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copy constructor and ascii type change.
[jalview.git]
/
src
/
jalview
/
gui
/
AppJMol.java
diff --git
a/src/jalview/gui/AppJMol.java
b/src/jalview/gui/AppJMol.java
index
14acb14
..
da94e4c
100644
(file)
--- a/
src/jalview/gui/AppJMol.java
+++ b/
src/jalview/gui/AppJMol.java
@@
-195,6
+195,8
@@
public synchronized void addSequence(SequenceI [] seq)
jmolpopup = JmolPopup.newJmolPopup(viewer);
viewer.evalStringQuiet(command);
jmolpopup = JmolPopup.newJmolPopup(viewer);
viewer.evalStringQuiet(command);
+
+ colourBySequence = true;
}
}
@@
-604,12
+606,13
@@
public synchronized void addSequence(SequenceI [] seq)
SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
boolean showFeatures = false;
SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
boolean showFeatures = false;
+
if (ap.av.showSequenceFeatures)
{
showFeatures = true;
if (fr == null)
{
if (ap.av.showSequenceFeatures)
{
showFeatures = true;
if (fr == null)
{
- fr = new jalview.gui.FeatureRenderer(ap.av);
+ fr = new jalview.gui.FeatureRenderer(ap);
}
fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
}
fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
@@
-622,7
+625,8
@@
public synchronized void addSequence(SequenceI [] seq)
{
for (int m = 0; m < mapping.length; m++)
{
{
for (int m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s])
+ if (mapping[m].getSequence() == sequence[s]
+ && ap.av.alignment.findIndex(sequence[s])>-1)
{
for (int r = 0; r < sequence[s].getLength(); r++)
{
{
for (int r = 0; r < sequence[s].getLength(); r++)
{