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