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 JalviewFileChooser chooser = new JalviewFileChooser(
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23 jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
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24 new String[]{"html"},
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25 new String[]{"HTML files"},
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28 chooser.setFileView(new JalviewFileView());
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29 chooser.setDialogTitle("Save as HTML");
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30 chooser.setToolTipText("Save");
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31 int value = chooser.showSaveDialog(null);
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32 if(value == JalviewFileChooser.APPROVE_OPTION)
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34 String choice = chooser.getSelectedFile().getPath();
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35 jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());
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37 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));
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38 out.println("<HTML>");
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39 out.println("<style type=\"text/css\">");
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40 out.println("<!--");
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41 out.print("td {font-family: \""+av.getFont().getFamily()+"\", \""+av.getFont().getName()+ "\", mono; "
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42 +"font-size: "+av.getFont().getSize()+"px; ");
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45 if (av.getFont().getStyle() == Font.BOLD)
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46 out.print("font-weight: BOLD; ");
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48 if (av.getFont().getStyle() == Font.ITALIC)
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49 out.print("font-style: italic; ");
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51 out.println("text-align: center; }");
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54 out.println("</style>");
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55 out.println("<BODY>");
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58 if(av.getWrapAlignment())
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59 drawWrappedAlignment(out);
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61 drawUnwrappedAlignment(out);
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63 out.println("\n</body>\n</html>");
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65 jalview.util.BrowserLauncher.openURL( "file:///"+choice );
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67 catch(Exception ex){ex.printStackTrace();}
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71 void drawUnwrappedAlignment(PrintWriter out)
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74 out.println("<table border=\"1\"><tr><td>\n");
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75 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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79 SequenceGroup [] groups;
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81 ColourSchemeI cs = null;
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82 AlignmentI alignment = av.getAlignment();
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85 // draws the top row, the measure rule
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86 out.println("<tr><td colspan=\"6\"></td>");
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88 for(i=10; i<alignment.getWidth()-10; i+=10)
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89 out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");
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91 out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");
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92 out.println("</tr>");
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94 for (i = 0; i < alignment.getHeight(); i++)
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96 seq = alignment.getSequenceAt(i);
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97 groups = alignment.findAllGroups( seq );
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98 if(av.getShowFullId())
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99 out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");
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101 out.println("<tr><td nowrap>"+seq.getName()+" </td>");
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105 for (int res = 0; res < seq.getLength(); res++)
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107 cs = av.getGlobalColourScheme();
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111 for (int k = 0; k < groups.length; k++)
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112 if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
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120 color = sr.getResidueBoxColour(cs, seq, res);
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122 if(color.getRGB()<-1)
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124 out.println("<td bgcolor=\"#"
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125 + jalview.util.Format.getHexString(color)
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126 + "\">"+seq.getCharAt(res)+"</td>");
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129 out.println("<td>"+seq.getCharAt(res)+"</td>");
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133 out.println("</tr>");
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136 out.println("</table>");
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137 out.println("</td></tr></table>");
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141 void drawWrappedAlignment(PrintWriter out)
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143 ////////////////////////////////////
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144 /// How many sequences and residues can we fit on a printable page?
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145 AlignmentI al = av.getAlignment();
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146 SequenceGroup [] groups;
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148 ColourSchemeI cs = null;
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151 out.println("<table border=\"1\"><tr><td>\n");
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152 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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154 for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())
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157 int endRes = startRes+av.getChunkWidth();
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158 if(endRes>al.getWidth())
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159 endRes = al.getWidth();
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161 out.println("<tr>");
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162 out.println("<td colspan=\"6\"> </td>");
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163 for (int i = startRes+10; i < endRes; i += 10)
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164 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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166 // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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168 out.println("</tr>");
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172 for (int s = 0; s < al.getHeight(); s++)
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174 out.println("<tr>");
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175 seq = al.getSequenceAt(s);
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176 groups = al.findAllGroups( seq );
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177 if(av.getShowFullId())
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178 out.println("<td nowrap>"+seq.getDisplayId()+" </td>");
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180 out.println("<td nowrap>"+seq.getName()+" </td>");
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182 for (int res = startRes; res < endRes; res++)
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184 cs = av.getGlobalColourScheme();
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187 for (int k = 0; k < groups.length; k++)
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188 if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
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195 color = sr.getResidueBoxColour(cs, seq, res);
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197 if(color.getRGB()<-1)
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199 r = Integer.toHexString(color.getRed());
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202 g = Integer.toHexString(color.getGreen());
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205 b = Integer.toHexString(color.getBlue());
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208 out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");
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211 out.println("<td>"+seq.getCharAt(res)+"</td>");
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215 out.println("</tr>");
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218 if(endRes<al.getWidth())
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219 out.println("<tr><td height=\"5\"></td></tr>");
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225 out.println("</table>");
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226 out.println("</table>");
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