Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / io / gff / GffHelperBase.java

diff --git a/src/jalview/io/gff/GffHelperBase.java b/src/jalview/io/gff/GffHelperBase.java
index d4a5358..1d4d3ac 100644 (file)
--- a/src/jalview/io/gff/GffHelperBase.java
+++ b/src/jalview/io/gff/GffHelperBase.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.analysis.SequenceIdMatcher;
@@ -130,8 +150,8 @@ public abstract class GffHelperBase implements GffHelperI
        * restrict from range to make them match up
        * it's kind of arbitrary which end we truncate - here it is the end
        */
-      System.err.print("Truncating mapping from " + Arrays.toString(from)
-              + " to ");
+      System.err.print(
+              "Truncating mapping from " + Arrays.toString(from) + " to ");
       if (from[1] > from[0])
       {
         from[1] -= fromOverlap / toRatio;
@@ -149,8 +169,8 @@ public abstract class GffHelperBase implements GffHelperI
       /*
        * restrict to range to make them match up
        */
-      System.err.print("Truncating mapping to " + Arrays.toString(to)
-              + " to ");
+      System.err.print(
+              "Truncating mapping to " + Arrays.toString(to) + " to ");
       if (to[1] > to[0])
       {
         to[1] -= fromOverlap / fromRatio;
@@ -241,7 +261,8 @@ public abstract class GffHelperBase implements GffHelperI
   /**
    * Parses the input line to a map of name / value(s) pairs. For example the
    * line <br>
-   * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal <br>
+   * Notes=Fe-S;Method=manual curation, prediction; source = Pfam; Notes = Metal
+   * <br>
    * if parsed with delimiter=";" and separators {' ', '='} <br>
    * would return a map with { Notes={Fe=S, Metal}, Method={manual curation,
    * prediction}, source={Pfam}} <br>
@@ -317,24 +338,44 @@ public abstract class GffHelperBase implements GffHelperI
   protected SequenceFeature buildSequenceFeature(String[] gff,
           Map<String, List<String>> attributes)
   {
+    return buildSequenceFeature(gff, TYPE_COL, gff[SOURCE_COL], attributes);
+  }
+
+  /**
+   * @param gff
+   * @param typeColumn
+   * @param group
+   * @param attributes
+   * @return
+   */
+  protected SequenceFeature buildSequenceFeature(String[] gff,
+          int typeColumn, String group, Map<String, List<String>> attributes)
+  {
     try
     {
       int start = Integer.parseInt(gff[START_COL]);
       int end = Integer.parseInt(gff[END_COL]);
-      float score = Float.NaN;
+
+      /*
+       * default 'score' is 0 rather than Float.NaN as the latter currently
+       * disables the 'graduated colour => colour by label' option
+       */
+      float score = 0f;
       try
       {
         score = Float.parseFloat(gff[SCORE_COL]);
       } catch (NumberFormatException nfe)
       {
-        // e.g. '.' - leave as NaN to indicate no score
+        // e.g. '.' - leave as zero
       }
 
-      SequenceFeature sf = new SequenceFeature(gff[TYPE_COL],
-              gff[SOURCE_COL], start, end, score, gff[SOURCE_COL]);
+      SequenceFeature sf = new SequenceFeature(gff[typeColumn],
+              gff[SOURCE_COL], start, end, score, group);
 
       sf.setStrand(gff[STRAND_COL]);
 
+      sf.setPhase(gff[PHASE_COL]);
+
       if (attributes != null)
       {
         /*
@@ -348,8 +389,8 @@ public abstract class GffHelperBase implements GffHelperI
          */
         for (Entry<String, List<String>> attr : attributes.entrySet())
         {
-          String values = StringUtils.listToDelimitedString(
-                  attr.getValue(), ",");
+          String values = StringUtils.listToDelimitedString(attr.getValue(),
+                  ",");
           sf.setValue(attr.getKey(), values);
           if (NOTE.equals(attr.getKey()))
           {
@@ -385,7 +426,8 @@ public abstract class GffHelperBase implements GffHelperI
    * @param toSeq
    * @return
    */
-  protected AlignedCodonFrame getMapping(AlignmentI align, SequenceI fromSeq, SequenceI toSeq)
+  protected AlignedCodonFrame getMapping(AlignmentI align,
+          SequenceI fromSeq, SequenceI toSeq)
   {
     AlignedCodonFrame acf = align.getMapping(fromSeq, toSeq);
     if (acf == null)