X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Futils%2FSeqSet.java;fp=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Futils%2FSeqSet.java;h=b6f48adc228f9e04cb6568ab5618252d99a6486f;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=e75bd54a569a4e47290fff8533f527cc417d15e5;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/utils/SeqSet.java b/src/uk/ac/vamsas/objects/utils/SeqSet.java
index e75bd54..b6f48ad 100644
--- a/src/uk/ac/vamsas/objects/utils/SeqSet.java
+++ b/src/uk/ac/vamsas/objects/utils/SeqSet.java
@@ -1,138 +1,166 @@
-/*
- * Created on 17-May-2005
- * Slurped into VamsasClient object set on 12th Jan 2006
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package uk.ac.vamsas.objects.utils;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.util.Hashtable;
-import java.util.Vector;
-import java.util.regex.Pattern;
-
-import uk.ac.vamsas.objects.core.*;
-
-/**
- * @author jimp
- *
- * TODO To change the template for this generated type comment go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-public class SeqSet {
-  
-  public static void write_Fasta(OutputStream os, SequenceType[] seqs) throws IOException {
-    write_Fasta(os, seqs, 80);
-  }
-  
-  public static void write_Fasta(OutputStream os, SequenceType[] seqs, boolean width80) throws IOException {
-    write_Fasta(os, seqs, (width80) ? 80 : 0);
-  }
-  
-  public static void write_Fasta(OutputStream os, SequenceType[] seqs, int width) throws IOException {
-    int i, nseq = seqs.length;
-    BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
-    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
-    for (i=0; i<nseq; i++) {
-      fasta_out.write(">"+seqs[i].getName()+"\n");
-      if (width<=0) {
-        fasta_out.write(seqs[i].getSequence()+"\n");
-      } else {
-        // TODO: adapt to SymbolDictionary labelwidths
-        String tempseq = seqs[i].getSequence();
-        int j=0, k=tempseq.length();
-        while (j<k) {
-          int d = k-j;
-          if (d>=width) {
-            fasta_out.write(tempseq, j, width);
-          } else {
-            fasta_out.write(tempseq, j, d);
-          }
-          fasta_out.write("\n");
-          j+=width;
-        }	  		    
-      }
-    }
-    fasta_out.flush();
-  }
-  /**
-   * TODO: introduce a dictionary parameter for qualified sequence symbols
-   * Reads a sequence set from a stream - will only read prescribed amino acid
-   * symbols. 
-   * @param os
-   * @return
-   * @throws IOException
-   */  
-  public static Sequence[] read_SeqFasta(InputStream os) throws IOException {
-    Vector seqs = new Vector();
-    int nseq = 0;
-    BufferedReader infasta = new BufferedReader(new InputStreamReader(os));
-    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
-    // TODO: decide on return type - SequenceType is a partly complete vamsas Vobject - either for a dataset or alignment sequence
-    // so could go in either!
-    String line;
-    Sequence seq = null;
-    Pattern aaMatch = Pattern.compile("[ARNDCQEGHILKMFPSTUWYV]", Pattern.CASE_INSENSITIVE);
-    String sname = "", seqstr=null;
-    do {
-      line = infasta.readLine();
-      if (line==null || line.startsWith(">")) {
-        if (seqstr!=null) 
-          seqs.add((Object) Seq.newSequence(sname.substring(1), seqstr, SymbolDictionary.STANDARD_AA, 0,0));
-        sname = line; // remove >
-        seqstr="";
-      } else {	
-        String subseq = Pattern.compile("//s+").matcher(line).replaceAll("");
-        seqstr += subseq; 			
-      }
-    } while (line!=null);
-    nseq = seqs.size();
-    if (nseq>0) {
-      // TODO:POSS: should really return a sequence if there's only one in the file.
-      Sequence[] seqset = new Sequence[nseq];
-      for (int i=0; i<nseq; i++) {
-        seqset[i] = (Sequence) seqs.elementAt(i);
-      }
-      return seqset;
-    }
-    
-    return null;
-  }
-  
-  public static Hashtable uniquify(SequenceType[] sequences) {
-    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
-    // TODO: do we need this with vamsas sequences ?
-    // Generate a safely named sequence set and a hash to recover the sequence names
-    Hashtable map = new Hashtable();
-    for (int i = 0; i < sequences.length; i++) {
-      String safename = new String("Sequence" + i);
-      map.put(safename, sequences[i].getName());
-      sequences[i].setName(safename);
-    }
-    return map;
-  }
-  
-  public static boolean deuniquify(Hashtable map, SequenceType[] sequences) {
-    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this method
-    // TODO: do we need this with vamsas sequences ?
-    // recover unsafe sequence names for a sequence set
-    boolean allfound = true;
-    for (int i = 0; i < sequences.length; i++) {
-      if (map.containsKey(sequences[i].getName())) {
-        String unsafename = (String) map.get(sequences[i].getName());
-        sequences[i].setName(unsafename);
-      } else {
-        allfound = false;
-      }
-    }
-    return allfound;
-  }
-  
-}
+/*
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client 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 Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package uk.ac.vamsas.objects.utils;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.util.Hashtable;
+import java.util.Vector;
+import java.util.regex.Pattern;
+
+import uk.ac.vamsas.objects.core.*;
+
+/**
+ * @author jimp
+ * 
+ *         TODO To change the template for this generated type comment go to
+ *         Window - Preferences - Java - Code Style - Code Templates
+ */
+public class SeqSet {
+
+  public static void write_Fasta(OutputStream os, SequenceType[] seqs)
+      throws IOException {
+    write_Fasta(os, seqs, 80);
+  }
+
+  public static void write_Fasta(OutputStream os, SequenceType[] seqs,
+      boolean width80) throws IOException {
+    write_Fasta(os, seqs, (width80) ? 80 : 0);
+  }
+
+  public static void write_Fasta(OutputStream os, SequenceType[] seqs, int width)
+      throws IOException {
+    int i, nseq = seqs.length;
+    BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
+    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this
+                                                  // method
+    for (i = 0; i < nseq; i++) {
+      fasta_out.write(">" + seqs[i].getName() + "\n");
+      if (width <= 0) {
+        fasta_out.write(seqs[i].getSequence() + "\n");
+      } else {
+        // TODO: adapt to SymbolDictionary labelwidths
+        String tempseq = seqs[i].getSequence();
+        int j = 0, k = tempseq.length();
+        while (j < k) {
+          int d = k - j;
+          if (d >= width) {
+            fasta_out.write(tempseq, j, width);
+          } else {
+            fasta_out.write(tempseq, j, d);
+          }
+          fasta_out.write("\n");
+          j += width;
+        }
+      }
+    }
+    fasta_out.flush();
+  }
+
+  /**
+   * TODO: introduce a dictionary parameter for qualified sequence symbols Reads
+   * a sequence set from a stream - will only read prescribed amino acid
+   * symbols.
+   * 
+   * @param os
+   * @return
+   * @throws IOException
+   */
+  public static Sequence[] read_SeqFasta(InputStream os) throws IOException {
+    Vector seqs = new Vector();
+    int nseq = 0;
+    BufferedReader infasta = new BufferedReader(new InputStreamReader(os));
+    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this
+                                                  // method
+    // TODO: decide on return type - SequenceType is a partly complete vamsas
+    // Vobject - either for a dataset or alignment sequence
+    // so could go in either!
+    String line;
+    Sequence seq = null;
+    Pattern aaMatch = Pattern.compile("[ARNDCQEGHILKMFPSTUWYV]",
+        Pattern.CASE_INSENSITIVE);
+    String sname = "", seqstr = null;
+    do {
+      line = infasta.readLine();
+      if (line == null || line.startsWith(">")) {
+        if (seqstr != null)
+          seqs.add((Object) Seq.newSequence(sname.substring(1), seqstr,
+              SymbolDictionary.STANDARD_AA, 0, 0));
+        sname = line; // remove >
+        seqstr = "";
+      } else {
+        String subseq = Pattern.compile("//s+").matcher(line).replaceAll("");
+        seqstr += subseq;
+      }
+    } while (line != null);
+    nseq = seqs.size();
+    if (nseq > 0) {
+      // TODO:POSS: should really return a sequence if there's only one in the
+      // file.
+      Sequence[] seqset = new Sequence[nseq];
+      for (int i = 0; i < nseq; i++) {
+        seqset[i] = (Sequence) seqs.elementAt(i);
+      }
+      return seqset;
+    }
+
+    return null;
+  }
+
+  public static Hashtable uniquify(SequenceType[] sequences) {
+    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this
+                                                  // method
+    // TODO: do we need this with vamsas sequences ?
+    // Generate a safely named sequence set and a hash to recover the sequence
+    // names
+    Hashtable map = new Hashtable();
+    for (int i = 0; i < sequences.length; i++) {
+      String safename = new String("Sequence" + i);
+      map.put(safename, sequences[i].getName());
+      sequences[i].setName(safename);
+    }
+    return map;
+  }
+
+  public static boolean deuniquify(Hashtable map, SequenceType[] sequences) {
+    System.err.println("NOT FULLY IMPLEMENTED!"); // TODO: Finish adapting this
+                                                  // method
+    // TODO: do we need this with vamsas sequences ?
+    // recover unsafe sequence names for a sequence set
+    boolean allfound = true;
+    for (int i = 0; i < sequences.length; i++) {
+      if (map.containsKey(sequences[i].getName())) {
+        String unsafename = (String) map.get(sequences[i].getName());
+        sequences[i].setName(unsafename);
+      } else {
+        allfound = false;
+      }
+    }
+    return allfound;
+  }
+
+}