-/*\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
-/**\r
- * <p>Title: </p>\r
- * PileUpfile\r
- * <p>Description: </p>\r
- *\r
- * Read and write PileUp style MSF Files.\r
- * This used to be the MSFFile class, and was written according to the EBI's idea\r
- * of a subset of the MSF alignment format. But, that was updated to reflect current\r
- * GCG style IO fashion, as found in Emboss (thanks David Martin!)\r
- *\r
- **/\r
-import java.io.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-\r
-public class PileUpfile\r
- extends MSFfile\r
-{\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- */\r
- public PileUpfile()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new MSFfile object.\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public PileUpfile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
-\r
- public String print(SequenceI[] s)\r
- {\r
- StringBuffer out = new StringBuffer("PileUp\n\n");\r
-\r
- int max = 0;\r
- int maxid = 0;\r
-\r
- int i = 0;\r
- int bigChecksum = 0;\r
- int[] checksums = new int[s.length];\r
- while (i < s.length)\r
- {\r
- checksums[i] = checkSum(s[i].getSequenceAsString());\r
- bigChecksum += checksums[i];\r
- i++;\r
- }\r
-\r
- out.append(" MSF: " + s[0].getSequence().length +\r
- " Type: P Check: " + bigChecksum % 10000 + " ..\n\n\n");\r
-\r
- i = 0;\r
- while ( (i < s.length) && (s[i] != null))\r
- {\r
- String seq = s[i].getSequenceAsString();\r
- out.append(" Name: " + printId(s[i]) +\r
- " oo Len: " +\r
- seq.length() + " Check: " + checksums[i] +\r
- " Weight: 1.00\n");\r
-\r
- if (seq.length() > max)\r
- {\r
- max = seq.length();\r
- }\r
-\r
- if (s[i].getName().length() > maxid)\r
- {\r
- maxid = s[i].getName().length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- if (maxid < 10)\r
- {\r
- maxid = 10;\r
- }\r
-\r
- maxid++;\r
- out.append("\n\n//\n\n");\r
-\r
- int len = 50;\r
-\r
- int nochunks = (max / len) + 1;\r
-\r
- if ( (max % len) == 0)\r
- {\r
- nochunks--;\r
- }\r
-\r
- for (i = 0; i < nochunks; i++)\r
- {\r
- int j = 0;\r
-\r
- while ( (j < s.length) && (s[j] != null))\r
- {\r
- String name = printId(s[j]);\r
-\r
- out.append(new Format("%-" + maxid + "s").form(name + " "));\r
-\r
- for (int k = 0; k < 5; k++)\r
- {\r
- int start = (i * 50) + (k * 10);\r
- int end = start + 10;\r
-\r
- if ( (end < s[j].getSequence().length) &&\r
- (start < s[j].getSequence().length))\r
- {\r
- out.append(s[j].getSequence(start, end));\r
-\r
- if (k < 4)\r
- {\r
- out.append(" ");\r
- }\r
- else\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- else\r
- {\r
- if (start < s[j].getSequence().length)\r
- {\r
- out.append(s[j].getSequenceAsString().substring(start));\r
- out.append("\n");\r
- }\r
- else\r
- {\r
- if (k == 0)\r
- {\r
- out.append("\n");\r
- }\r
- }\r
- }\r
- }\r
-\r
- j++;\r
- }\r
-\r
- out.append("\n");\r
- }\r
-\r
- return out.toString();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.io;
+
+/**
+ * <p>
+ * Title:
+ * </p>
+ * PileUpfile
+ * <p>
+ * Description:
+ * </p>
+ *
+ * Read and write PileUp style MSF Files. This used to be the MSFFile class, and
+ * was written according to the EBI's idea of a subset of the MSF alignment
+ * format. But, that was updated to reflect current GCG style IO fashion, as
+ * found in Emboss (thanks David Martin!)
+ *
+ */
+import java.io.*;
+
+import jalview.datamodel.*;
+import jalview.util.*;
+
+public class PileUpfile extends MSFfile
+{
+
+ /**
+ * Creates a new MSFfile object.
+ */
+ public PileUpfile()
+ {
+ }
+
+ /**
+ * Creates a new MSFfile object.
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public PileUpfile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public PileUpfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ public String print(SequenceI[] s)
+ {
+ StringBuffer out = new StringBuffer("PileUp");
+ out.append(newline);
+ out.append(newline);
+
+ int max = 0;
+ int maxid = 0;
+
+ int i = 0;
+ int bigChecksum = 0;
+ int[] checksums = new int[s.length];
+ while (i < s.length)
+ {
+ checksums[i] = checkSum(s[i].getSequenceAsString());
+ bigChecksum += checksums[i];
+ i++;
+ }
+
+ out.append(" MSF: " + s[0].getSequence().length
+ + " Type: P Check: " + bigChecksum % 10000
+ + " ..");
+ out.append(newline);
+ out.append(newline);
+ out.append(newline);
+
+ i = 0;
+ while ((i < s.length) && (s[i] != null))
+ {
+ String seq = s[i].getSequenceAsString();
+ out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length()
+ + " Check: " + checksums[i] + " Weight: 1.00");
+ out.append(newline);
+
+ if (seq.length() > max)
+ {
+ max = seq.length();
+ }
+
+ if (s[i].getName().length() > maxid)
+ {
+ maxid = s[i].getName().length();
+ }
+
+ i++;
+ }
+
+ if (maxid < 10)
+ {
+ maxid = 10;
+ }
+
+ maxid++;
+ out.append(newline);out.append(newline);out.append("//");
+ out.append(newline);out.append(newline);
+
+ int len = 50;
+
+ int nochunks = (max / len) + 1;
+
+ if ((max % len) == 0)
+ {
+ nochunks--;
+ }
+
+ for (i = 0; i < nochunks; i++)
+ {
+ int j = 0;
+
+ while ((j < s.length) && (s[j] != null))
+ {
+ String name = printId(s[j]);
+
+ out.append(new Format("%-" + maxid + "s").form(name + " "));
+
+ for (int k = 0; k < 5; k++)
+ {
+ int start = (i * 50) + (k * 10);
+ int end = start + 10;
+
+ if ((end < s[j].getSequence().length)
+ && (start < s[j].getSequence().length))
+ {
+ out.append(s[j].getSequence(start, end));
+
+ if (k < 4)
+ {
+ out.append(" ");
+ }
+ else
+ {
+ out.append(newline);
+ }
+ }
+ else
+ {
+ if (start < s[j].getSequence().length)
+ {
+ out.append(s[j].getSequenceAsString().substring(start));
+ out.append(newline);
+ }
+ else
+ {
+ if (k == 0)
+ {
+ out.append(newline);
+ }
+ }
+ }
+ }
+
+ j++;
+ }
+
+ out.append(newline);
+ }
+
+ return out.toString();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff