+ * Initialises the hmmer tabbed panel.
+ *
+ * @return
+ */
+ private JPanel initHMMERTab()
+ {
+ JPanel hmmerTab = new JPanel();
+ hmmerTab.setLayout(null);
+
+ hmmalign.setFont(LABEL_FONT);
+ hmmalign.setText(MessageManager.getString("label.hmmalign_label"));
+ hmmalign.setBounds(new Rectangle(22, 10, 200, 23));
+
+ trimTermini.setFont(LABEL_FONT);
+ trimTermini.setText(MessageManager.getString("label.trim_termini"));
+ trimTermini.setBounds(new Rectangle(22, 30, 200, 23));
+
+ hmmsearch.setFont(LABEL_FONT);
+ hmmsearch.setText(MessageManager.getString("label.hmmsearch_label"));
+ hmmsearch.setBounds(new Rectangle(250, 10, 200, 23));
+
+ sequencesToKeep.setFont(LABEL_FONT);
+ sequencesToKeep
+ .setText(MessageManager.getString("label.no_of_sequences"));
+ sequencesToKeep.setBounds(new Rectangle(250, 30, 125, 23));
+ numberOfSequencesToKeepField.setBounds(new Rectangle(375, 30, 40, 23));
+
+ installationLocation.setFont(LABEL_FONT);
+ installationLocation.setText(
+ MessageManager.getString("label.change_hmmer_location"));
+ installationLocation.setBounds(new Rectangle(22, 200, 200, 23));
+ installationLocationField.setBounds(new Rectangle(22, 220, 200, 23));
+ installationLocationField.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ if (e.getClickCount() == 2)
+ {
+ String chosen = openFileChooser();
+ if (chosen != null)
+ {
+ installationLocationField.setText(chosen);
+ }
+ }
+ }
+ });
+
+ backgroundFreqSource.add(uniprot);
+ backgroundFreqSource.add(alignment);
+ backgroundFreqSource.setSelected(uniprot.getModel(), true);
+
+ uniprot.setText(MessageManager.getString("label.freq_uniprot"));
+ uniprot.setFont(LABEL_FONT);
+ uniprot.setBounds(new Rectangle(22, 260, 255, 23));
+
+ alignment.setText(MessageManager.getString("label.freq_alignment"));
+ alignment.setFont(LABEL_FONT);
+ alignment.setBounds(new Rectangle(22, 280, 255, 23));
+
+ hmmerTab.add(uniprot);
+ hmmerTab.add(alignment);
+ hmmerTab.add(hmmalign);
+ hmmerTab.add(hmmsearch);
+ hmmerTab.add(installationLocation);
+ hmmerTab.add(installationLocationField);
+ hmmerTab.add(trimTermini);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(sequencesToKeep);
+ hmmerTab.add(numberOfSequencesToKeepField);
+ return hmmerTab;
+ }
+
+ /**