/*\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
{\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
else\r
{\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- colours.put(type, ucs.findColour("A"));\r
+ colours.put(type, ucs.findColour('A'));\r
if (st.hasMoreElements())\r
{\r
String link = st.nextToken();\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
// Probably the old style groups file\r
UserColourScheme ucs = new UserColourScheme(type);\r
- colours.put(type, ucs.findColour("A"));\r
+ colours.put(type, ucs.findColour('A'));\r
}\r
\r
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
catch (Exception ex)\r
{\r
System.out.println(line);\r
- ex.printStackTrace();\r
System.out.println("Error parsing feature file: " + ex +"\n"+line);\r
return false;\r
}\r
return true;\r
}\r
\r
- void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
{\r
+ if(sf.getDescription()==null)\r
+ return;\r
+\r
+ if(removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>")==-1)\r
+ removeHTML = false;\r
+\r
StringBuffer sb = new StringBuffer();\r
StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
String token, link;\r
+ int startTag;\r
+ String tag=null;\r
while(st.hasMoreElements())\r
{\r
- token = st.nextToken("<>");\r
+ token = st.nextToken("&>");\r
if(token.equalsIgnoreCase("html") || token.startsWith("/"))\r
+ {\r
continue;\r
+ }\r
+\r
+ tag = null;\r
+ startTag = token.indexOf("<");\r
\r
- if(token.startsWith("a href="))\r
+ if (startTag > -1)\r
{\r
- link = token.substring(token.indexOf("\"")+1, token.length()-1);\r
+ tag = token.substring(startTag+1);\r
+ token = token.substring(0, startTag);\r
+ }\r
+\r
+ if (tag != null && tag.toUpperCase().startsWith("A HREF="))\r
+ {\r
+ if(token.length()>0)\r
+ sb.append(token);\r
+ link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);\r
String label = st.nextToken("<>");\r
- sf.addLink(label+"|"+link);\r
- sb.append(label+"%LINK%");\r
+ sf.addLink(label + "|" + link);\r
+ sb.append(label + "%LINK%");\r
}\r
- else if(token.equalsIgnoreCase("br"))\r
+ else if (tag != null && tag.equalsIgnoreCase("br"))\r
sb.append("\n");\r
+ else if (token.startsWith("lt;"))\r
+ sb.append("<" + token.substring(3));\r
+ else if (token.startsWith("gt;"))\r
+ sb.append(">" + token.substring(3));\r
+ else if (token.startsWith("amp;"))\r
+ sb.append("&" + token.substring(4));\r
else\r
+ {\r
sb.append(token);\r
+ }\r
}\r
\r
if(removeHTML)\r
sf.description = sb.toString();\r
+\r
}\r
\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
+ if(next[j].links!=null\r
+ && next[j].getDescription().indexOf("<html>")==-1)\r
+ out.append("<html>");\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
+ if (next[j].getDescription().indexOf("</html>") == -1)\r
+ out.append("</html>");\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
git://source.jalview.org / jalview.git / blobdiff