/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
\r
import jalview.datamodel.*;\r
\r
- import java.util.Vector;\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
public class AppletFormatAdapter\r
{\r
/** DOCUMENT ME!! */\r
- public static final Vector formats = new Vector();\r
+ public static final String [] READABLE_FORMATS = new String[]\r
+ {\r
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB"\r
+ };\r
+\r
+ public static final String [] WRITEABLE_FORMATS = new String[]\r
+ {\r
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" //, "AMSA"\r
+ };\r
+\r
\r
public static String INVALID_CHARACTERS = "Contains invalid characters";\r
\r
public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +\r
"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM";\r
\r
- static\r
- {\r
- formats.addElement("BLC");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("PileUp");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
+\r
+ public static String FILE = "File";\r
+ public static String URL = "URL";\r
+ public static String PASTE = "Paste";\r
+ public static String CLASSLOADER = "ClassLoader";\r
+\r
\r
AlignFile afile = null;\r
+ String inFile;\r
+\r
+ public static final boolean isValidFormat(String format)\r
+ {\r
+ boolean valid = false;\r
+ for(int i=0; i<READABLE_FORMATS.length; i++)\r
+ if(READABLE_FORMATS[i].equalsIgnoreCase(format))\r
+ return true;\r
+\r
+ return valid;\r
+ }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public SequenceI[] readFile(String inFile, String type, String format)\r
+ public Alignment readFile(String inFile, String type, String format)\r
throws java.io.IOException\r
{\r
+ this.inFile = inFile;\r
try\r
{\r
- if (format.equals("FASTA"))\r
- {\r
- afile = new FastaFile(inFile, type);\r
- }\r
- else if (format.equals("MSF"))\r
- {\r
- afile = new MSFfile(inFile, type);\r
- }\r
- else if (format.equals("PileUp"))\r
- {\r
- afile = new PileUpfile(inFile, type);\r
- }\r
- else if (format.equals("CLUSTAL"))\r
- {\r
- afile = new ClustalFile(inFile, type);\r
- }\r
- else if (format.equals("BLC"))\r
- {\r
- afile = new BLCFile(inFile, type);\r
- }\r
- else if (format.equals("PIR"))\r
- {\r
- afile = new PIRFile(inFile, type);\r
- }\r
- else if (format.equals("PFAM"))\r
- {\r
- afile = new PfamFile(inFile, type);\r
- }\r
+ if (format.equals("FASTA"))\r
+ {\r
+ afile = new FastaFile(inFile, type);\r
+ }\r
+ else if (format.equals("MSF"))\r
+ {\r
+ afile = new MSFfile(inFile, type);\r
+ }\r
+ else if (format.equals("PileUp"))\r
+ {\r
+ afile = new PileUpfile(inFile, type);\r
+ }\r
+ else if (format.equals("CLUSTAL"))\r
+ {\r
+ afile = new ClustalFile(inFile, type);\r
+ }\r
+ else if (format.equals("BLC"))\r
+ {\r
+ afile = new BLCFile(inFile, type);\r
+ }\r
+ else if (format.equals("PIR"))\r
+ {\r
+ afile = new PIRFile(inFile, type);\r
+ }\r
+ else if (format.equals("PFAM"))\r
+ {\r
+ afile = new PfamFile(inFile, type);\r
+ }\r
+ else if (format.equals("JnetFile"))\r
+ {\r
+ afile = new JPredFile(inFile, type);\r
+ ( (JPredFile) afile).removeNonSequences();\r
+ }\r
+ else if (format.equals("PDB"))\r
+ {\r
+ afile = new MCview.PDBfile(inFile, type);\r
+ }\r
+ else if (format.equals("STH"))\r
+ {\r
+ afile = new StockholmFile(inFile, type);\r
+ }\r
+\r
+ Alignment al = new Alignment(afile.getSeqsAsArray());\r
+\r
+ afile.addAnnotations(al);\r
\r
- return afile.getSeqsAsArray();\r
+ return al;\r
}\r
catch (Exception e)\r
{\r
+ e.printStackTrace();\r
System.err.println("Failed to read alignment using the '" + format +\r
"' reader.\n"+e);\r
\r
try{\r
// Possible sequence is just residues with no label\r
afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");\r
- return afile.getSeqsAsArray();\r
+ Alignment al = new Alignment(afile.getSeqsAsArray());\r
+ afile.addAnnotations(al);\r
+ return al;\r
+\r
}\r
catch(Exception ex)\r
{\r
* @return DOCUMENT ME!\r
*/\r
public String formatSequences(String format,\r
- Vector seqs,\r
+ AlignmentI alignment,\r
boolean jvsuffix)\r
{\r
- SequenceI[] s = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- s[i] = (SequenceI) seqs.elementAt(i);\r
-\r
try\r
{\r
AlignFile afile = null;\r
{\r
afile = new PfamFile();\r
}\r
+ else if (format.equalsIgnoreCase("STH"))\r
+ {\r
+ afile = new StockholmFile();\r
+ }\r
+ else if (format.equals("AMSA"))\r
+ {\r
+ afile = new AMSAFile(alignment);\r
+ }\r
\r
afile.addJVSuffix(jvsuffix);\r
\r
- afile.setSeqs(s);\r
+ afile.setSeqs( alignment.getSequencesArray() );\r
\r
return afile.print();\r
}\r
git://source.jalview.org / jalview.git / blobdiff