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JAL-1233 JAL-1576 copy constructor to propagate helix colours and applyTo implementat...
[jalview.git]
/
src
/
jalview
/
io
/
TCoffeeScoreFile.java
diff --git
a/src/jalview/io/TCoffeeScoreFile.java
b/src/jalview/io/TCoffeeScoreFile.java
index
42a2caa
..
ca8a22a
100644
(file)
--- a/
src/jalview/io/TCoffeeScoreFile.java
+++ b/
src/jalview/io/TCoffeeScoreFile.java
@@
-1,19
+1,22
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
*/
package jalview.io;
@@
-30,6
+33,8
@@
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
/**
* A file parse for T-Coffee score ascii format. This file contains the
/**
* A file parse for T-Coffee score ascii format. This file contains the
@@
-86,7
+91,6
@@
import java.util.Map;
*/
public class TCoffeeScoreFile extends AlignFile
{
*/
public class TCoffeeScoreFile extends AlignFile
{
-
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
public TCoffeeScoreFile(String inFile, String type) throws IOException
{
super(inFile, type);
@@
-138,7
+142,7
@@
public class TCoffeeScoreFile extends AlignFile
/**
* @return The 'width' of the score matrix i.e. the number of columns. Since
/**
* @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()
* all the entries have to have the same width.
*/
public int getWidth()
@@
-393,6
+397,9
@@
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.
*
/**
* Read a scores block ihe provided stream.
*
@@
-452,6
+459,12
@@
public class TCoffeeScoreFile extends AlignFile
String id = line.substring(0, p).trim();
String val = line.substring(p + 1).trim();
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);
result.items.put(id, val);
} while ((line = reader.nextLine()) != null);
@@
-540,7
+553,11
@@
public class TCoffeeScoreFile extends AlignFile
{
if (al.getHeight() != getHeight() || al.getWidth() != getWidth())
{
{
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;
return false;
}
boolean added = false;