\n");
+ out.println(
+ "\n");
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save as HTML");
- chooser.setToolTipText("Save");
+ //////////////
+ SequenceI seq;
+ AlignmentI alignment = av.getAlignment();
- int value = chooser.showSaveDialog(null);
+ // draws the top row, the measure rule
+ out.println(" | ");
- if (value == JalviewFileChooser.APPROVE_OPTION) {
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ int i = 0;
- try {
- PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
- choice));
- out.println("");
- out.println("");
- out.println("");
+ out.println(" | " + id +
+ " | ");
- 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();
- }
- }
- }
+ for (int res = 0; res < seq.getLength(); res++)
+ {
- void drawUnwrappedAlignment(PrintWriter out) {
- out.println("\n");
- out.println(
- "\n");
+ color = sr.findSequenceColour(Color.white, seq, res);
- //////////////
- SequenceGroup[] groups;
- SequenceI seq;
- ColourSchemeI cs = null;
- AlignmentI alignment = av.getAlignment();
- String r;
- String g;
- String b;
+ color = fr.findFeatureColour(color, seq, res);
- // draws the top row, the measure rule
- out.println(" | ");
+ if (color.getRGB() < -1)
+ {
+ out.println("" +
+ seq.getCharAt(res) + " | ");
+ }
+ else
+ {
+ out.println("" + seq.getCharAt(res) + " | ");
+ }
+ }
- int i = 0;
+ out.println(" ");
+ }
- for (i = 10; i < (alignment.getWidth() - 10); i += 10)
- out.println("" + i + "
| | | ");
+ //////////////
+ out.println(" ");
+ out.println(" |
");
+ }
+
+ void drawWrappedAlignment(PrintWriter out)
+ {
+ ////////////////////////////////////
+ /// How many sequences and residues can we fit on a printable page?
+ AlignmentI al = av.getAlignment();
+ SequenceI seq;
+ String r;
+ String g;
+ String b;
+
+ 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(" | ");
+
+
+ for (int i = startRes + 10; i < endRes; 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);
+ int startPos, endPos;
+ for (int s = 0; s < al.getHeight(); s++)
+ {
+ out.println("");
+ seq = al.getSequenceAt(s);
- if (av.getShowFullId()) {
- out.println(" | " + seq.getDisplayId() +
- " | ");
- } else {
- out.println(" | " + seq.getName() +
- " | ");
- }
+ startPos = seq.findPosition( startRes );
+ endPos = seq.findPosition( endRes )-1;
- for (int res = 0; res < seq.getLength(); res++) {
- cs = av.getGlobalColourScheme();
+ String id = seq.getDisplayId(av.getShowJVSuffix());
- if (groups != null) {
- for (int k = 0; k < groups.length; k++)
- if ((groups[k].getStartRes() <= res) &&
- (groups[k].getEndRes() >= res)) {
- cs = groups[k].cs;
+ out.println("" + id +
+ " | ");
- break;
- }
- }
-
- color = sr.getResidueBoxColour(cs, seq, res);
-
- if (color.getRGB() < -1) {
- out.println("" +
- seq.getCharAt(res) + " | ");
- } else {
- out.println("" + seq.getCharAt(res) + " | ");
- }
- }
- out.println(" ");
+ if(av.getScaleLeftWrapped())
+ {
+ if(startPos > seq.getEnd() || endPos==0)
+ out.println(" | ");
+ else
+ out.println("" + startPos +
+ " | ");
}
- //////////////
- 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;
- String g;
- String b;
-
- 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 res = startRes; res < endRes; res++)
+ {
+ color = sr.findSequenceColour(Color.white, seq, res);
- for (int s = 0; s < al.getHeight(); s++) {
- out.println("");
- seq = al.getSequenceAt(s);
- groups = al.findAllGroups(seq);
+ color = fr.findFeatureColour(color, seq, res);
- if (av.getShowFullId()) {
- out.println("| " + seq.getDisplayId() +
- " | ");
- } else {
- out.println("" + seq.getName() +
- " | ");
- }
+ if (color.getRGB() < -1)
+ {
+ r = Integer.toHexString(color.getRed());
- for (int res = startRes; res < endRes; res++) {
- cs = av.getGlobalColourScheme();
+ if (r.length() < 2)
+ {
+ r = "0" + r;
+ }
- if (groups != null) {
- for (int k = 0; k < groups.length; k++)
- if ((groups[k].getStartRes() <= res) &&
- (groups[k].getEndRes() >= res)) {
- cs = groups[k].cs;
+ g = Integer.toHexString(color.getGreen());
- break;
- }
- }
+ if (g.length() < 2)
+ {
+ g = "0" + g;
+ }
- color = sr.getResidueBoxColour(cs, seq, res);
+ b = Integer.toHexString(color.getBlue());
- if (color.getRGB() < -1) {
- r = Integer.toHexString(color.getRed());
+ if (b.length() < 2)
+ {
+ b = "0" + b;
+ }
- if (r.length() < 2) {
- r = "0" + r;
- }
+ out.println("" +
+ seq.getCharAt(res) + " | ");
+ }
+ else
+ {
+ out.println("" + seq.getCharAt(res) + " | ");
+ }
- g = Integer.toHexString(color.getGreen());
- if (g.length() < 2) {
- g = "0" + g;
- }
+ }
- b = Integer.toHexString(color.getBlue());
+ if(av.getScaleRightWrapped() &&
+ endRes < startRes + av.getWrappedWidth())
+ {
+ out.println(""
+ +" | ");
+ }
- if (b.length() < 2) {
- b = "0" + b;
- }
- out.println("" +
- seq.getCharAt(res) + " | ");
- } else {
- out.println("" + seq.getCharAt(res) + " | ");
- }
- }
+ if(av.getScaleRightWrapped() && startPos " + endPos +
+ " ");
+ }
- out.println(" ");
- }
- if (endRes < al.getWidth()) {
- out.println(" | ");
- }
- }
+ out.println("");
+ }
- out.println(" ");
- out.println(" |
");
+ if (endRes < al.getWidth())
+ {
+ out.println(" | ");
+ }
}
+
+ out.println(" ");
+ out.println(" |