Must be 1.1 compliant

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 3a5946c..ca52083 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -49,12 +49,22 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);\r
   }\r
 \r
+  public void showAll()\r
+  {\r
+   for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)\r
+     showSequence(i);\r
+  }\r
+\r
   public void showSequence(int alignmentIndex)\r
   {\r
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);\r
-    if(repSequence.getHiddenSequences()==null && alignmentIndex>0)\r
+    if(repSequence!=null\r
+       && repSequence.getHiddenSequences()==null\r
+       && alignmentIndex>0)\r
       repSequence = alignment.getSequenceAt(alignmentIndex-1);\r
-    if(repSequence.getHiddenSequences()==null)\r
+\r
+    if(repSequence!=null\r
+       && repSequence.getHiddenSequences()==null)\r
       repSequence = null;\r
 \r
     int start = adjustForHiddenSeqs(alignmentIndex-1);\r
@@ -76,6 +86,11 @@ public class HiddenSequences
     }\r
   }\r
 \r
+  public Hashtable getHiddenSequences()\r
+  {\r
+    return hiddenSequences;\r
+  }\r
+\r
   public SequenceI getHiddenSequence(int alignmentIndex)\r
   {\r
     return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));\r
@@ -111,4 +126,36 @@ public class HiddenSequences
 \r
     return alignmentIndex ;\r
   }\r
+\r
+  public AlignmentI getFullAlignment()\r
+  {\r
+    int isize = alignment.getHeight()+hiddenSequences.size();\r
+    SequenceI [] seq = new Sequence[isize];\r
+\r
+    Enumeration en = hiddenSequences.keys();\r
+    while(en.hasMoreElements())\r
+    {\r
+      Integer key = (Integer)en.nextElement();\r
+      seq[key.intValue()] = (SequenceI)hiddenSequences.get(key);\r
+    }\r
+\r
+    int index = 0;\r
+    for(int i=0; i<isize; i++)\r
+    {\r
+      if(seq[i]!=null)\r
+      {\r
+        continue;\r
+      }\r
+\r
+      seq[i] = alignment.getSequenceAt(index);\r
+      index++;\r
+    }\r
+\r
+    return new Alignment(seq);\r
+  }\r
+\r
+  public boolean isHidden(SequenceI seq)\r
+  {\r
+    return hiddenSequences.contains(seq);\r
+  }\r
 }\r