src/jalview/io/HTMLOutput.java

   1 package jalview.io;\r
   2 \r
   3 import jalview.gui.*;\r
   4 import jalview.datamodel.*;\r
   5 import jalview.schemes.*;\r
   6 import java.awt.*;\r
   7 import javax.swing.*;\r
   8 import java.io.*;\r
   9 import java.util.*;\r
  10 \r
  11 \r
  12 public class HTMLOutput\r
  13 {\r
  14   AlignViewport av;\r
  15   SequenceRenderer sr;\r
  16   Color color;\r
  17 \r
  18   public HTMLOutput(AlignViewport av)\r
  19   {\r
  20     this.av = av;\r
  21     sr = new SequenceRenderer(av);\r
  22     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
  23     chooser.setFileView(new JalviewFileView());\r
  24     chooser.setDialogTitle("Save as HTML");\r
  25     chooser.setToolTipText("Save");\r
  26     int value = chooser.showSaveDialog(null);\r
  27     if(value == JalviewFileChooser.APPROVE_OPTION)\r
  28     {\r
  29       String choice =  chooser.getSelectedFile().getPath();\r
  30       jalview.bin.Cache.setProperty("LAST_DIRECTORY",  choice);\r
  31       try{\r
  32         PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(choice));\r
  33         out.println("<HTML>");\r
  34         out.println("<style type=\"text/css\">");\r
  35         out.println("<!--");\r
  36         out.print("td {font-family: \""+av.getFont().getFamily()+"\", \""+av.getFont().getName()+ "\", mono; "\r
  37                    +"font-size: "+av.getFont().getSize()+"px; ");\r
  38 \r
  39 \r
  40         if (av.getFont().getStyle() == Font.BOLD)\r
  41            out.print("font-weight: BOLD; ");\r
  42 \r
  43         if (av.getFont().getStyle() == Font.ITALIC)\r
  44            out.print("font-style: italic; ");\r
  45 \r
  46         out.println("text-align: center; }");\r
  47 \r
  48         out.println("-->");\r
  49         out.println("</style>");\r
  50         out.println("<BODY>");\r
  51 \r
  52 \r
  53         if(av.getWrapAlignment())\r
  54            drawWrappedAlignment(out);\r
  55         else\r
  56            drawUnwrappedAlignment(out);\r
  57 \r
  58         out.println("\n</body>\n</html>");\r
  59         out.close();\r
  60         jalview.util.BrowserLauncher.openURL( "file:///"+choice );\r
  61       }\r
  62       catch(Exception ex){ex.printStackTrace();}\r
  63     }\r
  64   }\r
  65 \r
  66   void drawUnwrappedAlignment(PrintWriter out)\r
  67   {\r
  68 \r
  69     out.println("<table border=\"1\"><tr><td>\n");\r
  70     out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
  71 \r
  72 \r
  73     //////////////\r
  74     SequenceGroup [] groups;\r
  75     SequenceI seq;\r
  76     ColourSchemeI cs = null;\r
  77     AlignmentI alignment = av.getAlignment();\r
  78     String r,g,b;\r
  79 \r
  80   // draws the top row, the measure rule\r
  81     out.println("<tr><td colspan=\"6\"></td>");\r
  82     int i=0;\r
  83     for(i=10; i<alignment.getWidth()-10; i+=10)\r
  84       out.println("<td colspan=\"9\">"+i+"<br>|</td><td></td>");\r
  85 \r
  86     out.println("<td colspan=\"3\"></td><td colspan=\"3\">"+i+"<br>|</td>");\r
  87     out.println("</tr>");\r
  88 \r
  89     for (i = 0; i < alignment.getHeight(); i++)\r
  90     {\r
  91       seq = alignment.getSequenceAt(i);\r
  92       groups = alignment.findAllGroups( seq );\r
  93       if(av.getShowFullId())\r
  94         out.println("<tr><td nowrap>"+seq.getDisplayId()+"&nbsp;&nbsp;</td>");\r
  95       else\r
  96         out.println("<tr><td nowrap>"+seq.getName()+"&nbsp;&nbsp;</td>");\r
  97 \r
  98 \r
  99 \r
 100       for (int res = 0; res < seq.getLength(); res++)\r
 101       {\r
 102         cs = av.getGlobalColourScheme();\r
 103 \r
 104         if(groups!=null)\r
 105          {\r
 106            for (int k = 0; k < groups.length; k++)\r
 107              if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
 108              {\r
 109                cs = groups[k].cs;\r
 110                break;\r
 111              }\r
 112          }\r
 113 \r
 114 \r
 115         color = sr.getResidueBoxColour(cs, seq, res);\r
 116 \r
 117         if(color.getRGB()<-1)\r
 118         {\r
 119           r = Integer.toHexString(color.getRed());\r
 120           if(r.length()<2)\r
 121             r = "0"+r;\r
 122           g = Integer.toHexString(color.getGreen());\r
 123           if(g.length()<2)\r
 124             g = "0"+g;\r
 125           b = Integer.toHexString(color.getBlue());\r
 126           if(b.length()<2)\r
 127             b = "0"+b;\r
 128           out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
 129         }\r
 130         else\r
 131           out.println("<td>"+seq.getCharAt(res)+"</td>");\r
 132 \r
 133       }\r
 134 \r
 135       out.println("</tr>");\r
 136     }\r
 137     //////////////\r
 138     out.println("</table>");\r
 139     out.println("</td></tr></table>");\r
 140 \r
 141   }\r
 142 \r
 143   void drawWrappedAlignment(PrintWriter out)\r
 144   {\r
 145      ////////////////////////////////////\r
 146      /// How many sequences and residues can we fit on a printable page?\r
 147      AlignmentI al = av.getAlignment();\r
 148      SequenceGroup [] groups;\r
 149      SequenceI seq;\r
 150      ColourSchemeI cs = null;\r
 151      String r,g,b;\r
 152 \r
 153      out.println("<table border=\"1\"><tr><td>\n");\r
 154      out.println("<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
 155 \r
 156      for(int startRes=0; startRes<al.getWidth(); startRes+=av.getChunkWidth())\r
 157      {\r
 158 \r
 159        int endRes = startRes+av.getChunkWidth();\r
 160        if(endRes>al.getWidth())\r
 161            endRes = al.getWidth();\r
 162 \r
 163      out.println("<tr>");\r
 164      out.println("<td colspan=\"6\">&nbsp;</td>");\r
 165      for (int i = startRes+10; i < endRes; i += 10)\r
 166        out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
 167 \r
 168     // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
 169     //             "<br>|</td>");\r
 170      out.println("</tr>");\r
 171 \r
 172 \r
 173 \r
 174        for (int s = 0; s < al.getHeight(); s++)\r
 175        {\r
 176          out.println("<tr>");\r
 177          seq = al.getSequenceAt(s);\r
 178          groups = al.findAllGroups( seq );\r
 179          if(av.getShowFullId())\r
 180            out.println("<td nowrap>"+seq.getDisplayId()+"&nbsp;&nbsp;</td>");\r
 181          else\r
 182            out.println("<td nowrap>"+seq.getName()+"&nbsp;&nbsp;</td>");\r
 183 \r
 184          for (int res = startRes; res < endRes; res++)\r
 185               {\r
 186                 cs = av.getGlobalColourScheme();\r
 187                 if(groups!=null)\r
 188                  {\r
 189                    for (int k = 0; k < groups.length; k++)\r
 190                      if (groups[k].getStartRes() <= res && groups[k].getEndRes() >= res)\r
 191                      {\r
 192                        cs = groups[k].cs;\r
 193                        break;\r
 194                      }\r
 195                  }\r
 196 \r
 197                 color = sr.getResidueBoxColour(cs, seq, res);\r
 198 \r
 199                 if(color.getRGB()<-1)\r
 200                 {\r
 201                   r = Integer.toHexString(color.getRed());\r
 202                   if(r.length()<2)\r
 203                     r = "0"+r;\r
 204                   g = Integer.toHexString(color.getGreen());\r
 205                   if(g.length()<2)\r
 206                     g = "0"+g;\r
 207                   b = Integer.toHexString(color.getBlue());\r
 208                   if(b.length()<2)\r
 209                     b = "0"+b;\r
 210                   out.println("<td bgcolor=\"#"+ r + g + b + "\">"+seq.getCharAt(res)+"</td>");\r
 211                 }\r
 212                 else\r
 213                   out.println("<td>"+seq.getCharAt(res)+"</td>");\r
 214 \r
 215               }\r
 216 \r
 217          out.println("</tr>");\r
 218 \r
 219        }\r
 220        if(endRes<al.getWidth())\r
 221            out.println("<tr><td height=\"5\"></td></tr>");\r
 222 \r
 223 \r
 224 \r
 225      }\r
 226 \r
 227     out.println("</table>");\r
 228     out.println("</table>");\r
 229 \r
 230 \r
 231 \r
 232   }\r
 233 \r
 234 \r
 235 }\r