X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=f5ca6512ecdeaecfd9506c86a90e8e0bd508b76a;hb=d4b1e4d0c74b1c6d0f3c3556b10be91a6aaea475;hp=00fbad5af0c96c23c20dd82dcc27d187017a15c9;hpb=6c4bc68ae8b1c5005e79661bb2d8246515cb787d;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 00fbad5..f5ca651 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -49,18 +49,25 @@ public class SeqsetUtils
     sqinfo.put("Name", seq.getName());
     sqinfo.put("Start", new Integer(seq.getStart()));
     sqinfo.put("End", new Integer(seq.getEnd()));
-    if (seq.getDescription()!=null)
+    if (seq.getDescription() != null)
+    {
       sqinfo.put("Description", seq.getDescription());
+    }
     Vector sfeat = new Vector();
-    jalview.datamodel.SequenceFeature[] sfarray=seq.getSequenceFeatures();
-    if (sfarray!=null && sfarray.length>0) {
-      for (int i=0;i<sfarray.length;i++)
+    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+    if (sfarray != null && sfarray.length > 0)
+    {
+      for (int i = 0; i < sfarray.length; i++)
+      {
         sfeat.add(sfarray[i]);
+      }
     }
     sqinfo.put("SeqFeatures", sfeat);
     sqinfo.put("PdbId",
                (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
-    sqinfo.put("datasetSequence", (seq.getDatasetSequence() !=null) ? seq.getDatasetSequence() : new Sequence("THISISAPLACEHOLDER",""));
+    sqinfo.put("datasetSequence",
+               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() :
+               new Sequence("THISISAPLACEHOLDER", ""));
     return sqinfo;
   }
 
@@ -74,15 +81,17 @@ public class SeqsetUtils
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
   {
     boolean namePresent = true;
-    if (sqinfo==null)
+    if (sqinfo == null)
+    {
       return false;
+    }
     String oldname = (String) sqinfo.get("Name");
     Integer start = (Integer) sqinfo.get("Start");
     Integer end = (Integer) sqinfo.get("End");
     Vector sfeatures = (Vector) sqinfo.get(
         "SeqFeatures");
     Vector pdbid = (Vector) sqinfo.get("PdbId");
-    String description=(String) sqinfo.get("Description");
+    String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
     if (oldname == null)
     {
@@ -92,7 +101,7 @@ public class SeqsetUtils
     {
       sq.setName(oldname);
     }
-    if (pdbid!=null && pdbid.size()>0)
+    if (pdbid != null && pdbid.size() > 0)
     {
       sq.setPDBId(pdbid);
     }
@@ -103,14 +112,19 @@ public class SeqsetUtils
       sq.setEnd(end.intValue());
     }
 
-    if ((sfeatures != null) && (sfeatures.size()>0))
+    if ( (sfeatures != null) && (sfeatures.size() > 0))
     {
       SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
       sq.setSequenceFeatures(sfarray);
     }
-    if (description!=null)
+    if (description != null)
+    {
       sq.setDescription(description);
-    if ((seqds!=null) && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds.getLength()==0)) {
+    }
+    if ( (seqds != null) &&
+        ! (seqds.getName().equals("THISISAPLACEHOLDER") &&
+           seqds.getLength() == 0))
+    {
       sq.setDatasetSequence(seqds);
     }
 
@@ -152,9 +166,9 @@ public class SeqsetUtils
       }
     }
 
-
     return map;
   }
+
   /**
    * recover unsafe sequence names and original properties for a sequence
    * set using a map generated by @see uniquify(sequences,true)
@@ -164,66 +178,88 @@ public class SeqsetUtils
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
   {
-    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
+    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
+        sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
     Vector unmatched = new Vector();
-    for (int i=0, j=sequences.length; i<j; i++)
+    for (int i = 0, j = sequences.length; i < j; i++)
+    {
       unmatched.add(sequences[i]);
-    while (keys.hasMoreElements()) {
+    }
+    while (keys.hasMoreElements())
+    {
       Object key = keys.nextElement();
-      if (key instanceof String) {
-        if ((msq = matcher.findIdMatch((String) key))!=null) {
+      if (key instanceof String)
+      {
+        if ( (msq = matcher.findIdMatch( (String) key)) != null)
+        {
           Hashtable sqinfo = (Hashtable) map.get(key);
           unmatched.remove(msq);
           SeqCharacterUnhash(msq, sqinfo);
         }
         else
         {
-          System.err.println("Can't find '"+((String) key)+"' in uniquified alignment");
+          System.err.println("Can't find '" + ( (String) key) +
+                             "' in uniquified alignment");
         }
       }
     }
-    if (unmatched.size()>0) {
+    if (unmatched.size() > 0)
+    {
       System.err.println("Did not find matches for :");
-      for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out.println(((SequenceI) i.nextElement()).getName()))
-           ;
+      for (Enumeration i = unmatched.elements(); i.hasMoreElements();
+           System.out.println( ( (SequenceI) i.nextElement()).getName()))
+      {
+        ;
+      }
       return false;
     }
 
     return true;
   }
+
   /**
    * returns a subset of the sequenceI seuqences,
    * including only those that contain at least one residue.
    * @param sequences SequenceI[]
    * @return SequenceI[]
    */
-  public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences) {
-      // Identify first row of alignment with residues for prediction
-      boolean ungapped[] = new boolean[sequences.length];
-      int msflen=0;
-      for (int i=0,j=sequences.length; i<j;i++) {
-        String tempseq = jalview.analysis.AlignSeq.extractGaps(
-            jalview.util.Comparison.GapChars,
-            sequences[i].getSequenceAsString());
-
-        if (tempseq.length()==0)
-          ungapped[i]=false;
-        else {
-          ungapped[i]=true;
-          msflen++;
-        }
+  public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
+  {
+    // Identify first row of alignment with residues for prediction
+    boolean ungapped[] = new boolean[sequences.length];
+    int msflen = 0;
+    for (int i = 0, j = sequences.length; i < j; i++)
+    {
+      String tempseq = jalview.analysis.AlignSeq.extractGaps(
+          jalview.util.Comparison.GapChars,
+          sequences[i].getSequenceAsString());
+
+      if (tempseq.length() == 0)
+      {
+        ungapped[i] = false;
       }
-      if (msflen==0)
-        return null; // no minimal set
-      // compose minimal set
-      SequenceI[] mset = new SequenceI[msflen];
-      for (int i=0,j=sequences.length,k=0; i<j;i++) {
-        if (ungapped[i])
-          mset[k++] = sequences[i];
+      else
+      {
+        ungapped[i] = true;
+        msflen++;
+      }
+    }
+    if (msflen == 0)
+    {
+      return null; // no minimal set
+    }
+    // compose minimal set
+    SequenceI[] mset = new SequenceI[msflen];
+    for (int i = 0, j = sequences.length, k = 0; i < j; i++)
+    {
+      if (ungapped[i])
+      {
+        mset[k++] = sequences[i];
       }
-      ungapped = null;
-      return mset;
+    }
+    ungapped = null;
+    return mset;
   }
 }