X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=b238383aca07d15196cf4e171e8f6ac9ff21d2c2;hb=fb94c80fc4ed42cb9b693d81a1c53aa150bb0dd6;hp=14a6ccb0ac5330d833b08ed42b2c50a1456da9b1;hpb=25effdb93ea664f42294ebf56d3b640d2f58a5f4;p=jalview.git
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 14a6ccb..b238383 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -13,7 +13,7 @@ public class HTMLOutput
{
SequenceRenderer sr = new SequenceRenderer(null);
- public HTMLOutput(AlignmentI alignment, ColourSchemeI cs)
+ public HTMLOutput(AlignViewport av)
{
Color color;
JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);
@@ -29,8 +29,7 @@ public class HTMLOutput
out.println("");
out.println("");
out.println("");
@@ -39,21 +38,37 @@ public class HTMLOutput
//////////////
+ SequenceGroup group;
+ SequenceI seq;
+ ColourSchemeI cs;
+ AlignmentI alignment = av.getAlignment();
+ String r,g,b;
for (int i = 0; i < alignment.getHeight(); i++)
{
- SequenceI seq = alignment.getSequenceAt(i);
+ seq = alignment.getSequenceAt(i);
+ group = alignment.findGroup( seq );
out.println("| "+seq.getName()+" | ");
for (int res = 0; res < seq.getLength(); res++)
{
+ if(group!=null && group.getStartRes()<=res && group.getEndRes()>=res)
+ cs = group.cs;
+ else
+ cs = av.getGlobalColourScheme();
+
color = sr.getResidueBoxColour(cs, seq, res);
if(color.getRGB()<-1)
{
- out.println(""+seq.getCharAt(res)+" | ");
+ r = Integer.toHexString(color.getRed());
+ if(r.length()<2)
+ r = "0"+r;
+ g = Integer.toHexString(color.getGreen());
+ if(g.length()<2)
+ g = "0"+g;
+ b = Integer.toHexString(color.getBlue());
+ if(b.length()<2)
+ b = "0"+b;
+ out.println(""+seq.getCharAt(res)+" | ");
}
else
out.println(""+seq.getCharAt(res)+" | ");