3 import jalview.gui.*;
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4 import jalview.datamodel.*;
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5 import jalview.schemes.*;
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7 import javax.swing.*;
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12 public class HTMLOutput
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15 SequenceRenderer sr;
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18 public HTMLOutput(AlignViewport av)
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21 sr = new SequenceRenderer(av);
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22 JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
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23 chooser.setDialogTitle("Save as HTML");
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24 chooser.setToolTipText("Save");
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25 int value = chooser.showSaveDialog(null);
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26 if(value == JFileChooser.APPROVE_OPTION)
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28 String choice = chooser.getSelectedFile().getPath();
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29 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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31 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));
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32 out.println("<HTML>");
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33 out.println("<style type=\"text/css\">");
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34 out.println("<!--");
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35 out.print("td {font-family: \""+av.getFont().getFamily()+"\", \""+av.getFont().getName()+ "\", mono; "
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36 +"font-size: "+av.getFont().getSize()+"px; ");
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39 if (av.getFont().getStyle() == Font.BOLD)
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40 out.print("font-weight: BOLD; ");
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42 if (av.getFont().getStyle() == Font.ITALIC)
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43 out.print("font-style: italic; ");
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45 out.println("text-align: center; }");
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48 out.println("</style>");
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49 out.println("<BODY>");
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52 if(av.getWrapAlignment())
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53 drawWrappedAlignment(out);
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55 drawUnwrappedAlignment(out);
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57 out.println("\n</body>\n</html>");
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59 jalview.util.BrowserLauncher.openURL( "file:///"+choice );
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61 catch(Exception ex){ex.printStackTrace();}
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65 void drawUnwrappedAlignment(PrintWriter out)
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68 out.println("<table border=\"1\"><tr><td>\n");
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69 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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73 SequenceGroup [] groups;
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75 ColourSchemeI cs = null;
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76 AlignmentI alignment = av.getAlignment();
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79 // draws the top row, the measure rule
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80 out.println("<tr><td colspan=\"6\"></td>");
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82 for(i=10; i<alignment.getWidth()-10; i+=10)
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83 out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");
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85 out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");
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86 out.println("</tr>");
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88 for (i = 0; i < alignment.getHeight(); i++)
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90 seq = alignment.getSequenceAt(i);
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91 groups = alignment.findAllGroups( seq );
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92 out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");
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95 for (int res = 0; res < seq.getLength(); res++)
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97 cs = av.getGlobalColourScheme();
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101 for (int k = 0; k < groups.length; k++)
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102 if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
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110 color = sr.getResidueBoxColour(cs, seq, res);
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112 if(color.getRGB()<-1)
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114 r = Integer.toHexString(color.getRed());
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117 g = Integer.toHexString(color.getGreen());
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120 b = Integer.toHexString(color.getBlue());
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123 out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");
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126 out.println("<td>"+seq.getCharAt(res)+"</td>");
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130 out.println("</tr>");
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133 out.println("</table>");
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134 out.println("</td></tr></table>");
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138 void drawWrappedAlignment(PrintWriter out)
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140 ////////////////////////////////////
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141 /// How many sequences and residues can we fit on a printable page?
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142 AlignmentI al = av.getAlignment();
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143 SequenceGroup [] groups;
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145 ColourSchemeI cs = null;
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148 out.println("<table border=\"1\"><tr><td>\n");
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149 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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151 for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())
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154 int endRes = startRes+av.getChunkWidth();
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155 if(endRes>al.getWidth())
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156 endRes = al.getWidth();
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158 out.println("<tr>");
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159 out.println("<td colspan=\"6\"> </td>");
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160 for (int i = startRes+10; i < endRes; i += 10)
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161 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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163 // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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165 out.println("</tr>");
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169 for (int s = 0; s < al.getHeight(); s++)
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171 out.println("<tr>");
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172 seq = al.getSequenceAt(s);
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173 groups = al.findAllGroups( seq );
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174 out.println("<td nowrap>"+seq.getDisplayId()+" </td>");
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176 for (int res = startRes; res < endRes; res++)
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178 cs = av.getGlobalColourScheme();
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181 for (int k = 0; k < groups.length; k++)
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182 if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
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189 color = sr.getResidueBoxColour(cs, seq, res);
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191 if(color.getRGB()<-1)
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193 r = Integer.toHexString(color.getRed());
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196 g = Integer.toHexString(color.getGreen());
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199 b = Integer.toHexString(color.getBlue());
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202 out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");
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205 out.println("<td>"+seq.getCharAt(res)+"</td>");
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209 out.println("</tr>");
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212 if(endRes<al.getWidth())
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213 out.println("<tr><td height=\"5\"></td></tr>");
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219 out.println("</table>");
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220 out.println("</table>");
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