X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FFeatureScoreModel.java;h=e2a8b9a57d3b2091ca77c1a662691a241436ef53;hb=872491e84ca43e8ec17ef8c0395d1b7a45e6b5d4;hp=e9347e41d7f342449ad8d1810eb4e9b05f73b321;hpb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/FeatureScoreModel.java b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
index e9347e4..e2a8b9a 100644
--- a/src/jalview/analysis/scoremodels/FeatureScoreModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
@@ -1,22 +1,24 @@
 package jalview.analysis.scoremodels;
 
-import java.awt.Color;
-
-import jalview.analysis.AlignSeq;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
-public class FeatureScoreModel implements ScoreModelI,ViewBasedAnalysisI
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+
+public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
 {
   jalview.api.FeatureRenderer fr;
-  
-  @Override 
-  public boolean configureFromAlignmentView(jalview.api.AlignmentViewPanel view)
+
+  @Override
+  public boolean configureFromAlignmentView(
+          jalview.api.AlignmentViewPanel view)
   {
     fr = view.cloneFeatureRenderer();
     return true;
@@ -25,60 +27,112 @@ public class FeatureScoreModel implements ScoreModelI,ViewBasedAnalysisI
   @Override
   public float[][] findDistances(AlignmentView seqData)
   {
-   
-    SequenceI[] sequenceString = seqData
-            .getVisibleAlignment(Comparison.GapChars.charAt(0)).getSequencesArray();
+    int nofeats = 0;
+    List<String> dft = Arrays.asList(fr.getDisplayedFeatureTypes());
+
+    if (dft != null)
+    {
+      nofeats = dft.size();
+    }
+
+    SequenceI[] sequenceString = seqData.getVisibleAlignment(
+            Comparison.GapChars.charAt(0)).getSequencesArray();
     int noseqs = sequenceString.length;
     int cpwidth = seqData.getWidth();
     float[][] distance = new float[noseqs][noseqs];
-    float max=0;
-    for (int cpos = 0;cpos<cpwidth;cpos++)
+    if (nofeats == 0)
+    {
+      for (float[] d : distance)
+      {
+        for (int i = 0; i < d.length; d[i++] = 0f)
+        {
+          ;
+        }
+      }
+      return distance;
+    }
+    float max = 0;
+    for (int cpos = 0; cpos < cpwidth; cpos++)
     {
-      // get visible features at cpos under view's display settings and compare them
+      // get visible features at cpos under view's display settings and compare
+      // them
+      List<Hashtable<String, SequenceFeature>> sfap = new ArrayList<Hashtable<String, SequenceFeature>>();
+      for (int i = 0; i < noseqs; i++)
+      {
+        Hashtable<String, SequenceFeature> types = new Hashtable<String, SequenceFeature>();
+        List<SequenceFeature> sfs = fr.findFeaturesAtRes(sequenceString[i],
+                sequenceString[i].findPosition(cpos));
+        for (SequenceFeature sf : sfs)
+        {
+          types.put(sf.getType(), sf);
+        }
+        sfap.add(types);
+      }
       for (int i = 0; i < (noseqs - 1); i++)
       {
-        SequenceFeature[] sf = fr.getVisible(sequenceString[i],cpos);
-        for (int j=i+1;j<noseqs;j++)
+        if (cpos == 0)
         {
-          SequenceFeature[] jsf = fr.getVisible(sequenceString[i],cpos);
-
-          
-        if (max < distance[i][j])
+          distance[i][i] = 0f;
+        }
+        for (int j = i + 1; j < noseqs; j++)
         {
-          max = distance[i][j];
+          int sfcommon = 0;
+          // compare the two lists of features...
+          Hashtable<String, SequenceFeature> fi = sfap.get(i), fk, fj = sfap
+                  .get(j);
+          if (fi.size() > fj.size())
+          {
+            fk = fj;
+          }
+          else
+          {
+            fk = fi;
+            fi = fj;
+          }
+          for (String k : fi.keySet())
+          {
+            SequenceFeature sfj = fk.get(k);
+            if (sfj != null)
+            {
+              sfcommon++;
+            }
+          }
+          distance[i][j] += (fi.size() + fk.size() - 2f * sfcommon);
+          distance[j][i] += distance[i][j];
         }
       }
     }
-    }
-
-    for (int i = 0; i < (noseqs - 1); i++)
+    for (int i = 0; i < noseqs; i++)
     {
-      for (int j = i; j < noseqs; j++)
+      for (int j = i + 1; j < noseqs; j++)
       {
-        distance[i][j] = max - distance[i][j];
+        distance[i][j] /= cpwidth;
         distance[j][i] = distance[i][j];
       }
     }
-     
     return distance;
   }
 
   @Override
   public String getName()
   {
-    return "Smith Waterman Score";
+    return "Sequence Feature Similarity";
   }
+
   @Override
   public boolean isDNA()
   {
     return true;
   }
+
   @Override
   public boolean isProtein()
   {
     return true;
   }
-  public String toString() {
-    return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+
+  public String toString()
+  {
+    return "Score between sequences based on hamming distance between binary vectors marking features displayed at each column";
   }
 }