3 import jalview.analysis.SequenceIdMatcher;
4 import jalview.datamodel.AlignmentAnnotation;
5 import jalview.datamodel.AlignmentI;
6 import jalview.datamodel.Annotation;
7 import jalview.datamodel.SequenceI;
10 import java.io.BufferedReader;
12 import java.io.FileNotFoundException;
13 import java.io.FileReader;
14 import java.io.IOException;
15 import java.io.Reader;
16 import java.util.ArrayList;
17 import java.util.HashMap;
18 import java.util.LinkedHashMap;
19 import java.util.List;
23 * A file parse for T-Coffee score ascii format. This file contains the alignment consensus
24 * for each resude in any sequence.
26 * This file is procuded by <code>t_coffee</code> providing the option
27 * <code>-output=score_ascii </code> to the program command line
29 * An example file is the following
32 * T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
49 * 1PHT 999999999999999999999999998762112222543211112134
50 * 1BB9 99999999999999999999999999987-------4322----2234
51 * 1UHC 99999999999999999999999999987-------5321----2246
52 * 1YCS 99999999999999999999999999986-------4321----1-35
53 * 1OOT 999999999999999999999999999861-------3------1135
54 * 1ABO 99999999999999999999999999986-------422-------34
55 * 1FYN 99999999999999999999999999985-------32--------35
56 * 1QCF 99999999999999999999999999974-------2---------24
57 * cons 999999999999999999999999999851000110321100001134
60 * 1PHT ----------5666642367889999999999889
61 * 1BB9 1111111111676653-355679999999999889
62 * 1UHC ----------788774--66789999999999889
63 * 1YCS ----------78777--356789999999999889
64 * 1OOT ----------78877--356789999999997-67
65 * 1ABO ----------687774--56779999999999889
66 * 1FYN ----------6888842356789999999999889
67 * 1QCF ----------6878742356789999999999889
68 * cons 00100000006877641356789999999999889
72 * @author Paolo Di Tommaso
75 public class TCoffeeScoreFile {
77 /** The {@link Header} structure holder */
81 * Holds the consensues values for each sequences. It uses a LinkedHashMap to maintaint the
84 LinkedHashMap<String,StringBuilder> scores = new LinkedHashMap<String,StringBuilder>();
89 * Parse the specified file.
91 * @param file The file to be parsed
93 public static TCoffeeScoreFile load(File file) {
95 return load(new FileReader(file));
97 catch (FileNotFoundException e) {
98 throw new RuntimeException(e);
103 * Parse the provided reader for the T-Coffee scores file format
107 public static TCoffeeScoreFile load(Reader reader) {
110 BufferedReader in = (BufferedReader) (reader instanceof BufferedReader ? reader : new BufferedReader(reader));
111 TCoffeeScoreFile result = new TCoffeeScoreFile();
112 result.doParsing(in);
113 return result.header != null && result.scores != null ? result : null;
115 catch( Exception e) {
116 throw new RuntimeException(e);
121 * @return The 'height' of the score matrix i.e. the numbers of score rows that should matches
122 * the number of sequences in the alignment
124 public int getHeight() {
125 // the last entry will always be the 'global' alingment consensus scores, so it is removed
126 // from the 'height' count to make this value compatible with the number of sequences in the MSA
127 return scores != null && scores.size() > 0 ? scores.size()-1 : 0;
131 * @return The 'width' of the score matrix i.e. the number of columns.
132 * Since teh score value are supposd to be calculated for an 'aligned' MSA, all the entries
133 * have to have the same width.
135 public int getWidth() {
136 return fWidth != null ? fWidth : 0;
140 * The default constructor is marked as {@code protected} since this class is meant to created
141 * through the {@link #load(File)} or {@link #load(Reader)} factory methods
143 protected TCoffeeScoreFile() { }
146 * Get the string of score values for the specified seqeunce ID.
147 * @param id The sequence ID
148 * @return The scores as a string of values e.g. {@code 99999987-------432}.
149 * It return an empty string when the specified ID is missing.
151 public String getScoresFor( String id ) {
152 return scores.containsKey(id) ? scores.get(id).toString() : "";
156 * @return The list of score string as a {@link List} object, in the same ordeer of the insertion i.e. in the MSA
158 public List<String> getScoresList() {
159 List<String> result = new ArrayList<String>( scores.size() );
160 for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
161 result.add(it.getValue().toString());
168 * @return The parsed score values a matrix of bytes
170 public byte[][] getScoresArray() {
171 byte[][] result = new byte[ scores.size() ][];
174 for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
175 String line = it.getValue().toString();
176 byte[] seqValues = new byte[ line.length() ];
177 for( int j=0, c=line.length(); j<c; j++ ) {
179 byte val = (byte)(line.charAt(j) - '0');
181 seqValues[j] = ( val >= 0 && val <= 9 ) ? val : -1;
184 result[rowCount++] = seqValues;
191 private void doParsing(BufferedReader in) throws IOException {
196 header = readHeader(in);
198 if( header == null ) { return; }
202 * initilize the structure
204 for( Map.Entry<String,Integer> entry : header.scores.entrySet() ) {
205 scores.put( entry.getKey(), new StringBuilder());
209 * go with the reading
212 while( (block = readBlock(in, header.scores.size())) != null ) {
215 * append sequences read in the block
217 for( Map.Entry<String,String> entry : block.items.entrySet() ) {
218 StringBuilder scoreStringBuilder = scores.get(entry.getKey());
219 if( scoreStringBuilder == null ) {
220 throw new RuntimeException(String.format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", entry.getKey()));
223 scoreStringBuilder.append( entry.getValue() );
228 * verify that all rows have the same width
230 for( StringBuilder str : scores.values() ) {
231 if( fWidth == null ) {
232 fWidth = str.length();
234 else if( fWidth != str.length() ) {
235 throw new RuntimeException("Invalid T-Coffee score file: All the score sequences must have the same length");
244 static int parseInt( String str ) {
246 return Integer.parseInt(str);
248 catch( NumberFormatException e ) {
249 // TODO report a warning ?
255 * Reaad the header section in the T-Coffee score file format
257 * @param reader The scores reader
258 * @return The parser {@link Header} instance
259 * @throws RuntimeException when the header is not in the expected format
261 static Header readHeader(BufferedReader reader) {
263 Header result = null;
265 result = new Header();
266 result.head = reader.readLine();
270 while( (line = reader.readLine()) != null ) {
271 if( line.startsWith("SCORE=")) {
272 result.score = parseInt( line.substring(6).trim() );
277 if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
278 if( (line=reader.readLine())==null || !"BAD AVG GOOD".equals(line.trim())) return null;
279 if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
282 * now are expected a list if sequences ID up to the first blank line
284 while( (line=reader.readLine()) != null ) {
285 if( "".equals(line) ) {
289 int p = line.indexOf(":");
291 // TODO report a warning
295 String id = line.substring(0,p).trim();
296 int val = parseInt(line.substring(p+1).trim());
297 if( "".equals(id) ) {
298 // TODO report warning
302 result.scores.put(id,val);
306 catch( IOException e ) {
307 throw new RuntimeException("Cannot parse T-Coffee score ascii file", e);
314 * Read a scores block ihe provided stream.
316 * @param reader The stream to parse
317 * @param size The expected number of the sequence to be read
318 * @return The {@link Block} instance read or {link null} null if the end of file has reached.
319 * @throws IOException Something went wrong on the 'wire'
321 static Block readBlock( BufferedReader reader, int size ) throws IOException {
322 Block result = new Block(size);
326 * read blank lines (eventually)
328 while( (line=reader.readLine()) != null && "".equals(line.trim())) {
329 // consume blank lines
332 if( line == null ) return null;
335 * read the scores block
338 if( "".equals(line.trim()) ) {
343 // split the line on the first blank
344 // the first part have to contain the sequence id
345 // theramining part are the scores values
346 int p = line.indexOf(" ");
348 //TODO This is an unexpected condition, log a warning or throw an exception ?
352 String id = line.substring(0,p).trim();
353 String val = line.substring(p+1).trim();
355 result.items.put(id, val);
357 } while( (line = reader.readLine()) != null );
364 * The score file header
366 static class Header {
370 LinkedHashMap<String,Integer> scores = new LinkedHashMap<String,Integer>();
372 public int getScoreAvg() { return score; }
374 public int getScoreFor( String ID ) {
376 return scores.containsKey(ID) ? scores.get(ID) : -1;
382 * Hold a single block values block in the score file
386 Map<String,String> items;
388 public Block( int size ) {
390 this.items = new HashMap<String,String>(size);
393 String getScoresFor( String id ) {
394 return items.get(id);
397 String getConsensus() {
398 return items.get("cons");
402 * TCOFFEE score colourscheme
404 static final Color[] colors = {
405 new Color( 102, 102, 255 ), // #6666FF
406 new Color( 0, 255, 0), // #00FF00
407 new Color( 102, 255, 0), // #66FF00
408 new Color( 204, 255, 0), // #CCFF00
409 new Color( 255, 255, 0), // #FFFF00
410 new Color( 255, 204, 0), // #FFCC00
411 new Color( 255, 153, 0), // #FF9900
412 new Color( 255, 102, 0), // #FF6600
413 new Color( 255, 51, 0), // #FF3300
414 new Color( 255, 34, 0) // #FF2000
416 public final static String TCOFFEE_SCORE="TCoffeeScore";
418 * generate annotation for this TCoffee score set on the given alignment
419 * @param al alignment to annotate
420 * @param matchids if true, annotate sequences based on matching sequence names
421 * @return true if alignment annotation was modified, false otherwise.
423 public boolean annotateAlignment(AlignmentI al, boolean matchids)
427 SequenceIdMatcher sidmatcher = new SequenceIdMatcher(al.getSequencesArray());
428 byte[][] scoreMatrix=getScoresArray();
429 // for 2.8 - we locate any existing TCoffee annotation and remove it first before adding this.
430 for (Map.Entry<String,StringBuilder> id:scores.entrySet())
432 byte[] srow=scoreMatrix[i];
436 s=sidmatcher.findIdMatch(id.getKey());
438 s=al.getSequenceAt(i);
441 if (s==null && i!=scores.size() && !id.getKey().equals("cons"))
443 System.err.println("No "+(matchids ? "match ":" sequences left ")+" for TCoffee score set : "+id.getKey());
446 int jSize=al.getWidth()< srow.length ? al.getWidth() : srow.length;
447 Annotation[] annotations=new Annotation[al.getWidth()];
448 for (int j=0;j<jSize;j++) {
450 annotations[j]=new Annotation(s==null ? ""+val:null,s==null ? ""+val:null,(char) val,val*1f,val >= 0 && val < colors.length ? colors[val] : Color.white);
452 AlignmentAnnotation aa=null;
455 // TODO - set per sequence score
456 aa=new AlignmentAnnotation(TCOFFEE_SCORE, "Score for "+id.getKey(), annotations);
458 aa.setSequenceRef(s);
460 aa.belowAlignment=false;
462 aa=new AlignmentAnnotation("T-COFFEE", "TCoffee column reliability score", annotations);
463 aa.belowAlignment=true;
467 al.addAnnotation(aa);