src/jalview/ext/varna/VarnaCommands.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.ext.varna;
  19
  20 import jalview.api.FeatureRenderer;
  21 import jalview.api.SequenceRenderer;
  22 import jalview.datamodel.AlignmentI;
  23 import jalview.datamodel.SequenceI;
  24 import jalview.structure.StructureMapping;
  25 import jalview.structure.StructureSelectionManager;
  26
  27 import java.awt.Color;
  28 import java.util.ArrayList;
  29
  30 /**
  31  * Routines for generating Jmol commands for Jalview/Jmol binding another
  32  * cruisecontrol test.
  33  *
  34  * @author JimP
  35  *
  36  */
  37 public class VarnaCommands
  38 {
  39
  40   /**
  41    * Jmol utility which constructs the commands to colour chains by the given
  42    * alignment
  43    *
  44    */
  45   public static String[] getColourBySequenceCommand(
  46           StructureSelectionManager ssm, String[] files,
  47           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
  48           AlignmentI alignment)
  49   {
  50     ArrayList<String> str = new ArrayList<String>();
  51     StringBuffer command = new StringBuffer();
  52
  53     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  54     {
  55       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  56
  57       if (mapping == null || mapping.length < 1)
  58         continue;
  59
  60       int lastPos = -1;
  61       for (int s = 0; s < sequence[pdbfnum].length; s++)
  62       {
  63         for (int sp, m = 0; m < mapping.length; m++)
  64         {
  65           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  66                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  67           {
  68             SequenceI asp = alignment.getSequenceAt(sp);
  69             for (int r = 0; r < asp.getLength(); r++)
  70             {
  71               // no mapping to gaps in sequence
  72               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  73               {
  74                 continue;
  75               }
  76               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  77
  78               if (pos < 1 || pos == lastPos)
  79                 continue;
  80
  81               lastPos = pos;
  82
  83               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  84
  85               if (fr != null)
  86                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  87               String newSelcom = (mapping[m].getChain() != " " ? ":"
  88                       + mapping[m].getChain() : "")
  89                       + "/"
  90                       + (pdbfnum + 1)
  91                       + ".1"
  92                       + ";color["
  93                       + col.getRed()
  94                       + ","
  95                       + col.getGreen()
  96                       + ","
  97                       + col.getBlue() + "]";
  98               if (command.length() > newSelcom.length()
  99                       && command.substring(
 100                               command.length() - newSelcom.length())
 101                               .equals(newSelcom))
 102               {
 103                 command = VarnaCommands.condenseCommand(command, pos);
 104                 continue;
 105               }
 106               // TODO: deal with case when buffer is too large for Jmol to parse
 107               // - execute command and flush
 108
 109               command.append(";");
 110               if (command.length() > 51200)
 111               {
 112                 // add another chunk
 113                 str.add(command.toString());
 114                 command.setLength(0);
 115               }
 116               command.append("select " + pos);
 117               command.append(newSelcom);
 118             }
 119             break;
 120           }
 121         }
 122       }
 123     }
 124     {
 125       // add final chunk
 126       str.add(command.toString());
 127       command.setLength(0);
 128     }
 129     return str.toArray(new String[str.size()]);
 130   }
 131
 132   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 133   {
 134
 135     // work back to last 'select'
 136     int p = command.length(), q = p;
 137     do
 138     {
 139       p -= 6;
 140       if (p < 1)
 141       {
 142         p = 0;
 143       }
 144       ;
 145     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 146
 147     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 148
 149     command = command.delete(0, q + 7);
 150
 151     String start;
 152
 153     if (command.indexOf("-") > -1)
 154     {
 155       start = command.substring(0, command.indexOf("-"));
 156     }
 157     else
 158     {
 159       start = command.substring(0, command.indexOf(":"));
 160     }
 161
 162     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 163
 164     return sb;
 165   }
 166
 167 }