X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=6c63f1c009a3078751f15f09ec02c9995f761e21;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=94aa5c9f6c4b663c07f2f59f469fe6b87f68ad39;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 94aa5c9..6c63f1c 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -35,15 +35,15 @@ import jalview.ws.seqfetcher.ASequenceFetcher;
 /**
  * Functions for cross-referencing sequence databases. user must first specify
  * if cross-referencing from protein or dna (set dna==true)
- *
+ * 
  * @author JimP
- *
+ * 
  */
 public class CrossRef
 {
   /**
    * get the DNA or protein references for a protein or dna sequence
-   *
+   * 
    * @param dna
    * @param rfs
    * @return
@@ -91,7 +91,7 @@ public class CrossRef
   /**
    * Indirect references are references from other sequences from the dataset to
    * any of the direct DBRefEntrys on the given sequences.
-   *
+   * 
    * @param dna
    *          true if seqs are DNA seqs
    * @param seqs
@@ -202,7 +202,7 @@ public class CrossRef
   }
 
   /**
-   *
+   * 
    * @param dna
    * @param seqs
    * @return
@@ -214,7 +214,7 @@ public class CrossRef
   }
 
   /**
-   *
+   * 
    * @param seqs
    * @param dna
    * @param source
@@ -416,7 +416,7 @@ public class CrossRef
    * find references to lrfs in the cross-reference set of each sequence in
    * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry
    * based on source and accession string only - Map and Version are nulled.
-   *
+   * 
    * @param sequenceI
    * @param lrfs
    * @param dataset
@@ -444,7 +444,7 @@ public class CrossRef
   /**
    * search a given sequence dataset for references matching cross-references to
    * the given sequence
-   *
+   * 
    * @param sequenceI
    * @param xrf
    * @param dataset
@@ -463,7 +463,7 @@ public class CrossRef
    * TODO: generalise to different protein classifications Search dataset for
    * DBRefEntrys matching the given one (xrf) and add the associated sequence to
    * rseq.
-   *
+   * 
    * @param sequenceI
    * @param xrf
    * @param dataset
@@ -488,78 +488,81 @@ public class CrossRef
       return false;
     }
     List<SequenceI> ds;
-    synchronized (ds=dataset.getSequences())
+    synchronized (ds = dataset.getSequences())
     {
-      for (SequenceI nxt:ds)
-      if (nxt != null)
-      {
-        if (nxt.getDatasetSequence() != null)
-        {
-          System.err
-                  .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
-        }
-        if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
+      for (SequenceI nxt : ds)
+        if (nxt != null)
         {
-          // check if this is the correct sequence type
+          if (nxt.getDatasetSequence() != null)
+          {
+            System.err
+                    .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
+          }
+          if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
           {
-            typer[0] = nxt;
-            boolean isDna = jalview.util.Comparison.isNucleotide(typer);
-            if ((direct && isDna == dna) || (!direct && isDna != dna))
+            // check if this is the correct sequence type
             {
-              // skip this sequence because it is same molecule type
-              continue;
+              typer[0] = nxt;
+              boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+              if ((direct && isDna == dna) || (!direct && isDna != dna))
+              {
+                // skip this sequence because it is same molecule type
+                continue;
+              }
             }
-          }
 
-          // look for direct or indirect references in common
-          DBRefEntry[] poss = nxt.getDBRef(), cands = null;
-          if (direct)
-          {
-            cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
-          }
-          else
-          {
-            poss = CrossRef.findXDbRefs(dna, poss); //
-            cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
-          }
-          if (cands != null)
-          {
-            if (!rseqs.contains(nxt))
+            // look for direct or indirect references in common
+            DBRefEntry[] poss = nxt.getDBRef(), cands = null;
+            if (direct)
+            {
+              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+            }
+            else
             {
-              rseqs.addElement(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++)
+              poss = CrossRef.findXDbRefs(dna, poss); //
+              cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+            }
+            if (cands != null)
+            {
+              if (!rseqs.contains(nxt))
               {
-                if (cands[r].hasMap())
+                rseqs.addElement(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].getMap().getTo() != null
-                          && cands[r].getMap().getMap().getFromRatio() != cands[r]
-                                  .getMap().getMap().getToRatio())
+                  if (cands[r].hasMap())
                   {
-                    foundmap = true;
-                    // get sense of map correct for adding to product alignment.
-                    if (dna)
-                    {
-                      // map is from dna seq to a protein product
-                      cf.addMap(sequenceI, nxt, cands[r].getMap().getMap());
-                    }
-                    else
+                    if (cands[r].getMap().getTo() != null
+                            && cands[r].getMap().getMap().getFromRatio() != cands[r]
+                                    .getMap().getMap().getToRatio())
                     {
-                      // map should be from protein seq to its coding dna
-                      cf.addMap(nxt, sequenceI, cands[r].getMap().getMap()
-                              .getInverse());
+                      foundmap = true;
+                      // get sense of map correct for adding to product
+                      // alignment.
+                      if (dna)
+                      {
+                        // map is from dna seq to a protein product
+                        cf.addMap(sequenceI, nxt, cands[r].getMap()
+                                .getMap());
+                      }
+                      else
+                      {
+                        // map should be from protein seq to its coding dna
+                        cf.addMap(nxt, sequenceI, cands[r].getMap()
+                                .getMap().getInverse());
+                      }
                     }
                   }
                 }
+                // TODO: add mapping between sequences if necessary
+                found = true;
               }
-              // TODO: add mapping between sequences if necessary
-              found = true;
             }
-          }
 
+          }
         }
-      }
     }
     return found;
   }
@@ -567,7 +570,7 @@ public class CrossRef
   /**
    * precalculate different products that can be found for seqs in dataset and
    * return them.
-   *
+   * 
    * @param dna
    * @param seqs
    * @param dataset