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Dispalys rule along top of output
author
amwaterhouse
<Andrew Waterhouse>
Fri, 14 Jan 2005 15:46:32 +0000
(15:46 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 14 Jan 2005 15:46:32 +0000
(15:46 +0000)
src/jalview/io/HTMLOutput.java
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diff --git
a/src/jalview/io/HTMLOutput.java
b/src/jalview/io/HTMLOutput.java
index
af6e255
..
d15a6e8
100755
(executable)
--- a/
src/jalview/io/HTMLOutput.java
+++ b/
src/jalview/io/HTMLOutput.java
@@
-50,22
+50,41
@@
public class HTMLOutput
\r
\r
//////////////
\r
\r
\r
//////////////
\r
- SequenceGroup group;
\r
+ SequenceGroup [] groups;
\r
SequenceI seq;
\r
SequenceI seq;
\r
- ColourSchemeI cs;
\r
+ ColourSchemeI cs = null;
\r
AlignmentI alignment = av.getAlignment();
\r
String r,g,b;
\r
AlignmentI alignment = av.getAlignment();
\r
String r,g,b;
\r
- for (int i = 0; i < alignment.getHeight(); i++)
\r
+
\r
+ // draws the top row, the measure rule
\r
+ out.println("<tr><td colspan=\"6\"></td>");
\r
+ int i=0;
\r
+ for(i=10; i<alignment.getWidth()-10; i+=10)
\r
+ out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");
\r
+
\r
+ out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");
\r
+ out.println("</tr>");
\r
+
\r
+ for (i = 0; i < alignment.getHeight(); i++)
\r
{
\r
seq = alignment.getSequenceAt(i);
\r
{
\r
seq = alignment.getSequenceAt(i);
\r
- group = alignment.findGroup( seq );
\r
+ groups = alignment.findAllGroups( seq );
\r
out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");
\r
out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");
\r
+
\r
+
\r
for (int res = 0; res < seq.getLength(); res++)
\r
{
\r
for (int res = 0; res < seq.getLength(); res++)
\r
{
\r
- if(group!=null && group.getStartRes()<=res && group.getEndRes()>=res)
\r
- cs = group.cs;
\r
- else
\r
- cs = av.getGlobalColourScheme();
\r
+ cs = av.getGlobalColourScheme();
\r
+
\r
+ if(groups!=null)
\r
+ {
\r
+ for (int k = 0; k < groups.length; k++)
\r
+ if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
\r
+ {
\r
+ cs = groups[k].cs;
\r
+ break;
\r
+ }
\r
+ }
\r
\r
\r
color = sr.getResidueBoxColour(cs, seq, res);
\r
\r
\r
color = sr.getResidueBoxColour(cs, seq, res);
\r