src/jalview/ext/jmol/JmolCommands.java

   1 /**\r
   2  * \r
   3  */\r
   4 package jalview.ext.jmol;\r
   5 \r
   6 import jalview.api.FeatureRenderer;\r
   7 import jalview.api.SequenceRenderer;\r
   8 import jalview.datamodel.AlignmentI;\r
   9 import jalview.datamodel.SequenceI;\r
  10 import jalview.structure.StructureMapping;\r
  11 import jalview.structure.StructureSelectionManager;\r
  12 import jalview.util.Comparison;\r
  13 \r
  14 import java.awt.Color;\r
  15 import java.util.ArrayList;\r
  16 \r
  17 /**\r
  18  * Routines for generating Jmol commands for Jalview/Jmol binding\r
  19  * another cruisecontrol test.\r
  20  * \r
  21  * @author JimP\r
  22  *\r
  23  */\r
  24 public class JmolCommands\r
  25 {\r
  26 \r
  27   /**\r
  28    * Jmol utility which constructs the commands to colour chains by the given alignment\r
  29    * \r
  30    */\r
  31   public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
  32   {\r
  33     ArrayList<String> str = new ArrayList<String>();\r
  34     StringBuffer command = new StringBuffer();\r
  35   \r
  36     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
  37     {\r
  38       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
  39   \r
  40       if (mapping == null || mapping.length < 1)\r
  41         continue;\r
  42   \r
  43       int lastPos = -1;\r
  44       for (int s = 0; s < sequence[pdbfnum].length; s++)\r
  45       {\r
  46         for (int sp, m = 0; m < mapping.length; m++)\r
  47         {\r
  48           if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
  49                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
  50           {\r
  51             SequenceI asp = alignment.getSequenceAt(sp);\r
  52             for (int r = 0; r < asp.getLength(); r++)\r
  53             {\r
  54               // no mapping to gaps in sequence\r
  55               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
  56               {\r
  57                 continue;\r
  58               }\r
  59               int pos = mapping[m].getPDBResNum(asp.findPosition(r));\r
  60   \r
  61               if (pos < 1 || pos == lastPos)\r
  62                 continue;\r
  63   \r
  64               lastPos = pos;\r
  65   \r
  66               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);\r
  67   \r
  68               if (fr != null)\r
  69                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);\r
  70               String newSelcom = (mapping[m].getChain() != " " ? ":"\r
  71                       + mapping[m].getChain() : "")\r
  72                       + "/"\r
  73                       + (pdbfnum + 1)\r
  74                       + ".1"\r
  75                       + ";color["\r
  76                       + col.getRed()\r
  77                       + ","\r
  78                       + col.getGreen()\r
  79                       + ","\r
  80                       + col.getBlue() + "]";\r
  81               if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))\r
  82               {\r
  83                 command = JmolCommands.condenseCommand(command, pos);\r
  84                 continue;\r
  85               }\r
  86               // TODO: deal with case when buffer is too large for Jmol to parse\r
  87               // - execute command and flush\r
  88   \r
  89               command.append(";");\r
  90               if (command.length()>51200)\r
  91               {\r
  92                 // add another chunk\r
  93                 str.add(command.toString());\r
  94                 command.setLength(0);\r
  95               }\r
  96               command.append("select " + pos);\r
  97               command.append(newSelcom);\r
  98             }\r
  99             break;\r
 100           }\r
 101         }\r
 102       }\r
 103     }\r
 104     {\r
 105       // add final chunk\r
 106       str.add(command.toString());\r
 107       command.setLength(0);\r
 108     }\r
 109     return str.toArray(new String[str.size()]);\r
 110   }\r
 111 \r
 112   public static StringBuffer condenseCommand(StringBuffer command, int pos)\r
 113   {\r
 114   \r
 115     // work back to last 'select'\r
 116     int p=command.length(),q=p;\r
 117     do {\r
 118       p-=6;\r
 119       if (p<1) { p=0; };\r
 120     } while ((q=command.indexOf("select",p))==-1 && p>0);\r
 121     \r
 122     StringBuffer sb = new StringBuffer(command.substring(0,q+7));\r
 123   \r
 124     command =  command.delete(0,q+7);\r
 125   \r
 126     String start;\r
 127   \r
 128     if (command.indexOf("-") > -1)\r
 129     {\r
 130       start = command.substring(0, command.indexOf("-"));\r
 131     }\r
 132     else\r
 133     {\r
 134       start = command.substring(0, command.indexOf(":"));\r
 135     }\r
 136   \r
 137     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));\r
 138   \r
 139     return sb;\r
 140   }\r
 141 \r
 142 }\r