JAL-2418 source formatting

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 73783e5..4be8d0e 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -35,11 +35,12 @@ import jalview.io.gff.GffHelperBase;
 import jalview.io.gff.GffHelperFactory;
 import jalview.io.gff.GffHelperI;
 import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 import jalview.util.MapList;
 import jalview.util.ParseHtmlBodyAndLinks;
 import jalview.util.StringUtils;
 
+import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -94,12 +95,13 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * Constructor which does not parse the file immediately
    * 
    * @param inFile
-   * @param type
+   * @param paste
    * @throws IOException
    */
-  public FeaturesFile(String inFile, String type) throws IOException
+  public FeaturesFile(String inFile, DataSourceType paste)
+          throws IOException
   {
-    super(false, inFile, type);
+    super(false, inFile, paste);
   }
 
   /**
@@ -119,8 +121,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @param type
    * @throws IOException
    */
-  public FeaturesFile(boolean parseImmediately, String inFile, String type)
-          throws IOException
+  public FeaturesFile(boolean parseImmediately, String inFile,
+          DataSourceType type) throws IOException
   {
     super(parseImmediately, inFile, type);
   }
@@ -302,7 +304,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    */
   protected boolean parseJalviewFeature(String line, String[] gffColumns,
           AlignmentI alignment, Map<String, FeatureColourI> featureColours,
-          boolean removeHTML, boolean relaxedIdMatching, String featureGroup)
+          boolean removeHTML, boolean relaxedIdMatching,
+          String featureGroup)
   {
     /*
      * tokens: description seqid seqIndex start end type [score]
@@ -353,11 +356,11 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
        * Perhaps an old style groups file with no colours -
        * synthesize a colour from the feature type
        */
-      UserColourScheme ucs = new UserColourScheme(ft);
-      featureColours.put(ft, new FeatureColour(ucs.findColour('A')));
+      Color colour = ColorUtils.createColourFromName(ft);
+      featureColours.put(ft, new FeatureColour(colour));
     }
-    SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos,
-            endPos, featureGroup);
+    SequenceFeature sf = new SequenceFeature(ft, desc, "", startPos, endPos,
+            featureGroup);
     if (gffColumns.length > 6)
     {
       float score = Float.NaN;
@@ -547,9 +550,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         for (int j = 0; j < features.length; j++)
         {
           isnonpos = features[j].begin == 0 && features[j].end == 0;
-          if ((!nonpos && isnonpos)
-                  || (!isnonpos && visOnly && !visible
-                          .containsKey(features[j].type)))
+          if ((!nonpos && isnonpos) || (!isnonpos && visOnly
+                  && !visible.containsKey(features[j].type)))
           {
             continue;
           }
@@ -588,18 +590,16 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
           {
             isnonpos = sequenceFeature.begin == 0
                     && sequenceFeature.end == 0;
-            if ((!nonpos && isnonpos)
-                    || (!isnonpos && visOnly && !visible
-                            .containsKey(sequenceFeature.type)))
+            if ((!nonpos && isnonpos) || (!isnonpos && visOnly
+                    && !visible.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
               continue;
             }
 
-            if (group != null
-                    && (sequenceFeature.featureGroup == null || !sequenceFeature.featureGroup
-                            .equals(group)))
+            if (group != null && (sequenceFeature.featureGroup == null
+                    || !sequenceFeature.featureGroup.equals(group)))
             {
               continue;
             }
@@ -617,8 +617,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
             }
             else
             {
-              if (sequenceFeature.links != null
-                      && sequenceFeature.getDescription().indexOf("<html>") == -1)
+              if (sequenceFeature.links != null && sequenceFeature
+                      .getDescription().indexOf("<html>") == -1)
               {
                 out.append("<html>");
               }
@@ -634,12 +634,13 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
 
                   if (sequenceFeature.description.indexOf(href) == -1)
                   {
-                    out.append(" <a href=\"" + href + "\">" + label
-                            + "</a>");
+                    out.append(
+                            " <a href=\"" + href + "\">" + label + "</a>");
                   }
                 }
 
-                if (sequenceFeature.getDescription().indexOf("</html>") == -1)
+                if (sequenceFeature.getDescription()
+                        .indexOf("</html>") == -1)
                 {
                   out.append("</html>");
                 }
@@ -710,7 +711,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       dataset = new Alignment(new SequenceI[] {});
     }
 
-    boolean parseResult = parse(dataset, null, false, true);
+    Map<String, FeatureColourI> featureColours = new HashMap<String, FeatureColourI>();
+    boolean parseResult = parse(dataset, featureColours, false, true);
     if (!parseResult)
     {
       // pass error up somehow
@@ -731,9 +733,10 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @return error message
    */
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
-    return "Use printGffFormat() or printJalviewFormat()";
+    System.out.println("Use printGffFormat() or printJalviewFormat()");
+    return null;
   }
 
   /**
@@ -894,8 +897,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         fromCount = Integer.parseInt(tokens[2]);
       } catch (NumberFormatException nfe)
       {
-        throw new IOException("Invalid number in Align field: "
-                + nfe.getMessage());
+        throw new IOException(
+                "Invalid number in Align field: " + nfe.getMessage());
       }
 
       /*
@@ -1115,9 +1118,8 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
    * @param newseqs
    * @throws IOException
    */
-  protected void processGffPragma(String line,
-          Map<String, String> gffProps, AlignmentI align,
-          List<SequenceI> newseqs) throws IOException
+  protected void processGffPragma(String line, Map<String, String> gffProps,
+          AlignmentI align, List<SequenceI> newseqs) throws IOException
   {
     line = line.trim();
     if ("###".equals(line))