/*\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
* @author $author$\r
* @version $Revision$\r
*/\r
-public class FormatAdapter\r
+public class FormatAdapter extends AppletFormatAdapter\r
{\r
- /** DOCUMENT ME!! */\r
- public static final Vector formats = new Vector();\r
\r
- static\r
+ public String formatSequences(String format,\r
+ SequenceI [] seqs,\r
+ String [] omitHiddenColumns)\r
{\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
-\r
- AlignFile afile = null;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param format DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI[] readFile(String inFile, String type, String format)\r
- {\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
-\r
- return afile.getSeqsAsArray();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
+ if(omitHiddenColumns!=null)\r
+ {\r
+ SequenceI [] tmp = new SequenceI[seqs.length];\r
+ for(int i=0; i<seqs.length; i++)\r
+ tmp [i] = new Sequence(\r
+ seqs[i].getName(), omitHiddenColumns[i],\r
+ seqs[i].getStart(), seqs[i].getEnd());\r
+\r
+ seqs = tmp;\r
+ }\r
+\r
+ return formatSequences(format, seqs);\r
}\r
\r
\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public String formatSequences(String format, Vector seqs)\r
+ public String formatSequences(String format,\r
+ SequenceI [] 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
if (format.equalsIgnoreCase("FASTA"))\r
{\r
afile = new FastaFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("MSF"))\r
{\r
- afile = new MSFfile();\r
+ afile = new MSFfile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PileUp"))\r
{\r
afile = new PileUpfile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("CLUSTAL"))\r
{\r
afile = new ClustalFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("BLC"))\r
{\r
afile = new BLCFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PIR"))\r
{\r
afile = new PIRFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PFAM"))\r
{\r
afile = new PfamFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
}\r
\r
- afile.setSeqs(s);\r
+ afile.setSeqs(seqs);\r
\r
return afile.print();\r
}\r