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JAL-1976 Added progress indicators for HTML_SVG and BioJS export operations
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
d20d62e
..
a616dc0
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-1369,7
+1369,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
- BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
+ BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel, this);
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
bjs.exportJalviewAlignmentAsBioJsHtmlFile();
}
@@
-2547,7
+2547,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
ColumnSelection colSel = viewport.getColumnSelection();
int column;
ColumnSelection colSel = viewport.getColumnSelection();
int column;
- if (colSel.size() > 0)
+ if (!colSel.isEmpty())
{
if (trimLeft)
{
{
if (trimLeft)
{
@@
-2966,6
+2966,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
viewport.showAllHiddenColumns();
repaint();
{
viewport.showAllHiddenColumns();
repaint();
+ viewport.sendSelection();
}
@Override
}
@Override
@@
-3056,6
+3057,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
toggleHiddenRegions(false, false);
+ viewport.sendSelection();
}
/*
}
/*
@@
-3073,6
+3075,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
/*
}
/*
@@
-3088,6
+3091,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
@Override
}
@Override
@@
-3095,6
+3099,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
{
viewport.hideSelectedColumns();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
@Override
}
@Override
@@
-5531,8
+5536,14
@@
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();
@@
-5601,9
+5612,14
@@
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();
@@
-5637,9
+5653,14
@@
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();
@@
-5688,9
+5709,14
@@
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();