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[jalview.git]
/
src
/
jalview
/
appletgui
/
SequenceRenderer.java
diff --git
a/src/jalview/appletgui/SequenceRenderer.java
b/src/jalview/appletgui/SequenceRenderer.java
index
e786b11
..
04defb7
100755
(executable)
--- a/
src/jalview/appletgui/SequenceRenderer.java
+++ b/
src/jalview/appletgui/SequenceRenderer.java
@@
-76,7
+76,7
@@
public class SequenceRenderer
{
\r
if (cs != null)
\r
{
\r
{
\r
if (cs != null)
\r
{
\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
\r
+ resBoxColour = cs.findColour(seq.getCharAt(i), i);
\r
}
\r
else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
\r
{
\r
}
\r
else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
\r
{
\r
@@
-99,6
+99,9
@@
public class SequenceRenderer
public void drawSequence(SequenceI seq, SequenceGroup[] sg,
\r
int start, int end, int y1)
\r
{
\r
public void drawSequence(SequenceI seq, SequenceGroup[] sg,
\r
int start, int end, int y1)
\r
{
\r
+ if(seq==null)
\r
+ return;
\r
+
\r
allGroups = sg;
\r
\r
drawBoxes(seq, start, end, y1);
\r
allGroups = sg;
\r
\r
drawBoxes(seq, start, end, y1);
\r
@@
-164,6
+167,14
@@
public class SequenceRenderer
\r
public void drawText(SequenceI seq, int start, int end, int y1)
\r
{
\r
\r
public void drawText(SequenceI seq, int start, int end, int y1)
\r
{
\r
+ Font boldFont = null;
\r
+ boolean bold = false;
\r
+ if(av.upperCasebold)
\r
+ {
\r
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
\r
+
\r
+ graphics.setFont(av.getFont());
\r
+ }
\r
\r
y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
\r
\r
\r
y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
\r
\r
@@
-219,6
+230,26
@@
public class SequenceRenderer
}
\r
}
\r
\r
}
\r
}
\r
\r
+ if (av.upperCasebold)
\r
+ {
\r
+ fm = graphics.getFontMetrics();
\r
+ if ('A' <= s && s <= 'Z')
\r
+ {
\r
+ if(!bold)
\r
+ {
\r
+
\r
+ graphics.setFont(boldFont);
\r
+ }
\r
+ bold = true;
\r
+ }
\r
+ else if(bold)
\r
+ {
\r
+ graphics.setFont(av.font);
\r
+ bold = false;
\r
+ }
\r
+
\r
+ }
\r
+
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r
graphics.drawString(String.valueOf(s),
\r
charOffset + av.charWidth * (i - start),
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r
graphics.drawString(String.valueOf(s),
\r
charOffset + av.charWidth * (i - start),
\r
@@
-262,7
+293,7
@@
public class SequenceRenderer
{
\r
if (i < seq.getLength())
\r
{
\r
{
\r
if (i < seq.getLength())
\r
{
\r
- s = seq.getSequence().charAt(i);
\r
+ s = seq.getCharAt(i);
\r
}
\r
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r
}
\r
\r
charOffset = (av.charWidth - fm.charWidth(s)) / 2;
\r