header updated

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

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 8436120..0a588a2 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -36,6 +36,19 @@ public class HiddenSequences
     return hiddenSequences == null ? 0 : hiddenSequences.size();\r
   }\r
 \r
+  public int getWidth()\r
+  {\r
+    Enumeration en = hiddenSequences.elements();\r
+    int width = 0;\r
+    while(en.hasMoreElements())\r
+    {\r
+      SequenceI seq = (SequenceI)en.nextElement();\r
+      if(seq.getLength()>width)\r
+        width = seq.getLength();\r
+    }\r
+    return width;\r
+  }\r
+\r
   public void hideSequence(SequenceI sequence)\r
   {\r
     if(hiddenSequences==null)\r
@@ -49,14 +62,21 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);\r
   }\r
 \r
-  public void showAll()\r
+  public Vector showAll()\r
   {\r
+   Vector revealedSeqs = new Vector();\r
    for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)\r
-     showSequence(i);\r
+    {\r
+      Vector tmp = showSequence(i);\r
+      for(int t=0; t<tmp.size(); t++)\r
+        revealedSeqs.addElement(tmp.elementAt(t));\r
+    }\r
+    return revealedSeqs;\r
   }\r
 \r
-  public void showSequence(int alignmentIndex)\r
+  public Vector showSequence(int alignmentIndex)\r
   {\r
+    Vector revealedSeqs = new Vector();\r
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);\r
     if(repSequence!=null\r
        && repSequence.getHiddenSequences()==null\r
@@ -75,8 +95,10 @@ public class HiddenSequences
       SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(\r
           index));\r
 \r
+\r
       if(seq!=null)\r
       {\r
+        revealedSeqs.addElement(seq);\r
         alignment.getSequences().insertElementAt(seq, alignmentIndex);\r
         if(repSequence!=null)\r
         {\r
@@ -84,6 +106,13 @@ public class HiddenSequences
         }\r
       }\r
     }\r
+\r
+    return revealedSeqs;\r
+  }\r
+\r
+  public Hashtable getHiddenSequences()\r
+  {\r
+    return hiddenSequences;\r
   }\r
 \r
   public SequenceI getHiddenSequence(int alignmentIndex)\r
@@ -121,4 +150,36 @@ 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