src/jalview/ext/varna/VarnaCommands.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   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
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.ext.varna;
  22
  23 import jalview.api.FeatureRenderer;
  24 import jalview.api.SequenceRenderer;
  25 import jalview.datamodel.AlignmentI;
  26 import jalview.datamodel.SequenceI;
  27 import jalview.structure.StructureMapping;
  28 import jalview.structure.StructureSelectionManager;
  29 import jalview.util.Comparison;
  30
  31 import java.awt.Color;
  32 import java.util.ArrayList;
  33
  34 /**
  35  * Routines for generating Jmol commands for Jalview/Jmol binding another
  36  * cruisecontrol test.
  37  *
  38  * @author JimP
  39  *
  40  */
  41 public class VarnaCommands
  42 {
  43
  44   /**
  45    * Jmol utility which constructs the commands to colour chains by the given
  46    * alignment
  47    *
  48    */
  49   public static String[] getColourBySequenceCommand(
  50           StructureSelectionManager ssm, String[] files,
  51           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
  52           AlignmentI alignment)
  53   {
  54     ArrayList<String> str = new ArrayList<String>();
  55     StringBuffer command = new StringBuffer();
  56
  57     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  58     {
  59       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  60
  61       if (mapping == null || mapping.length < 1)
  62       {
  63         continue;
  64       }
  65
  66       int lastPos = -1;
  67       for (int s = 0; s < sequence[pdbfnum].length; s++)
  68       {
  69         for (int sp, m = 0; m < mapping.length; m++)
  70         {
  71           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  72                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  73           {
  74             SequenceI asp = alignment.getSequenceAt(sp);
  75             for (int r = 0; r < asp.getLength(); r++)
  76             {
  77               // no mapping to gaps in sequence
  78               if (Comparison.isGap(asp.getCharAt(r)))
  79               {
  80                 continue;
  81               }
  82               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  83
  84               if (pos < 1 || pos == lastPos)
  85               {
  86                 continue;
  87               }
  88
  89               lastPos = pos;
  90
  91               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  92
  93               if (fr != null)
  94               {
  95                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  96               }
  97               String newSelcom = (mapping[m].getChain() != " " ? ":"
  98                       + mapping[m].getChain() : "")
  99                       + "/"
 100                       + (pdbfnum + 1)
 101                       + ".1"
 102                       + ";color["
 103                       + col.getRed()
 104                       + ","
 105                       + col.getGreen()
 106                       + ","
 107                       + col.getBlue() + "]";
 108               if (command.length() > newSelcom.length()
 109                       && command.substring(
 110                               command.length() - newSelcom.length())
 111                               .equals(newSelcom))
 112               {
 113                 command = VarnaCommands.condenseCommand(command, pos);
 114                 continue;
 115               }
 116               // TODO: deal with case when buffer is too large for Jmol to parse
 117               // - execute command and flush
 118
 119               command.append(";");
 120               if (command.length() > 51200)
 121               {
 122                 // add another chunk
 123                 str.add(command.toString());
 124                 command.setLength(0);
 125               }
 126               command.append("select " + pos);
 127               command.append(newSelcom);
 128             }
 129             break;
 130           }
 131         }
 132       }
 133     }
 134     {
 135       // add final chunk
 136       str.add(command.toString());
 137       command.setLength(0);
 138     }
 139     return str.toArray(new String[str.size()]);
 140   }
 141
 142   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 143   {
 144
 145     // work back to last 'select'
 146     int p = command.length(), q = p;
 147     do
 148     {
 149       p -= 6;
 150       if (p < 1)
 151       {
 152         p = 0;
 153       }
 154       ;
 155     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 156
 157     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 158
 159     command = command.delete(0, q + 7);
 160
 161     String start;
 162
 163     if (command.indexOf("-") > -1)
 164     {
 165       start = command.substring(0, command.indexOf("-"));
 166     }
 167     else
 168     {
 169       start = command.substring(0, command.indexOf(":"));
 170     }
 171
 172     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 173
 174     return sb;
 175   }
 176
 177 }