X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=be7dbe209481c7a6c6e1ee36fc14581bc47e7071;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=3a5946c0552982ff91b3073c413881879b9552c7;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 3a5946c..be7dbe2 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,114 +1,185 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-
-package jalview.datamodel;
-
-import java.util.*;
-
-public class HiddenSequences
-{
-  Hashtable hiddenSequences;
-  AlignmentI alignment;
-
-  public HiddenSequences(AlignmentI al)
-  {
-    alignment = al;
-  }
-
-  public int getSize()
-  {
-    return hiddenSequences == null ? 0 : hiddenSequences.size();
-  }
-
-  public void hideSequence(SequenceI sequence)
-  {
-    if(hiddenSequences==null)
-      hiddenSequences = new Hashtable();
-
-    int alignmentIndex = alignment.findIndex(sequence);
-    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
-
-    hiddenSequences.put(new Integer(alignmentIndex), sequence);
-
-    alignment.deleteSequence(sequence);
-  }
-
-  public void showSequence(int alignmentIndex)
-  {
-    SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
-    if(repSequence.getHiddenSequences()==null && alignmentIndex>0)
-      repSequence = alignment.getSequenceAt(alignmentIndex-1);
-    if(repSequence.getHiddenSequences()==null)
-      repSequence = null;
-
-    int start = adjustForHiddenSeqs(alignmentIndex-1);
-    int end = adjustForHiddenSeqs(alignmentIndex);
-
-    for(int index = end; index > start; index--)
-    {
-      SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(
-          index));
-
-      if(seq!=null)
-      {
-        alignment.getSequences().insertElementAt(seq, alignmentIndex);
-        if(repSequence!=null)
-        {
-          repSequence.showHiddenSequence(seq);
-        }
-      }
-    }
-  }
-
-  public SequenceI getHiddenSequence(int alignmentIndex)
-  {
-    return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));
-  }
-
-  public int findIndexWithoutHiddenSeqs(int alignmentIndex)
-  {
-    int index = 0;
-    int hiddenSeqs = 0;
-    while(index <= alignmentIndex)
-    {
-     if(hiddenSequences.containsKey(new Integer(index)))
-     {
-       hiddenSeqs ++;
-     }
-      index ++;
-    };
-
-    return (alignmentIndex - hiddenSeqs) ;
-  }
-
-  public int adjustForHiddenSeqs(int alignmentIndex)
-  {
-    int index = 0;
-    while(index <= alignmentIndex)
-    {
-     if(hiddenSequences.containsKey(new Integer(index)))
-     {
-       alignmentIndex ++;
-     }
-      index ++;
-    };
-
-    return alignmentIndex ;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package jalview.datamodel;
+
+import java.util.*;
+
+public class HiddenSequences
+{
+  Hashtable hiddenSequences;
+  AlignmentI alignment;
+
+  public HiddenSequences(AlignmentI al)
+  {
+    alignment = al;
+  }
+
+  public int getSize()
+  {
+    return hiddenSequences == null ? 0 : hiddenSequences.size();
+  }
+
+  public int getWidth()
+  {
+    Enumeration en = hiddenSequences.elements();
+    int width = 0;
+    while(en.hasMoreElements())
+    {
+      SequenceI seq = (SequenceI)en.nextElement();
+      if(seq.getLength()>width)
+        width = seq.getLength();
+    }
+    return width;
+  }
+
+  public void hideSequence(SequenceI sequence)
+  {
+    if(hiddenSequences==null)
+      hiddenSequences = new Hashtable();
+
+    int alignmentIndex = alignment.findIndex(sequence);
+    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+
+    hiddenSequences.put(new Integer(alignmentIndex), sequence);
+
+    alignment.deleteSequence(sequence);
+  }
+
+  public Vector showAll()
+  {
+   Vector revealedSeqs = new Vector();
+   for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)
+    {
+      Vector tmp = showSequence(i);
+      for(int t=0; t<tmp.size(); t++)
+        revealedSeqs.addElement(tmp.elementAt(t));
+    }
+    return revealedSeqs;
+  }
+
+  public Vector showSequence(int alignmentIndex)
+  {
+    Vector revealedSeqs = new Vector();
+    SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
+    if(repSequence!=null
+       && repSequence.getHiddenSequences()==null
+       && alignmentIndex>0)
+      repSequence = alignment.getSequenceAt(alignmentIndex-1);
+
+    if(repSequence!=null
+       && repSequence.getHiddenSequences()==null)
+      repSequence = null;
+
+    int start = adjustForHiddenSeqs(alignmentIndex-1);
+    int end = adjustForHiddenSeqs(alignmentIndex);
+
+    for(int index = end; index > start; index--)
+    {
+      SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(
+          index));
+
+
+      if(seq!=null)
+      {
+        revealedSeqs.addElement(seq);
+        alignment.getSequences().insertElementAt(seq, alignmentIndex);
+        if(repSequence!=null)
+        {
+          repSequence.showHiddenSequence(seq);
+        }
+      }
+    }
+
+    return revealedSeqs;
+  }
+
+  public Hashtable getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
+
+  public SequenceI getHiddenSequence(int alignmentIndex)
+  {
+    return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));
+  }
+
+  public int findIndexWithoutHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    int hiddenSeqs = 0;
+    while(index <= alignmentIndex)
+    {
+     if(hiddenSequences.containsKey(new Integer(index)))
+     {
+       hiddenSeqs ++;
+     }
+      index ++;
+    };
+
+    return (alignmentIndex - hiddenSeqs) ;
+  }
+
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    while(index <= alignmentIndex)
+    {
+     if(hiddenSequences.containsKey(new Integer(index)))
+     {
+       alignmentIndex ++;
+     }
+      index ++;
+    };
+
+    return alignmentIndex ;
+  }
+
+  public AlignmentI getFullAlignment()
+  {
+    int isize = alignment.getHeight()+hiddenSequences.size();
+    SequenceI [] seq = new Sequence[isize];
+
+    Enumeration en = hiddenSequences.keys();
+    while(en.hasMoreElements())
+    {
+      Integer key = (Integer)en.nextElement();
+      seq[key.intValue()] = (SequenceI)hiddenSequences.get(key);
+    }
+
+    int index = 0;
+    for(int i=0; i<isize; i++)
+    {
+      if(seq[i]!=null)
+      {
+        continue;
+      }
+
+      seq[i] = alignment.getSequenceAt(index);
+      index++;
+    }
+
+    return new Alignment(seq);
+  }
+
+  public boolean isHidden(SequenceI seq)
+  {
+    return hiddenSequences.contains(seq);
+  }
+}