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JAL-1136 JAL-811 JAL-812 store/recover autocalc alignment annotation based on calcId...
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
4c042b3
..
7fb7f0b
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-3367,7
+3367,16
@@
public class Jalview2XML
);
}
}
);
}
}
-
+ if (view.getCalcIdParam()!=null)
+ {
+ for (CalcIdParam calcIdParam:view.getCalcIdParam())
+ {
+ if (recoverCalcIdParam(calcIdParam, af.viewport)) {
+ } else {
+ warn("Couldn't recover parameters for "+calcIdParam.getCalcId());
+ }
+ }
+ }
af.setMenusFromViewport(af.viewport);
// TODO: we don't need to do this if the viewport is aready visible.
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
af.setMenusFromViewport(af.viewport);
// TODO: we don't need to do this if the viewport is aready visible.
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
@@
-3397,10
+3406,13
@@
public class Jalview2XML
}
for (JvAnnotRow auan : autoAlan)
{
}
for (JvAnnotRow auan : autoAlan)
{
- visan.put(auan.template.label, auan);
+ visan.put(auan.template.label+(auan.template.getCalcId()==null ? "" : "\t"+auan.template.getCalcId()), auan);
}
int hSize = al.getAlignmentAnnotation().length;
ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
}
int hSize = al.getAlignmentAnnotation().length;
ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ // work through any autoCalculated annotation already on the view
+ // removing it if it should be placed in a different location on the
+ // annotation panel.
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
@@
-3408,10
+3420,15
@@
public class Jalview2XML
if (jalan.autoCalculated)
{
JvAnnotRow valan = visan.get(jalan.label);
if (jalan.autoCalculated)
{
JvAnnotRow valan = visan.get(jalan.label);
+ if (jalan.getCalcId()!=null)
+ {
+ valan = visan.get(jalan.label+ "\t"+jalan.getCalcId());
+ }
+
if (valan != null)
{
// delete the auto calculated row from the alignment
if (valan != null)
{
// delete the auto calculated row from the alignment
- al.deleteAnnotation(al.getAlignmentAnnotation()[h], false);
+ al.deleteAnnotation(jalan, false);
hSize--;
h--;
if (valan != nullAnnot)
hSize--;
h--;
if (valan != nullAnnot)