if (av.hasHiddenRows())
{
- row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
}
ap.setScrollValues(col, row);
int row, col, sameRow = 0, sameCol = 0;
jalview.datamodel.SequenceI seq;
boolean hiddenRow = false;
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (row = 0; row <= sequencesHeight; row++)
{
if ((int) (row * sampleRow) == lastrow)
sameRow = 1;
}
- if (av.getAlignmentConservationAnnotation()!= null)
+ if (av.getAlignmentConservationAnnotation() != null)
{
for (col = 0; col < width; col++)
{
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
- ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
+ ap.annotationPanel.renderer.drawGraph(mg,
+ av.getAlignmentConservationAnnotation(),
+ av.getAlignmentConservationAnnotation().annotations,
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
{
int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
- .getHiddenSequences().getSize()) * av.getCharHeight();
+ .getHiddenSequences().getSize())
+ * av.getCharHeight();
int startRes = av.getStartRes();
int endRes = av.getEndRes();
if (av.hasHiddenRows())
{
- startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);