src/jalview/ext/varna/VarnaCommands.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 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 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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.ext.varna;
  20
  21 import jalview.api.FeatureRenderer;
  22 import jalview.api.SequenceRenderer;
  23 import jalview.datamodel.AlignmentI;
  24 import jalview.datamodel.SequenceI;
  25 import jalview.structure.StructureMapping;
  26 import jalview.structure.StructureSelectionManager;
  27
  28 import java.awt.Color;
  29 import java.util.ArrayList;
  30
  31 /**
  32  * Routines for generating Jmol commands for Jalview/Jmol binding another
  33  * cruisecontrol test.
  34  *
  35  * @author JimP
  36  *
  37  */
  38 public class VarnaCommands
  39 {
  40
  41   /**
  42    * Jmol utility which constructs the commands to colour chains by the given
  43    * alignment
  44    *
  45    */
  46   public static String[] getColourBySequenceCommand(
  47           StructureSelectionManager ssm, String[] files,
  48           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
  49           AlignmentI alignment)
  50   {
  51     ArrayList<String> str = new ArrayList<String>();
  52     StringBuffer command = new StringBuffer();
  53
  54     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
  55     {
  56       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
  57
  58       if (mapping == null || mapping.length < 1)
  59         continue;
  60
  61       int lastPos = -1;
  62       for (int s = 0; s < sequence[pdbfnum].length; s++)
  63       {
  64         for (int sp, m = 0; m < mapping.length; m++)
  65         {
  66           if (mapping[m].getSequence() == sequence[pdbfnum][s]
  67                   && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
  68           {
  69             SequenceI asp = alignment.getSequenceAt(sp);
  70             for (int r = 0; r < asp.getLength(); r++)
  71             {
  72               // no mapping to gaps in sequence
  73               if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
  74               {
  75                 continue;
  76               }
  77               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
  78
  79               if (pos < 1 || pos == lastPos)
  80                 continue;
  81
  82               lastPos = pos;
  83
  84               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
  85
  86               if (fr != null)
  87                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
  88               String newSelcom = (mapping[m].getChain() != " " ? ":"
  89                       + mapping[m].getChain() : "")
  90                       + "/"
  91                       + (pdbfnum + 1)
  92                       + ".1"
  93                       + ";color["
  94                       + col.getRed()
  95                       + ","
  96                       + col.getGreen()
  97                       + ","
  98                       + col.getBlue() + "]";
  99               if (command.length() > newSelcom.length()
 100                       && command.substring(
 101                               command.length() - newSelcom.length())
 102                               .equals(newSelcom))
 103               {
 104                 command = VarnaCommands.condenseCommand(command, pos);
 105                 continue;
 106               }
 107               // TODO: deal with case when buffer is too large for Jmol to parse
 108               // - execute command and flush
 109
 110               command.append(";");
 111               if (command.length() > 51200)
 112               {
 113                 // add another chunk
 114                 str.add(command.toString());
 115                 command.setLength(0);
 116               }
 117               command.append("select " + pos);
 118               command.append(newSelcom);
 119             }
 120             break;
 121           }
 122         }
 123       }
 124     }
 125     {
 126       // add final chunk
 127       str.add(command.toString());
 128       command.setLength(0);
 129     }
 130     return str.toArray(new String[str.size()]);
 131   }
 132
 133   public static StringBuffer condenseCommand(StringBuffer command, int pos)
 134   {
 135
 136     // work back to last 'select'
 137     int p = command.length(), q = p;
 138     do
 139     {
 140       p -= 6;
 141       if (p < 1)
 142       {
 143         p = 0;
 144       }
 145       ;
 146     } while ((q = command.indexOf("select", p)) == -1 && p > 0);
 147
 148     StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
 149
 150     command = command.delete(0, q + 7);
 151
 152     String start;
 153
 154     if (command.indexOf("-") > -1)
 155     {
 156       start = command.substring(0, command.indexOf("-"));
 157     }
 158     else
 159     {
 160       start = command.substring(0, command.indexOf(":"));
 161     }
 162
 163     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
 164
 165     return sb;
 166   }
 167
 168 }