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JAL-1942 JAL-1479 DBRefFetcher refactor
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
eda4a1c
..
a41e519
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-845,6
+845,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
+ @Override
public void setMenusForViewport()
{
setMenusFromViewport(viewport);
public void setMenusForViewport()
{
setMenusFromViewport(viewport);
@@
-1401,6
+1402,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.makeEPS(f);
}
alignPanel.makeEPS(f);
}
+ @Override
public void createSVG(File f)
{
alignPanel.makeSVG(f);
public void createSVG(File f)
{
alignPanel.makeSVG(f);
@@
-1574,6
+1576,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
}
+ @Override
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
public void addHistoryItem(CommandI command)
{
if (command.getSize() > 0)
@@
-2415,7
+2418,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
}
-
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-3498,6
+3500,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param cs
* DOCUMENT ME!
*/
* @param cs
* DOCUMENT ME!
*/
+ @Override
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
public void changeColour(ColourSchemeI cs)
{
// TODO: pull up to controller method
@@
-3517,6
+3520,11
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
cs, "Background"));
}
+ if (cs instanceof TCoffeeColourScheme)
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ }
}
viewport.setGlobalColourScheme(cs);
}
viewport.setGlobalColourScheme(cs);
@@
-5527,8
+5535,14
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
new jalview.ws.DBRefFetcher(alignPanel.av
- .getSequenceSelection(), alignPanel.alignFrame)
+ .getSequenceSelection(),
+ alignPanel.alignFrame, null,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
.fetchDBRefs(false);
}
}).start();
@@
-5597,9
+5611,14
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassource)
+ alignPanel.alignFrame, dassource,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
.fetchDBRefs(false);
}
}).start();
@@
-5633,9
+5652,14
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassource)
+ alignPanel.alignFrame, dassource,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
.fetchDBRefs(false);
}
}).start();
@@
-5684,9
+5708,14
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void run()
{
@Override
public void run()
{
+ boolean isNuclueotide = alignPanel.alignFrame
+ .getViewport().getAlignment()
+ .isNucleotide();
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
new jalview.ws.DBRefFetcher(alignPanel.av
.getSequenceSelection(),
- alignPanel.alignFrame, dassrc)
+ alignPanel.alignFrame, dassrc,
+ alignPanel.alignFrame.featureSettings,
+ isNuclueotide)
.fetchDBRefs(false);
}
}).start();
.fetchDBRefs(false);
}
}).start();
@@
-5751,6
+5780,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.firePropertyChange("alignment", null, al);
}
viewport.firePropertyChange("alignment", null, al);
}
+ @Override
public void setShowSeqFeatures(boolean b)
{
showSeqFeatures.setSelected(b);
public void setShowSeqFeatures(boolean b)
{
showSeqFeatures.setSelected(b);