAlignment().getWidth()
+ / (float) av.getAlignment().getHeight();
- if (av.conservation == null)
+ if (av.getAlignmentConservationAnnotation()== null)
{
graphHeight = 0;
}
- if (av.alignment.getWidth() > av.alignment.getHeight())
+ if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
{
// wider
width = 400;
if (boxX > (width - boxWidth))
{
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
// Try smallest possible box
boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
int col = (int) (boxX / scalew / av.getCharWidth());
int row = (int) (boxY / scaleh / av.getCharHeight());
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
if (!av.getColumnSelection().isVisible(col))
{
col = av.getColumnSelection().findColumnPosition(col);
}
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
+ row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
row);
}
fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
}
- int alwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight()
- + av.alignment.getHiddenSequences().getSize();
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight()
+ + av.getAlignment().getHiddenSequences().getSize();
setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
lastrow = (int) (row * sampleRow);
hiddenRow = false;
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+ seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow);
if (seq == null)
{
- int index = av.alignment.getHiddenSequences()
+ int index = av.getAlignment().getHiddenSequences()
.findIndexWithoutHiddenSeqs(lastrow);
- seq = av.alignment.getSequenceAt(index);
+ seq = av.getAlignment().getSequenceAt(index);
}
else
{
}
else
{
- seq = av.alignment.getSequenceAt(lastrow);
+ seq = av.getAlignment().getSequenceAt(lastrow);
}
if (seq == null)
}
if (hiddenRow
- || (av.hasHiddenColumns && !av.getColumnSelection()
+ || (av.hasHiddenColumns() && !av.getColumnSelection()
.isVisible(lastcol)))
{
color = new Color(color).darker().darker().getRGB();
}
}
- if (av.conservation != null)
+ if (av.getAlignmentConservationAnnotation()!= null)
{
renderer.updateFromAlignViewport(av);
for (col = 0; col < width; col++)
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
- renderer.drawGraph(mg, av.conservation,
+ renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
*/
public void setBoxPosition()
{
- int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
- int fullsizeHeight = (av.alignment.getHeight() + av.alignment
+ int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
+ int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
.getHiddenSequences().getSize()) * av.getCharHeight();
int startRes = av.getStartRes();
int endRes = av.getEndRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
int startSeq = av.startSeq;
int endSeq = av.endSeq;
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
+ startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
startSeq);
- endSeq = av.alignment.getHiddenSequences()
+ endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
}
boxX = (int) (startRes * av.getCharWidth() * scalew);
boxY = (int) (startSeq * av.getCharHeight() * scaleh);
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
}