2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import jalview.datamodel.*;
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23 import jalview.gui.*;
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25 import jalview.schemes.*;
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33 import javax.swing.*;
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36 public class HTMLOutput {
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38 SequenceRenderer sr;
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41 public HTMLOutput(AlignViewport av) {
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43 sr = new SequenceRenderer(av);
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45 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
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46 "LAST_DIRECTORY"), new String[] { "html" },
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47 new String[] { "HTML files" }, "HTML files");
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49 chooser.setFileView(new JalviewFileView());
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50 chooser.setDialogTitle("Save as HTML");
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51 chooser.setToolTipText("Save");
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53 int value = chooser.showSaveDialog(null);
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55 if (value == JalviewFileChooser.APPROVE_OPTION) {
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56 String choice = chooser.getSelectedFile().getPath();
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57 jalview.bin.Cache.setProperty("LAST_DIRECTORY",
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58 chooser.getSelectedFile().getParent());
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61 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
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63 out.println("<HTML>");
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64 out.println("<style type=\"text/css\">");
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65 out.println("<!--");
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66 out.print("td {font-family: \"" + av.getFont().getFamily() +
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67 "\", \"" + av.getFont().getName() + "\", mono; " +
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68 "font-size: " + av.getFont().getSize() + "px; ");
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70 if (av.getFont().getStyle() == Font.BOLD) {
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71 out.print("font-weight: BOLD; ");
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74 if (av.getFont().getStyle() == Font.ITALIC) {
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75 out.print("font-style: italic; ");
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78 out.println("text-align: center; }");
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81 out.println("</style>");
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82 out.println("<BODY>");
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84 if (av.getWrapAlignment()) {
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85 drawWrappedAlignment(out);
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87 drawUnwrappedAlignment(out);
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90 out.println("\n</body>\n</html>");
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92 jalview.util.BrowserLauncher.openURL("file:///" + choice);
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93 } catch (Exception ex) {
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94 ex.printStackTrace();
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99 void drawUnwrappedAlignment(PrintWriter out) {
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100 out.println("<table border=\"1\"><tr><td>\n");
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102 "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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105 SequenceGroup[] groups;
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107 ColourSchemeI cs = null;
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108 AlignmentI alignment = av.getAlignment();
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113 // draws the top row, the measure rule
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114 out.println("<tr><td colspan=\"6\"></td>");
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118 for (i = 10; i < (alignment.getWidth() - 10); i += 10)
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119 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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121 out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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123 out.println("</tr>");
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125 for (i = 0; i < alignment.getHeight(); i++) {
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126 seq = alignment.getSequenceAt(i);
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127 groups = alignment.findAllGroups(seq);
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129 if (av.getShowFullId()) {
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130 out.println("<tr><td nowrap>" + seq.getDisplayId() +
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131 " </td>");
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133 out.println("<tr><td nowrap>" + seq.getName() +
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134 " </td>");
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137 for (int res = 0; res < seq.getLength(); res++) {
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138 cs = av.getGlobalColourScheme();
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140 if (groups != null) {
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141 for (int k = 0; k < groups.length; k++)
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142 if ((groups[k].getStartRes() <= res) &&
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143 (groups[k].getEndRes() >= res)) {
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150 color = sr.getResidueBoxColour(cs, seq, res);
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152 if (color.getRGB() < -1) {
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153 out.println("<td bgcolor=\"#" +
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154 jalview.util.Format.getHexString(color) + "\">" +
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155 seq.getCharAt(res) + "</td>");
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157 out.println("<td>" + seq.getCharAt(res) + "</td>");
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161 out.println("</tr>");
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165 out.println("</table>");
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166 out.println("</td></tr></table>");
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169 void drawWrappedAlignment(PrintWriter out) {
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170 ////////////////////////////////////
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171 /// How many sequences and residues can we fit on a printable page?
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172 AlignmentI al = av.getAlignment();
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173 SequenceGroup[] groups;
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175 ColourSchemeI cs = null;
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180 out.println("<table border=\"1\"><tr><td>\n");
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182 "<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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184 for (int startRes = 0; startRes < al.getWidth();
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185 startRes += av.getChunkWidth()) {
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186 int endRes = startRes + av.getChunkWidth();
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188 if (endRes > al.getWidth()) {
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189 endRes = al.getWidth();
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192 out.println("<tr>");
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193 out.println("<td colspan=\"6\"> </td>");
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195 for (int i = startRes + 10; i < endRes; i += 10)
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196 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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198 // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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200 out.println("</tr>");
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202 for (int s = 0; s < al.getHeight(); s++) {
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203 out.println("<tr>");
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204 seq = al.getSequenceAt(s);
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205 groups = al.findAllGroups(seq);
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207 if (av.getShowFullId()) {
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208 out.println("<td nowrap>" + seq.getDisplayId() +
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209 " </td>");
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211 out.println("<td nowrap>" + seq.getName() +
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212 " </td>");
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215 for (int res = startRes; res < endRes; res++) {
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216 cs = av.getGlobalColourScheme();
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218 if (groups != null) {
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219 for (int k = 0; k < groups.length; k++)
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220 if ((groups[k].getStartRes() <= res) &&
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221 (groups[k].getEndRes() >= res)) {
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228 color = sr.getResidueBoxColour(cs, seq, res);
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230 if (color.getRGB() < -1) {
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231 r = Integer.toHexString(color.getRed());
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233 if (r.length() < 2) {
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237 g = Integer.toHexString(color.getGreen());
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239 if (g.length() < 2) {
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243 b = Integer.toHexString(color.getBlue());
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245 if (b.length() < 2) {
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249 out.println("<td bgcolor=\"#" + r + g + b + "\">" +
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250 seq.getCharAt(res) + "</td>");
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252 out.println("<td>" + seq.getCharAt(res) + "</td>");
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256 out.println("</tr>");
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259 if (endRes < al.getWidth()) {
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260 out.println("<tr><td height=\"5\"></td></tr>");
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264 out.println("</table>");
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265 out.println("</table>");
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