/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
((i - starty) * charHeight) + ypos + charHeight
- (charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, ypos);
}
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
for (int i = starty; i < alheight; i++)
{
- SequenceI s = av.alignment.getSequenceAt(i);
+ SequenceI s = av.getAlignment().getSequenceAt(i);
gg.setFont(italic);
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
setHiddenFont(s);
}
for (int i = starty; i < endy; i++)
{
- seq = av.alignment.getSequenceAt(i);
+ seq = av.getAlignment().getSequenceAt(i);
if (seq == null)
{
continue;
}
gg.setFont(italic);
// boolean isrep=false;
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
// isrep =
setHiddenFont(seq);
(((i - starty) * av.charHeight) + av.charHeight)
- (av.charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, 0);
}
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
+ SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
.getSize());
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.getHiddenRepSequences() != null
+ && av.getHiddenRepSequences().containsKey(seq))
{
gg.setFont(bold);
return true;