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