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Merge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099
[jalview.git]
/
src
/
jalview
/
gui
/
AlignFrame.java
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
a2336a0
..
b080a25
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-64,6
+64,7
@@
import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
@@
-963,6
+964,11
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
return progressBar.operationInProgress();
}
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
@Override
public void setStatus(String text)
{
@Override
public void setStatus(String text)
{
@@
-1154,7
+1160,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().saveAlignment(this, file, shortName);
+ success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+ shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
@@
-1186,9
+1193,13
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
}
else
{
+ // create backupfiles object and get new temp filename destination
+ BackupFiles backupfiles = new BackupFiles(file);
+
try
{
try
{
- PrintWriter out = new PrintWriter(new FileWriter(file));
+ PrintWriter out = new PrintWriter(
+ new FileWriter(backupfiles.getTempFilePath()));
out.print(output);
out.close();
out.print(output);
out.close();
@@
-1201,6
+1212,11
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
success = false;
ex.printStackTrace();
}
success = false;
ex.printStackTrace();
}
+
+ backupfiles.setWriteSuccess(success);
+ // do the backup file roll and rename the temp file to actual file
+ success = backupfiles.rollBackupsAndRenameTempFile();
+
}
}
}
}
@@
-2397,15
+2413,12
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
+ SequenceGroup sg = new SequenceGroup(
+ viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
@@
-2701,7
+2714,8
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
if (!copyAnnotation)
{
/*
@@
-2888,7
+2902,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setFollowHighlight(state);
if (state)
{
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
}
}
@@
-3035,6
+3049,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
@@
-3059,6
+3074,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
@@
-5399,7
+5415,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
}
/**