}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, 1);
+ alignPanel.getSeqPanel().moveCursor(0, 1,
+ evt.isShiftDown() && !evt.isAltDown());
}
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1);
+ alignPanel.getSeqPanel().moveCursor(0, -1,
+ evt.isShiftDown() && !evt.isAltDown());
}
-
break;
case KeyEvent.VK_LEFT:
}
else
{
- alignPanel.getSeqPanel().moveCursor(-1, 0);
+ alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(1, 0);
+ alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
}
break;
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
+ { file, format }));
}
else
else
{
// create backupfiles object and get new temp filename destination
- Cache.log.debug("ALIGNFRAME making backupfiles object for " + file);
+ Cache.log.trace("ALIGNFRAME making backupfiles object for " + file);
BackupFiles backupfiles = new BackupFiles(file);
try
{
- Cache.log.debug("ALIGNFRAME setting PrintWriter");
- PrintWriter out = new PrintWriter(
- new FileWriter(backupfiles.getTempFilePath()));
+ String tempFilePath = backupfiles.getTempFilePath();
+ Cache.log.trace(
+ "ALIGNFRAME setting PrintWriter to " + tempFilePath);
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
- Cache.log.debug("ALIGNFRAME about to write to temp file "
- + backupfiles.getTempFilePath());
+ Cache.log.trace(
+ "ALIGNFRAME about to write to temp file " + tempFilePath);
out.print(output);
- Cache.log.debug("ALIGNFRAME about to close file");
+ Cache.log.trace("ALIGNFRAME about to close file");
out.close();
- Cache.log.debug("ALIGNFRAME closed file");
+ Cache.log.trace("ALIGNFRAME closed file");
this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
+ { file, format.getName() }));
} catch (IOException e)
{
success = false;
Cache.log.error(
"ALIGNFRAME Something happened writing the temp file");
Cache.log.error(e.getMessage());
- Cache.log.debug(e.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
success = false;
Cache.log.error(
- "ALIGNFRAME Something else happened writing the temp file");
+ "ALIGNFRAME Something unexpected happened writing the temp file");
Cache.log.error(ex.getMessage());
- Cache.log.debug(ex.getStackTrace());
+ Cache.log.debug(Cache.getStackTraceString(ex));
}
backupfiles.setWriteSuccess(success);
Cache.log.debug("ALIGNFRAME writing temp file was "
+ (success ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
- Cache.log.debug("ALIGNFRAME about to rollBackupsAndRenameTempFile");
+ Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
success = backupfiles.rollBackupsAndRenameTempFile();
Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ (success ? "" : "un") + "successfully");
{
JvOptionPane.showInternalMessageDialog(this, MessageManager
.formatMessage("label.couldnt_save_file", new Object[]
- { fileName }),
+ { file }),
MessageManager.getString("label.error_saving_file"),
JvOptionPane.WARNING_MESSAGE);
}
synchronized void slideSequences(boolean right, int size)
{
List<SequenceI> sg = new ArrayList<>();
- if (viewport.cursorMode)
- {
- sg.add(viewport.getAlignment()
- .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
- }
- else if (viewport.getSelectionGroup() != null
- && viewport.getSelectionGroup().getSize() != viewport
- .getAlignment().getHeight())
+ if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
+ .getSize() != viewport.getAlignment().getHeight())
{
sg = viewport.getSelectionGroup()
.getSequences(viewport.getHiddenRepSequences());
}
+ if (sg.size() == 0 && viewport.cursorMode)
+ {
+ sg.add(viewport.getAlignment()
+ .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
+ }
+
if (sg.size() < 1)
{
return;
}
viewport.setSelectionGroup(null);
viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
+ viewport.setSearchResults(null);
alignPanel.getIdPanel().getIdCanvas().searchResults = null;
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
}
/**
- * DOCUMENT ME!
+ * Opens a Finder dialog
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder();
+ new Finder(alignPanel);
}
/**