From 9e0407286fe32d01dfe4fea4d0bb6141f999f145 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 21 Nov 2014 08:56:52 +0000
Subject: [PATCH] JAL-1140 sensible name for seuqences in RNAML files that
 have no ID

---
 src/jalview/io/RnamlFile.java |   39 +++++++++++++++++++++++++++------------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index d366edc..9f0c8d5 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -20,12 +20,6 @@
  */
 package jalview.io;
 
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-
 import jalview.analysis.SecStrConsensus.SimpleBP;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -33,6 +27,14 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import com.stevesoft.pat.Regex;
+
 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
@@ -139,6 +141,14 @@ public class RnamlFile extends AlignFile
       int end = seq.length();
 
       id = current.getName();
+      if (id == null || id.trim().length() == 0)
+      {
+        id = safeName(getDataName());
+        if (result.size() > 1)
+        {
+          id += "." + i;
+        }
+      }
       seqs[i] = new Sequence(id, seq, begin, end);
 
       seqs[i].setEnd(seqs[i].findPosition(seqs[i].getLength()));
@@ -204,13 +214,18 @@ public class RnamlFile extends AlignFile
   private String safeName(String dataName)
   {
     int b = 0;
-    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length())
+    if ((b = dataName.lastIndexOf(".")) > 0)
     {
-      dataName = dataName.substring(b + 1).trim();
-
+      dataName = dataName.substring(0, b - 1);
+    }
+    b = 0;
+    Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
+    String mm = dataName;
+    while (m.searchFrom(dataName, b))
+    {
+      mm = m.stringMatched();
+      b = m.matchedTo();
     }
-    int e = (dataName.length() - dataName.indexOf(".")) + 1;
-    dataName = dataName.substring(1, e).trim();
-    return dataName;
+    return mm;
   }
 }
-- 
1.7.10.2