2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
22 * JalviewX / Vamsas Project
23 * JPred.seq.concise reader
27 import jalview.datamodel.*;
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29 import jalview.util.*;
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36 public class JPredFile extends AlignFile {
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39 Hashtable Scores; // Hash of names and score vectors
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40 Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
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41 private int QuerySeqPosition;
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43 public JPredFile(String inStr) {
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47 public JPredFile(String inFile, String type) throws IOException {
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48 super(inFile, type);
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51 public void setQuerySeqPosition(int QuerySeqPosition) {
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52 this.QuerySeqPosition = QuerySeqPosition;
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55 public int getQuerySeqPosition() {
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56 return QuerySeqPosition;
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59 public Hashtable getScores() {
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63 public Hashtable getSymscores() {
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67 public void initData() {
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69 Scores = new Hashtable();
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75 * parse a JPred concise file into a sequence-alignment like object.
77 public void parse() throws IOException {
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78 // JBPNote log.System.out.println("all read in ");
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80 QuerySeqPosition = -1;
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83 Vector seq_entries = new Vector();
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84 Vector ids = new Vector();
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85 Hashtable Symscores = new Hashtable();
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87 while ((line = nextLine()) != null) {
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88 // Concise format allows no comments or non comma-formatted data
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89 StringTokenizer str = new StringTokenizer(line, ":");
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92 if (!str.hasMoreTokens()) {
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96 id = str.nextToken();
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98 String seqsym = str.nextToken();
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99 StringTokenizer symbols = new StringTokenizer(seqsym, ",");
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101 // decide if we have more than just alphanumeric symbols
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102 int numSymbols = symbols.countTokens();
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104 if (numSymbols == 0) {
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108 if (seqsym.length() != (2 * numSymbols)) {
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109 // Set of scalars for some property
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110 if (Scores.containsKey(id)) {
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113 while (Scores.containsKey(id + "_" + i)) {
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120 Vector scores = new Vector();
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122 // Typecheck from first entry
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124 String ascore = "dead";
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127 // store elements as floats...
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128 while (symbols.hasMoreTokens()) {
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129 ascore = symbols.nextToken();
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131 Float score = new Float(ascore);
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132 scores.addElement((Object) score);
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135 Scores.put(id, scores);
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136 } catch (Exception e) {
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137 // or just keep them as strings
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140 for (int j = 0; j < i; j++) {
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142 (Object) ((Float) scores.get(j)).toString());
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145 scores.addElement((Object) ascore);
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147 while (symbols.hasMoreTokens()) {
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148 ascore = symbols.nextToken();
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149 scores.addElement((Object) ascore);
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152 Scores.put(id, scores);
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154 } else if (id.equals("jnetconf")) {
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155 // log.debug System.out.println("here");
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156 id = "Prediction Confidence";
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157 this.conf = new Vector(numSymbols);
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159 for (int i = 0; i < numSymbols; i++) {
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160 conf.set(i, (Object) symbols.nextToken());
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163 // Sequence or a prediction string (rendered as sequence)
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164 StringBuffer newseq = new StringBuffer();
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166 for (int i = 0; i < numSymbols; i++) {
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167 newseq.append(symbols.nextToken());
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170 if (id.indexOf(";") > -1) {
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171 seq_entries.addElement(newseq);
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174 String name = id.substring(id.indexOf(";") + 1);
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176 while (ids.lastIndexOf(name) > -1) {
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177 name = id.substring(id.indexOf(";") + 1) + "_" + 1;
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180 ids.addElement(name);
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184 if (id.equals("JNETPRED")) {
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185 id = "Predicted Secondary Structure";
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188 seq_entries.addElement(newseq.toString());
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189 ids.addElement(id);
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190 Symscores.put((Object) id,
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191 (Object) new Integer(ids.size() - 1));
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197 throw new IOException(
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198 "JpredFile Parser: No sequence in the prediction!");
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201 maxLength = seq_entries.elementAt(0).toString().length();
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203 for (int i = 0; i < ids.size(); i++) {
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204 // Add all sequence like objects
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205 Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
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206 seq_entries.elementAt(i).toString(), 1,
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207 seq_entries.elementAt(i).toString().length());
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209 if (!Symscores.containsKey(ids.elementAt(i)) &&
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210 !isValidProteinSequence(newSeq.getSequence())) {
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211 throw new IOException(
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212 "JPredConcise: Not a valid protein sequence - (" +
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213 ids.elementAt(i).toString() + ")");
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216 if (maxLength != seq_entries.elementAt(i).toString().length()) {
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217 throw new IOException("JPredConcise: Entry (" +
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218 ids.elementAt(i).toString() +
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219 ") has an unexpected number of columns");
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222 if (newSeq.getName().startsWith("QUERY") &&
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223 (QuerySeqPosition == -1)) {
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224 QuerySeqPosition = seqs.size();
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227 seqs.addElement(newSeq);
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236 public String print() {
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237 return "Not Supported";
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240 public static void main(String[] args) {
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242 JPredFile blc = new JPredFile(args[0], "File");
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244 for (int i = 0; i < blc.seqs.size(); i++) {
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245 System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() +
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246 "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequence() +
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249 } catch (java.io.IOException e) {
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250 System.err.println("Exception " + e);
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251 e.printStackTrace();
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258 StringBuffer out = new StringBuffer();
260 out.append("START PRED\n");
261 for (int i = 0; i < s[0].sequence.length(); i++)
263 out.append(s[0].sequence.substring(i, i + 1) + " ");
264 out.append(s[1].sequence.substring(i, i + 1) + " ");
265 out.append(s[1].score[0].elementAt(i) + " ");
266 out.append(s[1].score[1].elementAt(i) + " ");
267 out.append(s[1].score[2].elementAt(i) + " ");
268 out.append(s[1].score[3].elementAt(i) + " ");
272 out.append("END PRED\n");
273 return out.toString();
276 public static void main(String[] args)
280 BLCFile blc = new BLCFile(args[0], "File");
281 DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
282 for (int i = 0; i < blc.seqs.size(); i++)
284 s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
286 String out = BLCFile.print(s);
288 AlignFrame af = new AlignFrame(null, s);
291 System.out.println(out);
293 catch (java.io.IOException e)
295 System.out.println("Exception " + e);