From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 30 Nov 2015 10:05:57 +0000 (+0000)
Subject: JAL-1421 generics loop syntax; 'bug?' comment added
X-Git-Tag: Release_2_10_0~296^2~113
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5c6b5740b5bc6ac8e89dc04fe0a3542ee76cc22e;p=jalview.git

JAL-1421 generics loop syntax; 'bug?' comment added
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 2e6431c..95d2396 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -25,6 +25,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
@@ -88,41 +89,54 @@ public class CrossRef
   {
     String[] dbrefs = null;
     List<String> refs = new ArrayList<String>();
-    for (int s = 0; s < seqs.length; s++)
+    for (SequenceI seq : seqs)
     {
-      if (seqs[s] != null)
+      if (seq != null)
       {
-        SequenceI dss = seqs[s];
+        SequenceI dss = seq;
         while (dss.getDatasetSequence() != null)
         {
           dss = dss.getDatasetSequence();
         }
         DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
-        for (int r = 0; rfs != null && r < rfs.length; r++)
+        if (rfs != null)
         {
-          if (!refs.contains(rfs[r].getSource()))
+          for (DBRefEntry ref : rfs)
           {
-            refs.add(rfs[r].getSource());
+            if (!refs.contains(ref.getSource()))
+            {
+              refs.add(ref.getSource());
+            }
           }
         }
         if (dataset != null)
         {
           // search for references to this sequence's direct references.
-          DBRefEntry[] lrfs = CrossRef
-                  .findXDbRefs(!dna, seqs[s].getDBRef());
+          DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
           List<SequenceI> rseqs = new ArrayList<SequenceI>();
-          CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
+          CrossRef.searchDatasetXrefs(seq, !dna, lrfs, dataset, rseqs,
                   null); // don't need to specify codon frame for mapping here
           for (SequenceI rs : rseqs)
           {
-            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef()); // not used??
-            for (int r = 0; rfs != null && r < rfs.length; r++)
+            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
+            if (xrs != null)
             {
-              if (!refs.contains(rfs[r].getSource()))
+              for (DBRefEntry ref : xrs)
               {
-                refs.add(rfs[r].getSource());
+                if (!refs.contains(ref.getSource()))
+                {
+                  refs.add(ref.getSource());
+                }
               }
             }
+            // looks like copy and paste - change rfs to xrs?
+            // for (int r = 0; rfs != null && r < rfs.length; r++)
+            // {
+            // if (!refs.contains(rfs[r].getSource()))
+            // {
+            // refs.add(rfs[r].getSource());
+            // }
+            // }
           }
         }
       }
@@ -135,13 +149,9 @@ public class CrossRef
     return dbrefs;
   }
 
-  /*
-   * if (dna) { if (rfs[r].hasMap()) { // most likely this is a protein cross
-   * reference if (!refs.contains(rfs[r].getSource())) {
-   * refs.addElement(rfs[r].getSource()); } } }
-   */
   public static boolean hasCdnaMap(SequenceI[] seqs)
   {
+    // TODO unused - remove?
     String[] reftypes = findSequenceXrefTypes(false, seqs);
     for (int s = 0; s < reftypes.length; s++)
     {
@@ -156,6 +166,7 @@ public class CrossRef
 
   public static SequenceI[] getCdnaMap(SequenceI[] seqs)
   {
+    // TODO unused - remove?
     Vector cseqs = new Vector();
     for (int s = 0; s < seqs.length; s++)
     {
@@ -199,7 +210,9 @@ public class CrossRef
   /**
    * 
    * @param seqs
+   *          sequences whose xrefs are being retrieved
    * @param dna
+   *          true if sequences are nucleotide
    * @param source
    * @param dataset
    *          alignment to search for product sequences.
@@ -209,11 +222,10 @@ public class CrossRef
           String source, AlignmentI dataset)
   {
     List<SequenceI> rseqs = new ArrayList<SequenceI>();
-    Alignment ral = null;
-    AlignedCodonFrame cf = new AlignedCodonFrame(); // nominal width
-    for (int s = 0; s < seqs.length; s++)
+    AlignedCodonFrame cf = new AlignedCodonFrame();
+    for (SequenceI seq : seqs)
     {
-      SequenceI dss = seqs[s];
+      SequenceI dss = seq;
       while (dss.getDatasetSequence() != null)
       {
         dss = dss.getDatasetSequence();
@@ -223,7 +235,8 @@ 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());
+        // FIXME should be dss not seq here?
+        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRef());
         // less ambiguous would be a 'find primary dbRefEntry' method.
         // filter for desired source xref here
         found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
@@ -321,7 +334,7 @@ public class CrossRef
             {
               System.err
                       .println("Problem whilst retrieving cross references for Sequence : "
-                              + seqs[s].getName());
+                              + seq.getName());
               e.printStackTrace();
             }
             if (retrieved != null)
@@ -329,15 +342,14 @@ public class CrossRef
               for (int rs = 0; rs < retrieved.length; rs++)
               {
                 // TODO: examine each sequence for 'redundancy'
-                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
-                        .getDBRef();
+                DBRefEntry[] dbr = retrieved[rs].getDBRef();
                 if (dbr != null && dbr.length > 0)
                 {
                   for (int di = 0; di < dbr.length; di++)
                   {
                     // find any entry where we should put in the sequence being
                     // cross-referenced into the map
-                    jalview.datamodel.Mapping map = dbr[di].getMap();
+                    Mapping map = dbr[di].getMap();
                     if (map != null)
                     {
                       if (map.getTo() != null && map.getMap() != null)
@@ -382,6 +394,8 @@ public class CrossRef
         }
       }
     }
+
+    Alignment ral = null;
     if (rseqs.size() > 0)
     {
       SequenceI[] rsqs = new SequenceI[rseqs.size()];