* @author Paolo Di Tommaso
*
*/
-public class TCoffeeScoreFile {
+public class TCoffeeScoreFile extends AlignFile {
+ public TCoffeeScoreFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+
+ }
+
+ 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<String,StringBuilder> scores = new LinkedHashMap<String,StringBuilder>();
+ LinkedHashMap<String,StringBuilder> scores;
Integer fWidth;
-
- /**
- * Parse the specified file.
- *
- * @param file The file to be parsed
- */
- public static TCoffeeScoreFile load(File file) {
- try {
- return load(new FileReader(file));
- }
- catch (FileNotFoundException e) {
- throw new RuntimeException(e);
- }
- }
/**
* Parse the provided reader for the T-Coffee scores file format
*
* @param reader
- */
public static TCoffeeScoreFile load(Reader reader) {
try {
throw new RuntimeException(e);
}
}
+ */
/**
* @return The 'height' of the score matrix i.e. the numbers of score rows that should matches
return fWidth != null ? fWidth : 0;
}
- /**
- * The default constructor is marked as {@code protected} since this class is meant to created
- * through the {@link #load(File)} or {@link #load(Reader)} factory methods
- */
- protected TCoffeeScoreFile() { }
/**
* Get the string of score values for the specified seqeunce ID.
* 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 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<String> getScoresList() {
+ if (scores==null)
+ {
+ return null;
+ }
List<String> result = new ArrayList<String>( scores.size() );
for( Map.Entry<String,StringBuilder> it : scores.entrySet() ) {
result.add(it.getValue().toString());
* @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;
}
- private void doParsing(BufferedReader in) throws IOException {
-
+ public void parse() throws IOException
+ {
/*
* read the header
*/
- header = readHeader(in);
+ header = readHeader(this);
- if( header == null ) { return; }
-
+ if( header == null ) { error=true; return;}
+ scores = new LinkedHashMap<String,StringBuilder>();
/*
* initilize the structure
* go with the reading
*/
Block block;
- while( (block = readBlock(in, header.scores.size())) != null ) {
+ while( (block = readBlock(this,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()));
+ 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() );
fWidth = str.length();
}
else if( fWidth != str.length() ) {
- throw new RuntimeException("Invalid T-Coffee score file: All the score sequences must have the same length");
+ error=true;
+ errormessage="Invalid T-Coffee score file: All the score sequences must have the same length";
+ return ;
}
}
-
+ return;
}
* @return The parser {@link Header} instance
* @throws RuntimeException when the header is not in the expected format
*/
- static Header readHeader(BufferedReader reader) {
+ static Header readHeader(FileParse reader) throws IOException {
Header result = null;
try {
result = new Header();
- result.head = reader.readLine();
+ result.head = reader.nextLine();
String line;
- while( (line = reader.readLine()) != null ) {
+ while( (line = reader.nextLine()) != 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;
+ 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.readLine()) != null ) {
+ while( (line=reader.nextLine()) != null ) {
if( "".equals(line) ) {
break;
}
result.scores.put(id,val);
}
+ if (result==null) {
+ error(reader, "T-COFFEE score file had no per-sequence scores");
+ }
+
}
catch( IOException e ) {
- throw new RuntimeException("Cannot parse T-Coffee score ascii file", 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.
*
* @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 {
+ static Block readBlock( FileParse reader, int size ) throws IOException {
Block result = new Block(size);
String line;
/*
* read blank lines (eventually)
*/
- while( (line=reader.readLine()) != null && "".equals(line.trim())) {
+ while( (line=reader.nextLine()) != null && "".equals(line.trim())) {
// consume blank lines
}
- if( line == null ) return null;
+ if( line == null ) { return null; }
/*
* read the scores block
// split the line on the first blank
// the first part have to contain the sequence id
- // theramining part are the scores values
+ // the remaining 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;
+ 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();
result.items.put(id, val);
- } while( (line = reader.readLine()) != null );
+ } while( (line = reader.nextLine()) != null );
return result;
*/
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());
Annotation[] annotations=new Annotation[al.getWidth()];
for (int j=0;j<jSize;j++) {
byte val = srow[j];
- 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);
+ 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);
+ }
}
- AlignmentAnnotation aa=null;
+ // this will overwrite any existing t-coffee scores for the alignment
+ AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,false,s,null);
if (s!=null)
{
- // TODO - set per sequence score
- aa=new AlignmentAnnotation(TCOFFEE_SCORE, "Score for "+id.getKey(), annotations);
-
- aa.setSequenceRef(s);
+ 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=new AlignmentAnnotation("T-COFFEE", "TCoffee column reliability score", annotations);
+ 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());
}
- al.addAnnotation(aa);
+ aa.showAllColLabels=true;
+ aa.validateRangeAndDisplay();
added=true;
}
+
return added;
}
-
+ @Override
+ public String print()
+ {
+ // TODO Auto-generated method stub
+ return "Not valid.";
+ }
}
git://source.jalview.org / jalview.git / blobdiff