/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\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
-* 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
-\r
/**\r
* DOCUMENT ME!\r
*\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class FormatAdapter extends AppletFormatAdapter\r
+public class FormatAdapter\r
+ extends AppletFormatAdapter\r
{\r
\r
- public String formatSequences(String format,\r
- SequenceI [] seqs,\r
- String [] omitHiddenColumns)\r
+ public String formatSequences(String format,\r
+ SequenceI[] seqs,\r
+ String[] omitHiddenColumns)\r
+ {\r
+ if (omitHiddenColumns != null)\r
{\r
- if(omitHiddenColumns!=null)\r
+ SequenceI[] tmp = new SequenceI[seqs.length];\r
+ for (int i = 0; i < seqs.length; i++)\r
{\r
- SequenceI [] tmp = new SequenceI[seqs.length];\r
- for(int i=0; i<seqs.length; i++)\r
- {\r
- tmp[i] = new Sequence(\r
- seqs[i].getName(), omitHiddenColumns[i],\r
- seqs[i].getStart(), seqs[i].getEnd());\r
- tmp[i].setDescription(seqs[i].getDescription());\r
- }\r
- seqs = tmp;\r
+ tmp[i] = new Sequence(\r
+ seqs[i].getName(), omitHiddenColumns[i],\r
+ seqs[i].getStart(), seqs[i].getEnd());\r
+ tmp[i].setDescription(seqs[i].getDescription());\r
}\r
-\r
- return formatSequences(format, seqs);\r
+ seqs = tmp;\r
}\r
\r
+ return formatSequences(format, seqs);\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param format DOCUMENT ME!\r
- * @param seqs DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String formatSequences(String format,\r
- SequenceI [] seqs)\r
- {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param format DOCUMENT ME!\r
+ * @param seqs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String formatSequences(String format,\r
+ SequenceI[] seqs)\r
+ {\r
\r
- try\r
- {\r
- AlignFile afile = null;\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.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
+ try\r
+ {\r
+ AlignFile afile = null;\r
\r
- afile.setSeqs(seqs);\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.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
- return afile.print();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Failed to write alignment as a '" + format +\r
- "' file\n");\r
- e.printStackTrace();\r
- }\r
+ afile.setSeqs(seqs);\r
\r
- return null;\r
+ return afile.print();\r
}\r
+ catch (Exception e)\r
+ {\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