- else\r
- {\r
- if( cs instanceof ResidueColourScheme)\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) cs;\r
- rcs.setThreshold(i);\r
- }\r
- else if( cs instanceof ScoreColourScheme)\r
- {\r
- ScoreColourScheme scs = (ScoreColourScheme) cs;\r
- scs.setThreshold(i);\r
- }\r
-\r
- }\r
-\r
- ap.seqPanel.seqCanvas.paintFlag=true;\r
- ap.seqPanel.repaint();\r
-\r
- }\r
-\r
- public void valueField_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- int i = Integer.parseInt(valueField.getText());\r
- slider.setValue(i);\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
+ {\r
+ allGroupsCheck.setEnabled(b);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void valueField_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ int i = Integer.parseInt(valueField.getText());\r
+ slider.setValue(i);\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ valueField.setText(slider.getValue() + "");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param value DOCUMENT ME!\r
+ */\r
+ public void setValue(int value)\r
+ {\r
+ slider.setValue(value);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getValue()\r
+ {\r
+ return Integer.parseInt(valueField.getText());\r