- * This file is procuded by t_coffee providing the option
+ * This file is procuded by t_coffee providing the option
* -output=score_ascii to the program command line
*
- * An example file is the following
+ * An example file is the following
*
*
* T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)
@@ -78,446 +87,560 @@ import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
*
*
* @author Paolo Di Tommaso
- *
+ *
*/
-public class TCoffeeScoreFile extends AlignFile {
-
- public TCoffeeScoreFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+public class TCoffeeScoreFile extends AlignFile
+{
+ public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
-
+
}
- public TCoffeeScoreFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
+ public TCoffeeScoreFile(FileParse source) throws IOException
{
super(source);
}
- /** The {@link Header} structure holder */
- Header header;
-
- /**
- * Holds the consensues values for each sequences. It uses a LinkedHashMap to maintaint the
- * insertion order.
- */
- LinkedHashMap scores;
-
- Integer fWidth;
-
- /**
- * Parse the provided reader for the T-Coffee scores file format
- *
- * @param reader
- public static TCoffeeScoreFile load(Reader reader) {
-
- try {
- BufferedReader in = (BufferedReader) (reader instanceof BufferedReader ? reader : new BufferedReader(reader));
- TCoffeeScoreFile result = new TCoffeeScoreFile();
- result.doParsing(in);
- return result.header != null && result.scores != null ? result : null;
- }
- catch( Exception e) {
- throw new RuntimeException(e);
- }
- }
- */
-
- /**
- * @return The 'height' of the score matrix i.e. the numbers of score rows that should matches
- * the number of sequences in the alignment
- */
- public int getHeight() {
- // the last entry will always be the 'global' alingment consensus scores, so it is removed
- // from the 'height' count to make this value compatible with the number of sequences in the MSA
- return scores != null && scores.size() > 0 ? scores.size()-1 : 0;
- }
-
- /**
- * @return The 'width' of the score matrix i.e. the number of columns.
- * Since teh score value are supposd to be calculated for an 'aligned' MSA, all the entries
- * have to have the same width.
- */
- public int getWidth() {
- return fWidth != null ? fWidth : 0;
- }
-
-
- /**
- * 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!=null && 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 getScoresList() {
- if (scores==null)
- {
- return null;
- }
- List result = new ArrayList( scores.size() );
- for( Map.Entry it : scores.entrySet() ) {
- result.add(it.getValue().toString());
- }
-
- return result;
- }
-
- /**
- * @return The parsed score values a matrix of bytes
- */
- public byte[][] getScoresArray() {
- if (scores==null)
- {
- return null;
- }
- byte[][] result = new byte[ scores.size() ][];
-
- int rowCount = 0;
- for( Map.Entry it : scores.entrySet() ) {
- String line = it.getValue().toString();
- byte[] seqValues = new byte[ line.length() ];
- for( int j=0, c=line.length(); j= 0 && val <= 9 ) ? val : -1;
- }
-
- result[rowCount++] = seqValues;
- }
-
- return result;
- }
-
-
- public void parse() throws IOException
- {
- /*
- * read the header
- */
- header = readHeader(this);
-
- if( header == null ) { error=true; return;}
- scores = new LinkedHashMap();
-
- /*
- * initilize the structure
- */
- for( Map.Entry entry : header.scores.entrySet() ) {
- scores.put( entry.getKey(), new StringBuilder());
- }
-
- /*
- * go with the reading
- */
- Block block;
- while( (block = readBlock(this,header.scores.size())) != null ) {
-
- /*
- * append sequences read in the block
- */
- for( Map.Entry entry : block.items.entrySet() ) {
- StringBuilder scoreStringBuilder = scores.get(entry.getKey());
- if( scoreStringBuilder == null ) {
- error=true;
- errormessage=String.format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", entry.getKey());
- return ;
- }
-
- scoreStringBuilder.append( entry.getValue() );
- }
- }
-
- /*
- * verify that all rows have the same width
- */
- for( StringBuilder str : scores.values() ) {
- if( fWidth == null ) {
- fWidth = str.length();
- }
- else if( fWidth != str.length() ) {
- error=true;
- errormessage="Invalid T-Coffee score file: All the score sequences must have the same length";
- return ;
- }
- }
-
-
- return;
- }
-
-
- 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(FileParse reader) throws IOException {
-
- Header result = null;
- try {
- result = new Header();
- result.head = reader.nextLine();
-
- String line;
-
- while( (line = reader.nextLine()) != null ) {
- if( line.startsWith("SCORE=")) {
- result.score = parseInt( line.substring(6).trim() );
- break;
- }
- }
-
- if( (line=reader.nextLine())==null || !"*".equals(line.trim())) { error(reader,"Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); return null;}
- if( (line=reader.nextLine())==null || !"BAD AVG GOOD".equals(line.trim())) { error(reader,"Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); return null;}
- if( (line=reader.nextLine())==null || !"*".equals(line.trim())) {error(reader,"Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)"); return null;}
-
- /*
- * now are expected a list if sequences ID up to the first blank line
- */
- while( (line=reader.nextLine()) != 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);
- }
-
- if (result==null) {
- error(reader, "T-COFFEE score file had no per-sequence scores");
- }
-
- }
- catch( IOException e ) {
- error(reader,"Unexpected problem parsing T-Coffee score ascii file");
- throw e;
- }
-
- return result;
- }
- private static void error(FileParse reader, String errm)
- {
- reader.error=true;
- if (reader.errormessage==null)
- { reader.errormessage=errm;
- } else {
- reader.errormessage+="\n"+errm;
- }
- }
- /**
- * 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( FileParse reader, int size ) throws IOException {
- Block result = new Block(size);
- String line;
-
- /*
- * read blank lines (eventually)
- */
- while( (line=reader.nextLine()) != 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
- // the remaining part are the scores values
- int p = line.indexOf(" ");
- if( p == -1 ) {
- if (reader.warningMessage==null) { reader.warningMessage=""; }
- reader.warningMessage+="Possible parsing error - expected to find a space in line: '"+line+"'\n";
- continue;
- }
-
- String id = line.substring(0,p).trim();
- String val = line.substring(p+1).trim();
-
- result.items.put(id, val);
-
- } while( (line = reader.nextLine()) != null );
-
-
- return result;
- }
-
- /*
- * The score file header
- */
- static class Header {
- String head;
- int score;
-
- LinkedHashMap scores = new LinkedHashMap();
-
- 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 items;
-
- public Block( int size ) {
- this.size = size;
- this.items = new HashMap(size);
- }
-
- String getScoresFor( String id ) {
- return items.get(id);
- }
-
- String getConsensus() {
- return items.get("cons");
- }
- }
- /**
- * TCOFFEE score colourscheme
- */
- static final Color[] colors = {
- new Color( 102, 102, 255 ), // #6666FF
- new Color( 0, 255, 0), // #00FF00
- new Color( 102, 255, 0), // #66FF00
- new Color( 204, 255, 0), // #CCFF00
- new Color( 255, 255, 0), // #FFFF00
- new Color( 255, 204, 0), // #FFCC00
- new Color( 255, 153, 0), // #FF9900
- new Color( 255, 102, 0), // #FF6600
- new Color( 255, 51, 0), // #FF3300
- new Color( 255, 34, 0) // #FF2000
- };
- public final static String TCOFFEE_SCORE="TCoffeeScore";
- /**
- * generate annotation for this TCoffee score set on the given alignment
- * @param al alignment to annotate
- * @param matchids if true, annotate sequences based on matching sequence names
- * @return true if alignment annotation was modified, false otherwise.
- */
- public boolean annotateAlignment(AlignmentI al, boolean matchids)
- {
- if (al.getHeight()!=getHeight() || al.getWidth()!=getWidth())
- {
- warningMessage="Alignment shape does not match T-Coffee score file shape.";
- return false;
- }
- boolean added=false;
- int i=0;
- SequenceIdMatcher sidmatcher = new SequenceIdMatcher(al.getSequencesArray());
- byte[][] scoreMatrix=getScoresArray();
- // for 2.8 - we locate any existing TCoffee annotation and remove it first before adding this.
- for (Map.Entry id:scores.entrySet())
- {
- byte[] srow=scoreMatrix[i];
- SequenceI s;
- if (matchids)
- {
- s=sidmatcher.findIdMatch(id.getKey());
- } else {
- s=al.getSequenceAt(i);
- }
- i++;
- if (s==null && i!=scores.size() && !id.getKey().equals("cons"))
- {
- System.err.println("No "+(matchids ? "match ":" sequences left ")+" for TCoffee score set : "+id.getKey());
- continue;
- }
- int jSize=al.getWidth()< srow.length ? al.getWidth() : srow.length;
- Annotation[] annotations=new Annotation[al.getWidth()];
- for (int j=0;j0)
- {
- System.err.println("Warning: non-zero value for positional T-COFFEE score for gap at "+j+" in sequence "+s.getName());
- }
- } else {
- annotations[j]=new Annotation(s==null ? ""+val:null,s==null ? ""+val:null,'\0',val*1f,val >= 0 && val < colors.length ? colors[val] : Color.white);
- }
- }
- // this will overwrite any existing t-coffee scores for the alignment
- AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,false,s,null);
- if (s!=null)
- {
- aa.label="T-COFFEE";
- aa.description=""+id.getKey();
- aa.annotations=annotations;
- aa.visible=false;
- aa.belowAlignment=false;
- aa.setScore(header.getScoreFor(id.getKey()));
- aa.createSequenceMapping(s, s.getStart(),true);
- s.addAlignmentAnnotation(aa);
- aa.adjustForAlignment();
- } else {
- aa.graph=AlignmentAnnotation.NO_GRAPH;
- aa.label="T-COFFEE";
- aa.description="TCoffee column reliability score";
- aa.annotations=annotations;
- aa.belowAlignment=true;
- aa.visible=true;
- aa.setScore(header.getScoreAvg());
- }
- aa.showAllColLabels=true;
- aa.validateRangeAndDisplay();
- added=true;
- }
-
- return added;
- }
+ /** The {@link Header} structure holder */
+ Header header;
+
+ /**
+ * Holds the consensues values for each sequences. It uses a LinkedHashMap to
+ * maintaint the insertion order.
+ */
+ LinkedHashMap scores;
+
+ Integer fWidth;
+
+ /**
+ * Parse the provided reader for the T-Coffee scores file format
+ *
+ * @param reader
+ * public static TCoffeeScoreFile load(Reader reader) {
+ *
+ * try { BufferedReader in = (BufferedReader) (reader instanceof
+ * BufferedReader ? reader : new BufferedReader(reader));
+ * TCoffeeScoreFile result = new TCoffeeScoreFile();
+ * result.doParsing(in); return result.header != null &&
+ * result.scores != null ? result : null; } catch( Exception e) {
+ * throw new RuntimeException(e); } }
+ */
+
+ /**
+ * @return The 'height' of the score matrix i.e. the numbers of score rows
+ * that should matches the number of sequences in the alignment
+ */
+ public int getHeight()
+ {
+ // the last entry will always be the 'global' alingment consensus scores, so
+ // it is removed
+ // from the 'height' count to make this value compatible with the number of
+ // sequences in the MSA
+ return scores != null && scores.size() > 0 ? scores.size() - 1 : 0;
+ }
+
+ /**
+ * @return The 'width' of the score matrix i.e. the number of columns. Since
+ * the score value are supposed to be calculated for an 'aligned' MSA,
+ * all the entries have to have the same width.
+ */
+ public int getWidth()
+ {
+ return fWidth != null ? fWidth : 0;
+ }
+
+ /**
+ * 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 != null && 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 getScoresList()
+ {
+ if (scores == null)
+ {
+ return null;
+ }
+ List result = new ArrayList(scores.size());
+ for (Map.Entry it : scores.entrySet())
+ {
+ result.add(it.getValue().toString());
+ }
+
+ return result;
+ }
+
+ /**
+ * @return The parsed score values a matrix of bytes
+ */
+ public byte[][] getScoresArray()
+ {
+ if (scores == null)
+ {
+ return null;
+ }
+ byte[][] result = new byte[scores.size()][];
+
+ int rowCount = 0;
+ for (Map.Entry 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;
+ }
+
+ public void parse() throws IOException
+ {
+ /*
+ * read the header
+ */
+ header = readHeader(this);
+
+ if (header == null)
+ {
+ error = true;
+ return;
+ }
+ scores = new LinkedHashMap();
+
+ /*
+ * initilize the structure
+ */
+ for (Map.Entry entry : header.scores.entrySet())
+ {
+ scores.put(entry.getKey(), new StringBuilder());
+ }
+
+ /*
+ * go with the reading
+ */
+ Block block;
+ while ((block = readBlock(this, header.scores.size())) != null)
+ {
+
+ /*
+ * append sequences read in the block
+ */
+ for (Map.Entry entry : block.items.entrySet())
+ {
+ StringBuilder scoreStringBuilder = scores.get(entry.getKey());
+ if (scoreStringBuilder == null)
+ {
+ error = true;
+ errormessage = String
+ .format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
+ entry.getKey());
+ return;
+ }
+
+ scoreStringBuilder.append(entry.getValue());
+ }
+ }
+
+ /*
+ * verify that all rows have the same width
+ */
+ for (StringBuilder str : scores.values())
+ {
+ if (fWidth == null)
+ {
+ fWidth = str.length();
+ }
+ else if (fWidth != str.length())
+ {
+ error = true;
+ errormessage = "Invalid T-Coffee score file: All the score sequences must have the same length";
+ return;
+ }
+ }
+
+ return;
+ }
+
+ 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(FileParse reader) throws IOException
+ {
+
+ Header result = null;
+ try
+ {
+ result = new Header();
+ result.head = reader.nextLine();
+
+ String line;
+
+ while ((line = reader.nextLine()) != null)
+ {
+ if (line.startsWith("SCORE="))
+ {
+ result.score = parseInt(line.substring(6).trim());
+ break;
+ }
+ }
+
+ if ((line = reader.nextLine()) == null || !"*".equals(line.trim()))
+ {
+ error(reader,
+ "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)");
+ return null;
+ }
+ if ((line = reader.nextLine()) == null
+ || !"BAD AVG GOOD".equals(line.trim()))
+ {
+ error(reader,
+ "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)");
+ return null;
+ }
+ if ((line = reader.nextLine()) == null || !"*".equals(line.trim()))
+ {
+ error(reader,
+ "Invalid T-COFFEE score format (NO BAD/AVG/GOOD header)");
+ return null;
+ }
+
+ /*
+ * now are expected a list if sequences ID up to the first blank line
+ */
+ while ((line = reader.nextLine()) != 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);
+ }
+
+ if (result == null)
+ {
+ error(reader, "T-COFFEE score file had no per-sequence scores");
+ }
+
+ } catch (IOException e)
+ {
+ error(reader, "Unexpected problem parsing T-Coffee score ascii file");
+ throw e;
+ }
+
+ return result;
+ }
+
+ private static void error(FileParse reader, String errm)
+ {
+ reader.error = true;
+ if (reader.errormessage == null)
+ {
+ reader.errormessage = errm;
+ }
+ else
+ {
+ reader.errormessage += "\n" + errm;
+ }
+ }
+
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
+
+ /**
+ * 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(FileParse reader, int size) throws IOException
+ {
+ Block result = new Block(size);
+ String line;
+
+ /*
+ * read blank lines (eventually)
+ */
+ while ((line = reader.nextLine()) != 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
+ // the remaining part are the scores values
+ int p = line.indexOf(" ");
+ if (p == -1)
+ {
+ if (reader.warningMessage == null)
+ {
+ reader.warningMessage = "";
+ }
+ reader.warningMessage += "Possible parsing error - expected to find a space in line: '"
+ + line + "'\n";
+ continue;
+ }
+
+ String id = line.substring(0, p).trim();
+ String val = line.substring(p + 1).trim();
+
+ Matcher m = SCORES_WITH_RESIDUE_NUMS.matcher(val);
+ if (m.matches())
+ {
+ val = m.group(1);
+ }
+
+ result.items.put(id, val);
+
+ } while ((line = reader.nextLine()) != null);
+
+ return result;
+ }
+
+ /*
+ * The score file header
+ */
+ static class Header
+ {
+ String head;
+
+ int score;
+
+ LinkedHashMap scores = new LinkedHashMap();
+
+ 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 items;
+
+ public Block(int size)
+ {
+ this.size = size;
+ this.items = new HashMap(size);
+ }
+
+ String getScoresFor(String id)
+ {
+ return items.get(id);
+ }
+
+ String getConsensus()
+ {
+ return items.get("cons");
+ }
+ }
+
+ /**
+ * TCOFFEE score colourscheme
+ */
+ static final Color[] colors = { new Color(102, 102, 255), // #6666FF
+ new Color(0, 255, 0), // #00FF00
+ new Color(102, 255, 0), // #66FF00
+ new Color(204, 255, 0), // #CCFF00
+ new Color(255, 255, 0), // #FFFF00
+ new Color(255, 204, 0), // #FFCC00
+ new Color(255, 153, 0), // #FF9900
+ new Color(255, 102, 0), // #FF6600
+ new Color(255, 51, 0), // #FF3300
+ new Color(255, 34, 0) // #FF2000
+ };
+
+ public final static String TCOFFEE_SCORE = "TCoffeeScore";
+
+ /**
+ * generate annotation for this TCoffee score set on the given alignment
+ *
+ * @param al
+ * alignment to annotate
+ * @param matchids
+ * if true, annotate sequences based on matching sequence names
+ * @return true if alignment annotation was modified, false otherwise.
+ */
+ public boolean annotateAlignment(AlignmentI al, boolean matchids)
+ {
+ if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
+ {
+ String info = String.format(
+ "align w: %s, h: %s; score: w: %s; h: %s ", al.getWidth(),
+ al.getHeight(), getWidth(), getHeight());
+ warningMessage = "Alignment shape does not match T-Coffee score file shape -- "
+ + info;
+ return false;
+ }
+ boolean added = false;
+ int i = 0;
+ SequenceIdMatcher sidmatcher = new SequenceIdMatcher(
+ al.getSequencesArray());
+ byte[][] scoreMatrix = getScoresArray();
+ // for 2.8 - we locate any existing TCoffee annotation and remove it first
+ // before adding this.
+ for (Map.Entry id : scores.entrySet())
+ {
+ byte[] srow = scoreMatrix[i];
+ SequenceI s;
+ if (matchids)
+ {
+ s = sidmatcher.findIdMatch(id.getKey());
+ }
+ else
+ {
+ s = al.getSequenceAt(i);
+ }
+ i++;
+ if (s == null && i != scores.size() && !id.getKey().equals("cons"))
+ {
+ System.err.println("No "
+ + (matchids ? "match " : " sequences left ")
+ + " for TCoffee score set : " + id.getKey());
+ continue;
+ }
+ int jSize = al.getWidth() < srow.length ? al.getWidth() : srow.length;
+ Annotation[] annotations = new Annotation[al.getWidth()];
+ for (int j = 0; j < jSize; j++)
+ {
+ byte val = srow[j];
+ if (s != null && jalview.util.Comparison.isGap(s.getCharAt(j)))
+ {
+ annotations[j] = null;
+ if (val > 0)
+ {
+ System.err
+ .println("Warning: non-zero value for positional T-COFFEE score for gap at "
+ + j + " in sequence " + s.getName());
+ }
+ }
+ else
+ {
+ annotations[j] = new Annotation(s == null ? "" + val : null,
+ s == null ? "" + val : null, '\0', val * 1f, val >= 0
+ && val < colors.length ? colors[val]
+ : Color.white);
+ }
+ }
+ // this will overwrite any existing t-coffee scores for the alignment
+ AlignmentAnnotation aa = al.findOrCreateAnnotation(TCOFFEE_SCORE,
+ TCOFFEE_SCORE, false, s, null);
+ if (s != null)
+ {
+ aa.label = "T-COFFEE";
+ aa.description = "" + id.getKey();
+ aa.annotations = annotations;
+ aa.visible = false;
+ aa.belowAlignment = false;
+ aa.setScore(header.getScoreFor(id.getKey()));
+ aa.createSequenceMapping(s, s.getStart(), true);
+ s.addAlignmentAnnotation(aa);
+ aa.adjustForAlignment();
+ }
+ else
+ {
+ aa.graph = AlignmentAnnotation.NO_GRAPH;
+ aa.label = "T-COFFEE";
+ aa.description = "TCoffee column reliability score";
+ aa.annotations = annotations;
+ aa.belowAlignment = true;
+ aa.visible = true;
+ aa.setScore(header.getScoreAvg());
+ }
+ aa.showAllColLabels = true;
+ aa.validateRangeAndDisplay();
+ added = true;
+ }
+
+ return added;
+ }
@Override
public String print()