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Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
a9d5b86
..
b655b2e
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-153,12
+153,15
@@
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
+import ext.vamsas.ServiceHandle;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
+@SuppressWarnings("serial")
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
@@
-392,12
+395,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- /**
- * BH 2018 ignore service listeners
- *
- * @j2sNative
- *
- */
+ if (!Platform.isJS())
{
addServiceListeners();
}
{
addServiceListeners();
}
@@
-851,7
+849,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
- };
+ }
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
@@
-1004,11
+1002,6
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void setStatus(String text)
{
@Override
public void setStatus(String text)
{
- // BH note: If text width and height are 0, then the layout manager
- // will dispense of it and change the frame height.
- // In JavaScript, we use \u00A0 -- unicode "non-breaking space"
- // which is the unicode encoding of
-
statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
@@
-1289,10
+1282,11
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
else
{
// create backupfiles object and get new temp filename destination
else
{
// create backupfiles object and get new temp filename destination
- BackupFiles backupfiles = new BackupFiles(file);
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
try
{
try
{
- String tempFilePath = backupfiles.getTempFilePath();
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
PrintWriter out = new PrintWriter(
new FileWriter(tempFilePath));
PrintWriter out = new PrintWriter(
new FileWriter(tempFilePath));
@@
-1302,15
+1296,19
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ fileName, format.getName() }));
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ fileName, format.getName() }));
+ lastSaveSuccessful = true;
} catch (Exception ex)
{
lastSaveSuccessful = false;
ex.printStackTrace();
}
} catch (Exception ex)
{
lastSaveSuccessful = false;
ex.printStackTrace();
}
- backupfiles.setWriteSuccess(lastSaveSuccessful);
- // do the backup file roll and rename the temp file to actual file
- lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ // do the backup file roll and rename the temp file to actual file
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ }
}
}
};
}
}
};
@@
-2086,7
+2084,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
+ Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
@@
-3034,7
+3033,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param toggleSeqs
* @param toggleCols
*/
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
{
boolean hide = false;
@@
-3169,7
+3168,7
@@
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);
}
@@
-3183,6
+3182,7
@@
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);
}
@@
-3196,6
+3196,7
@@
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);
}
@@
-3321,6
+3322,11
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
((JPanel) pane).add(textLabel, BorderLayout.NORTH);
}
else
((JPanel) pane).add(textLabel, BorderLayout.NORTH);
}
else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
@@
-3369,7
+3375,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
overview.dispose();
alignPanel.setOverviewPanel(null);
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
});
if (getKeyListeners().length > 0)
{
@@
-3807,7
+3813,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
+ Hashtable<String, String> scoreSorts = new Hashtable<>();
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
@@
-3820,11
+3826,11
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
}
}
}
}
- Enumeration labels = scoreSorts.keys();
+ Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
addSortByAnnotScoreMenuItem(sortByAnnotScore,
while (labels.hasMoreElements())
{
addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
+ labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
@@
-4152,14
+4158,14
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
+ Vector<ServiceHandle> secstrpr = Discoverer.services
.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
+ final ext.vamsas.ServiceHandle sh = secstrpr
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
@@
-4269,7
+4275,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
*
* @param webService
*/
*
* @param webService
*/
- private void build_urlServiceMenu(JMenu webService)
+ protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
@@
-5004,7
+5010,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
@@
-5733,7
+5739,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
Cache.setProperty("LAST_DIRECTORY", choice);
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
new VCFLoader(choice).loadVCF(seqs, us);
Cache.setProperty("LAST_DIRECTORY", choice);
SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
new VCFLoader(choice).loadVCF(seqs, us);
- };
+ }
});
chooser.showOpenDialog(null);
});
chooser.showOpenDialog(null);