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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
io
/
RnamlFile.java
diff --git
a/src/jalview/io/RnamlFile.java
b/src/jalview/io/RnamlFile.java
index
fb72bca
..
f48f825
100644
(file)
--- a/
src/jalview/io/RnamlFile.java
+++ b/
src/jalview/io/RnamlFile.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.
*
*
* This file is part of Jalview.
*
@@
-20,7
+20,7
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.Rna;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
@@
-32,6
+32,7
@@
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.List;
import com.stevesoft.pat.Regex;
import com.stevesoft.pat.Regex;
@@
-79,6
+80,7
@@
public class RnamlFile extends AlignFile
*
* @see jalview.io.AlignFile#parse()
*/
*
* @see jalview.io.AlignFile#parse()
*/
+ @Override
public void parse() throws IOException
{
if (System.getProperty("java.version").indexOf("1.6") > -1
public void parse() throws IOException
{
if (System.getProperty("java.version").indexOf("1.6") > -1
@@
-134,10
+136,10
@@
public class RnamlFile extends AlignFile
result = RNAFactory.loadSecStrRNAML(getReader());
result = RNAFactory.loadSecStrRNAML(getReader());
- ArrayList<ArrayList> allarray = new ArrayList();
- ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
- ArrayList strucinarray = new ArrayList();
- SequenceI[] seqs = new SequenceI[result.size()];
+ // ArrayList<ArrayList> allarray = new ArrayList();
+ // ArrayList<ArrayList<SimpleBP>> BP = new ArrayList();
+ // ArrayList strucinarray = new ArrayList();
+ SequenceI[] sqs = new SequenceI[result.size()];
for (int i = 0; i < result.size(); i++)
{
for (int i = 0; i < result.size(); i++)
{
@@
-157,9
+159,9
@@
public class RnamlFile extends AlignFile
id += "." + i;
}
}
id += "." + i;
}
}
- seqs[i] = new Sequence(id, seq, begin, end);
+ sqs[i] = new Sequence(id, seq, begin, end);
- seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
+ sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
String[] annot = new String[rna.length()];
Annotation[] ann = new Annotation[rna.length()];
String[] annot = new String[rna.length()];
Annotation[] ann = new Annotation[rna.length()];
@@
-170,9
+172,8
@@
public class RnamlFile extends AlignFile
}
for (int k = 0; k < rna.length(); k++)
{
}
for (int k = 0; k < rna.length(); k++)
{
- ann[k] = new Annotation(annot[k], "",
- jalview.schemes.ResidueProperties.getRNASecStrucState(
- annot[k]).charAt(0), 0f);
+ ann[k] = new Annotation(annot[k], "", Rna.getRNASecStrucState(
+ annot[k]).charAt(0), 0f);
}
AlignmentAnnotation align = new AlignmentAnnotation(
}
AlignmentAnnotation align = new AlignmentAnnotation(
@@
-181,17
+182,17
@@
public class RnamlFile extends AlignFile
+ current.getID()
: "", ann);
+ current.getID()
: "", ann);
- seqs[i].addAlignmentAnnotation(align);
- seqs[i].setRNA(result.get(i));
+ sqs[i].addAlignmentAnnotation(align);
+ sqs[i].setRNA(result.get(i));
- allarray.add(strucinarray);
+ // allarray.add(strucinarray);
annotations.addElement(align);
annotations.addElement(align);
- BP.add(align.bps);
+ // BP.add(align.bps);
}
}
- setSeqs(seqs);
+ setSeqs(sqs);
}
public static String print(SequenceI[] s)
}
public static String print(SequenceI[] s)
@@
-199,13
+200,14
@@
public class RnamlFile extends AlignFile
return "not yet implemented";
}
return "not yet implemented";
}
+ @Override
public String print()
{
System.out.print("print :");
return print(getSeqsAsArray());
}
public String print()
{
System.out.print("print :");
return print(getSeqsAsArray());
}
- public ArrayList getRNA()
+ public List<RNA> getRNA()
{
return result;
}
{
return result;
}