+ 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
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public static void showPIDSlider()\r
+ {\r
+ try\r
+ {\r
+ conservationSlider.setClosed(true);\r
+ conservationSlider = null;\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ if (!PIDSlider.isVisible())\r
+ {\r
+ Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,\r
+ false);\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ PIDSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent e)\r
+ {\r
+ PIDSlider = null;\r
+ }\r
+ });\r
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param i DOCUMENT ME!\r
+ */\r
+ public void valueChanged(int i)\r
+ {\r
+ if (cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ ColourSchemeI toChange = null;\r
+ Vector allGroups = null;\r
+ int groupIndex = 0;\r
+\r
+ if (allGroupsCheck.isSelected())\r
+ {\r
+ allGroups = ap.av.alignment.getGroups();\r
+ groupIndex = allGroups.size() - 1;\r
+ }\r
+ else\r
+ {\r
+ toChange = cs;\r
+ }\r
+\r
+\r
+ while (groupIndex > -1)\r
+ {\r
+ if (allGroups != null)\r
+ {\r
+ toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;\r
+\r
+ if (toChange == null)\r
+ {\r
+ groupIndex--;\r
+\r
+ continue;\r
+ }\r
+ }\r
+\r
+ if (forConservation)\r
+ {\r
+ if (toChange.conservationApplied())\r
+ {\r
+ toChange.setConservationInc(i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());\r
+ }\r
+\r
+ groupIndex--;\r
+ }\r
+\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setAllGroupsCheckEnabled(boolean b)\r