+ * Save HMMER settings
+ */
+ Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
+ Boolean.toString(hmmrTrimTermini.isSelected()));
+ Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
+ Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+ Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
+ hmmerSequenceCount.getText());
+ Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
+ if (cygwinPath != null)
+ {
+ 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(HMMALIGN_TRIM_TERMINI, false));
+ if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
+ {
+ hmmerBackgroundUniprot.setSelected(true);
+ }
+ else
+ {
+ hmmerBackgroundAlignment.setSelected(true);
+ }
+ hmmerSequenceCount
+ .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
+ hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+ /*
+ * Save Overview settings
+ */
+ Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+ Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+ Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+ Boolean.toString(useLegacyGap.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+ Boolean.toString(showHiddenAtStart.isSelected()));
+
+ /*