+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 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
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
package jalview.io;\r
\r
import jalview.datamodel.*;\r
+\r
import java.util.Vector;\r
-public class FormatAdapter\r
-{\r
-\r
- public static Vector formats = new Vector();\r
- static{\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("BLC");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
-\r
- public static SequenceI[] readFile(String inFile, String type, String format)\r
- {\r
-\r
- try\r
- {\r
- AlignFile afile = null;\r
- if (format.equals("FASTA"))\r
- afile = new FastaFile(inFile, type);\r
- else if (format.equals("MSF"))\r
- afile = new MSFfile(inFile, type);\r
- else if (format.equals("CLUSTAL"))\r
- afile = new ClustalFile(inFile, type);\r
- else if (format.equals("BLC"))\r
- afile = new BLCFile(inFile, type);\r
- else if (format.equals("PIR"))\r
- afile = new PIRFile(inFile, type);\r
- else if (format.equals("PFAM"))\r
- afile = new PfamFile(inFile, type);\r
-\r
- return afile.getSeqsAsArray();\r
+\r
+\r
+public class FormatAdapter {\r
+ public static Vector formats = new Vector();\r
+\r
+ static {\r
+ formats.addElement("FASTA");\r
+ formats.addElement("MSF");\r
+ formats.addElement("PileUp");\r
+ formats.addElement("CLUSTAL");\r
+ formats.addElement("BLC");\r
+ formats.addElement("PIR");\r
+ formats.addElement("PFAM");\r
}\r
- catch (Exception e) {}\r
-\r
- return null;\r
- }\r
-\r
-\r
- public static String formatSequences(String format, Vector seqs)\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
- if (format.equals("FASTA"))\r
- afile = new FastaFile();\r
- else if (format.equals("MSF"))\r
- afile = new MSFfile();\r
- else if (format.equals("CLUSTAL"))\r
- afile = new ClustalFile();\r
- else if (format.equals("BLC"))\r
- afile = new BLCFile();\r
- else if (format.equals("PIR"))\r
- afile = new PIRFile();\r
- else if (format.equals("PFAM"))\r
- afile = new PfamFile();\r
-\r
- afile.setSeqs(s);\r
- return afile.print();\r
+\r
+ public static SequenceI[] readFile(String inFile, String type, String format) {\r
+ try {\r
+ AlignFile afile = null;\r
+\r
+ if (format.equals("FASTA")) {\r
+ afile = new FastaFile(inFile, type);\r
+ } else if (format.equals("MSF")) {\r
+ afile = new MSFfile(inFile, type);\r
+ } else if (format.equals("PileUp")) {\r
+ afile = new PileUpfile(inFile, type);\r
+ } else if (format.equals("CLUSTAL")) {\r
+ afile = new ClustalFile(inFile, type);\r
+ } else if (format.equals("BLC")) {\r
+ afile = new BLCFile(inFile, type);\r
+ } else if (format.equals("PIR")) {\r
+ afile = new PIRFile(inFile, type);\r
+ } else if (format.equals("PFAM")) {\r
+ afile = new PfamFile(inFile, type);\r
+ }\r
+\r
+ return afile.getSeqsAsArray();\r
+ } catch (Exception e) {\r
+ System.err.println("Failed to read alignment using the '" + format +\r
+ "' reader.");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r
}\r
- catch (Exception e) {}\r
\r
- return null;\r
- }\r
+ public static String formatSequences(String format, Vector seqs) {\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
+ AlignFile afile = null;\r
+\r
+ if (format.equals("FASTA")) {\r
+ afile = new FastaFile();\r
+ } else if (format.equals("MSF")) {\r
+ afile = new MSFfile();\r
+ } else if (format.equals("PileUp")) {\r
+ afile = new PileUpfile();\r
+ } else if (format.equals("CLUSTAL")) {\r
+ afile = new ClustalFile();\r
+ } else if (format.equals("BLC")) {\r
+ afile = new BLCFile();\r
+ } else if (format.equals("PIR")) {\r
+ afile = new PIRFile();\r
+ } else if (format.equals("PFAM")) {\r
+ afile = new PfamFile();\r
+ }\r
+\r
+ afile.setSeqs(s);\r
+\r
+ return afile.print();\r
+ } catch (Exception e) {\r
+ System.err.println("Failed to write alignment as a '" + format +\r
+ "' file\n");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff