From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 4 Dec 2012 16:12:03 +0000 (+0000)
Subject: JAL-1140 - handle VARNA specific RNA exceptions within the IO class and generate... 
X-Git-Tag: Jalview_2_9~257
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c893db0d67d7708d5fa5d08566168a06a61df13e;p=jalview.git

JAL-1140 - handle VARNA specific RNA exceptions within the IO class and generate appropriate error messages
---

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index bc6b385..122e6e1 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -19,354 +19,161 @@ package jalview.io;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.SecondaryStructureAnnotation;
 import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.ws.jws1.Annotate3D;
 
 import java.io.BufferedReader;
 import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.Reader;
 import java.io.FileReader;
-import java.lang.reflect.Array;
+import java.io.IOException;
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
-
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-
-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.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
 import fr.orsay.lri.varna.factories.RNAFactory;
-import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
 import fr.orsay.lri.varna.models.rna.RNA;
-import fr.orsay.lri.varna.utils.RNAMLParser;
-
-
-
 
 public class RnamlFile extends AlignFile
 {
-	 public String id;
-	 protected ArrayList<RNA> result;
-	 
-	 public RnamlFile()
-	  {
-		 super();
-		
-	  }
-	 
-	 public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
-	  {
-	    super(inFile, type);
-	    
-	  }
-
-	  public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
-	  {
-	    super(source);
-	    
-	  }
-	  
-//	  public RnamlFile(BufferedReader r) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
-//	  {
-//		  	super();	    
-//		    parse(r);
-//		    // sets the index of each sequence in the alignment
-//		    for( int i=0,c=seqs.size(); i<c; i++ ) {  
-//		    	seqs.get(i).setIndex(i);  
-//		    }
-//		  
-//	    
-//	  }
-	  
-	public BufferedReader CreateReader() throws FileNotFoundException
-	{
-		 FileReader fr = null;
-		  fr = new FileReader(inFile); 
-		  
-		  BufferedReader r = new BufferedReader (fr);
-		  return r;
-	}
-	
-	
-	@SuppressWarnings("unchecked")
-	public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
-	{
-		 result = RNAFactory.loadSecStrRNAML(getReader());
-		  
-		 System.out.println("this is the secondary scructure:" +result.size());
-		  //System.out.println("this is the secondary scructure:" +result.toString());
-		  //System.out.println("this is the secondary scructure:" +result.size());
-		 SequenceI[] seqs = new SequenceI[result.size()];
-		  System.out.println(type); //the type is "File"
-		  System.out.println(inFile );//inFile is the path
-		  
-		 for(int i=0;i<result.size();i++)
-			{
-			 RNA current = result.get(i);
-		  System.out.println(current.getSeq());
-		  //System.out.println(result.get(i).getStructBPSEQ());
-		  System.out.println(result.get(i).getStructDBN(true));
-		  System.out.println(i);
-		  String rna =current.getStructDBN(true);
-		  //System.out.println(result.get(0).getAnnotations());
-		  String seq = current.getSeq();
-	
-		  int begin=1;
-		  int end = seq.length();
-		  
-		  id = current.getName();
-		  seqs[i] = new Sequence(id, seq, begin, end);
-		  //System.out.println(seq);
-		  System.out.println("Rna is still "+rna);
-		  //SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
-		  //seqs[i].addSequenceFeature(feat);
-		  
-		  String[] annot=new String[rna.length()] ;
-		  Annotation[] ann = new Annotation[rna.length()];
-		
-		  for(int j=0;j<rna.length();j++)
-			{
-			  annot[j] =rna.substring(j,j+1);
-		  
-			}
-		  
-		  for(int k=0;k<rna.length();k++)
-		{
-			  ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);
-			  			  
-		}
-		  AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);
-		  
-		  seqs[i].addAlignmentAnnotation(align);
-		  seqs[i].setRNA(result.get(i));
-		  this.annotations.addElement(align);
-		}
-   	  this.setSeqs(seqs);
-		 
-		 
-		
-
-	}
-	  
-	
-	  public void parse(BufferedReader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax 
-	  {
-		   System.out.println("parse with Buffer (RnamlFile");
-		  Hashtable seqhash = new Hashtable();
-		  Vector headers = new Vector();
-		  //ArrayList<String> seq =new ArrayList();
-		  //System.out.println(r);
-		  
-		  result = RNAFactory.loadSecStr(r,RNAFileType.FILE_TYPE_RNAML);
-		  
-		  System.out.println("this is the secondary scructure:" +result.toArray());
-		  System.out.println("this is the secondary scructure:" +result.toString());
-		  System.out.println("this is the secondary scructure:" +result.size());
-			for(int i=0;i<result.size();i++)
-			{
-		  System.out.println(result.get(0).getSeq());
-		  System.out.println(result.get(0).getStructBPSEQ());
-		  System.out.println(result.get(0).getStructDBN(true));
-		  String rna1 =result.get(0).getStructDBN(true);
-		  System.out.println(result.get(0).getAnnotations());
-		  String seq = result.get(0).getSeq();
-		  System.out.println(type); //the type is "File"
-		  System.out.println(inFile );//inFile is the path
-		  int begin=0;
-		  int end = seq.length()-1;
-		  SequenceI[] seqs = new SequenceI[1];
-		  id = safeName(getDataName());
-		  seqs[0] = new Sequence(id, seq, begin, end);
-		  SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
-		  seqs[0].addSequenceFeature(feat);
-		  this.setSeqs(seqs);
-		  
-		  String[] annot=new String[10000] ;
-		  Annotation[] ann = new Annotation[1000];
-		  for(int j=0;j<rna1.length();j++)
-			{
-		  annot[j] =rna1.substring(j,j+1);
-		  //System.out.println(annot[j]);
-			}
-		  
-		  for(int k=0;k<rna1.length();k++)
-		{
-			  ann[k] = new Annotation(annot[k], "", ' ', 0f);
-			  
-			  ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
-			  
-		}
-		  AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
-		  seqs[0].addAlignmentAnnotation(align);
-		  this.annotations.addElement(align);
-		}
-		//Annotate3D tintin = new Annotate3D();
-		  
-		//System.out.println(tintin);  
-		  
-		  
-		  
-		  
-		  
-		  
-		 
-	
-//					for(RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
-//					{
-//						// Retrieving parsed data
-//						seq = rnaTmp.getSequence(); //contient la séquence sous forme de liste
-//						System.out.println(seq);
-//						String seqAsStr = "";
-//						for(String s:seq)
-//						{
-//							// Only consider last character, e.g. in case of modified nucleotide
-//							seqAsStr += s.charAt(s.length()-1);
-//						}
-//						int begin=0;
-//						int end = seqAsStr.length()-1;
-//						SequenceI[] seqs = new SequenceI[1];
-//						id = safeName(getDataName());
-//						seqs[0] = new Sequence(id, seqAsStr, begin, end);
-//						SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
-//
-//	                    seqs[0].addSequenceFeature(feat);
-//						this.setSeqs(seqs);
-						
-						//String pos = annot.substring(1, 2);
-						//System.out.println(annot);
-						//System.out.println(pos);
-						
-					   // ann[1] = new Annotation(pos, "", ' ', 0f);
-					   // ann[1].secondaryStructure = 'A';
-					    //System.out.println(ann[1]);
-					    
-					   // toto.annotations=ann;
-					    
-
-					    
-////						 Annotation[] els = new Annotation[seq.size()];
-//						
-//						//System.err.println(""+seq.size());
-//					    Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
-//					    String[] annot = new String[10000];
-//					  
-//						//Annotation[] ann = new Annotation[allbpsTmp.size()];
-//						for (int i = 0; i < allbpsTmp.size(); i++) {
-//						RNAMLParser.BPTemp bp = allbpsTmp.get(i);
-//						//System.err.println("toto ="+bp);
-//						int bp5 = bp.pos5;
-//						annot[bp5]= "(";
-//						//annot[bp5]= '(';
-//						System.out.println(annot[bp5]);
-//						//System.out.println("bp5 ="+bp5);
-//						int bp3 = bp.pos3;
-//					
-//						annot[bp3]= ")";
-//						System.out.println(annot[bp3]);
-//						//System.out.println(annot.get(bp3));
-//						
-//						//String pos1 = annot.substring(bp5, bp5+1);
-//						//String pos2 = annot.substring(bp3, bp3+1);
-//						//ann[i] = new Annotation(pos1, "", ' ', 0f);
-//						//ann[i+1] = new Annotation(pos2, "", ' ', 0f);
-//						//System.out.println(pos1);
-//						
-//						//System.out.println("bp3 ="+bp3);
-//						//ModeleBP newStyle = bp.createBPStyle(mb, part);
-//						}	
-//						Annotation[] ann = new Annotation[annot.length+1];
-//						for(int i=0;i<annot.length;i++)
-//						{		
-//							if(annot[i]==null)
-//							{
-//								annot[i]=".";
-//							}
-//							
-//							ann[i] = new Annotation(annot[i], "", ' ', 0f);
-//						//System.out.print(annot[i]);
-//						}
-//						
-//						AlignmentAnnotation toto = new AlignmentAnnotation("Secondary structure","",ann);
-//						this.annotations.addElement(toto);
-					
-						// Creating empty structure of suitable size
-//						int[] str = new int[seq.size()];
-//						for (int i=0;i<str.length;i++)
-//						{ str[i] = -1; }
-//						Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
-//						for (int i = 0; i < allbpsTmp.size(); i++) {
-//							RNAMLParser.BPTemp bp = allbpsTmp.get(i);
-//							//System.err.println("toto ="+bp);
-//							int bp5 = bp.pos5;
-//							//System.out.println("bp5 ="+bp5);
-//							int bp3 = bp.pos3;
-							//System.out.println("bp3 ="+bp3);
-							//ModeleBP newStyle = bp.createBPStyle(mb, part);
-//						}
-						//Annotation ann;
-					    //ann = new Annotation(bp5, "", ' ', 0f);
-				
-					//}
-
-			
-
-//				return result;
-	  
-}
-
-	  
-	  public static String print(SequenceI[] s)
-	  {
-	    return "not yet implemented";
-	  }
-	  
-	  public String print()
-	  {
-		System.out.print("affiche :");
-	    return print(getSeqsAsArray());
-	  }
-	  
-	  /**
-	   * make a friendly ID string.
-	   * 
-	   * @param dataName
-	   * @return truncated dataName to after last '/'
-	   */
-	  private String safeName(String dataName)
-	  {
-	    int b = 0;
-	    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )
-	    {	    	   
-	    	dataName = dataName.substring(b + 1).trim();
-	    	
-	    }
-	    int e = (dataName.length() - dataName.indexOf("."))+1;
-	    dataName = dataName.substring(1,e).trim();
-	    return dataName;
-	  }
-	  
-	  public ArrayList getRNA()
-	  {
-		  return result;
-	  }
-	  
-	  public Vector getAnnot()
-	  {
-		  return annotations;
-	  }
+  public String id;
+
+  protected ArrayList<RNA> result;
+
+  public RnamlFile()
+  {
+    super();
+
+  }
+
+  public RnamlFile(String inFile, String type) throws IOException
+  {
+    super(inFile, type);
+
+  }
+
+  public RnamlFile(FileParse source) throws IOException
+  {
+    super(source);
+
+  }
+
+  // public RnamlFile(BufferedReader r) throws IOException,
+  // ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException,
+  // ExceptionPermissionDenied, ExceptionLoadingFailed
+  // {
+  // super();
+  // parse(r);
+  // // sets the index of each sequence in the alignment
+  // for( int i=0,c=seqs.size(); i<c; i++ ) {
+  // seqs.get(i).setIndex(i);
+  // }
+  //
+  //
+  // }
+
+  public BufferedReader CreateReader() throws FileNotFoundException
+  {
+    FileReader fr = null;
+    fr = new FileReader(inFile);
+
+    BufferedReader r = new BufferedReader(fr);
+    return r;
+  }
+
+  public void parse() throws IOException
+  {
+    result = null;
+    try
+    {
+      result = RNAFactory.loadSecStrRNAML(getReader());
+
+    } catch (ExceptionPermissionDenied pdx)
+    {
+      errormessage = "Couldn't access datasource (" + pdx.getMessage()
+              + ")";
+      throw new IOException(pdx);
+    } catch (ExceptionLoadingFailed lf)
+    {
+      errormessage = "Couldn't process data as RNAML file ("
+              + lf.getMessage() + ")";
+      throw new IOException(lf);
+    } catch (ExceptionFileFormatOrSyntax iff)
+    {
+      errormessage = "Invalid RNAML file (" + iff.getMessage() + ")";
+      throw new IOException(iff);
+    }
+
+    SequenceI[] seqs = new SequenceI[result.size()];
+
+    for (int i = 0; i < result.size(); i++)
+    {
+      // DEBUG System.err.println("RNAML entry "+i);
+      RNA current = result.get(i);
+      String seq = current.getSeq();
+      // DEBUG System.err.println(seq);
+      String rna = current.getStructDBN(true);
+      // DEBUG System.err.println(rna);
+
+      int begin = 1;
+      int end = seq.length(); // TODO: compute non-gapped length for sequence
+
+      id = current.getName();
+      seqs[i] = new Sequence(id, seq, begin, end);
+
+      String[] annot = new String[rna.length()];
+      Annotation[] ann = new Annotation[rna.length()];
+
+      for (int j = 0; j < rna.length(); j++)
+      {
+        annot[j] = rna.substring(j, j + 1);
+
+      }
+
+      for (int k = 0; k < rna.length(); k++)
+      {
+        ann[k] = new Annotation(annot[k], "",
+                jalview.schemes.ResidueProperties.getRNASecStrucState(
+                        annot[k]).charAt(0), 0f);
+
+      }
+      AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",
+              current.getID(), ann);
+
+      seqs[i].addAlignmentAnnotation(align);
+      seqs[i].setRNA(result.get(i));
+      annotations.addElement(align);
+    }
+    setSeqs(seqs);
+  }
+
+  public static String print(SequenceI[] s)
+  {
+    // TODO: implement RNAML export option
+    return "not yet implemented";
+  }
+
+  public String print()
+  {
+    return print(getSeqsAsArray());
+  }
+
+  /**
+   * make a friendly ID string.
+   * 
+   * @param dataName
+   * @return truncated dataName to after last '/'
+   */
+  private String safeName(String dataName)
+  {
+    int b = 0;
+    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+    {
+      dataName = dataName.substring(b + 1).trim();
+
+    }
+    int e = (dataName.length() - dataName.indexOf(".")) + 1;
+    dataName = dataName.substring(1, e).trim();
+    return dataName;
+  }
 }