- * This file is procuded by t_coffee providing the option
+ * This file is produced by t_coffee providing the option
* -output=score_ascii to the program command line
*
* An example file is the following
@@ -92,16 +92,25 @@ import java.util.Map;
public class TCoffeeScoreFile extends AlignFile
{
- public TCoffeeScoreFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
+ /**
+ * TCOFFEE score colourscheme
+ */
+ static final Color[] colors = { new Color(102, 102, 255), // 0: lilac #6666FF
+ new Color(0, 255, 0), // 1: green #00FF00
+ new Color(102, 255, 0), // 2: lime green #66FF00
+ new Color(204, 255, 0), // 3: greeny yellow #CCFF00
+ new Color(255, 255, 0), // 4: yellow #FFFF00
+ new Color(255, 204, 0), // 5: orange #FFCC00
+ new Color(255, 153, 0), // 6: deep orange #FF9900
+ new Color(255, 102, 0), // 7: ochre #FF6600
+ new Color(255, 51, 0), // 8: red #FF3300
+ new Color(255, 34, 0) // 9: redder #FF2000
+ };
- }
+ public final static String TCOFFEE_SCORE = "TCoffeeScore";
- public TCoffeeScoreFile(FileParse source) throws IOException
- {
- super(source);
- }
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
/** The {@link Header} structure holder */
Header header;
@@ -114,6 +123,18 @@ public class TCoffeeScoreFile extends AlignFile
Integer fWidth;
+ public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+ throws IOException
+ {
+ super(inFile, fileSourceType);
+
+ }
+
+ public TCoffeeScoreFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
/**
* Parse the provided reader for the T-Coffee scores file format
*
@@ -143,7 +164,7 @@ public class TCoffeeScoreFile extends AlignFile
/**
* @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,
+ * the score value are supposed to be calculated for an 'aligned' MSA,
* all the entries have to have the same width.
*/
public int getWidth()
@@ -161,8 +182,9 @@ public class TCoffeeScoreFile extends AlignFile
*/
public String getScoresFor(String id)
{
- return scores != null && scores.containsKey(id) ? scores.get(id)
- .toString() : "";
+ return scores != null && scores.containsKey(id)
+ ? scores.get(id).toString()
+ : "";
}
/**
@@ -214,6 +236,7 @@ public class TCoffeeScoreFile extends AlignFile
return result;
}
+ @Override
public void parse() throws IOException
{
/*
@@ -252,9 +275,9 @@ public class TCoffeeScoreFile extends AlignFile
if (scoreStringBuilder == null)
{
error = true;
- errormessage = String
- .format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
- entry.getKey());
+ errormessage = String.format(
+ "Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
+ entry.getKey());
return;
}
@@ -457,6 +480,12 @@ public class TCoffeeScoreFile extends AlignFile
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);
@@ -515,24 +544,6 @@ public class TCoffeeScoreFile extends AlignFile
}
/**
- * 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
@@ -545,7 +556,11 @@ public class TCoffeeScoreFile extends AlignFile
{
if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
{
- warningMessage = "Alignment shape does not match T-Coffee score file shape.";
+ 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;
@@ -570,9 +585,9 @@ public class TCoffeeScoreFile extends AlignFile
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());
+ 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;
@@ -585,16 +600,16 @@ public class TCoffeeScoreFile extends AlignFile
annotations[j] = null;
if (val > 0)
{
- System.err
- .println("Warning: non-zero value for positional T-COFFEE score for gap at "
+ 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]
+ s == null ? "" + val : null, '\0', val * 1f,
+ val >= 0 && val < colors.length ? colors[val]
: Color.white);
}
}
@@ -632,7 +647,7 @@ public class TCoffeeScoreFile extends AlignFile
}
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
// TODO Auto-generated method stub
return "Not valid.";