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
{
String tempFilePath = backupfiles.getTempFilePath();
- Cache.log.debug(
+ Cache.log.trace(
"ALIGNFRAME setting PrintWriter to " + tempFilePath);
PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
- Cache.log.debug(
+ 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[]
{
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(Cache.getStackTraceString(ex));
}
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");
}
/**
- * DOCUMENT ME!
+ * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode
*
* @param up
- * DOCUMENT ME!
+ * or down (if !up)
*/
public void moveSelectedSequences(boolean up)
{
if (sg == null)
{
- return;
+ if (viewport.cursorMode)
+ {
+ sg = new SequenceGroup();
+ sg.addSequence(viewport.getAlignment()
+ .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
+ } else {
+ return;
+ }
+ }
+
+ if (sg.getSize() < 1)
+ {
+ return;
}
+
+ // TODO: JAL-3733 - add an event to the undo buffer for this !
+
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true, false);
}
/**
- * DOCUMENT ME!
+ * Opens a Finder dialog
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder();
+ new Finder(alignPanel);
}
/**