\n");
- out.println("\n");
+ public HTMLOutput(AlignViewport av) {
+ this.av = av;
+ sr = new SequenceRenderer(av);
+
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+ "LAST_DIRECTORY"), new String[] { "html" },
+ new String[] { "HTML files" }, "HTML files");
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Save as HTML");
+ chooser.setToolTipText("Save");
+
+ int value = chooser.showSaveDialog(null);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION) {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+
+ try {
+ PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+ choice));
+ out.println("");
+ out.println("");
+ out.println("");
+
+ if (av.getWrapAlignment()) {
+ drawWrappedAlignment(out);
+ } else {
+ drawUnwrappedAlignment(out);
+ }
+
+ out.println("\n\n");
+ out.close();
+ jalview.util.BrowserLauncher.openURL("file:///" + choice);
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ }
+ }
+
+ void drawUnwrappedAlignment(PrintWriter out) {
+ out.println("\n");
+ out.println(
+ "\n");
//////////////
- SequenceGroup group;
+ SequenceGroup[] groups;
SequenceI seq;
- ColourSchemeI cs;
+ ColourSchemeI cs = null;
AlignmentI alignment = av.getAlignment();
- String r,g,b;
- for (int i = 0; i < alignment.getHeight(); 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)
- {
- 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)+" | ");
+ String r;
+ String g;
+ String b;
+
+ // draws the top row, the measure rule
+ out.println(" | ");
+
+ 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);
+
+ if (av.getShowFullId()) {
+ out.println("| " + seq.getDisplayId() +
+ " | ");
+ } else {
+ out.println(" | " + seq.getName() +
+ " | ");
}
- else
- out.println(""+seq.getCharAt(res)+" | ");
- }
+ 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;
+ }
+ }
- out.println(" ");
+ color = sr.getResidueBoxColour(cs, seq, res);
+
+ if (color.getRGB() < -1) {
+ out.println("" +
+ seq.getCharAt(res) + " | ");
+ } else {
+ out.println("" + seq.getCharAt(res) + " | ");
+ }
+ }
+
+ out.println("");
}
+
//////////////
out.println(" ");
- out.println(" |
\n\n");
+ out.println(" ");
+ }
- out.close();
+ 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;
+ String g;
+ String b;
- jalview.util.BrowserLauncher.openURL( choice );
- }
- catch(Exception ex){ex.printStackTrace();}
- }
- }
+ out.println("\n");
+ out.println(
+ "\n");
+
+ for (int startRes = 0; startRes < al.getWidth();
+ startRes += av.getChunkWidth()) {
+ int endRes = startRes + av.getChunkWidth();
+
+ if (endRes > al.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);
+
+ if (av.getShowFullId()) {
+ out.println("| " + seq.getDisplayId() +
+ " | ");
+ } else {
+ out.println("" + seq.getName() +
+ " | ");
+ }
+
+ 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(" ");
+ }
+
+ if (endRes < al.getWidth()) {
+ out.println(" | ");
+ }
+ }
+
+ out.println(" ");
+ out.println(" |
");
+ }
}
|