+ * Save HMMER settings
+ */
+ Cache.applicationProperties.setProperty("TRIM_TERMINI",
+ Boolean.toString(hmmrTrimTermini.isSelected()));
+ Cache.applicationProperties.setProperty("USE_UNIPROT",
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+ Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+ hmmerSequenceCount.getText());
+ Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
+ Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null && frames.length > 0)
+ {
+ for (AlignFrame f : frames)
+ {
+ f.updateHMMERStatus();
+ }
+ }
+
+ hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+ if (Cache.getDefault("USE_UNIPROT", false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*