/*\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
import java.io.*;\r
\r
-import java.util.*;\r
-\r
+import jalview.datamodel.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class FastaFile extends AlignFile\r
+public class FastaFile\r
+ extends AlignFile\r
{\r
/**\r
* Length of a sequence line\r
\r
StringBuffer out;\r
\r
- /**\r
- * Creates a new FastaFile object.\r
- */\r
- public FastaFile()\r
- {\r
- }\r
+ /**\r
+ * Creates a new FastaFile object.\r
+ */\r
+ public FastaFile()\r
+ {\r
+ }\r
\r
- /**\r
- * Creates a new FastaFile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public FastaFile(String inFile, String type) throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
+ /**\r
+ * Creates a new FastaFile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public FastaFile(String inFile, String type)\r
+ throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public void parse() throws IOException\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- boolean firstLine = true;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public void parse()\r
+ throws IOException\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ boolean firstLine = true;\r
\r
- String line;\r
- Sequence seq = null;\r
+ String line;\r
+ Sequence seq = null;\r
\r
- boolean annotation = false;\r
+ boolean annotation = false;\r
\r
- while ((line = nextLine()) != null)\r
+ while ( (line = nextLine()) != null)\r
+ {\r
+ line = line.trim();\r
+ if (line.length() > 0)\r
+ {\r
+ if (line.charAt(0) == '>')\r
{\r
- line = line.trim();\r
- if (line.length() > 0)\r
+ if (line.startsWith(">#_"))\r
+ {\r
+ if (annotation)\r
{\r
- if (line.charAt(0)=='>')\r
- {\r
- if (line.startsWith(">#_"))\r
- {\r
- if (annotation)\r
- {\r
- Annotation[] anots = new Annotation[sb.length()];\r
- String anotString = sb.toString();\r
- for (int i = 0; i < sb.length(); i++)\r
- {\r
- anots[i] = new Annotation(anotString.substring(i, i+1),\r
- null,\r
- ' ', 0);\r
- }\r
- AlignmentAnnotation aa = new AlignmentAnnotation(\r
- seq.getName().substring(2), seq.getDescription(),\r
- anots);\r
-\r
- annotations.addElement(aa);\r
- }\r
- }\r
- else\r
- annotation = false;\r
-\r
- if (!firstLine)\r
- {\r
- seq.setSequence(sb.toString());\r
-\r
- if (!annotation)\r
- seqs.addElement(seq);\r
- }\r
-\r
- seq = parseId(line.substring(1));\r
- firstLine = false;\r
-\r
- sb = new StringBuffer();\r
-\r
- if (line.startsWith(">#_"))\r
- annotation = true;\r
- }\r
- else\r
- {\r
- sb.append(line);\r
- }\r
+ Annotation[] anots = new Annotation[sb.length()];\r
+ String anotString = sb.toString();\r
+ for (int i = 0; i < sb.length(); i++)\r
+ {\r
+ anots[i] = new Annotation(anotString.substring(i, i + 1),\r
+ null,\r
+ ' ', 0);\r
+ }\r
+ AlignmentAnnotation aa = new AlignmentAnnotation(\r
+ seq.getName().substring(2), seq.getDescription(),\r
+ anots);\r
+\r
+ annotations.addElement(aa);\r
}\r
- }\r
+ }\r
+ else\r
+ {\r
+ annotation = false;\r
+ }\r
\r
- if (annotation)\r
- {\r
- Annotation[] anots = new Annotation[sb.length()];\r
- String anotString = sb.toString();\r
- for (int i = 0; i < sb.length(); i++)\r
+ if (!firstLine)\r
{\r
- anots[i] = new Annotation(anotString.substring(i, i + 1),\r
- null,\r
- ' ', 0);\r
+ seq.setSequence(sb.toString());\r
+\r
+ if (!annotation)\r
+ {\r
+ seqs.addElement(seq);\r
+ }\r
}\r
- AlignmentAnnotation aa = new AlignmentAnnotation(\r
- seq.getName().substring(2), seq.getDescription(),\r
- anots);\r
\r
- annotations.addElement(aa);\r
- }\r
+ seq = parseId(line.substring(1));\r
+ firstLine = false;\r
+\r
+ sb = new StringBuffer();\r
\r
- else if (!firstLine)\r
+ if (line.startsWith(">#_"))\r
+ {\r
+ annotation = true;\r
+ }\r
+ }\r
+ else\r
{\r
- seq.setSequence(sb.toString());\r
- seqs.addElement(seq);\r
+ sb.append(line);\r
}\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- * @param gaps DOCUMENT ME!\r
- * @param displayId DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print(SequenceI[] s)\r
+ if (annotation)\r
{\r
- out = new StringBuffer();\r
- int i = 0;\r
+ Annotation[] anots = new Annotation[sb.length()];\r
+ String anotString = sb.toString();\r
+ for (int i = 0; i < sb.length(); i++)\r
+ {\r
+ anots[i] = new Annotation(anotString.substring(i, i + 1),\r
+ null,\r
+ ' ', 0);\r
+ }\r
+ AlignmentAnnotation aa = new AlignmentAnnotation(\r
+ seq.getName().substring(2), seq.getDescription(),\r
+ anots);\r
+\r
+ annotations.addElement(aa);\r
+ }\r
\r
- while ((i < s.length) && (s[i] != null))\r
- {\r
- out.append(">" + printId(s[i]));\r
- if(s[i].getDescription()!=null)\r
- out.append(" "+s[i].getDescription());\r
+ else if (!firstLine)\r
+ {\r
+ seq.setSequence(sb.toString());\r
+ seqs.addElement(seq);\r
+ }\r
+ }\r
\r
- out.append("\n");\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ * @param len DOCUMENT ME!\r
+ * @param gaps DOCUMENT ME!\r
+ * @param displayId DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print(SequenceI[] s)\r
+ {\r
+ out = new StringBuffer();\r
+ int i = 0;\r
\r
- int nochunks = (s[i].getLength() / len) + 1;\r
+ while ( (i < s.length) && (s[i] != null))\r
+ {\r
+ out.append(">" + printId(s[i]));\r
+ if (s[i].getDescription() != null)\r
+ {\r
+ out.append(" " + s[i].getDescription());\r
+ }\r
\r
- for (int j = 0; j < nochunks; j++)\r
- {\r
- int start = j * len;\r
- int end = start + len;\r
-\r
- if (end < s[i].getLength())\r
- {\r
- out.append(s[i].getSequenceAsString(start, end) + "\n");\r
- }\r
- else if (start < s[i].getLength())\r
- {\r
- out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");\r
- }\r
- }\r
+ out.append("\n");\r
+\r
+ int nochunks = (s[i].getLength() / len) + 1;\r
\r
- i++;\r
+ for (int j = 0; j < nochunks; j++)\r
+ {\r
+ int start = j * len;\r
+ int end = start + len;\r
+\r
+ if (end < s[i].getLength())\r
+ {\r
+ out.append(s[i].getSequenceAsString(start, end) + "\n");\r
}\r
+ else if (start < s[i].getLength())\r
+ {\r
+ out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");\r
+ }\r
+ }\r
\r
- return out.toString();\r
+ i++;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
+ return out.toString();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
+ {\r
+ return print(getSeqsAsArray());\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff