X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPIRFile.java;h=5f5c23c4c834e4f79788f56bb3a93e454ba65996;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=fa9a28bf6b99eb04ffaefa5982493f9f9450569f;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index fa9a28b..5f5c23c 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -1,189 +1,205 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 java.io.*;
-import java.util.*;
-
-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
-
-  public PIRFile()
-  {
-  }
-
-  public PIRFile(String inFile, String type)
-      throws IOException
-  {
-    super(inFile, type);
-  }
-
-  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());
-          if (!isValidProteinSequence(newSeq.getSequence()))
-          {
-            throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
-                                  +" : "+ newSeq.getName()
-                                  +" : "+invalidCharacter);
-          }
-
-          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].getSequence();
-      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
-      {
-
-       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;
-        int end = start + len;
-
-        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();
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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);
+  }
+
+  @Override
+  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);
+      }
+    }
+  }
+
+  @Override
+  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)
+              + (seq.length() % len > 0 ? 1 : 0);
+
+      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();
+  }
+
+}