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