-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\r
- */\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-public class BLCFile extends AlignFile {\r
-\r
- Vector titles;\r
-\r
- public BLCFile()\r
- {}\r
-\r
- public BLCFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public void initData() {\r
- super.initData();\r
- titles = new Vector();\r
- }\r
-\r
- public BLCFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
-\r
-\r
- public void parse()\r
- {\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
- try{\r
- do{\r
- line = nextLine();\r
-\r
- // seek end of ids\r
- if (line.indexOf("*") > -1)\r
- {\r
- idsFound=true;\r
- break;\r
- }\r
-\r
- int abracket = line.indexOf(">");\r
-\r
- if (abracket > -1)\r
- {\r
-\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
-\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
- int value = Integer.parseInt(line.substring(0, line.indexOf(" ")));\r
- starts.addElement(value+"");\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- value = Integer.parseInt(line.substring(0, line.indexOf(" ")));\r
- ends.addElement(value+"");\r
-\r
- }catch(Exception ex)\r
- {\r
- System.out.println("err");\r
- starts.addElement("0");\r
- ends.addElement("0");\r
- }\r
-\r
- }\r
- else\r
- {\r
- ids.addElement( line.substring(abracket + 1, 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
- for(int i=0; i<ids.size(); i++)\r
- {\r
- if(seqstrings[i]==null)\r
- seqstrings[i] = new StringBuffer();\r
- }\r
-\r
- while ((line = nextLine()).indexOf("*")==-1)\r
- {\r
- for(int i=0; i<ids.size(); i++)\r
- {\r
- if(line.length()>i+starCol)\r
- seqstrings[i].append(line.charAt(i + starCol));\r
- }\r
- }\r
-\r
- for(int i=0; i<ids.size(); i++)\r
- {\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
-\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
- public static String print(SequenceI[] s) {\r
- StringBuffer out = new StringBuffer();\r
-\r
- int i=0;\r
- int max = -1;\r
- while (i < s.length && s[i] != null) {\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n");\r
- if (s[i].getSequence().length() > max) { max = s[i].getSequence().length();}\r
- i++;\r
- }\r
-\r
- out.append("* iteration 1\n");\r
- for (int j = 0; j < max; j++) {\r
- i=0;\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
- i++;\r
- }\r
- out.append("\n");\r
- }\r
- out.append("*\n");\r
- return out.toString();\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.IOException;
+import java.util.Vector;
+
+/**
+ * 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);
+ }
+
+ public BLCFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void initData()
+ {
+ super.initData();
+ titles = new Vector();
+ }
+
+ /**
+ * Control the number of block iterations to skip before returning. set to 0
+ * to read first block file entry only set to -1 to read last block file entry
+ * only set to greater than zero to skip at most that many entries before
+ * parsing
+ */
+ int iterationSkips = 0;
+
+ /**
+ * The iteration number for the alignment actually parsed from the blc file
+ */
+ int iterationCount = 0;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void parse() throws IOException
+ {
+ StringBuffer headerLines = new StringBuffer();
+ int numHeaderLines = 0; // number of lines appended.
+ StringBuffer[] seqstrings = null;
+ if (suffix != null)
+ {
+ try
+ {
+ iterationSkips = Integer.parseInt(suffix);
+ } catch (NumberFormatException e)
+ {
+ iterationSkips = 0; // first
+ }
+ }
+
+ String line = null;
+
+ do
+ {
+ boolean idsFound = false;
+ boolean newids = false;
+ // search for ID header.
+ do
+ {
+ line = nextLine();
+ if (line == null)
+ {
+ break;
+ }
+ // seek end of ids
+ if (line.indexOf("*") > -1)
+ {
+ idsFound = true;
+
+ break;
+ }
+
+ int abracket = line.indexOf(">");
+
+ if (abracket > -1)
+ {
+
+ if (iterationCount > 0 && !newids)
+ {
+ // we have a new set of IDs to record.
+ newids = true;
+ seqs.removeAllElements();
+ }
+
+ line = line.substring(abracket + 1);
+
+ Sequence seq = parseId(line);
+ seqs.addElement(seq);
+ }
+ else
+ {
+ // header lines - keep them for the alignment comments.
+ headerLines.append(line);
+ headerLines.append(newline);
+ numHeaderLines++;
+ }
+ } while (!idsFound);
+ if (line == null)
+ {
+ break; // end of file.
+ }
+ int starCol = line.indexOf("*");
+ seqstrings = new StringBuffer[seqs.size()];
+
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ if (seqstrings[i] == null)
+ {
+ seqstrings[i] = new StringBuffer();
+ }
+ }
+
+ try
+ {
+ line = nextLine();
+ while (line != null && line.indexOf("*") == -1)
+ {
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ if (line.length() > (i + starCol))
+ {
+ seqstrings[i].append(line.charAt(i + starCol));
+ }
+ }
+ line = nextLine();
+ }
+ } catch (IOException e)
+ {
+ if (iterationCount == 0)
+ {
+ throw (e); // otherwise we've just run out of iterations.
+ }
+ else
+ {
+ iterationSkips = 0;
+ }
+ }
+ iterationCount++;
+ } while (--iterationSkips != -1);
+
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ Sequence newSeq = (Sequence) seqs.elementAt(i);
+
+ newSeq.setSequence(seqstrings[i].toString());
+ }
+ if (seqs.size() > 0)
+ {
+ if (headerLines.length() > 1 + numHeaderLines)
+ {
+ // just whitespace or not.
+ setAlignmentProperty("Comments", headerLines.toString());
+ }
+ setAlignmentProperty("iteration", "" + iterationCount);
+ }
+ }
+
+ /**
+ * 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]));
+ if (s[i].getDescription() != null)
+ {
+ out.append(" " + s[i].getDescription());
+ }
+
+ out.append(newline);
+
+ if (s[i].getSequence().length > max)
+ {
+ max = s[i].getSequence().length;
+ }
+
+ i++;
+ }
+
+ out.append("* iteration 1");
+ out.append(newline);
+
+ 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].getSequenceAsString(j, j + 1));
+ }
+ else
+ {
+ out.append("-");
+ }
+
+ i++;
+ }
+
+ out.append(newline);
+ }
+
+ out.append("*");
+ out.append(newline);
+
+ return out.toString();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff