\n");
- out.println("\n");
-
+ out.println(
+ "\n");
//////////////
- SequenceGroup [] groups;
SequenceI seq;
- ColourSchemeI cs = null;
AlignmentI alignment = av.getAlignment();
- String r,g,b;
- // draws the top row, the measure rule
+ // draws the top row, the measure rule
out.println(" | ");
- int i=0;
- for(i=10; i"+i+"
| | ");
- out.println(" | "+i+"
| | ");
+ int i = 0;
+
+ for (i = 10; i < (alignment.getWidth() - 10); i += 10)
+ {
+ out.println("" + i + "
| | | ");
+ }
+
+ out.println(" | " + i +
+ "
| | ");
out.println(" ");
for (i = 0; i < alignment.getHeight(); i++)
{
seq = alignment.getSequenceAt(i);
- groups = alignment.findAllGroups( seq );
- out.println("| "+seq.getDisplayId()+" | ");
+
+ String id = seq.getDisplayId(av.getShowJVSuffix());
+
+ out.println(" | " + id +
+ " | ");
for (int res = 0; res < seq.getLength(); res++)
{
- cs = av.getGlobalColourScheme();
-
- if(groups!=null)
- {
- for (int k = 0; k < groups.length; k++)
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
- {
- cs = groups[k].cs;
- break;
- }
- }
+ color = sr.findSequenceColour(Color.white, seq, res);
- color = sr.getResidueBoxColour(cs, seq, res);
+ color = fr.findFeatureColour(color, seq, res);
- if(color.getRGB()<-1)
+ if (color.getRGB() < -1)
{
- 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)+" | ");
+ out.println("" +
+ seq.getCharAt(res) + " | ");
}
else
- out.println(""+seq.getCharAt(res)+" | ");
-
+ {
+ out.println("" + seq.getCharAt(res) + " | ");
+ }
}
out.println(" ");
}
+
//////////////
out.println(" ");
out.println(" ");
-
}
void drawWrappedAlignment(PrintWriter out)
{
- ////////////////////////////////////
- /// How many sequences and residues can we fit on a printable page?
- AlignmentI al = av.getAlignment();
- SequenceGroup [] groups;
- SequenceI seq;
- ColourSchemeI cs = null;
- String r,g,b;
-
- out.println("\n");
- out.println("\n");
-
- for(int startRes=0; startResal.getWidth())
- endRes = al.getWidth();
-
- out.println("");
- out.println("| | ");
- for (int i = startRes+10; i < endRes; i += 10)
- out.println("" + i + "
| | | ");
-
- // out.println(" | " + i +
- // "
| | ");
- out.println(" ");
-
-
-
- for (int s = 0; s < al.getHeight(); s++)
- {
- out.println("");
- seq = al.getSequenceAt(s);
- groups = al.findAllGroups( seq );
- out.println("| "+seq.getDisplayId()+" | ");
-
- for (int res = startRes; res < endRes; res++)
- {
- cs = av.getGlobalColourScheme();
- if(groups!=null)
- {
- for (int k = 0; k < groups.length; k++)
- if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
- {
- cs = groups[k].cs;
- break;
- }
- }
-
- color = sr.getResidueBoxColour(cs, seq, res);
-
- if(color.getRGB()<-1)
- {
- 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)+" | ");
-
- }
-
- out.println(" ");
+ ////////////////////////////////////
+ /// How many sequences and residues can we fit on a printable page?
+ AlignmentI al = av.getAlignment();
+ SequenceI seq;
+ String r;
+ String g;
+ String b;
- }
- if(endRes | ");
+ out.println("\n");
+ out.println(
+ "\n");
+
+ for (int startRes = 0; startRes < al.getWidth();
+ startRes += av.getWrappedWidth())
+ {
+ int endRes = startRes + av.getWrappedWidth();
+
+ if (endRes > al.getWidth())
+ {
+ endRes = al.getWidth();
+ }
+ if(av.getScaleAboveWrapped())
+ {
+ out.println("");
+ if (av.getScaleLeftWrapped())
+ out.println("| | ");
+ else
+ out.println(" | ");
- }
- out.println(" ");
- out.println(" |
");
+ for (int i = startRes + 10; i < endRes; i += 10)
+ {
+ out.println("" + i + "
| | | ");
+ }
+
+ out.println("");
+ }
+
+ int startPos, endPos;
+ for (int s = 0; s < al.getHeight(); s++)
+ {
+ out.println("");
+ seq = al.getSequenceAt(s);
+
+ startPos = seq.findPosition( startRes );
+ endPos = seq.findPosition( endRes )-1;
+
+ String id = seq.getDisplayId(av.getShowJVSuffix());
+
+ out.println("| " + id +
+ " | ");
+
+
+ if(av.getScaleLeftWrapped())
+ {
+ if(startPos > seq.getEnd() || endPos==0)
+ out.println(" | ");
+ else
+ out.println("" + startPos +
+ " | ");
+ }
+
+
+ for (int res = startRes; res < endRes; res++)
+ {
+ color = sr.findSequenceColour(Color.white, seq, res);
+
+ color = fr.findFeatureColour(color, seq, res);
+
+ if (color.getRGB() < -1)
+ {
+ 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) + " | ");
+ }
+
+
+ }
+
+ if(av.getScaleRightWrapped() &&
+ endRes < startRes + av.getWrappedWidth())
+ {
+ out.println(""
+ +" | ");
+ }
+
+
+ if(av.getScaleRightWrapped() && startPos " + endPos +
+ " ");
+ }
+
+
+ out.println(" ");
+ }
+
+ if (endRes < al.getWidth())
+ {
+ out.println(" | ");
+ }
+ }
+
+ out.println(" ");
+ out.println(" |
");
}
+ public static String getImageMapHTML()
+ {
+ return new String(
+ "\n"
+ +"\n"
+ +"\n"
+ +"\n"
+ +"\n"
+ +"\n"
+ +"\n");
+ }
}
|