+ if (comps == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Enumeration e = comps.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ comp = (Component) e.nextElement();\r
+\r
+ if (comp == source)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (validateSequences\r
+ && comp instanceof AlignmentPanel\r
+ && source instanceof AlignmentPanel)\r
+ {\r
+ validateSequences( ( (AlignmentPanel) source).av.alignment,\r
+ ( (AlignmentPanel) comp).av.alignment);\r
+ }\r
+\r
+ if (comp instanceof AlignmentPanel && alignmentChanged)\r
+ {\r
+ ( (AlignmentPanel) comp).alignmentChanged();\r
+ }\r
+\r
+ comp.repaint();\r
+ }\r
+ }\r
+\r
+ static void validateSequences(AlignmentI source, AlignmentI comp)\r
+ {\r
+ SequenceI[] a1;\r
+ if (source.getHiddenSequences().getSize() > 0)\r
+ {\r
+ a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ a1 = source.getSequencesArray();\r
+ }\r
+\r
+ SequenceI[] a2;\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ {\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ a2 = comp.getSequencesArray();\r
+ }\r
+\r
+ int i, iSize = a1.length, j, jSize = a2.length;\r
+\r
+ if (iSize == jSize)\r
+ {\r
+ return;\r
+ }\r
+\r
+ boolean exists = false;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ exists = false;\r
+\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ if (a2[j] == a1[i])\r
+ {\r
+ exists = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!exists)\r
+ {\r
+ if (i < comp.getHeight())\r
+ {\r
+ comp.getSequences().insertElementAt(a1[i], i);\r
+ }\r
+ else\r
+ {\r
+ comp.addSequence(a1[i]);\r
+ }\r
+\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ {\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ }\r
+ else\r
+ {\r
+ a2 = comp.getSequencesArray();\r
+ }\r
+\r
+ jSize = a2.length;\r
+ }\r
+ }\r
+\r
+ iSize = a1.length;\r
+ jSize = a2.length;\r
+\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ exists = false;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (a2[j] == a1[i])\r
+ {\r
+ exists = true;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!exists)\r
+ {\r
+ comp.deleteSequence(a2[j]);\r
+ }\r
+ }\r
+ }\r
+\r
+ static AlignmentPanel[] getAssociatedPanels(String id)\r
+ {\r
+ Vector comps = (Vector) components.get(id);\r
+ Vector tmp = new Vector();\r
+ int i, iSize = comps.size();\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
+ {\r
+ tmp.addElement( ( (AlignmentPanel) comps.elementAt(i)));\r
+ }\r