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 another\r
  19  * 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\r
  29    * alignment\r
  30    * \r
  31    */\r
  32   public static String[] getColourBySequenceCommand(\r
  33           StructureSelectionManager ssm, String[] files,\r
  34           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,\r
  35           AlignmentI alignment)\r
  36   {\r
  37     ArrayList<String> str = new ArrayList<String>();\r
  38     StringBuffer command = new StringBuffer();\r
  39 \r
  40     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
  41     {\r
  42       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\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()\r
  86                       && command.substring(\r
  87                               command.length() - newSelcom.length())\r
  88                               .equals(newSelcom))\r
  89               {\r
  90                 command = VarnaCommands.condenseCommand(command, pos);\r
  91                 continue;\r
  92               }\r
  93               // TODO: deal with case when buffer is too large for Jmol to parse\r
  94               // - execute command and flush\r
  95 \r
  96               command.append(";");\r
  97               if (command.length() > 51200)\r
  98               {\r
  99                 // add another chunk\r
 100                 str.add(command.toString());\r
 101                 command.setLength(0);\r
 102               }\r
 103               command.append("select " + pos);\r
 104               command.append(newSelcom);\r
 105             }\r
 106             break;\r
 107           }\r
 108         }\r
 109       }\r
 110     }\r
 111     {\r
 112       // add final chunk\r
 113       str.add(command.toString());\r
 114       command.setLength(0);\r
 115     }\r
 116     return str.toArray(new String[str.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     {\r
 126       p -= 6;\r
 127       if (p < 1)\r
 128       {\r
 129         p = 0;\r
 130       }\r
 131       ;\r
 132     } while ((q = command.indexOf("select", p)) == -1 && p > 0);\r
 133 \r
 134     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));\r
 135 \r
 136     command = command.delete(0, q + 7);\r
 137 \r
 138     String start;\r
 139 \r
 140     if (command.indexOf("-") > -1)\r
 141     {\r
 142       start = command.substring(0, command.indexOf("-"));\r
 143     }\r
 144     else\r
 145     {\r
 146       start = command.substring(0, command.indexOf(":"));\r
 147     }\r
 148 \r
 149     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));\r
 150 \r
 151     return sb;\r
 152   }\r
 153 \r
 154 }\r