X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=46467c53296759899ff575543c1369d5b6be5c25;hp=40f83d3559c65a731b6934c8168657c203d46663;hb=refs%2Fheads%2Ffeatures%2FJAL-2094_colourInterface;hpb=d737688dfdb8d00ed63a699fb86548499d75bcf2

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 40f83d3..46467c5 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -36,7 +36,6 @@ import jalview.io.gff.GffHelperFactory;
 import jalview.io.gff.GffHelperI;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.UserColourScheme;
-import jalview.util.Format;
 import jalview.util.MapList;
 import jalview.util.ParseHtmlBodyAndLinks;
 import jalview.util.StringUtils;
@@ -233,12 +232,18 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           else if (ft.equalsIgnoreCase("endgroup"))
           {
             // We should check whether this is the current group,
-            // but at present theres no way of showing more than 1 group
+            // but at present there's no way of showing more than 1 group
             featureGroup = null;
           }
           else
           {
-            parseFeatureColour(line, ft, gffColumns, colours);
+            String colscheme = gffColumns[1];
+            FeatureColourI colour = FeatureColour
+                    .parseJalviewFeatureColour(colscheme);
+            if (colour != null)
+            {
+              colours.put(ft, colour);
+            }
           }
           continue;
         }
@@ -744,50 +749,14 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       // viewed features
       // TODO: decide if feature links should also be written here ?
       Iterator<String> en = featureColours.keySet().iterator();
-      String featureType, color;
       while (en.hasNext())
       {
-        featureType = en.next();
-        FeatureColourI fc = featureColours.get(featureType);
-        if (fc.isSimpleColour())
-        {
-          color = Format.getHexString(fc.getColour());
-        }
-        else
-        {
-          color = (fc.isColourByLabel() ? "label|" : "")
-                  + Format.getHexString(fc.getMinColour()) + "|"
-                  + Format.getHexString(fc.getMaxColour())
-                  + (fc.isAutoScaled() ? "|" : "|abso|") + fc.getMin() + "|"
-                  + fc.getMax() + "|";
-            if (fc.isBelowThreshold())
-            {
-              color += "below";
-            }
-            else if (fc.isAboveThreshold())
-            {
-              color += "above";
-            }
-            // add the value
-            color += "|" + fc.getThreshold();
-          }
-//          else
-//          {
-//            color += "none";
-//          }
-        // else
-        // {
-        // // legacy support for integer objects containing colour triplet
-        // values
-        // color = Format.getHexString(new Color(Integer
-        // .parseInt(fc.toString())));
-        // }
-        out.append(featureType);
-        out.append(TAB);
-        out.append(color);
-        out.append(newline);
+        String featureType = en.next();
+        FeatureColourI colour = featureColours.get(featureType);
+        out.append(colour.toJalviewFormat(featureType)).append(newline);
       }
     }
+
     // Work out which groups are both present and visible
     List<String> groups = new ArrayList<String>();
     int groupIndex = 0;
@@ -839,12 +808,12 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         features = sequences[i].getSequenceFeatures();
         if (features != null)
         {
-          for (int j = 0; j < features.length; j++)
+          for (SequenceFeature sequenceFeature : features)
           {
-            isnonpos = features[j].begin == 0 && features[j].end == 0;
+            isnonpos = sequenceFeature.begin == 0 && sequenceFeature.end == 0;
             if ((!nonpos && isnonpos)
                     || (!isnonpos && visOnly && !featureColours
-                            .containsKey(features[j].type)))
+                            .containsKey(sequenceFeature.type)))
             {
               // skip if feature is nonpos and we ignore them or if we only
               // output visible and it isn't non-pos and it's not visible
@@ -852,47 +821,48 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             }
 
             if (group != null
-                    && (features[j].featureGroup == null || !features[j].featureGroup
+                    && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
                             .equals(group)))
             {
               continue;
             }
 
-            if (group == null && features[j].featureGroup != null)
+            if (group == null && sequenceFeature.featureGroup != null)
             {
               continue;
             }
             // we have features to output
             featuresGen = true;
-            if (features[j].description == null
-                    || features[j].description.equals(""))
+            if (sequenceFeature.description == null
+                    || sequenceFeature.description.equals(""))
             {
-              out.append(features[j].type).append(TAB);
+              out.append(sequenceFeature.type).append(TAB);
             }
             else
             {
-              if (features[j].links != null
-                      && features[j].getDescription().indexOf("<html>") == -1)
+              if (sequenceFeature.links != null
+                      && sequenceFeature.getDescription().indexOf("<html>") == -1)
               {
                 out.append("<html>");
               }
 
-              out.append(features[j].description + " ");
-              if (features[j].links != null)
+              out.append(sequenceFeature.description);
+              if (sequenceFeature.links != null)
               {
-                for (int l = 0; l < features[j].links.size(); l++)
+                for (int l = 0; l < sequenceFeature.links.size(); l++)
                 {
-                  String label = features[j].links.elementAt(l).toString();
+                  String label = sequenceFeature.links.elementAt(l);
                   String href = label.substring(label.indexOf("|") + 1);
                   label = label.substring(0, label.indexOf("|"));
 
-                  if (features[j].description.indexOf(href) == -1)
+                  if (sequenceFeature.description.indexOf(href) == -1)
                   {
-                    out.append("<a href=\"" + href + "\">" + label + "</a>");
+                    out.append(" <a href=\"" + href + "\">" + label
+                            + "</a>");
                   }
                 }
 
-                if (features[j].getDescription().indexOf("</html>") == -1)
+                if (sequenceFeature.getDescription().indexOf("</html>") == -1)
                 {
                   out.append("</html>");
                 }
@@ -902,15 +872,15 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             }
             out.append(sequences[i].getName());
             out.append("\t-1\t");
-            out.append(features[j].begin);
+            out.append(sequenceFeature.begin);
             out.append(TAB);
-            out.append(features[j].end);
+            out.append(sequenceFeature.end);
             out.append(TAB);
-            out.append(features[j].type);
-            if (!Float.isNaN(features[j].score))
+            out.append(sequenceFeature.type);
+            if (!Float.isNaN(sequenceFeature.score))
             {
               out.append(TAB);
-              out.append(features[j].score);
+              out.append(sequenceFeature.score);
             }
             out.append(newline);
           }
@@ -1022,7 +992,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           boolean includeNonPositionalFeatures)
   {
     StringBuilder out = new StringBuilder(256);
-    out.append(String.format("%s %d\n", GFF_VERSION, gffVersion));
+    int version = gffVersion == 0 ? 2 : gffVersion;
+    out.append(String.format("%s %d\n", GFF_VERSION, version));
     String source;
     boolean isnonpos;
     for (SequenceI seq : sequences)