/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\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
if(next[j].description==null || next[j].description.equals(""))\r
out.append(next[j].type+"\t");\r
else\r
- out.append(next[j].description + "\t");\r
+ {\r
+ out.append(next[j].description+" ");\r
+ if(next[j].links!=null)\r
+ {\r
+ for(int l=0; l<next[j].links.size(); l++)\r
+ {\r
+ String label = next[j].links.elementAt(l).toString();\r
+ String href = label.substring(label.indexOf("|")+1);\r
+ label = label.substring(0, label.indexOf("|"));\r
+\r
+ if(next[j].description.indexOf(href)==-1)\r
+ {\r
+ out.append("<a href=\""\r
+ + href\r
+ + "\">"\r
+ + label\r
+ + "</a>");\r
+ }\r
+ }\r
+ }\r
+ out.append("\t");\r
+ }\r
+\r
\r
out.append( seqs[i].getName() + "\t-1\t"\r
+ next[j].begin + "\t"\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