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Now outputs features and groups, and wrapped alignment limits
author
amwaterhouse
<Andrew Waterhouse>
Thu, 17 Nov 2005 15:17:08 +0000
(15:17 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 17 Nov 2005 15:17:08 +0000
(15:17 +0000)
src/jalview/io/HTMLOutput.java
patch
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blob
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diff --git
a/src/jalview/io/HTMLOutput.java
b/src/jalview/io/HTMLOutput.java
index
257e9fa
..
7290828
100755
(executable)
--- a/
src/jalview/io/HTMLOutput.java
+++ b/
src/jalview/io/HTMLOutput.java
@@
-30,12
+30,14
@@
public class HTMLOutput
{
\r
AlignViewport av;
\r
SequenceRenderer sr;
\r
{
\r
AlignViewport av;
\r
SequenceRenderer sr;
\r
+ FeatureRenderer fr;
\r
Color color;
\r
\r
Color color;
\r
\r
- public HTMLOutput(AlignViewport av)
\r
+ public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr)
\r
{
\r
this.av = av;
\r
{
\r
this.av = av;
\r
- sr = new SequenceRenderer(av);
\r
+ this.sr = sr;
\r
+ this.fr = fr;
\r
\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
getProperty(
\r
\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
\r
getProperty(
\r
@@
-110,9
+112,7
@@
public class HTMLOutput
"<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
\r
\r
//////////////
\r
"<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
\r
\r
//////////////
\r
- SequenceGroup[] groups;
\r
SequenceI seq;
\r
SequenceI seq;
\r
- ColourSchemeI cs = null;
\r
AlignmentI alignment = av.getAlignment();
\r
\r
// draws the top row, the measure rule
\r
AlignmentI alignment = av.getAlignment();
\r
\r
// draws the top row, the measure rule
\r
@@
-132,7
+132,6
@@
public class HTMLOutput
for (i = 0; i < alignment.getHeight(); i++)
\r
{
\r
seq = alignment.getSequenceAt(i);
\r
for (i = 0; i < alignment.getHeight(); i++)
\r
{
\r
seq = alignment.getSequenceAt(i);
\r
- groups = alignment.findAllGroups(seq);
\r
\r
String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
\r
\r
\r
String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
\r
\r
@@
-142,25
+141,12
@@
public class HTMLOutput
\r
for (int res = 0; res < seq.getLength(); res++)
\r
{
\r
\r
for (int res = 0; res < seq.getLength(); res++)
\r
{
\r
- cs = av.getGlobalColourScheme();
\r
\r
\r
- if (groups != null)
\r
- {
\r
- for (int k = 0; k < groups.length; k++)
\r
- {
\r
- if ( (groups[k].getStartRes() <= res) &&
\r
- (groups[k].getEndRes() >= res))
\r
- {
\r
- cs = groups[k].cs;
\r
-
\r
- break;
\r
- }
\r
- }
\r
- }
\r
+ color = sr.findSequenceColour(Color.white, seq, res);
\r
\r
\r
- color = sr.getResidueBoxColour(cs, seq, res);
\r
+ color = fr.findFeatureColour(color, seq, res);
\r
\r
\r
- if (color.getRGB() < -1)
\r
+ if (color.getRGB() < -1)
\r
{
\r
out.println("<td bgcolor=\"#" +
\r
jalview.util.Format.getHexString(color) + "\">" +
\r
{
\r
out.println("<td bgcolor=\"#" +
\r
jalview.util.Format.getHexString(color) + "\">" +
\r
@@
-185,9
+171,7
@@
public class HTMLOutput
////////////////////////////////////
\r
/// How many sequences and residues can we fit on a printable page?
\r
AlignmentI al = av.getAlignment();
\r
////////////////////////////////////
\r
/// How many sequences and residues can we fit on a printable page?
\r
AlignmentI al = av.getAlignment();
\r
- SequenceGroup[] groups;
\r
SequenceI seq;
\r
SequenceI seq;
\r
- ColourSchemeI cs = null;
\r
String r;
\r
String g;
\r
String b;
\r
String r;
\r
String g;
\r
String b;
\r
@@
-206,49
+190,54
@@
public class HTMLOutput
endRes = al.getWidth();
\r
}
\r
\r
endRes = al.getWidth();
\r
}
\r
\r
- out.println("<tr>");
\r
- out.println("<td colspan=\"6\"> </td>");
\r
-
\r
- for (int i = startRes + 10; i < endRes; i += 10)
\r
+ if(av.getScaleAboveWrapped())
\r
{
\r
{
\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
\r
- }
\r
+ out.println("<tr>");
\r
\r
\r
- // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
\r
- // "<br>|</td>");
\r
- out.println("</tr>");
\r
+ if (av.getScaleLeftWrapped())
\r
+ out.println("<td colspan=\"7\"> </td>");
\r
+ else
\r
+ out.println("<td colspan=\"6\"> </td>");
\r
+
\r
+
\r
+ for (int i = startRes + 10; i < endRes; i += 10)
\r
+ {
\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
\r
+ }
\r
\r
\r
+ out.println("</tr>");
\r
+ }
\r
+
\r
+ int startPos, endPos;
\r
for (int s = 0; s < al.getHeight(); s++)
\r
{
\r
out.println("<tr>");
\r
seq = al.getSequenceAt(s);
\r
for (int s = 0; s < al.getHeight(); s++)
\r
{
\r
out.println("<tr>");
\r
seq = al.getSequenceAt(s);
\r
- groups = al.findAllGroups(seq);
\r
+
\r
+ startPos = seq.findPosition( startRes );
\r
+ endPos = seq.findPosition( endRes )-1;
\r
\r
String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
\r
\r
\r
String id = seq.getDisplayId(av.getShowDBPrefix(), av.getShowJVSuffix());
\r
\r
- out.println("<td nowrap>" + id +
\r
+ out.println("<td nowrap>" + id +
\r
" </td>");
\r
\r
\r
" </td>");
\r
\r
\r
- for (int res = startRes; res < endRes; res++)
\r
+ if(av.getScaleLeftWrapped())
\r
{
\r
{
\r
- cs = av.getGlobalColourScheme();
\r
+ if(startPos > seq.getEnd() || endPos==0)
\r
+ out.println("<td nowrap> </td>");
\r
+ else
\r
+ out.println("<td nowrap>" + startPos +
\r
+ " </td>");
\r
+ }
\r
\r
\r
- if (groups != null)
\r
- {
\r
- for (int k = 0; k < groups.length; k++)
\r
- {
\r
- if ( (groups[k].getStartRes() <= res) &&
\r
- (groups[k].getEndRes() >= res))
\r
- {
\r
- cs = groups[k].cs;
\r
\r
\r
- break;
\r
- }
\r
- }
\r
- }
\r
+ for (int res = startRes; res < endRes; res++)
\r
+ {
\r
+ color = sr.findSequenceColour(Color.white, seq, res);
\r
\r
\r
- color = sr.getResidueBoxColour(cs, seq, res);
\r
+ color = fr.findFeatureColour(color, seq, res);
\r
\r
if (color.getRGB() < -1)
\r
{
\r
\r
if (color.getRGB() < -1)
\r
{
\r
@@
-280,8
+269,25
@@
public class HTMLOutput
{
\r
out.println("<td>" + seq.getCharAt(res) + "</td>");
\r
}
\r
{
\r
out.println("<td>" + seq.getCharAt(res) + "</td>");
\r
}
\r
+
\r
+
\r
+ }
\r
+
\r
+ if(av.getScaleRightWrapped() &&
\r
+ endRes < startRes + av.getWrappedWidth())
\r
+ {
\r
+ out.println("<td colspan=\""+ (startRes+av.getWrappedWidth()-endRes) +"\">"
\r
+ +" </td>");
\r
+ }
\r
+
\r
+
\r
+ if(av.getScaleRightWrapped() && startPos<endPos)
\r
+ {
\r
+ out.println("<td nowrap> " + endPos +
\r
+ " </td>");
\r
}
\r
\r
}
\r
\r
+
\r
out.println("</tr>");
\r
}
\r
\r
out.println("</tr>");
\r
}
\r
\r