X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=0a246015213216c6d065ddfc636b3c31eb6d3420;hb=8a18973f7e4521c7dd3705ebd8fabd3ca08cfcaf;hp=410628f4dab5dd7aef266b436919f1a5d7add2db;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 410628f..0a24601 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,135 +1,192 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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 jalview.analysis.*;
-
 import java.io.*;
 import java.util.*;
 
-public class PIRFile extends AlignFile {
+import jalview.analysis.*;
+import jalview.datamodel.*;
 
-  Vector words = new Vector();  //Stores the words in a line after splitting
+public class PIRFile
+    extends AlignFile
+{
+  Vector words = new Vector(); //Stores the words in a line after splitting
 
   public PIRFile()
-  {}
+  {
+  }
 
-  public PIRFile(String inStr) {
+  public PIRFile(String inStr)
+  {
     super(inStr);
   }
 
-  public PIRFile(String inFile, String type) throws IOException {
-    super(inFile,type);
+  public PIRFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
   }
 
-  public void parse() {
-    try{
-      String id, start, end;
+  public void parse()
+  {
+    try
+    {
+      String id;
+      String start;
+      String end;
       StringBuffer sequence;
       String line = null;
-      while( (line = nextLine())!=null)
+
+      while ( (line = nextLine()) != null)
       {
-        try{
-          id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
-          line = line.substring(line.indexOf("/") + 1);
-          start = line.substring(0, line.indexOf("-"));
-          end = line.substring(line.indexOf("-") + 1);
-        }catch(Exception ex)
-        {  id="No id"; start="0"; end="0"; }
+        if(line.length()==0)
+        {
+          //System.out.println("blank line");
+          continue;
+        }
+
+        id = "No id";
+        start = "1";
+        end = "-1";
+
+        try
+        {
+          int slashIndex = line.indexOf("/");
+          if(slashIndex!=-1)
+          {
+            id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));
+            line = line.substring(line.indexOf("/") + 1);
+            start = line.substring(0, line.indexOf("-"));
+            end = line.substring(line.indexOf("-") + 1);
+          }
+          else
+          {
+            id = line.substring(line.indexOf(";")+1);
+          }
+        }
+        catch (Exception ex)
+        {    }// Default id, start and end unchanged
 
         sequence = new StringBuffer();
 
         line = nextLine(); // this is the title line
 
         boolean starFound = false;
-        do
+
+        while(!starFound)
         {
           line = nextLine();
-          sequence.append( line );
-          if(line.indexOf("*")>-1)
-            starFound = true;
+          sequence.append(line);
 
-        }while(!starFound);
+          if (line == null)
+            break;
 
-        sequence.setLength( sequence.length()-1);
+          if (line.indexOf("*") > -1)
+          {
+            starFound = true;
+          }
+        }
 
-       Sequence newSeq = new Sequence(id,
-                               sequence.toString(),
-                               Integer.parseInt(start),
-                               Integer.parseInt(end));
-         seqs.addElement(newSeq);
-      }
+        if(sequence.length()>0)
+        {
+          sequence.setLength(sequence.length() - 1);
 
+          Sequence newSeq = new Sequence(id, sequence.toString(),
+                                         Integer.parseInt(start),
+                                         Integer.parseInt(end));
+          seqs.addElement(newSeq);
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
     }
-    catch(Exception ex){ex.printStackTrace();}
   }
 
-  public String print() {
+  public String print()
+  {
     return print(getSeqsAsArray());
   }
-  public static String print(SequenceI[] s) {
-    return print(s,72,true);
+
+  public static String print(SequenceI[] s)
+  {
+    return print(s, 72, true);
   }
-  public static String print(SequenceI[] s, int len) {
-    return print(s,len,true);
+
+  public static String print(SequenceI[] s, int len)
+  {
+    return print(s, len, true);
   }
-  public static String print(SequenceI[] s, int len,boolean gaps) {
+
+  public static String print(SequenceI[] s, int len, boolean gaps)
+  {
     StringBuffer out = new StringBuffer();
     int i = 0;
 
-    while (i < s.length && s[i] != null) {
+    while ( (i < s.length) && (s[i] != null))
+    {
       String seq = "";
-      if (gaps) {
+
+      if (gaps)
+      {
         seq = s[i].getSequence() + "*";
-      } else {
-        seq = AlignSeq.extractGaps(s[i].getSequence(),"-");
-        seq = AlignSeq.extractGaps(seq,".");
-        seq = AlignSeq.extractGaps(seq," ");
+      }
+      else
+      {
+        seq = AlignSeq.extractGaps(s[i].getSequence(), "-");
+        seq = AlignSeq.extractGaps(seq, ".");
+        seq = AlignSeq.extractGaps(seq, " ");
         seq = seq + "*";
       }
 
-      out.append(">P1;" + s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd() + "\n");
+      out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +
+                 s[i].getEnd() + "\n");
       out.append(" Dummy title\n");
-      int nochunks = seq.length() / len + 1;
 
-      for (int j = 0; j < nochunks; j++) {
-        int start = j*len;
+      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) + "\n");
-        } else if (start < seq.length()) {
+        if (end < seq.length())
+        {
+          out.append(seq.substring(start, end) + "\n");
+        }
+        else if (start < seq.length())
+        {
           out.append(seq.substring(start) + "\n");
         }
       }
+
       i++;
     }
+
     return out.toString();
   }
 
-  public static void main(String[] args) {
+  public static void main(String[] args)
+  {
     String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";
     PIRFile fa = new PIRFile(inStr);
   }
 }
-
-
-