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009fc42
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Groups file is now feature file
author
amwaterhouse
<Andrew Waterhouse>
Wed, 26 Oct 2005 16:23:18 +0000
(16:23 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 26 Oct 2005 16:23:18 +0000
(16:23 +0000)
src/jalview/gui/AlignFrame.java
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diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
7fbd14f
..
f2d0b69
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-175,7
+175,7
@@
public class AlignFrame
BufferedReader in = new BufferedReader(new FileReader(file));
\r
SequenceI seq = null;
\r
String line, type, desc, token;
\r
BufferedReader in = new BufferedReader(new FileReader(file));
\r
SequenceI seq = null;
\r
String line, type, desc, token;
\r
- UserColourScheme ucs;
\r
+
\r
int index, start, end;
\r
StringTokenizer st;
\r
SequenceFeature sf;
\r
int index, start, end;
\r
StringTokenizer st;
\r
SequenceFeature sf;
\r
@@
-185,17
+185,16
@@
public class AlignFrame
{
\r
lineNo++;
\r
st = new StringTokenizer(line, "\t");
\r
{
\r
lineNo++;
\r
st = new StringTokenizer(line, "\t");
\r
- if (st.countTokens() != 7)
\r
+ if (st.countTokens() == 2)
\r
{
\r
{
\r
- System.out.println("Groups file " + file +
\r
- " is invalid. Read help file.\nLine: \n"
\r
- +lineNo +": "+line);
\r
- break;
\r
+ type = st.nextToken();
\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());
\r
+ fr.setColour(type, ucs.findColour("A"));
\r
+ continue;
\r
}
\r
\r
while (st.hasMoreElements())
\r
{
\r
}
\r
\r
while (st.hasMoreElements())
\r
{
\r
- type = st.nextToken();
\r
desc = st.nextToken();
\r
token = st.nextToken();
\r
if (!token.equals("ID_NOT_SPECIFIED"))
\r
desc = st.nextToken();
\r
token = st.nextToken();
\r
if (!token.equals("ID_NOT_SPECIFIED"))
\r
@@
-211,14
+210,14
@@
public class AlignFrame
\r
start = Integer.parseInt(st.nextToken());
\r
end = Integer.parseInt(st.nextToken());
\r
\r
start = Integer.parseInt(st.nextToken());
\r
end = Integer.parseInt(st.nextToken());
\r
- ucs = new UserColourScheme(st.nextToken());
\r
\r
seq = viewport.alignment.getSequenceAt(index);
\r
start = seq.findIndex(start) - 1;
\r
end = seq.findIndex(end) - 1;
\r
\r
\r
seq = viewport.alignment.getSequenceAt(index);
\r
start = seq.findIndex(start) - 1;
\r
end = seq.findIndex(end) - 1;
\r
\r
+ type = st.nextToken();
\r
+
\r
sf = new SequenceFeature(type, desc, "", start, end);
\r
sf = new SequenceFeature(type, desc, "", start, end);
\r
- fr.setColour(type, ucs.findColour("A"));
\r
\r
seq.addSequenceFeature(sf);
\r
\r
\r
seq.addSequenceFeature(sf);
\r
\r