X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=fc0c9131294edcd2bc5d93492724b05984cb3d55;hb=efb5cfa00ee832a62dfdf59f5fb847a0e16424d9;hp=ae023dcfe160135430485683e0d047d15a26ff49;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java index ae023dc..fc0c913 100644 --- a/src/jalview/io/TCoffeeScoreFile.java +++ b/src/jalview/io/TCoffeeScoreFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -37,10 +37,10 @@ import java.util.regex.Matcher; import java.util.regex.Pattern; /** - * A file parse for T-Coffee score ascii format. This file contains the - * alignment consensus for each resude in any sequence. + * A file parser for T-Coffee score ascii format. This file contains the + * alignment consensus for each residue in any sequence. *
- * 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
@@ -91,16 +91,26 @@ import java.util.regex.Pattern;
*/
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 TCoffeeScoreFile(FileParse source) throws IOException
- {
- super(source);
- }
+ public final static String TCOFFEE_SCORE = "TCoffeeScore";
+
+ static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
/** The {@link Header} structure holder */
Header header;
@@ -113,6 +123,18 @@ public class TCoffeeScoreFile extends AlignFile
Integer fWidth;
+ public TCoffeeScoreFile(String inFile, DataSourceType fileSourceType)
+ throws IOException
+ {
+ super(inFile, fileSourceType);
+
+ }
+
+ public TCoffeeScoreFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
/**
* Parse the provided reader for the T-Coffee scores file format
*
@@ -160,8 +182,9 @@ public class TCoffeeScoreFile extends AlignFile
*/
public String getScoresFor(String id)
{
- return scores != null && scores.containsKey(id) ? scores.get(id)
- .toString() : "";
+ return scores != null && scores.containsKey(id)
+ ? scores.get(id).toString()
+ : "";
}
/**
@@ -213,6 +236,7 @@ public class TCoffeeScoreFile extends AlignFile
return result;
}
+ @Override
public void parse() throws IOException
{
/*
@@ -251,9 +275,9 @@ public class TCoffeeScoreFile extends AlignFile
if (scoreStringBuilder == null)
{
error = true;
- errormessage = String
- .format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
- entry.getKey());
+ errormessage = String.format(
+ "Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section",
+ entry.getKey());
return;
}
@@ -397,9 +421,6 @@ public class TCoffeeScoreFile extends AlignFile
}
}
- static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
- .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
-
/**
* Read a scores block ihe provided stream.
*
@@ -523,23 +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
@@ -581,9 +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;
@@ -596,16 +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);
}
}
@@ -643,7 +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.";