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