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