+ public static void Refresh(Component source,\r
+ String id,\r
+ boolean alignmentChanged,\r
+ boolean validateSequences)\r
+ {\r
+ if (components == null)\r
+ return;\r
+\r
+ Component comp;\r
+ Vector comps = (Vector) components.get(id);\r
+\r
+ 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
+ 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
+\r
+ if(iSize == jSize)\r
+ return;\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
+ 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
+ }\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
+ }\r
+ AlignmentPanel [] result = new AlignmentPanel[tmp.size()];\r
+ tmp.toArray(result);\r
+\r
+ return result;\r
+ }\r