{\r
}\r
\r
- /**\r
- * Creates a new FeaturesFile object.\r
- *\r
- * @param inStr DOCUMENT ME!\r
- */\r
- public FeaturesFile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
\r
/**\r
* Creates a new FeaturesFile object.\r
end = Integer.parseInt(st.nextToken());\r
try\r
{\r
- score = Float.parseFloat(st.nextToken());\r
+ score = new Float(st.nextToken()).floatValue();\r
}\r
catch (NumberFormatException ex)\r
{\r
catch (Exception ex)\r
{}\r
\r
- seq.getDatasetSequence().addSequenceFeature(sf);\r
+ if(st.hasMoreTokens())\r
+ {\r
+ StringBuffer attributes = new StringBuffer();\r
+ while (st.hasMoreTokens())\r
+ {\r
+ attributes.append("\t"+st.nextElement());\r
+ }\r
+ sf.setValue("ATTRIBUTES", attributes.toString());\r
+ }\r
+\r
+ seq.addSequenceFeature(sf);\r
\r
break;\r
}\r
{\r
StringBuffer out = new StringBuffer();\r
SequenceFeature [] next;\r
+ String source;\r
\r
for(int i=0; i<seqs.length; i++)\r
{\r
if(!visible.containsKey(next[j].type))\r
continue;\r
\r
+ source = next[j].featureGroup;\r
+ if(source==null)\r
+ source = next[j].getDescription();\r
+\r
out.append(seqs[i].getName() + "\t"\r
- + next[j].description + "\t"\r
+ + source + "\t"\r
+ next[j].type + "\t"\r
+ next[j].begin + "\t"\r
+ next[j].end + "\t"\r
out.append(next[j].getValue("STRAND")+"\t");\r
else\r
out.append(".\t");\r
+\r
if(next[j].getValue("FRAME")!=null)\r
- out.append(next[j].getValue("FRAME")+"\n");\r
+ out.append(next[j].getValue("FRAME"));\r
else\r
- out.append(".\n");\r
+ out.append(".");\r
+\r
+ if(next[j].getValue("ATTRIBUTES")!=null)\r
+ out.append(next[j].getValue("ATTRIBUTES"));\r
+\r
+ out.append("\n");\r
\r
}\r
}\r