MyGraphics added to enhance applet GUI

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 61735ee..309fdae 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -29,10 +29,15 @@ import java.util.*;
  */\r
 public class Alignment implements AlignmentI\r
 {\r
+    protected Alignment dataset;\r
     protected Vector sequences;\r
     protected Vector groups = new Vector();\r
     protected Vector superGroup = new Vector();\r
     protected char gapCharacter = '-';\r
+    protected Provenance provenance;\r
+    protected int type = NUCLEOTIDE;\r
+    public static final int PROTEIN = 0;\r
+    public static final int NUCLEOTIDE = 1;\r
 \r
     /** DOCUMENT ME!! */\r
     public AlignmentAnnotation[] annotations;\r
@@ -46,9 +51,16 @@ public class Alignment implements AlignmentI
      */\r
     public Alignment(SequenceI[] seqs)\r
     {\r
+        int i=0;\r
+\r
+        if( jalview.util.Comparison.isNucleotide(seqs))\r
+          type = NUCLEOTIDE;\r
+        else\r
+          type = PROTEIN;\r
+\r
         sequences = new Vector();\r
 \r
-        for (int i = 0; i < seqs.length; i++)\r
+        for (i = 0; i < seqs.length; i++)\r
         {\r
             sequences.addElement(seqs[i]);\r
         }\r
@@ -658,6 +670,7 @@ public class Alignment implements AlignmentI
             aSize = annotations.length + 1;\r
         }\r
 \r
+\r
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
         int i = 0;\r
 \r
@@ -683,4 +696,62 @@ public class Alignment implements AlignmentI
     {\r
         return annotations;\r
     }\r
+\r
+    public void setNucleotide(boolean b)\r
+    {\r
+      if(b)\r
+        type = NUCLEOTIDE;\r
+      else\r
+        type = PROTEIN;\r
+    }\r
+\r
+    public boolean isNucleotide()\r
+    {\r
+      if(type==NUCLEOTIDE)\r
+        return true;\r
+      else\r
+        return false;\r
+    }\r
+\r
+    public void setDataset(Alignment data)\r
+    {\r
+      if(dataset==null && data==null)\r
+      {\r
+        // Create a new dataset for this alignment.\r
+        // Can only be done once, if dataset is not null\r
+        // This will not be performed\r
+        Sequence[] seqs = new Sequence[getHeight()];\r
+        for (int i = 0; i < getHeight(); i++)\r
+        {\r
+\r
+          seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
+                                 AlignSeq.extractGaps(\r
+                                     jalview.util.Comparison.GapChars,\r
+                                     getSequenceAt(i).getSequence()\r
+                                 ),\r
+                                 getSequenceAt(i).getStart(),\r
+                                 getSequenceAt(i).getEnd());\r
+        }\r
+\r
+        dataset = new Alignment(seqs);\r
+      }\r
+      else if(dataset==null && data!=null)\r
+      {\r
+        dataset = data;\r
+      }\r
+    }\r
+\r
+    public Alignment getDataset()\r
+    {\r
+      return dataset;\r
+    }\r
+\r
+    public void setProvenance(Provenance prov)\r
+    {\r
+      provenance = prov;\r
+    }\r
+    public Provenance getProvenance()\r
+    {\r
+      return provenance;\r
+    }\r
 }\r