X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FTCoffeeScoreFile.java;h=d069e5e6e3429b921519390409e8f06df9e24244;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=97de459be5f199ea3e3dceeafa71bc93d5b5f9ac;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java index 97de459..d069e5e 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 2.9.0b2) - * 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";
+
+ private final static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+ .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
/** The {@link Header} structure holder */
Header header;
@@ -113,6 +123,19 @@ public class TCoffeeScoreFile extends AlignFile
Integer fWidth;
+ public TCoffeeScoreFile(Object inFile, DataSourceType fileSourceType)
+ throws IOException
+ {
+ // BH 2018 allows File or String
+ super(inFile, fileSourceType);
+
+ }
+
+ public TCoffeeScoreFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
/**
* Parse the provided reader for the T-Coffee scores file format
*
@@ -160,8 +183,9 @@ 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()
+ : "";
}
/**
@@ -174,7 +198,7 @@ public class TCoffeeScoreFile extends AlignFile
{
return null;
}
- List