X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=e96d9d7afb8c632fef1e0f6ec74d597a0014100a;hb=b4fac54ddfb91688f281a6a2ede0d8d44ec1dd13;hp=68f6c93ed1f3eb760348f8267f57baba7e824564;hpb=cb6d2306e75ecea509fb1fde9736ff593e8e5837;p=jalview.git

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 68f6c93..e96d9d7 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -27,22 +27,13 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.io.gff.SequenceOntology;
-import jalview.schemes.ResidueProperties;
 import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-import jalview.util.StringUtils;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 
 import java.util.ArrayList;
-import java.util.Collections;
-import java.util.LinkedHashMap;
 import java.util.List;
-import java.util.Map.Entry;
 import java.util.Vector;
 
 /**
@@ -278,12 +269,6 @@ public class CrossRef
                 // map should be from protein seq to its coding dna
                 cf.addMap(rsq, dss, xref.getMap().getMap().getInverse());
               }
-
-              /*
-               * compute peptide variants from dna variants
-               */
-              rsq.createDatasetSequence();
-              computeProteinVariants(seq, rsq, xref.getMap().getMap());
             }
             found = true;
           }
@@ -585,195 +570,6 @@ public class CrossRef
   }
 
   /**
-   * Computes variants in peptide product generated by variants in dna, and adds
-   * them as sequence_variant features on the protein sequence. Returns the
-   * number of variant features added.
-   * 
-   * @param dnaSeq
-   * @param peptide
-   * @param dnaToProtein
-   */
-  protected static int computeProteinVariants(SequenceI dnaSeq,
-          SequenceI peptide, MapList dnaToProtein)
-  {
-    /*
-     * map from peptide position to all variant features of the codon for it
-     * LinkedHashMap ensures we add the peptide features in sequence order
-     */
-    LinkedHashMap<Integer, String[][]> variants = new LinkedHashMap<Integer, String[][]>();
-    SequenceOntology so = SequenceOntology.getInstance();
-  
-    SequenceFeature[] dnaFeatures = dnaSeq.getSequenceFeatures();
-    if (dnaFeatures == null)
-    {
-      return 0;
-    }
-  
-    int[] lastCodon = null;
-    int lastPeptidePostion = 0;
-
-    /*
-     * build a map of codon variations for peptides
-     */
-    for (SequenceFeature sf : dnaFeatures)
-    {
-      int dnaCol = sf.getBegin();
-      if (dnaCol != sf.getEnd())
-      {
-        // not handling multi-locus variant features
-        continue;
-      }
-      if (so.isSequenceVariant(sf.getType()))
-      {
-        int[] mapsTo = dnaToProtein.locateInTo(dnaCol, dnaCol);
-        if (mapsTo == null)
-        {
-          // feature doesn't lie within coding region
-          continue;
-        }
-        int peptidePosition = mapsTo[0];
-        String[][] codonVariants = variants.get(peptidePosition);
-        if (codonVariants == null)
-        {
-          codonVariants = new String[3][];
-          variants.put(peptidePosition, codonVariants);
-        }
-
-        /*
-         * extract dna variants to a string array
-         */
-        String alls = (String) sf.getValue("alleles");
-        if (alls == null)
-        {
-          continue;
-        }
-        String[] alleles = alls.split(",");
-
-        /*
-         * get this peptides codon positions e.g. [3, 4, 5] or [4, 7, 10]
-         */
-        int[] codon = peptidePosition == lastPeptidePostion ? lastCodon
-                : MappingUtils.flattenRanges(dnaToProtein.locateInFrom(
-                        peptidePosition, peptidePosition));
-        lastPeptidePostion = peptidePosition;
-        lastCodon = codon;
-
-        /*
-         * save nucleotide (and this variant) for each codon position
-         */
-        for (int codonPos = 0; codonPos < 3; codonPos++)
-        {
-          String nucleotide = String.valueOf(dnaSeq
-                  .getCharAt(codon[codonPos] - 1));
-          if (codon[codonPos] == dnaCol)
-          {
-            /*
-             * record current dna base and its alleles
-             */
-            String[] dnaVariants = new String[alleles.length + 1];
-            dnaVariants[0] = nucleotide;
-            System.arraycopy(alleles, 0, dnaVariants, 1, alleles.length);
-            codonVariants[codonPos] = dnaVariants;
-          }
-          else if (codonVariants[codonPos] == null)
-          {
-            /*
-             * record current dna base only 
-             * (at least until we find any variation and overwrite it)
-             */
-            codonVariants[codonPos] = new String[] { nucleotide };
-          }
-        }
-      }
-    }
-  
-    /*
-     * scan codon variations, compute peptide variants and add to peptide sequence
-     */
-    int count = 0;
-    for (Entry<Integer, String[][]> variant : variants.entrySet())
-    {
-      int peptidePos = variant.getKey();
-      String[][] codonVariants = variant.getValue();
-      String residue = String.valueOf(peptide.getCharAt(peptidePos - 1)); // 0-based
-      List<String> peptideVariants = computePeptideVariants(codonVariants,
-              residue);
-      if (!peptideVariants.isEmpty())
-      {
-        Collections.sort(peptideVariants);
-        String desc = StringUtils.listToDelimitedString(peptideVariants,
-                ", ");
-        SequenceFeature sf = new SequenceFeature(
-                SequenceOntology.SEQUENCE_VARIANT, desc, peptidePos,
-                peptidePos, Float.NaN, null);
-        peptide.getDatasetSequence().addSequenceFeature(sf);
-        count++;
-      }
-    }
-    return count;
-  }
-
-  /**
-   * Returns a non-redundant list of all peptide translations generated by the
-   * given dna variants, excluding the current residue value
-   * 
-   * @param codonVariants
-   *          an array of base values for codon positions 1, 2, 3
-   * @param residue
-   *          the current residue translation
-   * @return
-   */
-  protected static List<String> computePeptideVariants(
-          String[][] codonVariants, String residue)
-  {
-    List<String> result = new ArrayList<String>();
-    for (String base1 : codonVariants[0])
-    {
-      for (String base2 : codonVariants[1])
-      {
-        for (String base3 : codonVariants[2])
-        {
-          String codon = base1 + base2 + base3;
-          // TODO: report frameshift/insertion/deletion
-          // and multiple-base variants?!
-          String peptide = codon.contains("-") ? "-" : ResidueProperties
-                  .codonTranslate(codon);
-          if (peptide != null && !result.contains(peptide)
-                  && !peptide.equals(residue))
-          {
-            result.add(peptide);
-          }
-        }
-      }
-    }
-    return result;
-  }
-
-  /**
-   * Computes a list of all peptide variants given dna variants
-   * 
-   * @param dnaSeq
-   *          the coding dna sequence
-   * @param codonVariants
-   *          variant features for each codon position (null if no variant)
-   * @param residue
-   *          the canonical protein translation
-   * @return
-   */
-  protected static List<String> computePeptideVariants(SequenceI dnaSeq,
-          SequenceFeature[] codonVariants, String residue)
-  {
-    List<String> result = new ArrayList<String>();
-    int[][] dnaVariants = new int[3][];
-    for (int i = 0; i < 3; i++)
-    {
-
-    }
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /**
    * precalculate different products that can be found for seqs in dataset and
    * return them.
    *