/*\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
+ * 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
-public class BLCFile extends AlignFile {\r
- Vector titles;\r
-\r
- public BLCFile() {\r
- }\r
-\r
- public BLCFile(String inStr) {\r
- super(inStr);\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class BLCFile\r
+ extends AlignFile\r
+{\r
+ Vector titles;\r
+\r
+ /**\r
+ * Creates a new BLCFile object.\r
+ */\r
+ public BLCFile()\r
+ {\r
+ }\r
+\r
+ /**\r
+ * Creates a new BLCFile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public BLCFile(String inFile, String type)\r
+ throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void initData()\r
+ {\r
+ super.initData();\r
+ titles = new Vector();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void parse()\r
+ throws IOException\r
+ {\r
+ boolean idsFound = false;\r
+ StringBuffer[] seqstrings;\r
+\r
+ String line = null;\r
+\r
+ do\r
+ {\r
+ line = nextLine();\r
+\r
+ // seek end of ids\r
+ if (line.indexOf("*") > -1)\r
+ {\r
+ idsFound = true;\r
+\r
+ break;\r
+ }\r
+\r
+ int abracket = line.indexOf(">");\r
+\r
+ if (abracket > -1)\r
+ {\r
+ line = line.substring(abracket + 1);\r
+\r
+ Sequence seq = parseId(line);\r
+ seqs.addElement(seq);\r
+ }\r
}\r
+ while (!idsFound);\r
\r
- public BLCFile(String inFile, String type) throws IOException {\r
- super(inFile, type);\r
- }\r
+ int starCol = line.indexOf("*");\r
+ seqstrings = new StringBuffer[seqs.size()];\r
\r
- public void initData() {\r
- super.initData();\r
- titles = new Vector();\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ if (seqstrings[i] == null)\r
+ {\r
+ seqstrings[i] = new StringBuffer();\r
+ }\r
}\r
\r
- public void parse() {\r
- boolean idsFound = false;\r
- Vector ids = new Vector();\r
- StringBuffer[] seqstrings;\r
- Vector starts = new Vector();\r
- Vector ends = new Vector();\r
-\r
- String line = null;\r
-\r
- try {\r
- do {\r
- line = nextLine();\r
-\r
- // seek end of ids\r
- if (line.indexOf("*") > -1) {\r
- idsFound = true;\r
-\r
- break;\r
- }\r
-\r
- int abracket = line.indexOf(">");\r
-\r
- if (abracket > -1) {\r
- if (line.indexOf(" ") > -1) //\r
- {\r
- ///Colur it be this format?\r
- //>54402046 0 1 137 137:\r
- // or this??\r
- // 1 >L1H14 30539 343\r
- try {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf(" ", abracket + 1)));\r
-\r
- // remove p Value\r
- line = line.substring(abracket + 1);\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
-\r
- int value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- starts.addElement(value + "");\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- ends.addElement(value + "");\r
- } catch (Exception ex) {\r
- System.err.println("Error during blockfile read.");\r
- ex.printStackTrace();\r
- starts.addElement("0");\r
- ends.addElement("0");\r
- }\r
- } else {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf("/")));\r
- line = line.substring(line.indexOf("/") + 1);\r
- starts.addElement(line.substring(0, line.indexOf("-")));\r
- ends.addElement(line.substring(line.indexOf("-") + 1));\r
- }\r
- }\r
- } while (!idsFound);\r
-\r
- int starCol = line.indexOf("*");\r
- seqstrings = new StringBuffer[ids.size()];\r
-\r
- for (int i = 0; i < ids.size(); i++) {\r
- if (seqstrings[i] == null) {\r
- seqstrings[i] = new StringBuffer();\r
- }\r
- }\r
-\r
- while ((line = nextLine()).indexOf("*") == -1) {\r
- for (int i = 0; i < ids.size(); i++) {\r
- if (line.length() > (i + starCol)) {\r
- seqstrings[i].append(line.charAt(i + starCol));\r
- }\r
- }\r
- }\r
-\r
- for (int i = 0; i < ids.size(); i++) {\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqstrings[i].toString(),\r
- Integer.parseInt(starts.elementAt(i).toString()),\r
- Integer.parseInt(ends.elementAt(i).toString()));\r
- seqs.addElement(newSeq);\r
- }\r
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
+ while ( (line = nextLine()).indexOf("*") == -1)\r
+ {\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ if (line.length() > (i + starCol))\r
+ {\r
+ seqstrings[i].append(line.charAt(i + starCol));\r
}\r
+ }\r
}\r
\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ Sequence newSeq = (Sequence) seqs.elementAt(i);\r
\r
- public static String print(SequenceI[] s) {\r
- StringBuffer out = new StringBuffer();\r
+ newSeq.setSequence(seqstrings[i].toString());\r
+ }\r
\r
- int i = 0;\r
- int max = -1;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
+ {\r
+ return print(getSeqsAsArray());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param s DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print(SequenceI[] s)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ /**\r
+ * A general parser for ids. Will look for dbrefs in\r
+ * Uniprot format source|id\r
+ * And also Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ int i = 0;\r
+ int max = -1;\r
+\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
+ out.append("\n");\r
+\r
+ if (s[i].getSequence().length > max)\r
+ {\r
+ max = s[i].getSequence().length;\r
+ }\r
+\r
+ i++;\r
+ }\r
\r
- while ((i < s.length) && (s[i] != null)) {\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
+ out.append("* iteration 1\n");\r
\r
- if (s[i].getSequence().length() > max) {\r
- max = s[i].getSequence().length();\r
- }\r
+ for (int j = 0; j < max; j++)\r
+ {\r
+ i = 0;\r
\r
- i++;\r
+ while ( (i < s.length) && (s[i] != null))\r
+ {\r
+ if (s[i].getSequence().length > j)\r
+ {\r
+ out.append(s[i].getSequenceAsString(j, j + 1));\r
}\r
-\r
- out.append("* iteration 1\n");\r
-\r
- for (int j = 0; j < max; j++) {\r
- i = 0;\r
-\r
- while ((i < s.length) && (s[i] != null)) {\r
- if (s[i].getSequence().length() > j) {\r
- out.append(s[i].getSequence().substring(j, j + 1));\r
- } else {\r
- out.append("-");\r
- }\r
-\r
- i++;\r
- }\r
-\r
- out.append("\n");\r
+ else\r
+ {\r
+ out.append("-");\r
}\r
\r
- out.append("*\n");\r
+ i++;\r
+ }\r
\r
- return out.toString();\r
+ out.append("\n");\r
}\r
+\r
+ out.append("*\n");\r
+\r
+ return out.toString();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff