Don't parse input id, leave it as it is

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 28849b6..3a1b44a 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
@@ -334,9 +346,16 @@ public class Alignment implements AlignmentI
     {\r
         Vector temp = new Vector();\r
 \r
-        for (int i = 0; i < this.groups.size(); i++)\r
+        int gSize = groups.size();\r
+        for (int i = 0; i < gSize; i++)\r
         {\r
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+            if(sg==null || sg.sequences==null)\r
+            {\r
+              this.deleteGroup(sg);\r
+              gSize--;\r
+              continue;\r
+            }\r
 \r
             if (sg.sequences.contains(s))\r
             {\r
@@ -439,11 +458,9 @@ public class Alignment implements AlignmentI
 \r
         while (i < sequences.size())\r
         {\r
-            SequenceI s = getSequenceAt(i);\r
-\r
-            if (s.getName().equals(name))\r
+            if (getSequenceAt(i).getName().equals(name))\r
             {\r
-                return s;\r
+                return getSequenceAt(i);\r
             }\r
 \r
             i++;\r
@@ -452,25 +469,6 @@ public class Alignment implements AlignmentI
         return null;\r
     }\r
 \r
-    /**    */\r
-    public SequenceI findbyDisplayId(String name)\r
-    {\r
-        int i = 0;\r
-\r
-        while (i < sequences.size())\r
-        {\r
-            SequenceI s = getSequenceAt(i);\r
-\r
-            if (s.getDisplayId().equals(name))\r
-            {\r
-                return s;\r
-            }\r
-\r
-            i++;\r
-        }\r
-\r
-        return null;\r
-    }\r
 \r
     /**    */\r
     public int findIndex(SequenceI s)\r
@@ -651,6 +649,7 @@ public class Alignment implements AlignmentI
             aSize = annotations.length + 1;\r
         }\r
 \r
+\r
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
         int i = 0;\r
 \r
@@ -676,4 +675,64 @@ 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).getDisplayId(true),\r
+                                 AlignSeq.extractGaps(\r
+                                     jalview.util.Comparison.GapChars,\r
+                                     getSequenceAt(i).getSequence()\r
+                                 ),\r
+                                 getSequenceAt(i).getStart(),\r
+                                 getSequenceAt(i).getEnd());\r
+\r
+          getSequenceAt(i).setDatasetSequence(seqs[i]);\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