JAL-653 trim initial tab in sequence feature ATTRIBUTES

[jalview.git] / src / jalview / io / FeaturesFile.java

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 804cefc..a9ad665 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,13 +20,28 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
-
 import jalview.analysis.SequenceIdMatcher;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
 import jalview.util.Format;
+import jalview.util.MapList;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 /**
  * Parse and create Jalview Features files Detects GFF format features files and
@@ -154,6 +169,10 @@ public class FeaturesFile extends AlignFile
     try
     {
       SequenceI seq = null;
+      /**
+       * keep track of any sequences we try to create from the data if it is a GFF3 file
+       */
+      ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
       String type, desc, token = null;
 
       int index, start, end;
@@ -427,7 +446,7 @@ public class FeaturesFile extends AlignFile
             // Still possible this is an old Jalview file,
             // which does not have type colours at the beginning
             seqId = token = st.nextToken();
-            seq = findName(align, seqId, relaxedIdmatching);
+            seq = findName(align, seqId, relaxedIdmatching, newseqs);
             if (seq != null)
             {
               desc = st.nextToken();
@@ -496,9 +515,11 @@ public class FeaturesFile extends AlignFile
               if (st.hasMoreTokens())
               {
                 StringBuffer attributes = new StringBuffer();
+                boolean sep = false;
                 while (st.hasMoreTokens())
                 {
-                  attributes.append("\t" + st.nextElement());
+                  attributes.append((sep ? "\t" : "") + st.nextElement());
+                  sep = true;
                 }
                 // TODO validate and split GFF2 attributes field ? parse out
                 // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
@@ -536,7 +557,7 @@ public class FeaturesFile extends AlignFile
 
           if (!token.equals("ID_NOT_SPECIFIED"))
           {
-            seq = findName(align, seqId = token, relaxedIdmatching);
+            seq = findName(align, seqId = token, relaxedIdmatching, null);
             st.nextToken();
           }
           else
@@ -632,7 +653,7 @@ public class FeaturesFile extends AlignFile
   }
 
   private SequenceI findName(AlignmentI align, String seqId,
-          boolean relaxedIdMatching)
+          boolean relaxedIdMatching, List<SequenceI> newseqs)
   {
     SequenceI match = null;
     if (relaxedIdMatching)
@@ -641,16 +662,29 @@ public class FeaturesFile extends AlignFile
       {
         matcher = new SequenceIdMatcher(
                 (lastmatchedAl = align).getSequencesArray());
+        if (newseqs != null)
+        {
+          matcher.addAll(newseqs);
+        }
       }
       match = matcher.findIdMatch(seqId);
     }
     else
     {
       match = align.findName(seqId, true);
+      
+    }
+    if (match==null && newseqs!=null)
+    {
+      match = new SequenceDummy(seqId);
+      if (relaxedIdMatching)
+      {
+        matcher.addAll(Arrays.asList(new SequenceI[]
+        { match }));
+      }
     }
     return match;
   }
-
   public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
   {
     if (sf.getDescription() == null)