features.setDescription(sf[index].getDescription());\r
features.setType(sf[index].getType());\r
features.setFeatureGroup(sf[index].getFeatureGroup());\r
+ features.setScore(sf[index].getScore());\r
+ if(sf[index].links!=null)\r
+ {\r
+ for(int l=0; l<sf[index].links.size(); l++)\r
+ {\r
+ OtherData keyValue = new OtherData();\r
+ keyValue.setKey("LINK_"+l);\r
+ keyValue.setValue(sf[index].links.elementAt(l).toString());\r
+ features.addOtherData(keyValue);\r
+ }\r
+ }\r
+ if(sf[index].otherDetails!=null)\r
+ {\r
+ String key;\r
+ Enumeration keys = sf[index].otherDetails.keys();\r
+ while(keys.hasMoreElements())\r
+ {\r
+ key = keys.nextElement().toString();\r
+ OtherData keyValue = new OtherData();\r
+ keyValue.setKey( key );\r
+ keyValue.setValue(\r
+ sf[index].otherDetails.get(key).toString());\r
+ features.addOtherData(keyValue);\r
+ }\r
+ }\r
+\r
jseq.addFeatures(features);\r
index ++;\r
}\r
\r
String [] renderOrder =\r
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
+\r
+ Vector settingsAdded = new Vector();\r
for(int ro=0; ro<renderOrder.length; ro++)\r
{\r
Setting setting = new Setting();\r
);\r
\r
fs.addSetting(setting);\r
+ settingsAdded.addElement(renderOrder[ro]);\r
+ }\r
+\r
+ //Make sure we save none displayed feature settings\r
+ Enumeration en =\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();\r
+ while(en.hasMoreElements())\r
+ {\r
+ String key = en.nextElement().toString();\r
+ if(settingsAdded.contains(key))\r
+ continue;\r
\r
+ Setting setting = new Setting();\r
+ setting.setType(key);\r
+ setting.setColour(\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()\r
+ );\r
+\r
+ setting.setDisplay(false);\r
+\r
+ fs.addSetting(setting);\r
+ settingsAdded.addElement(key);\r
}\r
+\r
jms.setFeatureSettings(fs);\r
\r
}\r
features[f].getBegin(), features[f].getEnd(),\r
features[f].getFeatureGroup());\r
\r
+ sf.setScore(features[f].getScore());\r
+ for(int od=0; od<features[f].getOtherDataCount(); od++)\r
+ {\r
+ OtherData keyValue = features[f].getOtherData(od);\r
+ if(keyValue.getKey().startsWith("LINK"))\r
+ sf.addLink(keyValue.getValue());\r
+ else\r
+ sf.setValue(keyValue.getKey(), keyValue.getValue());\r
+\r
+ }\r
+\r
al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
}\r
}\r