+/*\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.io.*;\r
-import java.util.*;\r
-\r
-public abstract class AlignFile extends FileParse {\r
- int noSeqs = 0;\r
- int maxLength = 0;\r
-\r
- Vector seqs;\r
- Vector headers;\r
\r
- long start;\r
- long end;\r
-\r
- public AlignFile()\r
- {}\r
+import java.util.*;\r
\r
- public AlignFile(String inStr) {\r
- initData();\r
-System.out.println("is this ever called??");\r
- try{\r
- parse();\r
- }catch(Exception ex){}\r
- }\r
\r
/**\r
- * Constructor which parses the data from a file of some specified type.\r
- * @param inFile Filename to read from.\r
- * @param type What type of file to read from (File, URL)\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
*/\r
- public AlignFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
+public abstract class AlignFile extends FileParse\r
+{\r
+ int noSeqs = 0;\r
+ int maxLength = 0;\r
+ Vector seqs;\r
+ Vector headers;\r
+ long start;\r
+ long end;\r
+\r
+ /**\r
+ * Creates a new AlignFile object.\r
+ */\r
+ public AlignFile()\r
+ {\r
+ }\r
\r
- initData();\r
+ /**\r
+ * Creates a new AlignFile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public AlignFile(String inStr)\r
+ {\r
+ initData();\r
+ System.out.println("is this ever called??");\r
+\r
+ try\r
+ {\r
+ parse();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
\r
- parse();\r
+ /**\r
+ * Constructor which parses the data from a file of some specified type.\r
+ * @param inFile Filename to read from.\r
+ * @param type What type of file to read from (File, URL)\r
+ */\r
+ public AlignFile(String inFile, String type) throws IOException\r
+ {\r
+ super(inFile, type);\r
\r
- }\r
+ initData();\r
\r
-/**\r
- * Return the seqs Vector\r
- */\r
- public Vector getSeqs() {\r
- return seqs;\r
- }\r
+ parse();\r
+ }\r
\r
-/**\r
- * Return the Sequences in the seqs Vector as an array of Sequences\r
- */\r
- public SequenceI [] getSeqsAsArray() {\r
- SequenceI [] s = new SequenceI[seqs.size()];\r
- for (int i=0;i < seqs.size();i++) {\r
- s[i] = (SequenceI)seqs.elementAt(i);\r
+ /**\r
+ * Return the seqs Vector\r
+ */\r
+ public Vector getSeqs()\r
+ {\r
+ return seqs;\r
}\r
- return s;\r
- }\r
\r
+ /**\r
+ * Return the Sequences in the seqs Vector as an array of Sequences\r
+ */\r
+ public SequenceI[] getSeqsAsArray()\r
+ {\r
+ SequenceI[] s = new SequenceI[seqs.size()];\r
\r
-/**\r
- * Initialise objects to store sequence data in.\r
- */\r
- protected void initData() {\r
- seqs = new Vector();\r
- headers = new Vector();\r
- }\r
-\r
- protected void setSeqs(SequenceI [] s) {\r
- seqs = new Vector();\r
- for (int i=0; i<s.length; i++) {\r
- seqs.addElement(s[i]);\r
- }\r
- }\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ s[i] = (SequenceI) seqs.elementAt(i);\r
+ }\r
\r
- // Checks whether sequence is valid aa characters\r
- protected boolean isValidProteinSequence(String sequence)\r
- {\r
- for (int i = 0; i < sequence.length(); i++)\r
- if (!jalview.schemes.ResidueProperties.aaHash.containsKey(String.valueOf(sequence.charAt(i))))\r
- return false;\r
+ return s;\r
+ }\r
\r
- return true;\r
- }\r
+ /**\r
+ * Initialise objects to store sequence data in.\r
+ */\r
+ protected void initData()\r
+ {\r
+ seqs = new Vector();\r
+ headers = new Vector();\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ */\r
+ protected void setSeqs(SequenceI[] s)\r
+ {\r
+ seqs = new Vector();\r
+\r
+ for (int i = 0; i < s.length; i++)\r
+ {\r
+ seqs.addElement(s[i]);\r
+ }\r
+ }\r
\r
-/**\r
- * This method must be implemented to parse the contents of the file.\r
- */\r
- public abstract void parse() throws IOException;\r
+ // Checks whether sequence is valid aa characters\r
+ protected boolean isValidProteinSequence(String sequence)\r
+ {\r
+ for (int i = 0; i < sequence.length(); i++)\r
+ if (!jalview.schemes.ResidueProperties.aaHash.containsKey(\r
+ String.valueOf(sequence.charAt(i))))\r
+ {\r
+ return false;\r
+ }\r
+\r
+ return true;\r
+ }\r
\r
+ /**\r
+ * This method must be implemented to parse the contents of the file.\r
+ */\r
+ public abstract void parse() throws IOException;\r
\r
-/**\r
- * Print out in alignment file format the Sequences in the seqs Vector.\r
- */\r
- public abstract String print();\r
+ /**\r
+ * Print out in alignment file format the Sequences in the seqs Vector.\r
+ */\r
+ public abstract String print();\r
}\r
git://source.jalview.org / jalview.git / blobdiff