X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=910d18929e48d60b65664bc33312104b556b1335;hb=9efc6af45120e24f7a11cc8ce6409139844e5001;hp=be60a4329b7d18eab7a4bc6919c92d2ef59667f2;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index be60a43..910d189 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,5 +1,6 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
@@ -13,121 +14,176 @@
  *
  * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * 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.datamodel.*;
+
+public class PIRFile
+    extends AlignFile
+{
+  public static boolean useModellerOutput = false;
 
-  Vector words = new Vector();  //Stores the words in a line after splitting
+  Vector words = new Vector(); //Stores the words in a line after splitting
 
   public PIRFile()
-  {}
-
-  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;
-      StringBuffer sequence;
-      String line = null;
-      while( (line = nextLine())!=null)
+  public void parse()
+      throws IOException
+  {
+    StringBuffer sequence;
+    String line = null;
+    ModellerDescription md;
+
+    while ( (line = nextLine()) != null)
+    {
+      if (line.length() == 0)
       {
-        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"; }
+        //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();
+      sequence = new StringBuffer();
 
-        line = nextLine(); // this is the title line
+      newSeq.setDescription(nextLine()); // this is the title line
 
-        boolean starFound = false;
-        do
-        {
-          line = nextLine();
-          sequence.append( line );
-          if(line.indexOf("*")>-1)
-            starFound = true;
+      boolean starFound = false;
 
-        }while(!starFound);
+      while (!starFound)
+      {
+        line = nextLine();
+        sequence.append(line);
 
-        sequence.setLength( sequence.length()-1);
+        if (line == null)
+        {
+          break;
+        }
 
-       Sequence newSeq = new Sequence(id,
-                               sequence.toString(),
-                               Integer.parseInt(start),
-                               Integer.parseInt(end));
-         seqs.addElement(newSeq);
+        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);
+      }
     }
-    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, int len) {
-    return print(s,len,true);
-  }
-  public static String print(SequenceI[] s, int len,boolean gaps) {
+
+  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 = "";
-      if (gaps) {
-        seq = s[i].getSequence() + "*";
-      } else {
-        seq = AlignSeq.extractGaps(s[i].getSequence(),"-");
-        seq = AlignSeq.extractGaps(seq,".");
-        seq = AlignSeq.extractGaps(seq," ");
-        seq = seq + "*";
+    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() + "\n");
+        if (s[i].getDescription() == null)
+        {
+          out.append(s[i].getName() + " " +
+                     (s[i].getEnd() - s[i].getStart() + 1));
+          out.append(is_NA ? " bases\n" : " residues\n");
+        }
+        else
+        {
+          out.append(s[i].getDescription() + "\n");
+        }
       }
+      else
+      {
 
-      out.append(">P1;" + s[i].getName() + "/" + s[i].getStart()+ "-" + s[i].getEnd() + "\n");
-      out.append(" Dummy title\n");
-      int nochunks = seq.length() / len + 1;
+        if (useModellerOutput)
+        {
+          out.append(">P1;" + s[i].getName() + "\n");
+          md = new ModellerDescription(s[i]);
+          out.append(md.getDescriptionLine() + "\n");
+        }
+        else
+        {
+          out.append(">P1;" + printId(s[i]) + "\n");
+          if (s[i].getDescription() != null)
+          {
+            out.append(s[i].getDescription() + "\n");
+          }
+          else
+          {
+            out.append(s[i].getName() + " "
+                       + (s[i].getEnd() - s[i].getStart() + 1)
+                       + " residues\n");
+          }
+        }
+      }
+      int nochunks = (seq.length() / len) + 1;
 
-      for (int j = 0; j < nochunks; j++) {
-        int start = j*len;
+      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) {
-    String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";
-    PIRFile fa = new PIRFile(inStr);
-  }
 }
-
-
-