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JAL-3489 ensure all chains mapped when loading local multimeric PDB file
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
4ff1b4f
..
39123d5
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-33,6
+33,7
@@
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
@@
-2092,7
+2093,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
@@
-2139,7
+2140,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
@@
-3104,7
+3105,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
alignPanel.paintAlignment(true, false);
}
@@
-3118,6
+3119,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
alignPanel.paintAlignment(true, false);
}
@@
-3131,6
+3133,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
alignPanel.paintAlignment(true, false);
}
@@
-4489,7
+4492,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
int assocfiles = 0;
if (filesmatched.size() > 0)
{
int assocfiles = 0;
if (filesmatched.size() > 0)
{
- boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ boolean autoAssociate = Cache
+ .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
if (!autoAssociate)
{
String msg = MessageManager.formatMessage(
if (!autoAssociate)
{
String msg = MessageManager.formatMessage(
@@
-4515,7
+4519,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
(DataSourceType) fm[1], toassoc, false,
PDBEntry pe = new AssociatePdbFileWithSeq()
.associatePdbWithSeq((String) fm[0],
(DataSourceType) fm[1], toassoc, false,
- Desktop.instance);
+ Desktop.instance, false);
if (pe != null)
{
System.err.println("Associated file : "
if (pe != null)
{
System.err.println("Associated file : "
@@
-4932,6
+4936,13
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void finished()
{
@Override
public void finished()
{
+
+ for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ .getFeatureSettingsModels())
+ {
+
+ alignPanel.av.mergeFeaturesStyle(srcSettings);
+ }
AlignFrame.this.setMenusForViewport();
}
});
AlignFrame.this.setMenusForViewport();
}
});
@@
-5017,6
+5028,10
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void finished()
{
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ alignPanel.av.mergeFeaturesStyle(
+ srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
AlignFrame.this.setMenusForViewport();
}
});