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