X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=83317c19ece9cda1cd7f1b323b2e304f38593883;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=17658b3aba7f3073be7b39e11f4a5c091fad62d5;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 17658b3..83317c1 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,38 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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/>.
+ * 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.analysis;
 
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-import java.util.Hashtable;
-
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
 /**
  * Functions for cross-referencing sequence databases. user must first specify
  * if cross-referencing from protein or dna (set dna==true)
@@ -43,39 +45,22 @@ import jalview.ws.seqfetcher.ASequenceFetcher;
 public class CrossRef
 {
   /**
-   * get the DNA or protein references for a protein or dna sequence
+   * Select just the DNA or protein references for a protein or dna sequence
    * 
-   * @param dna
-   * @param rfs
+   * @param fromDna
+   *          if true, select references from DNA (i.e. Protein databases), else
+   *          DNA database references
+   * @param refs
+   *          a set of references to select from
    * @return
    */
-  public static DBRefEntry[] findXDbRefs(boolean dna, DBRefEntry[] rfs)
+  public static DBRefEntry[] findXDbRefs(boolean fromDna, DBRefEntry[] refs)
   {
-    if (dna)
-    {
-      rfs = jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS);
-    }
-    else
-    {
-      rfs = jalview.util.DBRefUtils.selectRefs(rfs,
-              DBRefSource.DNACODINGDBS); // could attempt to find other cross
-      // refs and return here - ie PDB xrefs
-      // (not dna, not protein seq)
-    }
-    return rfs;
-  }
-
-  public static Hashtable classifyDbRefs(DBRefEntry[] rfs)
-  {
-    Hashtable classes = new Hashtable();
-    classes.put(DBRefSource.PROTEINDBS,
-            jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS));
-    classes.put(DBRefSource.DNACODINGDBS, jalview.util.DBRefUtils
-            .selectRefs(rfs, DBRefSource.DNACODINGDBS));
-    classes.put(DBRefSource.DOMAINDBS,
-            jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.DOMAINDBS));
-    // classes.put(OTHER, )
-    return classes;
+    return DBRefUtils.selectRefs(refs, fromDna ? DBRefSource.PROTEINDBS
+            : DBRefSource.DNACODINGDBS);
+    // could attempt to find other cross
+    // refs here - ie PDB xrefs
+    // (not dna, not protein seq)
   }
 
   /**
@@ -102,12 +87,11 @@ public class CrossRef
           SequenceI[] seqs, AlignmentI dataset)
   {
     String[] dbrefs = null;
-    Vector refs = new Vector();
+    List<String> refs = new ArrayList<String>();
     for (int s = 0; s < seqs.length; s++)
     {
       if (seqs[s] != null)
       {
-
         SequenceI dss = seqs[s];
         while (dss.getDatasetSequence() != null)
         {
@@ -118,7 +102,7 @@ public class CrossRef
         {
           if (!refs.contains(rfs[r].getSource()))
           {
-            refs.addElement(rfs[r].getSource());
+            refs.add(rfs[r].getSource());
           }
         }
         if (dataset != null)
@@ -126,19 +110,17 @@ public class CrossRef
           // search for references to this sequence's direct references.
           DBRefEntry[] lrfs = CrossRef
                   .findXDbRefs(!dna, seqs[s].getDBRef());
-          Vector rseqs = new Vector();
+          List<SequenceI> rseqs = new ArrayList<SequenceI>();
           CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
                   null); // don't need to specify codon frame for mapping here
-          Enumeration lr = rseqs.elements();
-          while (lr.hasMoreElements())
+          for (SequenceI rs : rseqs)
           {
-            SequenceI rs = (SequenceI) lr.nextElement();
-            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
+            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef()); // not used??
             for (int r = 0; rfs != null && r < rfs.length; r++)
             {
               if (!refs.contains(rfs[r].getSource()))
               {
-                refs.addElement(rfs[r].getSource());
+                refs.add(rfs[r].getSource());
               }
             }
           }
@@ -148,7 +130,7 @@ public class CrossRef
     if (refs.size() > 0)
     {
       dbrefs = new String[refs.size()];
-      refs.copyInto(dbrefs);
+      refs.toArray(dbrefs);
     }
     return dbrefs;
   }
@@ -226,9 +208,9 @@ public class CrossRef
   public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
           String source, AlignmentI dataset)
   {
-    Vector rseqs = new Vector();
+    List<SequenceI> rseqs = new ArrayList<SequenceI>();
     Alignment ral = null;
-    AlignedCodonFrame cf = new AlignedCodonFrame(0); // nominal width
+    AlignedCodonFrame cf = new AlignedCodonFrame(); // nominal width
     for (int s = 0; s < seqs.length; s++)
     {
       SequenceI dss = seqs[s];
@@ -241,14 +223,8 @@ public class CrossRef
       if ((xrfs == null || xrfs.length == 0) && dataset != null)
       {
         System.out.println("Attempting to find ds Xrefs refs.");
-        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less
-        // ambiguous
-        // would
-        // be a
-        // 'find
-        // primary
-        // dbRefEntry'
-        // method.
+        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
+        // less ambiguous would be a 'find primary dbRefEntry' method.
         // filter for desired source xref here
         found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
                 rseqs, cf);
@@ -256,13 +232,15 @@ public class CrossRef
       for (int r = 0; xrfs != null && r < xrfs.length; r++)
       {
         if (source != null && !source.equals(xrfs[r].getSource()))
+        {
           continue;
+        }
         if (xrfs[r].hasMap())
         {
           if (xrfs[r].getMap().getTo() != null)
           {
-            Sequence rsq = new Sequence(xrfs[r].getMap().getTo());
-            rseqs.addElement(rsq);
+            SequenceI rsq = new Sequence(xrfs[r].getMap().getTo());
+            rseqs.add(rsq);
             if (xrfs[r].getMap().getMap().getFromRatio() != xrfs[r]
                     .getMap().getMap().getToRatio())
             {
@@ -289,7 +267,9 @@ public class CrossRef
           {
             found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf); // ,false,!dna);
             if (found)
+            {
               xrfs[r] = null; // we've recovered seqs for this one.
+            }
           }
         }
       }
@@ -326,7 +306,9 @@ public class CrossRef
             for (int r = 0; r < xrfs.length; r++)
             {
               if (xrfs[r] != null)
+              {
                 t[l++] = xrfs[r];
+              }
             }
             xrfs = t;
             try
@@ -393,7 +375,7 @@ public class CrossRef
                   }
                 }
                 retrieved[rs].updatePDBIds();
-                rseqs.addElement(retrieved[rs]);
+                rseqs.add(retrieved[rs]);
               }
             }
           }
@@ -403,7 +385,7 @@ public class CrossRef
     if (rseqs.size() > 0)
     {
       SequenceI[] rsqs = new SequenceI[rseqs.size()];
-      rseqs.copyInto(rsqs);
+      rseqs.toArray(rsqs);
       ral = new Alignment(rsqs);
       if (cf != null && cf.getProtMappings() != null)
       {
@@ -425,12 +407,14 @@ public class CrossRef
    * @return true if matches were found.
    */
   private static boolean searchDatasetXrefs(SequenceI sequenceI,
-          boolean dna, DBRefEntry[] lrfs, AlignmentI dataset, Vector rseqs,
-          AlignedCodonFrame cf)
+          boolean dna, DBRefEntry[] lrfs, AlignmentI dataset,
+          List<SequenceI> rseqs, AlignedCodonFrame cf)
   {
     boolean found = false;
     if (lrfs == null)
+    {
       return false;
+    }
     for (int i = 0; i < lrfs.length; i++)
     {
       DBRefEntry xref = new DBRefEntry(lrfs[i]);
@@ -455,7 +439,7 @@ public class CrossRef
    * @return true if one or more unique sequences were found and added
    */
   public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
-          AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf)
+          AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf)
   {
     return searchDataset(sequenceI, xrf, dataset, rseqs, cf, true, false);
   }
@@ -476,13 +460,15 @@ public class CrossRef
    * @return true if relationship found and sequence added.
    */
   public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
-          AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf,
+          AlignmentI dataset, List<SequenceI> rseqs, AlignedCodonFrame cf,
           boolean direct, boolean dna)
   {
     boolean found = false;
     SequenceI[] typer = new SequenceI[1];
     if (dataset == null)
+    {
       return false;
+    }
     if (dataset.getSequences() == null)
     {
       System.err.println("Empty dataset sequence set - NO VECTOR");
@@ -492,6 +478,7 @@ public class CrossRef
     synchronized (ds = dataset.getSequences())
     {
       for (SequenceI nxt : ds)
+      {
         if (nxt != null)
         {
           if (nxt.getDatasetSequence() != null)
@@ -527,10 +514,9 @@ public class CrossRef
             {
               if (!rseqs.contains(nxt))
               {
-                rseqs.addElement(nxt);
-                boolean foundmap = cf != null; // don't search if we aren't
-                                               // given
-                // a codon map object
+                rseqs.add(nxt);
+                boolean foundmap = cf != null;
+                // don't search if we aren't given a codon map object
                 for (int r = 0; foundmap && r < cands.length; r++)
                 {
                   if (cands[r].hasMap())
@@ -564,6 +550,7 @@ public class CrossRef
 
           }
         }
+      }
     }
     return found;
   }