From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 24 May 2018 14:59:49 +0000 (+0100)
Subject: JAL-2997 additional tests
X-Git-Tag: Release_2_10_5~70
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=acf9118bba86938c8406e7041b4e5a507f4f37a3;p=jalview.git

JAL-2997 additional tests
---

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index a37afd9..afb2009 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -77,7 +77,9 @@ public class ClustalFile extends AlignFile
         {
           top = true;
         }
-        if (line.indexOf(" ") != 0)
+        boolean isConservation = line.startsWith(SPACE)
+                || line.startsWith(TAB);
+        if (!isConservation)
         {
           str = new StringTokenizer(line);
 
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d2282b1..e0722c0 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -72,8 +72,6 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
   private static final String NOTE = "Note";
 
-  protected static final String TAB = "\t";
-
   protected static final String GFF_VERSION = "##gff-version";
 
   private AlignmentI lastmatchedAl = null;
@@ -180,11 +178,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           Map<String, FeatureColourI> colours, boolean removeHTML,
           boolean relaxedIdmatching)
   {
-    Map<String, String> gffProps = new HashMap<String, String>();
+    Map<String, String> gffProps = new HashMap<>();
     /*
      * keep track of any sequences we try to create from the data
      */
-    List<SequenceI> newseqs = new ArrayList<SequenceI>();
+    List<SequenceI> newseqs = new ArrayList<>();
 
     String line = null;
     try
@@ -534,7 +532,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
      * sort groups alphabetically, and ensure that features with a
      * null or empty group are output after those in named groups
      */
-    List<String> sortedGroups = new ArrayList<String>(visibleFeatureGroups);
+    List<String> sortedGroups = new ArrayList<>(visibleFeatureGroups);
     sortedGroups.remove(null);
     sortedGroups.remove("");
     Collections.sort(sortedGroups);
@@ -577,7 +575,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       for (int i = 0; i < sequences.length; i++)
       {
         String sequenceName = sequences[i].getName();
-        List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+        List<SequenceFeature> features = new ArrayList<>();
         if (types.length > 0)
         {
           features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
@@ -688,7 +686,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       dataset = new Alignment(new SequenceI[] {});
     }
 
-    Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
+    Map<String, FeatureColourI> featureColours = new HashMap<>();
     boolean parseResult = parse(dataset, featureColours, false, true);
     if (!parseResult)
     {
@@ -748,7 +746,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
     for (SequenceI seq : sequences)
     {
-      List<SequenceFeature> features = new ArrayList<SequenceFeature>();
+      List<SequenceFeature> features = new ArrayList<>();
       if (includeNonPositionalFeatures)
       {
         features.addAll(seq.getFeatures().getNonPositionalFeatures());
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index c0328d5..7117d0f 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -45,6 +45,10 @@ import java.util.zip.GZIPInputStream;
  */
 public class FileParse
 {
+  protected static final String SPACE = " ";
+
+  protected static final String TAB = "\t";
+
   /**
    * text specifying source of data. usually filename or url.
    */
diff --git a/test/jalview/io/ClustalFileTest.java b/test/jalview/io/ClustalFileTest.java
index a912d96..1da2c75 100644
--- a/test/jalview/io/ClustalFileTest.java
+++ b/test/jalview/io/ClustalFileTest.java
@@ -25,7 +25,35 @@ public class ClustalFileTest
             + "FER_CAPAN/1-55     SYKVKLI 55\n"
             + "FER1_SOLLC/1-55    SYKVKLI 55\n"
             + "Q93XJ9_SOLTU/1-55  SYKVKLI 55\n"
-            + "FER1_PEA/1-60      SYKVKLV 60\n";
+            + "FER1_PEA/1-60      SYKVKLV 60\n"
+            + "                   .*     .:....*******..** ..........**  ********...*:::*  ...\n"
+            + "\t\t.:.::.  *\n";
+    //@formatter:on
+    ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
+    cf.parse();
+    SequenceI[] seqs = cf.getSeqsAsArray();
+    assertEquals(seqs.length, 5);
+    assertEquals(seqs[0].getName(), "FER_CAPAA");
+    assertEquals(seqs[0].getStart(), 1);
+    assertEquals(seqs[0].getEnd(), 8);
+    assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
+  }
+
+  @Test(groups="Functional")
+  public void testParse_noNumbering() throws IOException
+  {
+    //@formatter:off
+    String data = "CLUSTAL\n\n"
+            + "FER_CAPAA/1-8      -----------------------------------------------------------A\n"
+            + "FER_CAPAN/1-55     MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMA\n"
+            + "FER1_SOLLC/1-55    MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
+            + "Q93XJ9_SOLTU/1-55  MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMA\n"
+            + "FER1_PEA/1-60      MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMA\n\n"
+            + "FER_CAPAA/1-8      SYKVKLI\n"
+            + "FER_CAPAN/1-55     SYKVKLI\n"
+            + "FER1_SOLLC/1-55    SYKVKLI\n"
+            + "Q93XJ9_SOLTU/1-55  SYKVKLI\n"
+            + "FER1_PEA/1-60      SYKVKLV\n";
     //@formatter:on
     ClustalFile cf = new ClustalFile(data, DataSourceType.PASTE);
     cf.parse();