/*\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
public class AppletFormatAdapter\r
{\r
/** DOCUMENT ME!! */\r
- public static final Vector formats = new Vector();\r
-\r
- static\r
+ public static final String [] READABLE_FORMATS = new String[]\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
+ "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"\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
+\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
* @return DOCUMENT ME!\r
*/\r
public SequenceI[] 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
\r
- return afile.getSeqsAsArray();\r
+ return afile.getSeqsAsArray();\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
+ if(e.getMessage()!=null && e.getMessage().startsWith(INVALID_CHARACTERS))\r
+ throw new java.io.IOException(e.getMessage());\r
+\r
// Finally test if the user has pasted just the sequence, no id\r
if(type.equalsIgnoreCase("Paste"))\r
{\r
// Possible sequence is just residues with no label\r
afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");\r
return afile.getSeqsAsArray();\r
- }catch(Exception ex)\r
+ }\r
+ catch(Exception ex)\r
{\r
- System.err.println("Failed to read alignment using the 'FASTA' reader.\n"+e);\r
+ if(ex.toString().startsWith(INVALID_CHARACTERS))\r
+ throw new java.io.IOException(e.getMessage());\r
+\r
ex.printStackTrace();\r
}\r
-\r
}\r
- }\r
\r
- return null;\r
+ // If we get to this stage, the format was not supported\r
+ throw new java.io.IOException(SUPPORTED_FORMATS);\r
+ }\r
}\r
\r
\r
{\r
afile = new PfamFile();\r
}\r
+ else if (format.equalsIgnoreCase("STH"))\r
+ {\r
+ afile = new StockholmFile();\r
+ }\r
+\r
\r
afile.addJVSuffix(jvsuffix);\r
\r
git://source.jalview.org / jalview.git / blobdiff