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(jalview.bin.Cache.getProperty("LAST_DIRECTORY")
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23 , new String[]{"html"}, "HTML files");
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25 chooser.setFileView(new JalviewFileView());
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26 chooser.setDialogTitle("Save as HTML");
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27 chooser.setToolTipText("Save");
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28 int value = chooser.showSaveDialog(null);
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29 if(value == JalviewFileChooser.APPROVE_OPTION)
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31 String choice = chooser.getSelectedFile().getPath();
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32 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
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34 PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));
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35 out.println("<HTML>");
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36 out.println("<style type=\"text/css\">");
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37 out.println("<!--");
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38 out.print("td {font-family: \""+av.getFont().getFamily()+"\", \""+av.getFont().getName()+ "\", mono; "
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39 +"font-size: "+av.getFont().getSize()+"px; ");
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42 if (av.getFont().getStyle() == Font.BOLD)
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43 out.print("font-weight: BOLD; ");
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45 if (av.getFont().getStyle() == Font.ITALIC)
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46 out.print("font-style: italic; ");
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48 out.println("text-align: center; }");
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51 out.println("</style>");
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52 out.println("<BODY>");
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55 if(av.getWrapAlignment())
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56 drawWrappedAlignment(out);
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58 drawUnwrappedAlignment(out);
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60 out.println("\n</body>\n</html>");
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62 jalview.util.BrowserLauncher.openURL( "file:///"+choice );
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64 catch(Exception ex){ex.printStackTrace();}
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68 void drawUnwrappedAlignment(PrintWriter out)
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71 out.println("<table border=\"1\"><tr><td>\n");
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72 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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76 SequenceGroup [] groups;
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78 ColourSchemeI cs = null;
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79 AlignmentI alignment = av.getAlignment();
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82 // draws the top row, the measure rule
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83 out.println("<tr><td colspan=\"6\"></td>");
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85 for(i=10; i<alignment.getWidth()-10; i+=10)
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86 out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");
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88 out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");
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89 out.println("</tr>");
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91 for (i = 0; i < alignment.getHeight(); i++)
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93 seq = alignment.getSequenceAt(i);
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94 groups = alignment.findAllGroups( seq );
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95 if(av.getShowFullId())
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96 out.println("<tr><td nowrap>"+seq.getDisplayId()+" </td>");
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98 out.println("<tr><td nowrap>"+seq.getName()+" </td>");
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102 for (int res = 0; res < seq.getLength(); res++)
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104 cs = av.getGlobalColourScheme();
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108 for (int k = 0; k < groups.length; k++)
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109 if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
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117 color = sr.getResidueBoxColour(cs, seq, res);
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119 if(color.getRGB()<-1)
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121 r = Integer.toHexString(color.getRed());
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124 g = Integer.toHexString(color.getGreen());
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127 b = Integer.toHexString(color.getBlue());
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130 out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");
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133 out.println("<td>"+seq.getCharAt(res)+"</td>");
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137 out.println("</tr>");
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140 out.println("</table>");
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141 out.println("</td></tr></table>");
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145 void drawWrappedAlignment(PrintWriter out)
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147 ////////////////////////////////////
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148 /// How many sequences and residues can we fit on a printable page?
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149 AlignmentI al = av.getAlignment();
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150 SequenceGroup [] groups;
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152 ColourSchemeI cs = null;
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155 out.println("<table border=\"1\"><tr><td>\n");
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156 out.println("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");
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158 for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())
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161 int endRes = startRes+av.getChunkWidth();
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162 if(endRes>al.getWidth())
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163 endRes = al.getWidth();
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165 out.println("<tr>");
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166 out.println("<td colspan=\"6\"> </td>");
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167 for (int i = startRes+10; i < endRes; i += 10)
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168 out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");
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170 // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +
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172 out.println("</tr>");
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176 for (int s = 0; s < al.getHeight(); s++)
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178 out.println("<tr>");
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179 seq = al.getSequenceAt(s);
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180 groups = al.findAllGroups( seq );
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181 if(av.getShowFullId())
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182 out.println("<td nowrap>"+seq.getDisplayId()+" </td>");
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184 out.println("<td nowrap>"+seq.getName()+" </td>");
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186 for (int res = startRes; res < endRes; res++)
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188 cs = av.getGlobalColourScheme();
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191 for (int k = 0; k < groups.length; k++)
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192 if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)
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199 color = sr.getResidueBoxColour(cs, seq, res);
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201 if(color.getRGB()<-1)
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203 r = Integer.toHexString(color.getRed());
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206 g = Integer.toHexString(color.getGreen());
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209 b = Integer.toHexString(color.getBlue());
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212 out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");
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215 out.println("<td>"+seq.getCharAt(res)+"</td>");
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219 out.println("</tr>");
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222 if(endRes<al.getWidth())
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223 out.println("<tr><td height=\"5\"></td></tr>");
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229 out.println("</table>");
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230 out.println("</table>");
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