X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=17348c2cf08763271f3bf1fc3300e8293f209fbb;hb=341e759bcdf94d50e58217f55a87f25a44eeef54;hp=9a6d022b2126db36ab253f88ef665a6bd2b235f8;hpb=ef23315db576f5451de0fcb850f645c5db222b20;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 9a6d022..17348c2 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,28 +1,37 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.
- * 
+ * 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/>.
+ * 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.*;
-
-import java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
 
-import jalview.analysis.*;
-import jalview.schemes.*;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
 
 /**
  * Collects a set contiguous ranges on a set of sequences
@@ -54,7 +63,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private Vector sequences = new Vector();
+  private Vector<SequenceI> sequences = new Vector<SequenceI>();
 
   /**
    * representative sequence for this group (if any)
@@ -91,12 +100,12 @@ public class SequenceGroup implements AnnotatedCollectionI
    * consensus calculation property
    */
   private boolean showSequenceLogo = false;
+
   /**
    * flag indicating if logo should be rendered normalised
    */
   private boolean normaliseSequenceLogo;
 
-
   /**
    * @return the includeAllConsSymbols
    */
@@ -152,7 +161,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     if (seqsel != null)
     {
       sequences = new Vector();
-      Enumeration sq = seqsel.sequences.elements();
+      Enumeration<SequenceI> sq = seqsel.sequences.elements();
       while (sq.hasMoreElements())
       {
         sequences.addElement(sq.nextElement());
@@ -285,7 +294,15 @@ public class SequenceGroup implements AnnotatedCollectionI
     return eres;
   }
 
-  public Vector getSequences(Hashtable hiddenReps)
+  @Override
+  public List<SequenceI> getSequences()
+  {
+    return sequences;
+  }
+
+  @Override
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     if (hiddenReps == null)
     {
@@ -294,17 +311,16 @@ public class SequenceGroup implements AnnotatedCollectionI
     else
     {
       Vector allSequences = new Vector();
-      SequenceI seq, seq2;
+      SequenceI seq;
       for (int i = 0; i < sequences.size(); i++)
       {
-        seq = (SequenceI) sequences.elementAt(i);
+        seq = sequences.elementAt(i);
         allSequences.addElement(seq);
         if (hiddenReps.containsKey(seq))
         {
-          SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
-          for (int h = 0; h < hsg.getSize(); h++)
+          SequenceCollectionI hsg = hiddenReps.get(seq);
+          for (SequenceI seq2 : hsg.getSequences())
           {
-            seq2 = hsg.getSequenceAt(h);
             if (seq2 != seq && !allSequences.contains(seq2))
             {
               allSequences.addElement(seq2);
@@ -317,20 +333,15 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
-  public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+  public SequenceI[] getSequencesAsArray(
+          Map<SequenceI, SequenceCollectionI> map)
   {
-    Vector tmp = getSequences(hiddenReps);
+    List<SequenceI> tmp = getSequences(map);
     if (tmp == null)
     {
       return null;
     }
-    SequenceI[] result = new SequenceI[tmp.size()];
-    for (int i = 0; i < result.length; i++)
-    {
-      result[i] = (SequenceI) tmp.elementAt(i);
-    }
-
-    return result;
+    return tmp.toArray(new SequenceI[tmp.size()]);
   }
 
   /**
@@ -468,12 +479,29 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * Max Gaps Threshold for performing a conservation calculation TODO: make
-   * this a configurable property - or global to an alignment view
+   * Max Gaps Threshold (percent) for performing a conservation calculation
    */
   private int consPercGaps = 25;
 
   /**
+   * @return Max Gaps Threshold for performing a conservation calculation
+   */
+  public int getConsPercGaps()
+  {
+    return consPercGaps;
+  }
+
+  /**
+   * set Max Gaps Threshold (percent) for performing a conservation calculation
+   * 
+   * @param consPercGaps
+   */
+  public void setConsPercGaps(int consPercGaps)
+  {
+    this.consPercGaps = consPercGaps;
+  }
+
+  /**
    * calculate residue conservation for group - but only if necessary.
    */
   public void recalcConservation()
@@ -482,26 +510,17 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       return;
     }
-    if (cs!=null)
-    {
-      cs.alignmentChanged(this);
-    }
     try
     {
       Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
-        _updateConsensusRow(cnsns);
+        _updateConsensusRow(cnsns, sequences.size());
       }
       if (cs != null)
       {
         cs.setConsensus(cnsns);
-
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-        }
       }
 
       if ((conservation != null)
@@ -521,15 +540,13 @@ public class SequenceGroup implements AnnotatedCollectionI
           if (cs.conservationApplied())
           {
             cs.setConservation(c);
-
-            if (cs instanceof ClustalxColourScheme)
-            {
-              ((ClustalxColourScheme) cs).resetClustalX(sequences,
-                      getWidth());
-            }
           }
         }
       }
+      if (cs != null)
+      {
+        cs.alignmentChanged(context != null ? context : this, null);
+      }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
@@ -560,7 +577,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public Hashtable[] consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns)
+  private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
   {
     if (consensus == null)
     {
@@ -577,9 +594,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
 
     AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
-            ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
-                                                      // for
-                                                      // ignoreGapsInConsensusCalculation);
+            ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+                                                            // container
+    // for
+    // ignoreGapsInConsensusCalculation);
   }
 
   /**
@@ -620,20 +638,21 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * 
+   * @return the first column selected by this group. Runs from 0<=i<N_cols
    */
+  @Override
   public int getStartRes()
   {
     return startRes;
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return the groups last selected column. Runs from 0<=i<N_cols
    */
+  @Override
   public int getEndRes()
   {
     return endRes;
@@ -679,7 +698,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public SequenceI getSequenceAt(int i)
   {
-    return (SequenceI) sequences.elementAt(i);
+    return sequences.elementAt(i);
   }
 
   /**
@@ -750,17 +769,18 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
     // MC This needs to get reset when characters are inserted and deleted
     if (sequences.size() > 0)
     {
-      width = ((SequenceI) sequences.elementAt(0)).getLength();
+      width = sequences.elementAt(0).getLength();
     }
 
     for (int i = 1; i < sequences.size(); i++)
     {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
+      SequenceI seq = sequences.elementAt(i);
 
       if (seq.getLength() > width)
       {
@@ -956,18 +976,19 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @param alignment
    *          (may not be null)
-   * @param hashtable
+   * @param map
    *          (may be null)
    * @return new group containing sequences common to this group and alignment
    */
-  public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable)
+  public SequenceGroup intersect(AlignmentI alignment,
+          Map<SequenceI, SequenceCollectionI> map)
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
     sgroup.sequences = new Vector();
     for (int s = 0; insect != null && s < insect.length; s++)
     {
-      if (hashtable == null || hashtable.containsKey(insect[s]))
+      if (map == null || map.containsKey(insect[s]))
       {
         sgroup.sequences.addElement(insect[s]);
       }
@@ -1041,12 +1062,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
               100f, AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
+      consensus.groupRef = this;
+      consensus.label = "Consensus for " + getName();
+      consensus.description = "Percent Identity";
     }
-    consensus.hasText = true;
-    consensus.autoCalculated = true;
-    consensus.groupRef = this;
-    consensus.label = "Consensus for " + getName();
-    consensus.description = "Percent Identity";
     return consensus;
   }
 
@@ -1178,55 +1199,113 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   /**
    * set flag indicating if logo should be normalised when rendered
+   * 
    * @param norm
    */
   public void setNormaliseSequenceLogo(boolean norm)
   {
-    normaliseSequenceLogo=norm;
+    normaliseSequenceLogo = norm;
   }
+
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
   }
+
   @Override
   /**
    * returns a new array with all annotation involving this group
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
   {
-    // TODO add in other methods like 'getAlignmentAnnotation(String label), etc'
+    // TODO add in other methods like 'getAlignmentAnnotation(String label),
+    // etc'
     ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
-    for (SequenceI seq:(Vector<SequenceI>)sequences)
+    for (SequenceI seq : sequences)
     {
-      for (AlignmentAnnotation al: seq.getAnnotation())
+      AlignmentAnnotation[] aa = seq.getAnnotation();
+      if (aa != null)
       {
-        if (al.groupRef==this)
+        for (AlignmentAnnotation al : aa)
         {
-          annot.add(al);
+          if (al.groupRef == this)
+          {
+            annot.add(al);
+          }
         }
       }
     }
-    if (consensus!=null)
+    if (consensus != null)
     {
       annot.add(consensus);
     }
-    if (conservation!=null)
+    if (conservation != null)
     {
       annot.add(conservation);
     }
     return annot.toArray(new AlignmentAnnotation[0]);
   }
+
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a:getAlignmentAnnotation())
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a : getAlignmentAnnotation())
     {
-      if (a.getCalcId()==calcId)
+      if (a.getCalcId() == calcId)
       {
         aa.add(a);
       }
     }
     return aa;
   }
+
+  /**
+   * Answer true if any annotation matches the calcId passed in (if not null).
+   * 
+   * @param calcId
+   * @return
+   */
+  public boolean hasAnnotation(String calcId)
+  {
+    if (calcId != null && !"".equals(calcId))
+    {
+      for (AlignmentAnnotation a : getAlignmentAnnotation())
+      {
+        if (a.getCalcId() == calcId)
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
+  public void clear()
+  {
+    sequences.clear();
+  }
+
+  private AnnotatedCollectionI context;
+
+  /**
+   * set the alignment or group context for this group
+   * 
+   * @param context
+   */
+  public void setContext(AnnotatedCollectionI context)
+  {
+    this.context = context;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+   */
+  @Override
+  public AnnotatedCollectionI getContext()
+  {
+    return context;
+  }
 }