sequences are private in SequenceGroup

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c62d707..070b927 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -73,6 +73,16 @@ public class Alignment implements AlignmentI
         return sequences;\r
     }\r
 \r
+    public SequenceI [] getSequencesArray()\r
+    {\r
+      SequenceI [] reply = new SequenceI[sequences.size()];\r
+      for(int i=0; i<sequences.size(); i++)\r
+      {\r
+        reply[i] = (SequenceI)sequences.elementAt(i);\r
+      }\r
+      return reply;\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -96,22 +106,21 @@ public class Alignment implements AlignmentI
      */\r
     public void addSequence(SequenceI snew)\r
     {\r
-        sequences.addElement(snew);\r
-    }\r
+      if(dataset!=null)\r
+      {\r
+        Sequence ds = new Sequence(snew.getName(),\r
+                                   AlignSeq.extractGaps("-. ", snew.getSequence()),\r
+                                   snew.getStart(),\r
+                                   snew.getEnd());\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param seq DOCUMENT ME!\r
-     */\r
-    public void addSequence(SequenceI[] seq)\r
-    {\r
-        for (int i = 0; i < seq.length; i++)\r
-        {\r
-            addSequence(seq[i]);\r
-        }\r
+        snew.setDatasetSequence(ds);\r
+        getDataset().addSequence(ds);\r
+      }\r
+\r
+      sequences.addElement(snew);\r
     }\r
 \r
+\r
     /** Adds a sequence to the alignment.  Recalculates maxLength and size.\r
      *\r
      * @param snew\r
@@ -268,62 +277,6 @@ public class Alignment implements AlignmentI
         sequences.removeElementAt(i);\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param threshold DOCUMENT ME!\r
-     * @param sel DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public Vector removeRedundancy(float threshold, Vector sel)\r
-    {\r
-        Vector del = new Vector();\r
-\r
-        for (int i = 1; i < sel.size(); i++)\r
-        {\r
-            for (int j = 0; j < i; j++)\r
-            {\r
-                // Only do the comparison if either have not been deleted\r
-                if (!del.contains((SequenceI) sel.elementAt(i)) ||\r
-                        !del.contains((SequenceI) sel.elementAt(j)))\r
-                {\r
-                    // use PID instead of Comparison (which is really not pleasant)\r
-                    float pid = Comparison.PID((SequenceI) sel.elementAt(j),\r
-                            (SequenceI) sel.elementAt(i));\r
-\r
-                    if (pid >= threshold)\r
-                    {\r
-                        // Delete the shortest one\r
-                        if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel\r
-                                                                                         .elementAt(\r
-                                    i)).getSequence().length())\r
-                        {\r
-                            del.addElement(sel.elementAt(i));\r
-                        }\r
-                        else\r
-                        {\r
-                            del.addElement(sel.elementAt(i));\r
-                        }\r
-                    }\r
-                }\r
-            }\r
-        }\r
-\r
-        // Now delete the sequences\r
-        for (int i = 0; i < del.size(); i++)\r
-        {\r
-            deleteSequence((SequenceI) del.elementAt(i));\r
-        }\r
-\r
-        return del;\r
-    }\r
-\r
-    /**    */\r
-    public SequenceGroup findGroup(int i)\r
-    {\r
-        return findGroup(getSequenceAt(i));\r
-    }\r
 \r
     /**    */\r
     public SequenceGroup findGroup(SequenceI s)\r
@@ -332,7 +285,7 @@ public class Alignment implements AlignmentI
         {\r
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
 \r
-            if (sg.sequences.contains(s))\r
+            if (sg.getSequences(false).contains(s))\r
             {\r
                 return sg;\r
             }\r
@@ -356,14 +309,14 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < gSize; i++)\r
         {\r
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-            if(sg==null || sg.sequences==null)\r
+            if(sg==null || sg.getSequences(false)==null)\r
             {\r
               this.deleteGroup(sg);\r
               gSize--;\r
               continue;\r
             }\r
 \r
-            if (sg.sequences.contains(s))\r
+            if (sg.getSequences(false).contains(s))\r
             {\r
                 temp.addElement(sg);\r
             }\r