JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index d069e5e..7e963d5 100644 (file)
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -109,7 +109,7 @@ public class TCoffeeScoreFile extends AlignFile
 
   public final static String TCOFFEE_SCORE = "TCoffeeScore";
 
-  private final static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
+  static Pattern SCORES_WITH_RESIDUE_NUMS = Pattern
           .compile("^\\d+\\s([^\\s]+)\\s+\\d+$");
 
   /** The {@link Header} structure holder */
@@ -198,7 +198,7 @@ public class TCoffeeScoreFile extends AlignFile
     {
       return null;
     }
-    List<String> result = new ArrayList<>(scores.size());
+    List<String> result = new ArrayList<String>(scores.size());
     for (Map.Entry<String, StringBuilder> it : scores.entrySet())
     {
       result.add(it.getValue().toString());
@@ -250,7 +250,7 @@ public class TCoffeeScoreFile extends AlignFile
       error = true;
       return;
     }
-    scores = new LinkedHashMap<>();
+    scores = new LinkedHashMap<String, StringBuilder>();
 
     /*
      * initilize the structure
@@ -503,7 +503,7 @@ public class TCoffeeScoreFile extends AlignFile
 
     int score;
 
-    LinkedHashMap<String, Integer> scores = new LinkedHashMap<>();
+    LinkedHashMap<String, Integer> scores = new LinkedHashMap<String, Integer>();
 
     public int getScoreAvg()
     {
@@ -530,7 +530,7 @@ public class TCoffeeScoreFile extends AlignFile
     public Block(int size)
     {
       this.size = size;
-      this.items = new HashMap<>(size);
+      this.items = new HashMap<String, String>(size);
     }
 
     String getScoresFor(String id)