+ resetTable(false);\r
+ }\r
+\r
+ //This routine adds and removes checkboxes depending on\r
+ //Group selection states\r
+ void resetTable(boolean groupsChanged)\r
+ {\r
+ SequenceFeature [] tmpfeatures;\r
+ String group=null, type;\r
+ Vector visibleChecks = new Vector();\r
+\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ if (av.alignment.getSequenceAt(i).getSequenceFeatures() == null)\r
+ continue;\r
+\r
+ tmpfeatures = av.alignment.getSequenceAt(i).getSequenceFeatures();\r
+ int index = 0;\r
+ while (index < tmpfeatures.length)\r
+ {\r
+ group = tmpfeatures[index].featureGroup;\r
+\r
+ if (group==null || fr.featureGroups.get(group)==null ||\r
+ ((Boolean) fr.featureGroups.get(group)).booleanValue())\r
+ {\r
+ type = tmpfeatures[index].getType();\r
+ if(!visibleChecks.contains(type) )\r
+ {\r
+ visibleChecks.addElement(type);\r
+ }\r
+ }\r
+ index++;\r
+ }\r
+ }\r
+\r
+ Component[] comps;\r
+ int cSize = featurePanel.getComponentCount();\r
+ Checkbox check;\r
+ //This will remove any checkboxes which shouldn't be\r
+ //visible\r
+ for (int i = 0; i < cSize; i++)\r
+ {\r
+ comps = featurePanel.getComponents();\r
+ check = (Checkbox) comps[i];\r
+ if (!visibleChecks.contains(check.getLabel()))\r
+ {\r
+ featurePanel.remove(i);\r
+ cSize --;\r
+ i--;\r
+ }\r
+ }\r
+\r
+ if(fr.renderOrder!=null)\r
+ {\r
+ //First add the checks in the previous render order,\r
+ //in case the window has been closed and reopened\r
+ for(int ro=fr.renderOrder.length-1; ro>-1; ro--)\r
+ {\r
+ String item = fr.renderOrder[ro];\r
+\r
+ if(!visibleChecks.contains(item))\r
+ continue;\r
+\r
+ visibleChecks.removeElement(item);\r
+\r
+ addCheck(false, item);\r
+ }\r
+ }\r
+\r
+ // now add checkboxes which should be visible,\r
+ // if they have not already been added\r
+ Enumeration en = visibleChecks.elements();\r
+\r
+ while(en.hasMoreElements())\r
+ {\r
+ addCheck(groupsChanged, en.nextElement().toString());\r
+ }\r
+\r
+\r
+ featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), 1, 10,5));\r
+ featurePanel.validate();\r
+\r
+\r
+ if(scrollPane!=null)\r
+ scrollPane.validate();\r
+\r
+ itemStateChanged(null);\r
+ }\r
+\r
+ void addCheck(boolean groupsChanged, String type)\r
+ {\r
+ boolean addCheck;\r
+ Component [] comps = featurePanel.getComponents();\r
+ Checkbox check;\r
+ addCheck = true;\r
+ for (int i = 0; i < featurePanel.getComponentCount(); i++)\r
+ {\r
+ check = (Checkbox) comps[i];\r
+ if (check.getLabel().equals(type))\r
+ {\r
+ addCheck = false;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (addCheck)\r
+ {\r
+ boolean selected = false;\r
+ if (groupsChanged || av.featuresDisplayed.containsKey(type))\r
+ {\r
+ selected = true;\r
+ }\r
+\r
+ check = new MyCheckbox(type,\r
+ selected,\r
+ (fr.featureLinks!=null && fr.featureLinks.containsKey(type))\r
+ );\r
+\r
+ check.addMouseListener(this);\r
+ check.addMouseMotionListener(this);\r
+ check.setBackground(fr.getColour(type));\r
+ check.addItemListener(this);\r
+ featurePanel.add(check);\r
+ }\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ for(int i=0; i<featurePanel.getComponentCount(); i++)\r
+ {\r
+ Checkbox check = (Checkbox)featurePanel.getComponent(i);\r
+ check.setState(!check.getState());\r
+ }\r
+ selectionChanged();\r