/*\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
}\r
\r
/**\r
- * DOCUMENT ME!\r
+ * The Application can render HTML, but the applet will\r
+ * remove HTML tags and replace links with %LINK%\r
+ * Both need to read links in HTML however\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public boolean parse(AlignmentI align,\r
+ Hashtable colours,\r
+ boolean removeHTML)\r
+ {\r
+ return parse(align, colours, null, removeHTML);\r
+ }\r
+ /**\r
+ * The Application can render HTML, but the applet will\r
+ * remove HTML tags and replace links with %LINK%\r
+ * Both need to read links in HTML however\r
*\r
* @throws IOException DOCUMENT ME!\r
*/\r
- public boolean parse(AlignmentI align, Hashtable colours)\r
- throws IOException\r
+ public boolean parse(AlignmentI align,\r
+ Hashtable colours,\r
+ Hashtable featureLink,\r
+ boolean removeHTML)\r
{\r
String line = null;\r
try\r
float score;\r
StringTokenizer st;\r
SequenceFeature sf;\r
- String featureGroup = null;\r
+ String featureGroup = null, groupLink = null;\r
+ Hashtable typeLink = new Hashtable();\r
\r
boolean GFFFile = true;\r
\r
if (type.equalsIgnoreCase("startgroup"))\r
{\r
featureGroup = st.nextToken();\r
+ if (st.hasMoreElements())\r
+ {\r
+ groupLink = st.nextToken();\r
+ featureLink.put(featureGroup, groupLink);\r
+ }\r
}\r
else if (type.equalsIgnoreCase("endgroup"))\r
{\r
//but at present theres no way of showing more than 1 group\r
st.nextToken();\r
featureGroup = null;\r
+ groupLink = null;\r
}\r
else\r
{\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
colours.put(type, ucs.findColour("A"));\r
+ if (st.hasMoreElements())\r
+ {\r
+ String link = st.nextToken();\r
+ typeLink.put(type, link);\r
+ if(featureLink==null)\r
+ featureLink = new Hashtable();\r
+ featureLink.put(type, link);\r
+ }\r
+\r
}\r
continue;\r
}\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
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
\r
- seq.getDatasetSequence().addSequenceFeature(sf);\r
+ seq.addSequenceFeature(sf);\r
+\r
+ if(groupLink!=null && removeHTML)\r
+ {\r
+ sf.addLink(groupLink);\r
+ sf.description += "%LINK%";\r
+ }\r
+ if(typeLink.containsKey(type) && removeHTML)\r
+ {\r
+ sf.addLink(typeLink.get(type).toString());\r
+ sf.description += "%LINK%";\r
+ }\r
+\r
+ parseDescriptionHTML(sf, removeHTML);\r
\r
//If we got here, its not a GFFFile\r
GFFFile = false;\r
catch (Exception ex)\r
{\r
System.out.println(line);\r
- ex.printStackTrace();\r
- System.out.println("Error parsing groups file: " + ex +"\n"+line);\r
+ System.out.println("Error parsing feature file: " + ex +"\n"+line);\r
return false;\r
}\r
\r
return true;\r
-\r
}\r
\r
+ void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
+ String token, link;\r
+ while(st.hasMoreElements())\r
+ {\r
+ token = st.nextToken("<>");\r
+ if(token.equalsIgnoreCase("html") || token.startsWith("/"))\r
+ continue;\r
+\r
+ if(token.startsWith("a href="))\r
+ {\r
+ link = token.substring(token.indexOf("\"")+1, token.length()-1);\r
+ String label = st.nextToken("<>");\r
+ sf.addLink(label+"|"+link);\r
+ sb.append(label+"%LINK%");\r
+ }\r
+ else if(token.equalsIgnoreCase("br"))\r
+ sb.append("\n");\r
+ else\r
+ sb.append(token);\r
+ }\r
+\r
+ if(removeHTML)\r
+ sf.description = sb.toString();\r
+ }\r
\r
/**\r
* DOCUMENT ME!\r
\r
do\r
{\r
- if (groups.size() > 0)\r
+\r
+\r
+ if (groups.size() > 0 && groupIndex < groups.size())\r
{\r
group = groups.elementAt(groupIndex).toString();\r
out.append("\nSTARTGROUP\t" + group + "\n");\r
}\r
-\r
+ else\r
+ group = null;\r
\r
for (int i = 0; i < seqs.length; i++)\r
{\r
if (!visible.containsKey(next[j].type))\r
continue;\r
\r
- if (group != null && !next[j].featureGroup.equals(group))\r
+ if (group != null\r
+ && (next[j].featureGroup==null\r
+ || !next[j].featureGroup.equals(group))\r
+ )\r
+ continue;\r
+\r
+ if(group==null && next[j].featureGroup!=null)\r
continue;\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
}\r
\r
- if(groups.size()>0)\r
+ if(group!=null)\r
{\r
out.append("ENDGROUP\t"+group+"\n");\r
+ groupIndex++;\r
}\r
+ else\r
+ break;\r
\r
- groupIndex++;\r
}\r
- while(groupIndex < groups.size());\r
+ while(groupIndex < groups.size()+1);\r
\r
\r
return out.toString();\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