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Any character non aa or nucleotide is a space
[jalview.git]
/
src
/
jalview
/
io
/
FeaturesFile.java
diff --git
a/src/jalview/io/FeaturesFile.java
b/src/jalview/io/FeaturesFile.java
index
d81141c
..
2c0b6d7
100755
(executable)
--- a/
src/jalview/io/FeaturesFile.java
+++ b/
src/jalview/io/FeaturesFile.java
@@
-125,7
+125,7
@@
public class FeaturesFile extends AlignFile
else
\r
{
\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());
\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
if (st.hasMoreElements())
\r
{
\r
String link = st.nextToken();
\r
@@
-230,7
+230,7
@@
public class FeaturesFile extends AlignFile
{
\r
// Probably the old style groups file
\r
UserColourScheme ucs = new UserColourScheme(type);
\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
}
\r
\r
sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
\r
@@
-267,6
+267,9
@@
public class FeaturesFile extends AlignFile
\r
public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
\r
{
\r
\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
if(removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>")==-1)
\r
removeHTML = false;
\r
\r
@@
-410,6
+413,10
@@
public class FeaturesFile extends AlignFile
out.append(next[j].type+"\t");
\r
else
\r
{
\r
out.append(next[j].type+"\t");
\r
else
\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
out.append(next[j].description+" ");
\r
if(next[j].links!=null)
\r
{
\r
@@
-428,7
+435,12
@@
public class FeaturesFile extends AlignFile
+ "</a>");
\r
}
\r
}
\r
+ "</a>");
\r
}
\r
}
\r
+
\r
+ if (next[j].getDescription().indexOf("</html>") == -1)
\r
+ out.append("</html>");
\r
}
\r
}
\r
+
\r
+
\r
out.append("\t");
\r
}
\r
\r
out.append("\t");
\r
}
\r
\r