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javadoc
[jalview.git]
/
src
/
jalview
/
gui
/
FeatureRenderer.java
diff --git
a/src/jalview/gui/FeatureRenderer.java
b/src/jalview/gui/FeatureRenderer.java
index
b584d89
..
12876ed
100755
(executable)
--- a/
src/jalview/gui/FeatureRenderer.java
+++ b/
src/jalview/gui/FeatureRenderer.java
@@
-212,7
+212,7
@@
public class FeatureRenderer
{
\r
type = renderOrder[renderIndex];
\r
\r
{
\r
type = renderOrder[renderIndex];
\r
\r
- if(!av.featuresDisplayed.containsKey(type))
\r
+ if(type==null || !av.featuresDisplayed.containsKey(type))
\r
continue;
\r
\r
// loop through all features in sequence to find
\r
continue;
\r
\r
// loop through all features in sequence to find
\r
@@
-309,7
+309,7
@@
public class FeatureRenderer
int pady = (y1 + av.charHeight) - av.charHeight / 5;
\r
for (i = fstart; i <= fend; i++)
\r
{
\r
int pady = (y1 + av.charHeight) - av.charHeight / 5;
\r
for (i = fstart; i <= fend; i++)
\r
{
\r
- s = seq.getSequence().charAt(i);
\r
+ s = seq.getCharAt(i);
\r
\r
if (jalview.util.Comparison.isGap(s))
\r
{
\r
\r
if (jalview.util.Comparison.isGap(s))
\r
{
\r
@@
-438,6
+438,8
@@
public class FeatureRenderer
final JTextArea description = new JTextArea(3,25);
\r
final JSpinner start = new JSpinner();
\r
final JSpinner end = new JSpinner();
\r
final JTextArea description = new JTextArea(3,25);
\r
final JSpinner start = new JSpinner();
\r
final JSpinner end = new JSpinner();
\r
+ start.setPreferredSize(new Dimension(80,20));
\r
+ end.setPreferredSize(new Dimension(80,20));
\r
final JPanel colour = new JPanel();
\r
colour.setBorder(BorderFactory.createEtchedBorder());
\r
colour.setMaximumSize(new Dimension(40,10));
\r
final JPanel colour = new JPanel();
\r
colour.setBorder(BorderFactory.createEtchedBorder());
\r
colour.setMaximumSize(new Dimension(40,10));
\r
@@
-477,9
+479,9
@@
public class FeatureRenderer
bigPanel.add(panel, BorderLayout.SOUTH);
\r
\r
panel = new JPanel();
\r
bigPanel.add(panel, BorderLayout.SOUTH);
\r
\r
panel = new JPanel();
\r
- panel.add(new JLabel(" Start: ", JLabel.RIGHT));
\r
+ panel.add(new JLabel(" Start:", JLabel.RIGHT));
\r
panel.add(start);
\r
panel.add(start);
\r
- panel.add(new JLabel(" End: ", JLabel.RIGHT));
\r
+ panel.add(new JLabel(" End:", JLabel.RIGHT));
\r
panel.add(end);
\r
bigPanel.add(panel, BorderLayout.CENTER);
\r
}
\r
panel.add(end);
\r
bigPanel.add(panel, BorderLayout.CENTER);
\r
}
\r
@@
-529,12
+531,10
@@
public class FeatureRenderer
if (getColour(lastFeatureAdded) != null)
\r
{
\r
colour.setBackground(getColour(lastFeatureAdded));
\r
if (getColour(lastFeatureAdded) != null)
\r
{
\r
colour.setBackground(getColour(lastFeatureAdded));
\r
- colour.setForeground(getColour(lastFeatureAdded));
\r
}
\r
else
\r
{
\r
colour.setBackground(new Color(60, 160, 115));
\r
}
\r
else
\r
{
\r
colour.setBackground(new Color(60, 160, 115));
\r
- colour.setForeground(new Color(60, 160, 115));
\r
}
\r
\r
}
\r
}
\r
\r
}
\r
@@
-566,8
+566,6
@@
public class FeatureRenderer
end.setValue(new Integer(features[index].getEnd()));
\r
colour.setBackground(
\r
getColour(name.getSelectedItem().toString()));
\r
end.setValue(new Integer(features[index].getEnd()));
\r
colour.setBackground(
\r
getColour(name.getSelectedItem().toString()));
\r
- colour.setForeground(
\r
- getColour(name.getSelectedItem().toString()));
\r
\r
SearchResults highlight = new SearchResults();
\r
highlight.addResult(sequences[0],
\r
\r
SearchResults highlight = new SearchResults();
\r
highlight.addResult(sequences[0],
\r
@@
-577,6
+575,13
@@
public class FeatureRenderer
ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
\r
\r
}
\r
ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
\r
\r
}
\r
+ Color col = getColour(name.getSelectedItem().toString());
\r
+ if (col == null)
\r
+ col = new
\r
+ jalview.schemes.UserColourScheme()
\r
+ .createColourFromName(name.getSelectedItem().toString());
\r
+
\r
+ colour.setBackground(col);
\r
}
\r
});
\r
\r
}
\r
});
\r
\r
@@
-607,6
+612,9
@@
public class FeatureRenderer
&& name.getSelectedItem() != null
\r
&& source.getSelectedItem() != null)
\r
{
\r
&& name.getSelectedItem() != null
\r
&& source.getSelectedItem() != null)
\r
{
\r
+ //This ensures that the last sequence
\r
+ //is refreshed and new features are rendered
\r
+ lastSeq=null;
\r
lastFeatureAdded = name.getSelectedItem().toString();
\r
lastFeatureGroupAdded = source.getSelectedItem().toString();
\r
lastDescriptionAdded = description.getText().replaceAll("\n", " ");
\r
lastFeatureAdded = name.getSelectedItem().toString();
\r
lastFeatureGroupAdded = source.getSelectedItem().toString();
\r
lastDescriptionAdded = description.getText().replaceAll("\n", " ");
\r