-/*\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
-\r
-package jalview.io;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-public class PIRFile extends AlignFile {\r
-\r
- Vector words = new Vector(); //Stores the words in a line after splitting\r
-\r
- public PIRFile()\r
- {}\r
-\r
- public PIRFile(String inStr) {\r
- super(inStr);\r
- }\r
-\r
- public PIRFile(String inFile, String type) throws IOException {\r
- super(inFile,type);\r
- }\r
-\r
- public void parse() {\r
- try{\r
- String id, start, end;\r
- StringBuffer sequence;\r
- String line = null;\r
- while( (line = nextLine())!=null)\r
- {\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"; start="0"; end="0"; }\r
-\r
- sequence = new StringBuffer();\r
-\r
- line = nextLine(); // this is the title line\r
-\r
- boolean starFound = false;\r
- do\r
- {\r
- line = nextLine();\r
- sequence.append( line );\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,\r
- sequence.toString(),\r
- Integer.parseInt(start),\r
- Integer.parseInt(end));\r
- seqs.addElement(newSeq);\r
- }\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
- return print(s,72,true);\r
- }\r
- public static String print(SequenceI[] s, int len) {\r
- return print(s,len,true);\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
- 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()+ "-" + s[i].getEnd() + "\n");\r
- out.append(" Dummy title\n");\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
- i++;\r
- }\r
- return out.toString();\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
-}\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;
+
+public class PIRFile extends AlignFile
+{
+ public static boolean useModellerOutput = false;
+
+ Vector words = new Vector(); // Stores the words in a line after splitting
+
+ public PIRFile()
+ {
+ }
+
+ public PIRFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ public PIRFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ public void parse() throws IOException
+ {
+ StringBuffer sequence;
+ String line = null;
+ ModellerDescription md;
+
+ while ((line = nextLine()) != null)
+ {
+ if (line.length() == 0)
+ {
+ // System.out.println("blank line");
+ continue;
+ }
+ if (line.indexOf("C;") == 0 || line.indexOf("#") == 0)
+ {
+ continue;
+ }
+ Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));
+
+ sequence = new StringBuffer();
+
+ newSeq.setDescription(nextLine()); // this is the title line
+
+ boolean starFound = false;
+
+ while (!starFound)
+ {
+ line = nextLine();
+ sequence.append(line);
+
+ if (line == null)
+ {
+ break;
+ }
+
+ if (line.indexOf("*") > -1)
+ {
+ starFound = true;
+ }
+ }
+
+ if (sequence.length() > 0)
+ {
+ sequence.setLength(sequence.length() - 1);
+ newSeq.setSequence(sequence.toString());
+
+ seqs.addElement(newSeq);
+
+ md = new ModellerDescription(newSeq.getDescription());
+ md.updateSequenceI(newSeq);
+ }
+ }
+ }
+
+ public String print()
+ {
+ return print(getSeqsAsArray());
+ }
+
+ public String print(SequenceI[] s)
+ {
+ boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+ int len = 72;
+ StringBuffer out = new StringBuffer();
+ int i = 0;
+ ModellerDescription md;
+
+ while ((i < s.length) && (s[i] != null))
+ {
+ String seq = s[i].getSequenceAsString();
+ seq = seq + "*";
+
+ if (is_NA)
+ {
+ // modeller doesn't really do nucleotides, so we don't do anything fancy
+ // Official tags area as follows, for now we'll use P1 and DL
+ // Protein (complete) P1
+ // Protein (fragment) F1
+ // DNA (linear) Dl
+ // DNA (circular) DC
+ // RNA (linear) RL
+ // RNA (circular) RC
+ // tRNA N3
+ // other functional RNA N1
+
+ out.append(">N1;" + s[i].getName());
+ out.append(newline);
+ if (s[i].getDescription() == null)
+ {
+ out.append(s[i].getName() + " "
+ + (s[i].getEnd() - s[i].getStart() + 1));
+ out.append(is_NA ? " bases" : " residues");
+ out.append(newline);
+ }
+ else
+ {
+ out.append(s[i].getDescription());
+ out.append(newline);
+ }
+ }
+ else
+ {
+
+ if (useModellerOutput)
+ {
+ out.append(">P1;" + s[i].getName());
+ out.append(newline);
+ md = new ModellerDescription(s[i]);
+ out.append(md.getDescriptionLine());
+ out.append(newline);
+ }
+ else
+ {
+ out.append(">P1;" + printId(s[i]));
+ out.append(newline);
+ if (s[i].getDescription() != null)
+ {
+ out.append(s[i].getDescription());
+ out.append(newline);
+ }
+ else
+ {
+ out.append(s[i].getName() + " "
+ + (s[i].getEnd() - s[i].getStart() + 1) + " residues");
+ out.append(newline);
+ }
+ }
+ }
+ int nochunks = (seq.length() / len) + 1;
+
+ for (int j = 0; j < nochunks; j++)
+ {
+ int start = j * len;
+ int end = start + len;
+
+ if (end < seq.length())
+ {
+ out.append(seq.substring(start, end));
+ out.append(newline);
+ }
+ else if (start < seq.length())
+ {
+ out.append(seq.substring(start));
+ out.append(newline);
+ }
+ }
+
+ i++;
+ }
+
+ return out.toString();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff