--- /dev/null
+package jalview.io;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A file parse for T-Coffee score ascii format. This file contains the alignment consensus
+ * for each resude in any sequence.
+ * <p>
+ * This file is procuded by <code>t_coffee</code> providing the option
+ * <code>-output=score_ascii </code> to the program command line
+ *
+ * An example file is the following
+ *
+ * <pre>
+ * T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
+ * Cedric Notredame
+ * CPU TIME:0 sec.
+ * SCORE=90
+ * *
+ * BAD AVG GOOD
+ * *
+ * 1PHT : 89
+ * 1BB9 : 90
+ * 1UHC : 94
+ * 1YCS : 94
+ * 1OOT : 93
+ * 1ABO : 94
+ * 1FYN : 94
+ * 1QCF : 94
+ * cons : 90
+ *
+ * 1PHT 999999999999999999999999998762112222543211112134
+ * 1BB9 99999999999999999999999999987-------4322----2234
+ * 1UHC 99999999999999999999999999987-------5321----2246
+ * 1YCS 99999999999999999999999999986-------4321----1-35
+ * 1OOT 999999999999999999999999999861-------3------1135
+ * 1ABO 99999999999999999999999999986-------422-------34
+ * 1FYN 99999999999999999999999999985-------32--------35
+ * 1QCF 99999999999999999999999999974-------2---------24
+ * cons 999999999999999999999999999851000110321100001134
+ *
+ *
+ * 1PHT ----------5666642367889999999999889
+ * 1BB9 1111111111676653-355679999999999889
+ * 1UHC ----------788774--66789999999999889
+ * 1YCS ----------78777--356789999999999889
+ * 1OOT ----------78877--356789999999997-67
+ * 1ABO ----------687774--56779999999999889
+ * 1FYN ----------6888842356789999999999889
+ * 1QCF ----------6878742356789999999999889
+ * cons 00100000006877641356789999999999889
+ * </pre>
+ *
+ *
+ * @author Paolo Di Tommaso
+ *
+ */
+public class TCoffeeScoreFile {
+
+ /** The {@link Header} structure holder */
+ Header header;
+
+ /**
+ * Holds the consensues values for each sequences. It uses a LinkedHashMap to maintaint the
+ * insertion order.
+ */
+ LinkedHashMap<String,StringBuilder> scores = new LinkedHashMap<String,StringBuilder>();
+
+
+ /**
+ * Get the string of score values for the specified seqeunce ID.
+ * @param id The sequence ID
+ * @return The scores as a string of values e.g. {@code 99999987-------432}.
+ * It return an empty string when the specified ID is missing.
+ */
+ public String getScoresFor( String id ) {
+ return scores.containsKey(id) ? scores.get(id).toString() : "";
+ }
+
+ /**
+ * @return The list of score string as a {@link List} object, in the same ordeer of the insertion i.e. in the MSA
+ */
+ public List<String> getScoresList() {
+ List<String> result = new ArrayList<String>( scores.size() );
+ for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
+ result.add(it.getValue().toString());
+ }
+
+ return result;
+ }
+
+ /**
+ * @return The parsed score values a matrix of bytes
+ */
+ public byte[][] getScoresArray() {
+ byte[][] result = new byte[ scores.size() ][];
+
+ int rowCount = 0;
+ for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
+ String line = it.getValue().toString();
+ byte[] seqValues = new byte[ line.length() ];
+ for( int j=0, c=line.length(); j<c; j++ ) {
+
+ byte val = (byte)(line.charAt(j) - '0');
+
+ seqValues[j] = ( val >= 0 && val <= 9 ) ? val : -1;
+ }
+
+ result[rowCount++] = seqValues;
+ }
+
+ return result;
+ }
+
+ /**
+ * Parse the specified file.
+ *
+ * @param file The file to be parsed
+ */
+ public void parse(File file) {
+ try {
+ parse(new FileReader(file));
+ }
+ catch (FileNotFoundException e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ /**
+ * Parse the provided reader for the T-Coffee scores file format
+ *
+ * @param reader
+ */
+ public void parse(Reader reader) {
+
+ try {
+ BufferedReader in = (BufferedReader) (reader instanceof BufferedReader ? reader : new BufferedReader(reader));
+ doParsing(in);
+ }
+ catch( Exception e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+ private void doParsing(BufferedReader in) throws IOException {
+
+ /*
+ * read the header
+ */
+ header = readHeader(in);
+
+ /*
+ * initilize the structure
+ */
+ for( Map.Entry<String,Integer> entry : header.scores.entrySet() ) {
+ scores.put( entry.getKey(), new StringBuilder());
+ }
+
+ /*
+ * go with the reading
+ */
+ Block block;
+ while( (block = readBlock(in, header.scores.size())) != null ) {
+
+ /*
+ * append sequences read in the block
+ */
+ for( Map.Entry<String,String> entry : block.items.entrySet() ) {
+ StringBuilder scoreStringBuilder = scores.get(entry.getKey());
+ if( scoreStringBuilder == null ) {
+ throw new RuntimeException(String.format("Invalid T-Coffee score file. Sequence ID '%s' is not declared in header section", entry.getKey()));
+ }
+
+ scoreStringBuilder.append( entry.getValue() );
+ }
+
+ }
+
+ }
+
+
+ static int parseInt( String str ) {
+ try {
+ return Integer.parseInt(str);
+ }
+ catch( NumberFormatException e ) {
+ // TODO report a warning ?
+ return 0;
+ }
+ }
+
+ /**
+ * Reaad the header section in the T-Coffee score file format
+ *
+ * @param reader The scores reader
+ * @return The parser {@link Header} instance
+ * @throws RuntimeException when the header is not in the expected format
+ */
+ static Header readHeader(BufferedReader reader) {
+
+ Header result = null;
+ try {
+ result = new Header();
+ result.head = reader.readLine();
+
+ String line;
+
+ while( (line = reader.readLine()) != null ) {
+ if( line.startsWith("SCORE=")) {
+ result.score = parseInt( line.substring(6).trim() );
+ break;
+ }
+ }
+
+ if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
+ if( (line=reader.readLine())==null || !"BAD AVG GOOD".equals(line.trim())) return null;
+ if( (line=reader.readLine())==null || !"*".equals(line.trim())) return null;
+
+ /*
+ * now are expected a list if sequences ID up to the first blank line
+ */
+ while( (line=reader.readLine()) != null ) {
+ if( "".equals(line) ) {
+ break;
+ }
+
+ int p = line.indexOf(":");
+ if( p == -1 ) {
+ // TODO report a warning
+ continue;
+ }
+
+ String id = line.substring(0,p).trim();
+ int val = parseInt(line.substring(p+1).trim());
+ if( "".equals(id) ) {
+ // TODO report warning
+ continue;
+ }
+
+ result.scores.put(id,val);
+ }
+
+ }
+ catch( IOException e ) {
+ throw new RuntimeException("Cannot parse T-Coffee score ascii file", e);
+ }
+
+ return result;
+ }
+
+ /**
+ * Read a scores block ihe provided stream.
+ *
+ * @param reader The stream to parse
+ * @param size The expected number of the sequence to be read
+ * @return The {@link Block} instance read or {link null} null if the end of file has reached.
+ * @throws IOException Something went wrong on the 'wire'
+ */
+ static Block readBlock( BufferedReader reader, int size ) throws IOException {
+ Block result = new Block(size);
+ String line;
+
+ /*
+ * read blank lines (eventually)
+ */
+ while( (line=reader.readLine()) != null && "".equals(line.trim())) {
+ // consume blank lines
+ }
+
+ if( line == null ) return null;
+
+ /*
+ * read the scores block
+ */
+ do {
+ if( "".equals(line.trim()) ) {
+ // terminated
+ break;
+ }
+
+ // split the line on the first blank
+ // the first part have to contain the sequence id
+ // theramining part are the scores values
+ int p = line.indexOf(" ");
+ if( p == -1 ) {
+ //TODO This is an unexpected condition, log a warning or throw an exception ?
+ continue;
+ }
+
+ String id = line.substring(0,p).trim();
+ String val = line.substring(p+1).trim();
+
+ result.items.put(id, val);
+
+ } while( (line = reader.readLine()) != null );
+
+
+ return result;
+ }
+
+ /*
+ * The score file header
+ */
+ static class Header {
+ String head;
+ int score;
+
+ LinkedHashMap<String,Integer> scores = new LinkedHashMap<String,Integer>();
+
+ public int getScoreAvg() { return score; }
+
+ public int getScoreFor( String ID ) {
+
+ return scores.containsKey(ID) ? scores.get(ID) : -1;
+
+ }
+ }
+
+ /*
+ * Hold a single block values block in the score file
+ */
+ static class Block {
+ int size;
+ Map<String,String> items;
+
+ public Block( int size ) {
+ this.size = size;
+ this.items = new HashMap<String,String>(size);
+ }
+
+ String getScoresFor( String id ) {
+ return items.get(id);
+ }
+
+ String getConsensus() {
+ return items.get("cons");
+ }
+ }
+
+
+
+}
--- /dev/null
+package jalview.io;
+
+import static org.junit.Assert.*;
+import jalview.io.TCoffeeScoreFile.Block;
+import jalview.io.TCoffeeScoreFile.Header;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.StringReader;
+import java.util.List;
+
+import org.junit.Test;
+
+public class TCoffeeScoreFileTest {
+
+ final static File SCORE_FILE = new File("./test/jalview/io/tcoffee.score_ascii");
+
+ @Test
+ public void testReadHeader() throws FileNotFoundException {
+
+ Header header = TCoffeeScoreFile.readHeader( new BufferedReader(new FileReader(SCORE_FILE)) );
+ assertNotNull(header);
+ assertEquals( "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)", header.head );
+ assertEquals( 90, header.score );
+ assertEquals( 89, header.getScoreFor("1PHT") );
+ assertEquals( 90, header.getScoreFor("1BB9") );
+ assertEquals( 94, header.getScoreFor("1UHC") );
+ assertEquals( 94, header.getScoreFor("1YCS") );
+ assertEquals( 93, header.getScoreFor("1OOT") );
+ assertEquals( 94, header.getScoreFor("1ABO") );
+ assertEquals( 94, header.getScoreFor("1FYN") );
+ assertEquals( 94, header.getScoreFor("1QCF") );
+ assertEquals( 90, header.getScoreFor("cons") );
+ }
+
+ @Test
+ public void testReadBlock( ) throws IOException {
+
+ String BLOCK = "\n" +
+ "\n" +
+ "\n" +
+ "1PHT 999999999999999999999999998762112222543211112134\n" +
+ "1BB9 99999999999999999999999999987-------4322----2234 \n" +
+ "1UHC 99999999999999999999999999987-------5321----2246\n" +
+ "1YCS 99999999999999999999999999986-------4321----1-35\n" +
+ "1OOT 999999999999999999999999999861-------3------1135 \n" +
+ "1ABO 99999999999999999999999999986-------422-------34\n" +
+ "1FYN 99999999999999999999999999985-------32--------35\n" +
+ "1QCF 99999999999999999999999999974-------2---------24\n" +
+ "cons 999999999999999999999999999851000110321100001134\n" +
+ "\n" +
+ "\n";
+
+ Block block = TCoffeeScoreFile.readBlock(new BufferedReader(new StringReader(BLOCK)), 0);
+ assertNotNull(block);
+ assertEquals( "999999999999999999999999998762112222543211112134", block.getScoresFor("1PHT") );
+ assertEquals( "99999999999999999999999999987-------4322----2234", block.getScoresFor("1BB9") );
+ assertEquals( "99999999999999999999999999987-------5321----2246", block.getScoresFor("1UHC") );
+ assertEquals( "99999999999999999999999999986-------4321----1-35", block.getScoresFor("1YCS") );
+ assertEquals( "999999999999999999999999999861-------3------1135", block.getScoresFor("1OOT") );
+ assertEquals( "99999999999999999999999999986-------422-------34", block.getScoresFor("1ABO") );
+ assertEquals( "99999999999999999999999999985-------32--------35", block.getScoresFor("1FYN") );
+ assertEquals( "99999999999999999999999999974-------2---------24", block.getScoresFor("1QCF") );
+ assertEquals( "999999999999999999999999999851000110321100001134", block.getConsensus() );
+ }
+
+ @Test
+ public void testParse() throws FileNotFoundException {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile();
+ parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+ assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", parser.getScoresFor("1PHT") );
+ assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", parser.getScoresFor("1BB9") );
+ assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", parser.getScoresFor("1UHC") );
+ assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", parser.getScoresFor("1YCS") );
+ assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", parser.getScoresFor("1OOT") );
+ assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", parser.getScoresFor("1ABO") );
+ assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", parser.getScoresFor("1FYN") );
+ assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", parser.getScoresFor("1QCF") );
+ assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", parser.getScoresFor("cons") );
+ }
+
+
+ @Test
+ public void testGetAsList() throws FileNotFoundException {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile();
+ parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+ List<String> scores = parser.getScoresList();
+ assertEquals( "999999999999999999999999998762112222543211112134----------5666642367889999999999889", scores.get(0) );
+ assertEquals( "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889", scores.get(1) );
+ assertEquals( "99999999999999999999999999987-------5321----2246----------788774--66789999999999889", scores.get(2) );
+ assertEquals( "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889", scores.get(3) );
+ assertEquals( "999999999999999999999999999861-------3------1135----------78877--356789999999997-67", scores.get(4) );
+ assertEquals( "99999999999999999999999999986-------422-------34----------687774--56779999999999889", scores.get(5) );
+ assertEquals( "99999999999999999999999999985-------32--------35----------6888842356789999999999889", scores.get(6) );
+ assertEquals( "99999999999999999999999999974-------2---------24----------6878742356789999999999889", scores.get(7) );
+ assertEquals( "99999999999999999999999999985100011032110000113400100000006877641356789999999999889", scores.get(8) );
+
+ }
+
+
+ @Test
+ public void testGetAsArray() throws FileNotFoundException {
+
+ TCoffeeScoreFile parser = new TCoffeeScoreFile();
+ parser.parse(new BufferedReader(new FileReader(SCORE_FILE)) );
+
+ byte[][] scores = parser.getScoresArray();
+
+ assertEquals( 9, scores[0][0] );
+ assertEquals( 9, scores[1][0] );
+ assertEquals( 9, scores[2][0] );
+ assertEquals( 9, scores[3][0] );
+ assertEquals( 9, scores[4][0] );
+ assertEquals( 9, scores[5][0] );
+ assertEquals( 9, scores[6][0] );
+ assertEquals( 9, scores[7][0] );
+ assertEquals( 9, scores[8][0] );
+
+ assertEquals( 5, scores[0][36] );
+ assertEquals( 4, scores[1][36] );
+ assertEquals( 5, scores[2][36] );
+ assertEquals( 4, scores[3][36] );
+ assertEquals( -1, scores[4][36] );
+ assertEquals( 4, scores[5][36] );
+ assertEquals( 3, scores[6][36] );
+ assertEquals( 2, scores[7][36] );
+ assertEquals( 3, scores[8][36] );
+
+ }
+
+
+
+}
--- /dev/null
+>1PHT
+YQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEI--
+--------GWLNGYNETTGERGDFPGTYVEYIG
+>1BB9
+FKVQAQHDYTATDTDELQLKAGDVVLVIP-------FQNP----EEQDEG
+WLMGVKESDWNQHK-ELEKCRGVFPENFTERVQ
+>1UHC
+QVYFAVYTFKARNPNELSVSANQKLKILE-------FKDV----TGNT--
+--------EWWLAE--VNGKKGYVPSNYIRKTE
+>1YCS
+GVIYALWDYEPQNDDELPMKEGDCMTIIH-------REDE----D-EI--
+--------EWWWA--RLNDKEGYVPRNLLGLYP
+>1OOT
+PKAVALYSFAGEESGDLPFRKGDVITILKK-------S------DSQN--
+--------DWWTG--RVNGREGIFPANYVE-LV
+>1ABO
+NLFVALYDFVASGDNTLSITKGEKLRVLG-------YNH-------NG--
+--------EWCEAQ--TKNGQGWVPSNYITPVN
+>1FYN
+TLFVALYDYEARTEDDLSFHKGEKFQILN-------SS--------EG--
+--------DWWEARSLTTGETGYIPSNYVAPVD
+>1QCF
+IIVVALYDYEAIHHEDLSFQKGDQMVVLE-------E---------SG--
+--------EWWKARSLATRKEGYIPSNYVARVD
\ No newline at end of file
--- /dev/null
+T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
+Cedric Notredame
+CPU TIME:0 sec.
+SCORE=90
+*
+ BAD AVG GOOD
+*
+1PHT : 89
+1BB9 : 90
+1UHC : 94
+1YCS : 94
+1OOT : 93
+1ABO : 94
+1FYN : 94
+1QCF : 94
+cons : 90
+
+1PHT 999999999999999999999999998762112222543211112134
+1BB9 99999999999999999999999999987-------4322----2234
+1UHC 99999999999999999999999999987-------5321----2246
+1YCS 99999999999999999999999999986-------4321----1-35
+1OOT 999999999999999999999999999861-------3------1135
+1ABO 99999999999999999999999999986-------422-------34
+1FYN 99999999999999999999999999985-------32--------35
+1QCF 99999999999999999999999999974-------2---------24
+cons 999999999999999999999999999851000110321100001134
+
+
+1PHT ----------5666642367889999999999889
+1BB9 1111111111676653-355679999999999889
+1UHC ----------788774--66789999999999889
+1YCS ----------78777--356789999999999889
+1OOT ----------78877--356789999999997-67
+1ABO ----------687774--56779999999999889
+1FYN ----------6888842356789999999999889
+1QCF ----------6878742356789999999999889
+cons 00100000006877641356789999999999889
git://source.jalview.org / jalview.git / commitdiff