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JAL-2885 ENSEMBL-DOMAIN -> ENSEMBL-BASEURL
[jalview.git]
/
src
/
jalview
/
gui
/
StructureViewerBase.java
diff --git
a/src/jalview/gui/StructureViewerBase.java
b/src/jalview/gui/StructureViewerBase.java
index
3ba9947
..
31c20ed
100644
(file)
--- a/
src/jalview/gui/StructureViewerBase.java
+++ b/
src/jalview/gui/StructureViewerBase.java
@@
-83,18
+83,18
@@
public abstract class StructureViewerBase extends GStructureViewer
/**
* list of sequenceSet ids associated with the view
*/
/**
* list of sequenceSet ids associated with the view
*/
- protected List<String> _aps = new ArrayList<String>();
+ protected List<String> _aps = new ArrayList<>();
/**
* list of alignment panels to use for superposition
*/
/**
* list of alignment panels to use for superposition
*/
- protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+ protected Vector<AlignmentPanel> _alignwith = new Vector<>();
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
- protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+ protected Vector<AlignmentPanel> _colourwith = new Vector<>();
private String viewId = null;
private String viewId = null;
@@
-170,7
+170,7
@@
public abstract class StructureViewerBase extends GStructureViewer
{
if (_alignwith == null)
{
{
if (_alignwith == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ _alignwith = new Vector<>();
}
if (_alignwith.size() == 0 && ap != null)
{
}
if (_alignwith.size() == 0 && ap != null)
{
@@
-310,6
+310,8
@@
public abstract class StructureViewerBase extends GStructureViewer
public abstract ViewerType getViewerType();
public abstract ViewerType getViewerType();
+ protected abstract IProgressIndicator getIProgressIndicator();
+
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
/**
* add a new structure (with associated sequences and chains) to this viewer,
* retrieving it if necessary first.
@@
-460,7
+462,7
@@
public abstract class StructureViewerBase extends GStructureViewer
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
* create the mappings
*/
apanel.getStructureSelectionManager().setMapping(seq, chains,
- pdbFilename, DataSourceType.FILE);
+ pdbFilename, DataSourceType.FILE, getIProgressIndicator());
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
@@
-468,7
+470,9
@@
public abstract class StructureViewerBase extends GStructureViewer
if (apanel.getSeqPanel().seqCanvas.fr != null)
{
apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
if (apanel.getSeqPanel().seqCanvas.fr != null)
{
apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
- apanel.paintAlignment(true);
+ // note - we don't do a refresh for structure here because we do it
+ // explicitly for all panels later on
+ apanel.paintAlignment(true, false);
}
/*
}
/*
@@
-717,11
+721,11
@@
public abstract class StructureViewerBase extends GStructureViewer
if (_colourwith == null)
{
if (_colourwith == null)
{
- _colourwith = new Vector<AlignmentPanel>();
+ _colourwith = new Vector<>();
}
if (_alignwith == null)
{
}
if (_alignwith == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ _alignwith = new Vector<>();
}
ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
}
ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
@@
-888,7
+892,7
@@
public abstract class StructureViewerBase extends GStructureViewer
binding.setColourBySequence(seqColour.isSelected());
if (_colourwith == null)
{
binding.setColourBySequence(seqColour.isSelected());
if (_colourwith == null)
{
- _colourwith = new Vector<AlignmentPanel>();
+ _colourwith = new Vector<>();
}
if (binding.isColourBySequence())
{
}
if (binding.isColourBySequence())
{