src/jalview/ext/varna/VarnaCommands.java

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