X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FRnamlFile.java;h=4d3ddc17241ba7cdd0b60123fd438e363efcc4a2;hb=d4ec118f86b5c9dee801e743c46aaacc7bb521d1;hp=7b89909b4509c65858c07c54e66b2a5035ed38cd;hpb=8af5dc25549fb2ba801ae889d44744a46dacf04e;p=jalview.git
diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index 7b89909..4d3ddc1 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -1,33 +1,40 @@
/*
- * 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
- * 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.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
+import jalview.analysis.Rna;
+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.util.List;
-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;
@@ -47,7 +54,7 @@ public class RnamlFile extends AlignFile
}
- public RnamlFile(String inFile, String type) throws IOException
+ public RnamlFile(String inFile, DataSourceType type) throws IOException
{
super(inFile, type);
@@ -73,6 +80,7 @@ public class RnamlFile extends AlignFile
*
* @see jalview.io.AlignFile#parse()
*/
+ @Override
public void parse() throws IOException
{
if (System.getProperty("java.version").indexOf("1.6") > -1
@@ -94,39 +102,44 @@ public class RnamlFile extends AlignFile
_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)
{
- 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)
{
- 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;
- 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);
}
}
@SuppressWarnings("unchecked")
- public void _parse() throws FileNotFoundException,
- ExceptionPermissionDenied, ExceptionLoadingFailed,
- ExceptionFileFormatOrSyntax
+ public void _parse()
+ throws FileNotFoundException, ExceptionPermissionDenied,
+ ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
{
result = RNAFactory.loadSecStrRNAML(getReader());
- ArrayList allarray = new ArrayList();
- ArrayList> BP = new ArrayList();
- ArrayList strucinarray = new ArrayList();
- SequenceI[] seqs = new SequenceI[result.size()];
+ // ArrayList allarray = new ArrayList();
+ // ArrayList> BP = new ArrayList();
+ // ArrayList strucinarray = new ArrayList();
+ SequenceI[] sqs = new SequenceI[result.size()];
for (int i = 0; i < result.size(); i++)
{
@@ -138,9 +151,17 @@ public class RnamlFile extends AlignFile
int end = seq.length();
id = current.getName();
- seqs[i] = new Sequence(id, seq, begin, end);
+ if (id == null || id.trim().length() == 0)
+ {
+ id = safeName(getDataName());
+ if (result.size() > 1)
+ {
+ id += "." + i;
+ }
+ }
+ 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()];
@@ -152,38 +173,36 @@ public class RnamlFile extends AlignFile
for (int k = 0; k < rna.length(); k++)
{
ann[k] = new Annotation(annot[k], "",
- jalview.schemes.ResidueProperties.getRNASecStrucState(
- annot[k]).charAt(0), 0f);
+ Rna.getRNASecStrucState(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));
+ sqs[i].addAlignmentAnnotation(align);
+ sqs[i].setRNA(result.get(i));
- allarray.add(strucinarray);
+ // allarray.add(strucinarray);
annotations.addElement(align);
- BP.add(align.bps);
+ // BP.add(align.bps);
}
- setSeqs(seqs);
+ setSeqs(sqs);
}
- public static String print(SequenceI[] s)
+ @Override
+ public String print(SequenceI[] s, boolean jvSuffix)
{
return "not yet implemented";
}
- public String print()
- {
- System.out.print("print :");
- return print(getSeqsAsArray());
- }
-
- public ArrayList getRNA()
+ public List getRNA()
{
return result;
}
@@ -203,13 +222,18 @@ public class RnamlFile extends AlignFile
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;
}
}