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Merge branch 'develop' into features/JAL-653_gffalignments
[jalview.git]
/
src
/
jalview
/
io
/
RnamlFile.java
diff --git
a/src/jalview/io/RnamlFile.java
b/src/jalview/io/RnamlFile.java
index
7b89909
..
c15bc6c
100644
(file)
--- a/
src/jalview/io/RnamlFile.java
+++ b/
src/jalview/io/RnamlFile.java
@@
-1,33
+1,39
@@
/*
/*
- * 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;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
+import com.stevesoft.pat.Regex;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
@@
-94,24
+100,21
@@
public class RnamlFile extends AlignFile
_parse();
} catch (ExceptionPermissionDenied pdx)
{
_parse();
} catch (ExceptionPermissionDenied pdx)
{
- errormessage = "Couldn't access datasource (" + pdx.getMessage()
- + ")";
+ errormessage = MessageManager.formatMessage("exception.rnaml_couldnt_access_datasource", new String[]{pdx.getMessage()});
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
throw new IOException(pdx);
} catch (ExceptionLoadingFailed lf)
{
- errormessage = "Couldn't process data as RNAML file ("
- + lf.getMessage() + ")";
+ errormessage = MessageManager.formatMessage("exception.ranml_couldnt_process_data", new String[]{lf.getMessage()});
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
throw new IOException(lf);
} catch (ExceptionFileFormatOrSyntax iff)
{
- errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+ errormessage = MessageManager.formatMessage("exception.ranml_invalid_file", new String[]{iff.getMessage()});
throw new IOException(iff);
} catch (Exception x)
{
error = true;
throw new IOException(iff);
} catch (Exception x)
{
error = true;
- errormessage = "Problem parsing data as RNAML (" + x.getMessage()
- + ")";
- throw new IOException("Couldn't parse the datasource as RNAML", x);
+ errormessage = MessageManager.formatMessage("exception.ranml_problem_parsing_data", new String[]{x.getMessage()});
+ throw new IOException(errormessage , x);
}
}
}
}
@@
-138,6
+141,14
@@
public class RnamlFile extends AlignFile
int end = seq.length();
id = current.getName();
int end = seq.length();
id = current.getName();
+ if (id == null || id.trim().length() == 0)
+ {
+ id = safeName(getDataName());
+ if (result.size() > 1)
+ {
+ id += "." + i;
+ }
+ }
seqs[i] = new Sequence(id, seq, begin, end);
seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
seqs[i] = new Sequence(id, seq, begin, end);
seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
@@
-156,8
+167,11
@@
public class RnamlFile extends AlignFile
annot[k]).charAt(0), 0f);
}
annot[k]).charAt(0), 0f);
}
- AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
- current.getID(), ann);
+ AlignmentAnnotation align = new AlignmentAnnotation(
+ "Secondary Structure",
+ current.getID().trim().length() > 0 ? "Secondary Structure for "
+ + current.getID()
+ : "", ann);
seqs[i].addAlignmentAnnotation(align);
seqs[i].setRNA(result.get(i));
seqs[i].addAlignmentAnnotation(align);
seqs[i].setRNA(result.get(i));
@@
-203,13
+217,18
@@
public class RnamlFile extends AlignFile
private String safeName(String dataName)
{
int b = 0;
private String safeName(String dataName)
{
int b = 0;
- while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+ if ((b = dataName.lastIndexOf(".")) > 0)
{
{
- dataName = dataName.substring(b + 1).trim();
-
+ dataName = dataName.substring(0, b - 1);
+ }
+ b = 0;
+ Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
+ String mm = dataName;
+ while (m.searchFrom(dataName, b))
+ {
+ mm = m.stringMatched();
+ b = m.matchedTo();
}
}
- int e = (dataName.length() - dataName.indexOf(".")) + 1;
- dataName = dataName.substring(1, e).trim();
- return dataName;
+ return mm;
}
}
}
}