X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=09c1b784878cf837e842cd0e183f9a1c0c666691;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=36c64989e80d9c9d85c6cb72bf10af213eac988c;hpb=32c056ffe34e60a1fde83bf4061af6e82d41f958;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 36c6498..09c1b78 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,174 +1,299 @@
-/*
- * 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 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 void showAll()
-  {
-   for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)
-     showSequence(i);
-  }
-
-  public void showSequence(int alignmentIndex)
-  {
-    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)
-      {
-        alignment.getSequences().insertElementAt(seq, alignmentIndex);
-        if(repSequence!=null)
-        {
-          repSequence.showHiddenSequence(seq);
-        }
-      }
-    }
-  }
-
-  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);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+public class HiddenSequences
+{
+  /**
+   * holds a list of hidden sequences associated with an alignment.
+   */
+  public SequenceI[] hiddenSequences;
+
+  AlignmentI alignment;
+
+  public HiddenSequences(AlignmentI al)
+  {
+    alignment = al;
+  }
+
+  public int getSize()
+  {
+    if (hiddenSequences == null)
+    {
+      return 0;
+    }
+    int count = 0;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        count++;
+      }
+    }
+
+    return count;
+  }
+
+  public int getWidth()
+  {
+    int width = 0;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null
+              && hiddenSequences[i].getLength() > width)
+      {
+        width = hiddenSequences[i].getLength();
+      }
+    }
+
+    return width;
+  }
+
+  /**
+   * Call this method if sequences are removed from the main alignment
+   */
+  public void adjustHeightSequenceDeleted(int seqIndex)
+  {
+    if (hiddenSequences == null)
+    {
+      return;
+    }
+
+    int alHeight = alignment.getHeight();
+
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+    int deletionIndex = adjustForHiddenSeqs(seqIndex);
+
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] == null)
+      {
+        continue;
+      }
+
+      if (i > deletionIndex)
+      {
+        tmp[i - 1] = hiddenSequences[i];
+      }
+      else
+      {
+        tmp[i] = hiddenSequences[i];
+      }
+    }
+
+    hiddenSequences = tmp;
+
+  }
+
+  /**
+   * Call this method if sequences are added to or removed from the main
+   * alignment
+   */
+  public void adjustHeightSequenceAdded()
+  {
+    if (hiddenSequences == null)
+    {
+      return;
+    }
+
+    int alHeight = alignment.getHeight();
+
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+    System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
+    hiddenSequences = tmp;
+  }
+
+  public void hideSequence(SequenceI sequence)
+  {
+    if (hiddenSequences == null)
+    {
+      hiddenSequences = new SequenceI[alignment.getHeight()];
+    }
+
+    int alignmentIndex = alignment.findIndex(sequence);
+    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+
+    if (hiddenSequences[alignmentIndex] != null)
+    {
+      System.out.println("ERROR!!!!!!!!!!!");
+    }
+
+    hiddenSequences[alignmentIndex] = sequence;
+
+    alignment.deleteSequence(sequence);
+  }
+
+  public List<SequenceI> showAll(
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        List<SequenceI> tmp = showSequence(i, hiddenRepSequences);
+        for (SequenceI seq : tmp)
+        {
+          revealedSeqs.add(seq);
+        }
+      }
+    }
+    return revealedSeqs;
+  }
+
+  public List<SequenceI> showSequence(int alignmentIndex,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
+    SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
+    if (repSequence != null && hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(repSequence))
+    {
+      hiddenRepSequences.remove(repSequence);
+      revealedSeqs.add(repSequence);
+    }
+
+    int start = adjustForHiddenSeqs(alignmentIndex - 1);
+    int end = adjustForHiddenSeqs(alignmentIndex);
+    if (end >= hiddenSequences.length)
+    {
+      end = hiddenSequences.length - 1;
+    }
+
+    List<SequenceI> asequences;
+    synchronized (asequences = alignment.getSequences())
+    {
+      for (int index = end; index > start; index--)
+      {
+        SequenceI seq = hiddenSequences[index];
+        hiddenSequences[index] = null;
+
+        if (seq != null)
+        {
+          if (seq.getLength() > 0)
+          {
+            revealedSeqs.add(seq);
+            asequences.add(alignmentIndex, seq);
+          }
+          else
+          {
+            System.out.println(seq.getName()
+                    + " has been deleted whilst hidden");
+          }
+        }
+
+      }
+    }
+
+    return revealedSeqs;
+  }
+
+  public SequenceI getHiddenSequence(int alignmentIndex)
+  {
+    return hiddenSequences[alignmentIndex];
+  }
+
+  public int findIndexWithoutHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    int hiddenSeqs = 0;
+    if (hiddenSequences.length <= alignmentIndex)
+    {
+      alignmentIndex = hiddenSequences.length - 1;
+    }
+
+    while (index <= alignmentIndex)
+    {
+      if (hiddenSequences[index] != null)
+      {
+        hiddenSeqs++;
+      }
+      index++;
+    }
+    ;
+
+    return (alignmentIndex - hiddenSeqs);
+  }
+
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    int index = 0;
+    int hSize = hiddenSequences.length;
+    while (index <= alignmentIndex && index < hSize)
+    {
+      if (hiddenSequences[index] != null)
+      {
+        alignmentIndex++;
+      }
+      index++;
+    }
+    ;
+
+    return alignmentIndex;
+  }
+
+  public AlignmentI getFullAlignment()
+  {
+    int isize = hiddenSequences.length;
+    SequenceI[] seq = new Sequence[isize];
+
+    int index = 0;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        seq[i] = hiddenSequences[i];
+      }
+      else
+      {
+        seq[i] = alignment.getSequenceAt(index);
+        index++;
+      }
+    }
+    Alignment fAlignmt = new Alignment(seq);
+    fAlignmt.annotations = alignment.getAlignmentAnnotation();
+    fAlignmt.alignmentProperties = alignment.getProperties();
+    fAlignmt.groups = alignment.getGroups();
+    fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+
+    return fAlignmt;
+  }
+
+  public boolean isHidden(SequenceI seq)
+  {
+    if (hiddenSequences != null)
+    {
+      for (int i = 0; i < hiddenSequences.length; i++)
+      {
+        if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+        {
+          return true;
+        }
+      }
+    }
+
+    return false;
+  }
+}