public void saveState(File statefile)
{
FileOutputStream fos = null;
- // create backupfiles object and get new temp filename destination
- BackupFiles backupfiles = new BackupFiles(statefile);
try
{
- fos = new FileOutputStream(backupfiles.getTempFilePath());
+ fos = new FileOutputStream(statefile);
JarOutputStream jout = new JarOutputStream(fos);
saveState(jout);
fos.close();
- backupfiles.setWriteSuccess(true);
- backupfiles.rollBackupsAndRenameTempFile();
} catch (Exception e)
{
- Cache.log.error("Couln't write Jalview state to " + statefile
- + ". Temporary file is at: " + backupfiles.getTempFile(), e);
+ Cache.log.error("Couln't write Jalview state to " + statefile, e);
// TODO: inform user of the problem - they need to know if their data was
// not saved !
if (errorMessage == null)
else
{
errorMessage += "(Didn't write Jalview Archive to output file '"
- + statefile + "\nTemporary file is at: "
- + backupfiles.getTempFile() + ")";
+ + statefile + ")";
}
e.printStackTrace();
} finally
float min = safeFloat(safeFloat(setting.getMin()));
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
- FeatureColourI gc = new FeatureColour(minColour, maxColour,
+ FeatureColourI gc = new FeatureColour(maxColour, minColour,
+ maxColour,
noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
fto, m.getMapFromUnit().intValue(),
m.getMapToUnit().intValue());
- // if (m.getMappingChoice() != null)
- // {
- // MappingChoice mc = m.getMappingChoice();
+
+ /*
+ * (optional) choice of dseqFor or Sequence
+ */
if (m.getDseqFor() != null)
{
String dsfor = m.getDseqFor();
if (seqRefIds.containsKey(dsfor))
{
- /**
+ /*
* recover from hash
*/
jmap.setTo(seqRefIds.get(dsfor));
frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
- else
+ else if (m.getSequence() != null)
{
- /**
+ /*
* local sequence definition
*/
Sequence ms = m.getSequence();
noValueColour = maxcol;
}
- colour = new FeatureColour(mincol, maxcol, noValueColour,
+ colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
final List<String> attributeName = colourModel.getAttributeName();