+ valueField.setText(value + "");\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ * @param cs DOCUMENT ME!\r
+ * @param source DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static int setConservationSlider(AlignmentPanel ap,\r
+ ColourSchemeI cs, String source)\r
+ {\r
+ SliderPanel sp = null;\r
+\r
+ if (conservationSlider == null)\r
+ {\r
+ sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);\r
+ conservationSlider = new JInternalFrame();\r
+ conservationSlider.setContentPane(sp);\r
+ conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+ else\r
+ {\r
+ sp = (SliderPanel) conservationSlider.getContentPane();\r
+ sp.cs = cs;\r
+ }\r
+\r
+ conservationSlider.setTitle("Conservation Colour Increment (" +\r
+ source + ")");\r
+\r
+ if (ap.av.alignment.getGroups() != null)\r
+ {\r
+ sp.setAllGroupsCheckEnabled(true);\r
+ }\r
+ else\r
+ {\r
+ sp.setAllGroupsCheckEnabled(false);\r
+ }\r
+\r
+ return sp.getValue();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public static void showConservationSlider()\r
+ {\r
+ try\r
+ {\r
+ PIDSlider.setClosed(true);\r
+ PIDSlider = null;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ if (!conservationSlider.isVisible())\r
+ {\r
+ Desktop.addInternalFrame(conservationSlider,\r
+ conservationSlider.getTitle(), 420, 90, false);\r
+ conservationSlider.addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent e)\r
+ {\r
+ conservationSlider = null;\r
+ }\r
+ });\r
+ conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ * @param cs DOCUMENT ME!\r
+ * @param source DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
+ String source)\r
+ {\r
+ SliderPanel pid = null;\r
+\r
+ int threshold = cs.getThreshold();\r
+\r
+ if (PIDSlider == null)\r
+ {\r
+ pid = new SliderPanel(ap, threshold, false, cs);\r
+ PIDSlider = new JInternalFrame();\r
+ PIDSlider.setContentPane(pid);\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+ else\r
+ {\r
+ pid = (SliderPanel) PIDSlider.getContentPane();\r
+ pid.cs = cs;\r
+ }\r
+\r
+ PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");\r
+\r
+ if (ap.av.alignment.getGroups() != null)\r
+ {\r
+ pid.setAllGroupsCheckEnabled(true);\r
+ }\r
+ else\r
+ {\r
+ pid.setAllGroupsCheckEnabled(false);\r
+ }\r
+\r
+ return pid.getValue();\r