sequences are private in SequenceGroup

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6de42b9..ecdf2bc 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -41,9 +41,7 @@ public class SequenceGroup
     boolean displayBoxes;\r
     boolean displayText;\r
     boolean colourText;\r
-\r
-    /** DOCUMENT ME!! */\r
-    public Vector sequences = new Vector();\r
+    private Vector sequences = new Vector();\r
     int width = -1;\r
 \r
     /** DOCUMENT ME!! */\r
@@ -115,6 +113,33 @@ public class SequenceGroup
         endRes = end;\r
     }\r
 \r
+    public Vector getSequences(boolean includeHidden)\r
+    {\r
+      if(!includeHidden)\r
+        return sequences;\r
+      else\r
+      {\r
+        Vector allSequences = new Vector();\r
+        SequenceI seq;\r
+        for (int i = 0; i < sequences.size(); i++)\r
+        {\r
+          seq = (SequenceI) sequences.elementAt(i);\r
+          allSequences.addElement(seq);\r
+          if (seq.getHiddenSequences() != null)\r
+          {\r
+            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)\r
+            {\r
+              allSequences.addElement(\r
+                  seq.getHiddenSequences().getSequenceAt(h)\r
+                  );\r
+            }\r
+          }\r
+        }\r
+\r
+        return allSequences;\r
+      }\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -344,9 +369,24 @@ public class SequenceGroup
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public int getSize()\r
+    public int getSize(boolean includeHidden)\r
     {\r
+      if(!includeHidden)\r
         return sequences.size();\r
+      else\r
+      {\r
+        int total = sequences.size();\r
+        SequenceI seq;\r
+        for (int i = 0; i < sequences.size(); i++)\r
+        {\r
+          seq = (SequenceI) sequences.elementAt(i);\r
+          if (seq.getHiddenSequences() != null)\r
+          {\r
+            total += seq.getHiddenSequences().getSize(false);\r
+          }\r
+        }\r
+        return total;\r
+      }\r
     }\r
 \r
     /**\r