+ if (!comp.isValid())\r
+ {\r
+ comps.removeElement(comp);\r
+ }\r
+ else 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
+ a1 = source.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a1 = source.getSequencesArray();\r
+\r
+ SequenceI[] a2;\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a2 = comp.getSequencesArray();\r
+\r
+ int i, iSize=a1.length, j, jSize=a2.length;\r
+ boolean exists = false;\r
+ for(i=0; i<iSize; i++)\r
+ {\r
+ exists = false;\r
+\r
+ for(j=0; j<jSize; j++)\r
+ if (a2[j]==a1[i] )\r
+ {\r
+ exists = true;\r
+ break;\r
+ }\r
+\r
+ if(!exists)\r
+ {\r
+ if (i < jSize)\r
+ comp.getSequences().insertElementAt(a1[i], i);\r
+ else\r
+ comp.addSequence(a1[i]);\r
+\r
+ jSize++;\r
+\r
+ if (comp.getHiddenSequences().getSize() > 0)\r
+ a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();\r
+ else\r
+ a2 = comp.getSequencesArray();\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