From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 15 May 2017 15:26:02 +0000 (+0100)
Subject: JAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0... 
X-Git-Tag: Release_2_10_2~3^2~88^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7e7c422421698d7a47a9bad846c5522556f066d6;p=jalview.git

JAL-2535 quick hack to implement posterior probabilities parsing. 0-9 parsed as 0..9, ‘*’ or any other non-whitespace symbol parsed as ’10’.
---

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index e4d9f60..7f3f93b 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -33,6 +33,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -817,12 +818,16 @@ public class StockholmFile extends AlignFile
       type = (label.indexOf("_cons") == label.length() - 5) ? label
               .substring(0, label.length() - 5) : label;
     }
-    boolean ss = false;
+    boolean ss = false, posterior = false;
     type = id2type(type);
     if (type.equals("secondary structure"))
     {
       ss = true;
     }
+    if (type.equalsIgnoreCase("posterior probability"))
+    {
+      posterior = true;
+    }
     // decide on secondary structure or not.
     Annotation[] els = new Annotation[annots.length()];
     for (int i = 0; i < annots.length(); i++)
@@ -857,6 +862,25 @@ public class StockholmFile extends AlignFile
         }
 
       }
+      if (posterior && !ann.isWhitespace()
+              && !Comparison.isGap(pos.charAt(0)))
+      {
+        float val = 0;
+        // symbol encodes values - 0..*==0..10
+        if (pos.charAt(0) == '*')
+        {
+          val = 10;
+        }
+        else
+        {
+          val = pos.charAt(0) - '0';
+          if (val > 9)
+          {
+            val = 10;
+          }
+        }
+        ann.value = val;
+      }
 
       els[i] = ann;
     }