X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=6c2c51ef5110a13b1849a0d250769e8d69332b75;hb=7157dfd20efd2e1db47db1ac12e879eb51c67b92;hp=32d8a1f6163357ef7f98bc1ab0095d8ba445ecea;hpb=312a01c56639fe2d5a94a7918e6968955533afc5;p=jalview.git
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 32d8a1f..6c2c51e 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,6 +1,6 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@ -137,8 +137,7 @@ public class HTMLOutput
String id = seq.getDisplayId(av.getShowJVSuffix());
out.println("
" + id +
- " | ");
-
+ " ");
for (int res = 0; res < seq.getLength(); res++)
{
@@ -149,10 +148,11 @@ public class HTMLOutput
color = fr.findFeatureColour(color, seq, res);
}
else
- color = Color.white;
-
+ {
+ color = Color.white;
+ }
- if (color.getRGB() < -1)
+ if (color.getRGB() < -1)
{
out.println("" +
@@ -196,15 +196,18 @@ public class HTMLOutput
endRes = al.getWidth();
}
- if(av.getScaleAboveWrapped())
+ if (av.getScaleAboveWrapped())
{
out.println(" |
");
if (av.getScaleLeftWrapped())
+ {
out.println(" | ");
+ }
else
+ {
out.println(" | ");
-
+ }
for (int i = startRes + 10; i < endRes; i += 10)
{
@@ -220,25 +223,27 @@ public class HTMLOutput
out.println("
");
seq = al.getSequenceAt(s);
- startPos = seq.findPosition( startRes );
- endPos = seq.findPosition( endRes )-1;
+ startPos = seq.findPosition(startRes);
+ endPos = seq.findPosition(endRes) - 1;
String id = seq.getDisplayId(av.getShowJVSuffix());
out.println("" + id +
- " | ");
-
+ " ");
- if(av.getScaleLeftWrapped())
+ if (av.getScaleLeftWrapped())
{
- if(startPos > seq.getEnd() || endPos==0)
+ if (startPos > seq.getEnd() || endPos == 0)
+ {
out.println(" | ");
+ }
else
+ {
out.println("" + startPos +
- " | ");
+ " ");
+ }
}
-
for (int res = startRes; res < endRes; res++)
{
if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
@@ -248,11 +253,14 @@ public class HTMLOutput
color = fr.findFeatureColour(color, seq, res);
}
else
+ {
color = Color.white;
+ }
if (color.getRGB() < -1)
{
- out.println("" +
+ out.println(" | " +
seq.getCharAt(res) + " | ");
}
else
@@ -260,24 +268,22 @@ public class HTMLOutput
out.println("" + seq.getCharAt(res) + " | ");
}
-
}
- if(av.getScaleRightWrapped() &&
- endRes < startRes + av.getWrappedWidth())
+ if (av.getScaleRightWrapped() &&
+ endRes < startRes + av.getWrappedWidth())
{
- out.println(""
- +" | ");
- }
-
+ out.println(""
+ + " | ");
+ }
- if(av.getScaleRightWrapped() && startPos " + endPos +
" ");
}
-
out.println("
");
}
@@ -294,88 +300,90 @@ public class HTMLOutput
public static String getImageMapHTML()
{
return new String(
- "\n"
- +"\n"
- +"\n"
- +"\n"
- +"\n"
- +"\n"
- +"\n");
+ "\n"
+ + "\n"
+ + "\n"
+ + "\n"
+ + "\n"
+ + "\n"
+ + "\n");
}
}