/*\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) 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.analysis.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
import java.io.*;\r
-\r
import java.util.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+\r
+public class PIRFile\r
+ extends AlignFile\r
+{\r
+ Vector words = new Vector(); //Stores the words in a line after splitting\r
+\r
+ public PIRFile()\r
+ {\r
+ }\r
+\r
+ public PIRFile(String inStr)\r
+ {\r
+ super(inStr);\r
+ }\r
+\r
+ public PIRFile(String inFile, String type)\r
+ throws IOException\r
+ {\r
+ super(inFile, type);\r
+ }\r
+\r
+ public void parse()\r
+ {\r
+ try\r
+ {\r
+ String id;\r
+ String start;\r
+ String end;\r
+ StringBuffer sequence;\r
+ String line = null;\r
+\r
+ while ( (line = nextLine()) != null)\r
+ {\r
+ try\r
+ {\r
+ id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
+ line = line.substring(line.indexOf("/") + 1);\r
+ start = line.substring(0, line.indexOf("-"));\r
+ end = line.substring(line.indexOf("-") + 1);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ id = "No id";\r
+ start = "0";\r
+ end = "0";\r
+ }\r
\r
-public class PIRFile extends AlignFile {\r
- Vector words = new Vector(); //Stores the words in a line after splitting\r
+ sequence = new StringBuffer();\r
\r
- public PIRFile() {\r
- }\r
+ line = nextLine(); // this is the title line\r
\r
- public PIRFile(String inStr) {\r
- super(inStr);\r
- }\r
+ boolean starFound = false;\r
\r
- public PIRFile(String inFile, String type) throws IOException {\r
- super(inFile, type);\r
- }\r
+ do\r
+ {\r
+ line = nextLine();\r
+ sequence.append(line);\r
\r
- public void parse() {\r
- try {\r
- String id;\r
- String start;\r
- String end;\r
- StringBuffer sequence;\r
- String line = null;\r
-\r
- while ((line = nextLine()) != null) {\r
- try {\r
- id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
- line = line.substring(line.indexOf("/") + 1);\r
- start = line.substring(0, line.indexOf("-"));\r
- end = line.substring(line.indexOf("-") + 1);\r
- } catch (Exception ex) {\r
- id = "No id";\r
- start = "0";\r
- end = "0";\r
- }\r
-\r
- sequence = new StringBuffer();\r
-\r
- line = nextLine(); // this is the title line\r
-\r
- boolean starFound = false;\r
-\r
- do {\r
- line = nextLine();\r
- sequence.append(line);\r
-\r
- if (line.indexOf("*") > -1) {\r
- starFound = true;\r
- }\r
- } while (!starFound);\r
-\r
- sequence.setLength(sequence.length() - 1);\r
-\r
- Sequence newSeq = new Sequence(id, sequence.toString(),\r
- Integer.parseInt(start), Integer.parseInt(end));\r
- seqs.addElement(newSeq);\r
- }\r
- } catch (Exception ex) {\r
- ex.printStackTrace();\r
+ if (line.indexOf("*") > -1)\r
+ {\r
+ starFound = true;\r
+ }\r
}\r
- }\r
+ while (!starFound);\r
\r
- public String print() {\r
- return print(getSeqsAsArray());\r
- }\r
+ sequence.setLength(sequence.length() - 1);\r
\r
- public static String print(SequenceI[] s) {\r
- return print(s, 72, true);\r
+ Sequence newSeq = new Sequence(id, sequence.toString(),\r
+ Integer.parseInt(start),\r
+ Integer.parseInt(end));\r
+ seqs.addElement(newSeq);\r
+ }\r
}\r
-\r
- public static String print(SequenceI[] s, int len) {\r
- return print(s, len, true);\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
}\r
-\r
- public static String print(SequenceI[] s, int len, boolean gaps) {\r
- StringBuffer out = new StringBuffer();\r
- int i = 0;\r
-\r
- while ((i < s.length) && (s[i] != null)) {\r
- String seq = "";\r
-\r
- if (gaps) {\r
- seq = s[i].getSequence() + "*";\r
- } else {\r
- seq = AlignSeq.extractGaps(s[i].getSequence(), "-");\r
- seq = AlignSeq.extractGaps(seq, ".");\r
- seq = AlignSeq.extractGaps(seq, " ");\r
- seq = seq + "*";\r
- }\r
-\r
- out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
- out.append(" Dummy title\n");\r
-\r
- int nochunks = (seq.length() / len) + 1;\r
-\r
- for (int j = 0; j < nochunks; j++) {\r
- int start = j * len;\r
- int end = start + len;\r
-\r
- if (end < seq.length()) {\r
- out.append(seq.substring(start, end) + "\n");\r
- } else if (start < seq.length()) {\r
- out.append(seq.substring(start) + "\n");\r
- }\r
- }\r
-\r
- i++;\r
+ }\r
+\r
+ public String print()\r
+ {\r
+ return print(getSeqsAsArray());\r
+ }\r
+\r
+ public static String print(SequenceI[] s)\r
+ {\r
+ return print(s, 72, true);\r
+ }\r
+\r
+ public static String print(SequenceI[] s, int len)\r
+ {\r
+ return print(s, len, true);\r
+ }\r
+\r
+ public static String print(SequenceI[] s, int len, boolean gaps)\r
+ {\r
+ StringBuffer out = new StringBuffer();\r
+ int i = 0;\r
+\r
+ while ( (i < s.length) && (s[i] != null))\r
+ {\r
+ String seq = "";\r
+\r
+ if (gaps)\r
+ {\r
+ seq = s[i].getSequence() + "*";\r
+ }\r
+ else\r
+ {\r
+ seq = AlignSeq.extractGaps(s[i].getSequence(), "-");\r
+ seq = AlignSeq.extractGaps(seq, ".");\r
+ seq = AlignSeq.extractGaps(seq, " ");\r
+ seq = seq + "*";\r
+ }\r
+\r
+ out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
+ s[i].getEnd() + "\n");\r
+ out.append(" Dummy title\n");\r
+\r
+ int nochunks = (seq.length() / len) + 1;\r
+\r
+ for (int j = 0; j < nochunks; j++)\r
+ {\r
+ int start = j * len;\r
+ int end = start + len;\r
+\r
+ if (end < seq.length())\r
+ {\r
+ out.append(seq.substring(start, end) + "\n");\r
}\r
+ else if (start < seq.length())\r
+ {\r
+ out.append(seq.substring(start) + "\n");\r
+ }\r
+ }\r
\r
- return out.toString();\r
+ i++;\r
}\r
\r
- public static void main(String[] args) {\r
- String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";\r
- PIRFile fa = new PIRFile(inStr);\r
- }\r
+ return out.toString();\r
+ }\r
+\r
+ public static void main(String[] args)\r
+ {\r
+ String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";\r
+ PIRFile fa = new PIRFile(inStr);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff