2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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21 import jalview.datamodel.*;
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23 import java.util.Vector;
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30 * @version $Revision$
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32 public class AppletFormatAdapter
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34 /** DOCUMENT ME!! */
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35 public static final String [] READABLE_FORMATS = new String[]
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37 "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"
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40 public static final String [] WRITEABLE_FORMATS = new String[]
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42 "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" //, "AMSA"
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46 public static String INVALID_CHARACTERS = "Contains invalid characters";
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48 public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
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49 "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";
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52 public static String FILE = "File";
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53 public static String URL = "URL";
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54 public static String PASTE = "Paste";
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55 public static String CLASSLOADER = "ClassLoader";
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58 AlignFile afile = null;
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61 public static final boolean isValidFormat(String format)
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63 boolean valid = false;
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64 for(int i=0; i<READABLE_FORMATS.length; i++)
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65 if(READABLE_FORMATS[i].equalsIgnoreCase(format))
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74 * @param inFile DOCUMENT ME!
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75 * @param type DOCUMENT ME!
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76 * @param format DOCUMENT ME!
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78 * @return DOCUMENT ME!
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80 public Alignment readFile(String inFile, String type, String format)
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81 throws java.io.IOException
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83 this.inFile = inFile;
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86 if (format.equals("FASTA"))
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88 afile = new FastaFile(inFile, type);
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90 else if (format.equals("MSF"))
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92 afile = new MSFfile(inFile, type);
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94 else if (format.equals("PileUp"))
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96 afile = new PileUpfile(inFile, type);
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98 else if (format.equals("CLUSTAL"))
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100 afile = new ClustalFile(inFile, type);
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102 else if (format.equals("BLC"))
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104 afile = new BLCFile(inFile, type);
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106 else if (format.equals("PIR"))
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108 afile = new PIRFile(inFile, type);
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110 else if (format.equals("PFAM"))
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112 afile = new PfamFile(inFile, type);
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114 else if (format.equals("JnetFile"))
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116 afile = new JPredFile(inFile, type);
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117 ( (JPredFile) afile).removeNonSequences();
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119 else if (format.equals("PDB"))
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121 afile = new MCview.PDBfile(inFile, type);
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123 else if (format.equals("STH"))
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125 afile = new StockholmFile(inFile, type);
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128 Alignment al = new Alignment(afile.getSeqsAsArray());
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130 afile.addAnnotations(al);
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134 catch (Exception e)
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136 e.printStackTrace();
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137 System.err.println("Failed to read alignment using the '" + format +
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140 if(e.getMessage()!=null && e.getMessage().startsWith(INVALID_CHARACTERS))
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141 throw new java.io.IOException(e.getMessage());
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143 // Finally test if the user has pasted just the sequence, no id
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144 if(type.equalsIgnoreCase("Paste"))
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147 // Possible sequence is just residues with no label
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148 afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
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149 Alignment al = new Alignment(afile.getSeqsAsArray());
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150 afile.addAnnotations(al);
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154 catch(Exception ex)
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156 if(ex.toString().startsWith(INVALID_CHARACTERS))
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157 throw new java.io.IOException(e.getMessage());
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159 ex.printStackTrace();
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163 // If we get to this stage, the format was not supported
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164 throw new java.io.IOException(SUPPORTED_FORMATS);
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172 * @param format DOCUMENT ME!
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173 * @param seqs DOCUMENT ME!
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175 * @return DOCUMENT ME!
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177 public String formatSequences(String format,
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178 AlignmentI alignment,
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183 AlignFile afile = null;
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185 if (format.equalsIgnoreCase("FASTA"))
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187 afile = new FastaFile();
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189 else if (format.equalsIgnoreCase("MSF"))
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191 afile = new MSFfile();
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193 else if (format.equalsIgnoreCase("PileUp"))
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195 afile = new PileUpfile();
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197 else if (format.equalsIgnoreCase("CLUSTAL"))
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199 afile = new ClustalFile();
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201 else if (format.equalsIgnoreCase("BLC"))
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203 afile = new BLCFile();
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205 else if (format.equalsIgnoreCase("PIR"))
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207 afile = new PIRFile();
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209 else if (format.equalsIgnoreCase("PFAM"))
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211 afile = new PfamFile();
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213 else if (format.equalsIgnoreCase("STH"))
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215 afile = new StockholmFile();
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217 else if (format.equals("AMSA"))
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219 afile = new AMSAFile(alignment);
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222 afile.addJVSuffix(jvsuffix);
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224 afile.setSeqs( alignment.getSequencesArray() );
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226 return afile.print();
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228 catch (Exception e)
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230 System.err.println("Failed to write alignment as a '" + format +
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232 e.printStackTrace();
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