temp push

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d2a9b0a..821384a 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -88,6 +88,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
   private static final String ID_NOT_SPECIFIED = "ID_NOT_SPECIFIED";
 
+  private static final String NOTE = "Note";
+
   protected static final String GFF_VERSION = "##gff-version";
 
   private AlignmentI lastmatchedAl = null;
@@ -591,6 +593,14 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             .getDisplayedFeatureCols();
     Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
 
+    // BH check this is out?
+//    if (!includeNonPositional
+//            && (visibleColours == null || visibleColours.isEmpty()))
+//    {
+//      // no point continuing.
+//      return "No Features Visible";
+//    }
+
     /*
      * write out feature colours (if we know them)
      */
@@ -908,7 +918,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @param sequenceName
    * @param sequenceFeature
    */
-  protected void formatJalviewFeature(
+  protected String formatJalviewFeature(
           StringBuilder out, String sequenceName,
           SequenceFeature sequenceFeature)
   {
@@ -962,6 +972,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       out.append(sequenceFeature.score);
     }
     out.append(newline);
+
+    return out.toString();
   }
 
   /**
@@ -973,14 +985,15 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     AlignViewportI av = getViewport();
     if (av != null)
     {
-      if (av.getAlignment() != null)
+      AlignmentI a = av.getAlignment();
+      if (a != null)
       {
-        dataset = av.getAlignment().getDataset();
+        dataset = a.getDataset();
       }
       if (dataset == null)
       {
         // working in the applet context ?
-        dataset = av.getAlignment();
+        dataset = a;
       }
     }
     else
@@ -1020,11 +1033,9 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * Returns features output in GFF2 format
    * 
    * @param sequences
-   *                                       the sequences whose features are to be
-   *                                       output
+   *          the sequences whose features are to be output
    * @param visible
-   *                                       a map whose keys are the type names of
-   *                                       visible features
+   *          a map whose keys are the type names of visible features
    * @param visibleFeatureGroups
    * @param includeNonPositionalFeatures
    * @param includeComplement
@@ -1036,7 +1047,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
   {
     FeatureRenderer fr2 = null;
     if (includeComplement)
-    {
+  {
       AlignViewportI comp = fr.getViewport().getCodingComplement();
       fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
     }
@@ -1063,6 +1074,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       {
         features.addAll(seq.getFeatures().getPositionalFeatures(types));
       }
+
       for (SequenceFeature sf : features)
       {
         if (sf.isNonPositional() || fr.isVisible(sf))
@@ -1099,34 +1111,34 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
   private void formatGffFeature(StringBuilder out, SequenceI seq,
           SequenceFeature sf)
   {
-    String source = sf.featureGroup;
-    if (source == null)
-    {
-      source = sf.getDescription();
-    }
-
-    out.append(seq.getName());
-    out.append(TAB);
-    out.append(source);
-    out.append(TAB);
-    out.append(sf.type);
-    out.append(TAB);
-    out.append(sf.begin);
-    out.append(TAB);
-    out.append(sf.end);
-    out.append(TAB);
-    out.append(sf.score);
-    out.append(TAB);
-
-    int strand = sf.getStrand();
-    out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
-    out.append(TAB);
+        String source = sf.featureGroup;
+        if (source == null)
+        {
+          source = sf.getDescription();
+        }
 
-    String phase = sf.getPhase();
-    out.append(phase == null ? "." : phase);
+        out.append(seq.getName());
+        out.append(TAB);
+        out.append(source);
+        out.append(TAB);
+        out.append(sf.type);
+        out.append(TAB);
+        out.append(sf.begin);
+        out.append(TAB);
+        out.append(sf.end);
+        out.append(TAB);
+        out.append(sf.score);
+        out.append(TAB);
+
+        int strand = sf.getStrand();
+        out.append(strand == 1 ? "+" : (strand == -1 ? "-" : "."));
+        out.append(TAB);
+
+        String phase = sf.getPhase();
+        out.append(phase == null ? "." : phase);
 
     if (sf.otherDetails != null && !sf.otherDetails.isEmpty())
-    {
+        {
       Map<String, Object> map = sf.otherDetails;
       formatAttributes(out, map);
     }
@@ -1237,11 +1249,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * format)
    * 
    * @param alignedRegions
-   *                         a list of "Align fromStart toStart fromCount"
+   *          a list of "Align fromStart toStart fromCount"
    * @param mapIsFromCdna
-   *                         if true, 'from' is dna, else 'from' is protein
+   *          if true, 'from' is dna, else 'from' is protein
    * @param strand
-   *                         either 1 (forward) or -1 (reverse)
+   *          either 1 (forward) or -1 (reverse)
    * @return
    * @throws IOException
    */
@@ -1376,6 +1388,39 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     return seq;
   }
 
+  // BH! check that we did not lose something here. 
+//  /**
+//   * Process the 'column 9' data of the GFF file. This is less formally defined,
+//   * and its interpretation will vary depending on the tool that has generated
+//   * it.
+//   * 
+//   * @param attributes
+//   * @param sf
+//   */
+//  protected void processGffColumnNine(String attributes, SequenceFeature sf)
+//  {
+//    sf.setAttributes(attributes);
+//
+//    /*
+//     * Parse attributes in column 9 and add them to the sequence feature's 
+//     * 'otherData' table; use Note as a best proxy for description
+//     */
+//    char nameValueSeparator = gffVersion == 3 ? '=' : ' ';
+//    // TODO check we don't break GFF2 values which include commas here
+//    Map<String, List<String>> nameValues = GffHelperBase
+//            .parseNameValuePairs(attributes, ";", nameValueSeparator, ",");
+//    for (Entry<String, List<String>> attr : nameValues.entrySet())
+//    {
+//      String values = StringUtils.listToDelimitedString(attr.getValue(),
+//              "; ");
+//      sf.setValue(attr.getKey(), values);
+//      if (NOTE.equals(attr.getKey()))
+//      {
+//        sf.setDescription(values);
+//      }
+//    }
+//  }
+
   /**
    * After encountering ##fasta in a GFF3 file, process the remainder of the
    * file as FAST sequence data. Any placeholder sequences created during