From 4a621265c074df3b90126a453bed7a0e7bed02c6 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 23 Apr 2016 18:37:04 +0100
Subject: [PATCH] JAL-2075 fix: use AlignmentView.getVisibleContigs and
 SeqCigar.findPosition to locate aligned features

---
 .../analysis/scoremodels/FeatureScoreModel.java    |   96 +++++++++++---------
 1 file changed, 51 insertions(+), 45 deletions(-)

diff --git a/src/jalview/analysis/scoremodels/FeatureScoreModel.java b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
index 1ca3342..7c81912 100644
--- a/src/jalview/analysis/scoremodels/FeatureScoreModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureScoreModel.java
@@ -23,9 +23,8 @@ package jalview.analysis.scoremodels;
 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;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -48,13 +47,10 @@ public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
   {
     int nofeats = 0;
     List<String> dft = fr.getDisplayedFeatureTypes();
-
     nofeats = dft.size();
-
-    SequenceI[] sequenceString = seqData.getVisibleAlignment(
-            Comparison.GapChars.charAt(0)).getSequencesArray();
-    int noseqs = sequenceString.length;
-    int cpwidth = seqData.getWidth();
+    SeqCigar[] seqs = seqData.getSequences();
+    int noseqs = seqs.length;
+    int cpwidth = 0;// = seqData.getWidth();
     float[][] distance = new float[noseqs][noseqs];
     if (nofeats == 0)
     {
@@ -67,54 +63,64 @@ public class FeatureScoreModel implements ScoreModelI, ViewBasedAnalysisI
       }
       return distance;
     }
-    float max = 0;
-    for (int cpos = 0; cpos < cpwidth; cpos++)
+    // need to get real position for view position
+    int[] viscont = seqData.getVisibleContigs();
+    for (int vc = 0; vc < viscont.length; vc += 2)
     {
-      // 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++)
+
+      for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++)
       {
-        if (cpos == 0)
-        {
-          distance[i][i] = 0f;
-        }
-        for (int j = i + 1; j < noseqs; j++)
+        cpwidth++;
+        // 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++)
         {
-          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())
+          Hashtable<String, SequenceFeature> types = new Hashtable<String, SequenceFeature>();
+          int spos = seqs[i].findPosition(cpos);
+          if (spos != -1)
           {
-            fk = fj;
+            List<SequenceFeature> sfs = fr.findFeaturesAtRes(
+                    seqs[i].getRefSeq(), spos);
+            for (SequenceFeature sf : sfs)
+            {
+              types.put(sf.getType(), sf);
+            }
           }
-          else
+          sfap.add(types);
+        }
+        for (int i = 0; i < (noseqs - 1); i++)
+        {
+          if (cpos == 0)
           {
-            fk = fi;
-            fi = fj;
+            distance[i][i] = 0f;
           }
-          for (String k : fi.keySet())
+          for (int j = i + 1; j < noseqs; j++)
           {
-            SequenceFeature sfj = fk.get(k);
-            if (sfj != null)
+            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())
             {
-              sfcommon++;
+              SequenceFeature sfj = fk.get(k);
+              if (sfj != null)
+              {
+                sfcommon++;
+              }
             }
+            distance[i][j] += (fi.size() + fk.size() - 2f * sfcommon);
+            distance[j][i] += distance[i][j];
           }
-          distance[i][j] += (fi.size() + fk.size() - 2f * sfcommon);
-          distance[j][i] += distance[i][j];
         }
       }
     }
-- 
1.7.10.2