git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Loads PDB files from jar file, new views can open PDB file
[jalview.git]
/
src
/
jalview
/
gui
/
AlignmentPanel.java
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
4b759fd
..
1574d03
100755
(executable)
--- a/
src/jalview/gui/AlignmentPanel.java
+++ b/
src/jalview/gui/AlignmentPanel.java
@@
-123,6
+123,8
@@
public class AlignmentPanel extends GAlignmentPanel
if (overviewPanel != null)
\r
overviewPanel.updateOverviewImage();
\r
\r
if (overviewPanel != null)
\r
overviewPanel.updateOverviewImage();
\r
\r
+ alignFrame.updateEditMenuBar();
\r
+
\r
repaint();
\r
}
\r
\r
repaint();
\r
}
\r
\r
@@
-712,18
+714,19
@@
public class AlignmentPanel extends GAlignmentPanel
pg.setFont(new Font(av.getFont().getName(),
\r
Font.ITALIC,
\r
av.getFont().getSize()));
\r
pg.setFont(new Font(av.getFont().getName(),
\r
Font.ITALIC,
\r
av.getFont().getSize()));
\r
+ SequenceI seq;
\r
for (int i = startSeq; i < endSeq; i++)
\r
{
\r
for (int i = startSeq; i < endSeq; i++)
\r
{
\r
+ seq = av.getAlignment().getSequenceAt(i);
\r
if ( (av.getSelectionGroup() != null) &&
\r
if ( (av.getSelectionGroup() != null) &&
\r
- av.getSelectionGroup().getSequences(false).contains(
\r
- av.getAlignment().getSequenceAt(i)))
\r
+ av.getSelectionGroup().getSequences(false).contains(seq))
\r
{
\r
currentColor = Color.gray;
\r
currentTextColor = Color.black;
\r
}
\r
else
\r
{
\r
{
\r
currentColor = Color.gray;
\r
currentTextColor = Color.black;
\r
}
\r
else
\r
{
\r
- currentColor = av.getAlignment().getSequenceAt(i).getColor();
\r
+ currentColor = av.getSequenceColour(seq);
\r
currentTextColor = Color.black;
\r
}
\r
\r
currentTextColor = Color.black;
\r
}
\r
\r
@@
-733,10
+736,17
@@
public class AlignmentPanel extends GAlignmentPanel
\r
pg.setColor(currentTextColor);
\r
\r
\r
pg.setColor(currentTextColor);
\r
\r
- String string = av.getAlignment().getSequenceAt(i).getDisplayId
\r
- ( av.getShowJVSuffix());
\r
+ int xPos = 0;
\r
+ if (av.rightAlignIds)
\r
+ {
\r
+ fm = pg.getFontMetrics();
\r
+ xPos = idWidth - fm.stringWidth(
\r
+ seq.getDisplayId(av.getShowJVSuffix())
\r
+ ) - 4;
\r
+ }
\r
\r
\r
- pg.drawString(string, 0,
\r
+ pg.drawString(seq.getDisplayId( av.getShowJVSuffix()),
\r
+ xPos,
\r
( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
\r
(av.getCharHeight() / 5));
\r
}
\r
( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -
\r
(av.getCharHeight() / 5));
\r
}
\r
@@
-827,8
+837,13
@@
public class AlignmentPanel extends GAlignmentPanel
{
\r
SequenceI s = av.alignment.getSequenceAt(i);
\r
String string = s.getDisplayId( av.getShowJVSuffix());
\r
{
\r
SequenceI s = av.alignment.getSequenceAt(i);
\r
String string = s.getDisplayId( av.getShowJVSuffix());
\r
-
\r
- pg.drawString(string, 0,
\r
+ int xPos = 0;
\r
+ if (av.rightAlignIds)
\r
+ {
\r
+ FontMetrics fm = getFontMetrics(italic);
\r
+ xPos = idWidth - fm.stringWidth( string ) - 4;
\r
+ }
\r
+ pg.drawString(string, xPos,
\r
( (i * av.charHeight) + ypos + av.charHeight) -
\r
(av.charHeight / 5));
\r
}
\r
( (i * av.charHeight) + ypos + av.charHeight) -
\r
(av.charHeight / 5));
\r
}
\r