-/*\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
-\r
-import java.util.*;\r
-\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
-\r
- public BLCFile(String inFile, String type) throws IOException {\r
- super(inFile, type);\r
- }\r
-\r
- public void initData() {\r
- super.initData();\r
- titles = new Vector();\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
- if(line.indexOf("/")>-1)\r
- {\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
- else{\r
- ids.addElement(line.substring(abracket+1));\r
- starts.addElement("0");\r
- ends.addElement("0");\r
- }\r
-\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
- }\r
- }\r
-\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
-\r
- public static String print(SequenceI[] s) {\r
- StringBuffer out = new StringBuffer();\r
-\r
- int i = 0;\r
- int max = -1;\r
-\r
- while ((i < s.length) && (s[i] != null)) {\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
-\r
- if (s[i].getSequence().length() > max) {\r
- max = s[i].getSequence().length();\r
- }\r
-\r
- i++;\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
- }\r
-\r
- out.append("*\n");\r
-\r
- return out.toString();\r
- }\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import java.io.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BLCFile extends AlignFile
+{
+ Vector titles;
+
+ /**
+ * Creates a new BLCFile object.
+ */
+ public BLCFile()
+ {
+ }
+
+
+ /**
+ * Creates a new BLCFile object.
+ *
+ * @param inFile DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public BLCFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initData()
+ {
+ super.initData();
+ titles = new Vector();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void parse() throws IOException
+ {
+ boolean idsFound = false;
+ Vector ids = new Vector();
+ StringBuffer[] seqstrings;
+ Vector starts = new Vector();
+ Vector ends = new Vector();
+
+ String line = null;
+
+ do
+ {
+ line = nextLine();
+
+ // seek end of ids
+ if (line.indexOf("*") > -1)
+ {
+ idsFound = true;
+
+ break;
+ }
+
+ int abracket = line.indexOf(">");
+
+ if (abracket > -1)
+ {
+ if (line.indexOf(" ") > -1) //
+ {
+ line = line.substring(abracket + 1,
+ line.indexOf(" ", abracket + 1));
+ }
+ else
+ line = line.substring(abracket+1);
+
+
+ Sequence seq = parseId(line);
+ ids.addElement(seq.getName());
+ starts.addElement(seq.getStart() + "");
+ ends.addElement(seq.getEnd() + "");
+ }
+ }
+ while (!idsFound);
+
+ int starCol = line.indexOf("*");
+ seqstrings = new StringBuffer[ids.size()];
+
+ for (int i = 0; i < ids.size(); i++)
+ {
+ if (seqstrings[i] == null)
+ {
+ seqstrings[i] = new StringBuffer();
+ }
+ }
+
+ while ((line = nextLine()).indexOf("*") == -1)
+ {
+ for (int i = 0; i < ids.size(); i++)
+ {
+ if (line.length() > (i + starCol))
+ {
+ seqstrings[i].append(line.charAt(i + starCol));
+ }
+ }
+ }
+
+ for (int i = 0; i < ids.size(); i++)
+ {
+ Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
+ seqstrings[i].toString(),
+ Integer.parseInt(starts.elementAt(i).
+ toString()),
+ Integer.parseInt(ends.elementAt(i).toString()));
+
+ if (!isValidProteinSequence(newSeq.getSequence()))
+ {
+ throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
+ +" : "+ newSeq.getName()
+ +" : "+invalidCharacter);
+
+ }
+
+ seqs.addElement(newSeq);
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print(SequenceI[] s)
+ {
+ StringBuffer out = new StringBuffer();
+ /**
+ * A general parser for ids. Will look for dbrefs in
+ * Uniprot format source|id
+ * And also Jalview /start-end
+ *
+ * @String id Id to be parsed
+ */
+ int i = 0;
+ int max = -1;
+
+ while ((i < s.length) && (s[i] != null))
+ {
+ out.append(">" + printId(s[i]) +"\n");
+
+ if (s[i].getSequence().length() > max)
+ {
+ max = s[i].getSequence().length();
+ }
+
+ i++;
+ }
+
+ out.append("* iteration 1\n");
+
+ for (int j = 0; j < max; j++)
+ {
+ i = 0;
+
+ while ((i < s.length) && (s[i] != null))
+ {
+ if (s[i].getSequence().length() > j)
+ {
+ out.append(s[i].getSequence().substring(j, j + 1));
+ }
+ else
+ {
+ out.append("-");
+ }
+
+ i++;
+ }
+
+ out.append("\n");
+ }
+
+ out.append("*\n");
+
+ return out.toString();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff