X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=9d3e6db930ab5688972d73748b3e9e67e8ff9f08;hb=5f7810e6c809dbc218fed92b811999807dec148a;hp=c0d8f5e64910e5da2b493ce6638c1b11c36cd9cf;hpb=1da593c9a6e87837ebe95e22cb138c8a682ddab5;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c0d8f5e..9d3e6db 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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
+ * 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/>.
  */
 package jalview.datamodel;
 
@@ -46,23 +45,27 @@ public class SequenceGroup
   boolean displayText = true;
 
   boolean colourText = false;
+
   /**
    * after Olivier's non-conserved only character display
    */
   boolean showUnconserved = false;
-  
+
   /**
    * group members
    */
   private Vector sequences = new Vector();
+
   /**
    * representative sequence for this group (if any)
    */
   private SequenceI seqrep = null;
+
   int width = -1;
 
   /**
-   * Colourscheme applied to group if any */
+   * Colourscheme applied to group if any
+   */
   public ColourSchemeI cs;
 
   int startRes = 0;
@@ -80,6 +83,24 @@ public class SequenceGroup
   public Color textColour2 = Color.white;
 
   /**
+   * consensus calculation property
+   */
+  private boolean ignoreGapsInConsensus = true;
+
+  /**
+   * consensus calculation property
+   */
+  private boolean showSequenceLogo = false;
+
+  /**
+   * @return the includeAllConsSymbols
+   */
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
+  /**
    * Creates a new SequenceGroup object.
    */
   public SequenceGroup()
@@ -97,9 +118,9 @@ public class SequenceGroup
    * @param displayText
    * @param colourText
    * @param start
-   *                first column of group
+   *          first column of group
    * @param end
-   *                last column of group
+   *          last column of group
    */
   public SequenceGroup(Vector sequences, String groupName,
           ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
@@ -115,20 +136,24 @@ public class SequenceGroup
     endRes = end;
     recalcConservation();
   }
+
   /**
    * copy constructor
+   * 
    * @param seqsel
    */
   public SequenceGroup(SequenceGroup seqsel)
   {
-    if (seqsel!=null)
+    if (seqsel != null)
     {
-      sequences=new Vector();
+      sequences = new Vector();
       Enumeration sq = seqsel.sequences.elements();
-      while (sq.hasMoreElements()) { 
-        sequences.addElement(sq.nextElement()); 
-      };
-      if (seqsel.groupName!=null)
+      while (sq.hasMoreElements())
+      {
+        sequences.addElement(sq.nextElement());
+      }
+      ;
+      if (seqsel.groupName != null)
       {
         groupName = new String(seqsel.groupName);
       }
@@ -137,8 +162,8 @@ public class SequenceGroup
       colourText = seqsel.colourText;
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
-      cs =seqsel.cs;
-      if (seqsel.description!=null)
+      cs = seqsel.cs;
+      if (seqsel.description != null)
         description = new String(seqsel.description);
       hidecols = seqsel.hidecols;
       hidereps = seqsel.hidereps;
@@ -149,9 +174,10 @@ public class SequenceGroup
       textColour2 = seqsel.textColour2;
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
-      if (seqsel.conserve!=null)
+      ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+      if (seqsel.conserve != null)
       {
-        recalcConservation(); // safer than 
+        recalcConservation(); // safer than
         // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
       }
     }
@@ -229,7 +255,7 @@ public class SequenceGroup
    * If sequence ends in gaps, the end residue can be correctly calculated here
    * 
    * @param seq
-   *                SequenceI
+   *          SequenceI
    * @return int
    */
   public int findEndRes(SequenceI seq)
@@ -306,7 +332,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param col
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -340,7 +366,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param col
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -379,11 +405,12 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setName(String name)
   {
     groupName = name;
+    // TODO: URGENT: update dependent objects (annotation row)
   }
 
   public void setDescription(String desc)
@@ -405,7 +432,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setConservation(Conservation c)
   {
@@ -416,9 +443,9 @@ public class SequenceGroup
    * Add s to this sequence group
    * 
    * @param s
-   *                alignment sequence to be added
+   *          alignment sequence to be added
    * @param recalc
-   *                true means Group's conservation should be recalculated
+   *          true means Group's conservation should be recalculated
    */
   public void addSequence(SequenceI s, boolean recalc)
   {
@@ -434,38 +461,60 @@ public class SequenceGroup
   }
 
   /**
-   * calculate residue conservation for group
+   * Max Gaps Threshold for performing a conservation calculation TODO: make
+   * this a configurable property - or global to an alignment view
+   */
+  private int consPercGaps = 25;
+
+  /**
+   * calculate residue conservation for group - but only if necessary.
    */
   public void recalcConservation()
   {
-    if (cs == null)
+    if (cs == null && consensus == null && conservation == null)
     {
       return;
     }
 
     try
     {
-      cs.setConsensus(AAFrequency
-              .calculate(sequences, startRes, endRes + 1));
-
-      if (cs instanceof ClustalxColourScheme)
+      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+              endRes + 1, showSequenceLogo);
+      if (consensus != null)
+      {
+        _updateConsensusRow(cnsns);
+      }
+      if (cs != null)
       {
-        ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        cs.setConsensus(cnsns);
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        }
       }
 
-      if (cs.conservationApplied())
+      if ((conservation != null)
+              || (cs != null && cs.conservationApplied()))
       {
         Conservation c = new Conservation(groupName,
                 ResidueProperties.propHash, 3, sequences, startRes,
                 endRes + 1);
         c.calculate();
-        c.verdict(false, 25);
-
-        cs.setConservation(c);
-
-        if (cs instanceof ClustalxColourScheme)
+        c.verdict(false, consPercGaps);
+        if (conservation != null)
         {
-          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+          _updateConservationRow(c);
+        }
+        if (cs != null)
+        {
+          cs.setConservation(c);
+
+          if (cs instanceof ClustalxColourScheme)
+          {
+            ((ClustalxColourScheme) cs)
+                    .resetClustalX(sequences, getWidth());
+          }
         }
       }
     } catch (java.lang.OutOfMemoryError err)
@@ -476,13 +525,56 @@ public class SequenceGroup
 
   }
 
+  private void _updateConservationRow(Conservation c)
+  {
+    if (conservation == null)
+    {
+      getConservation();
+    }
+    // update Labels
+    conservation.label = "Conservation for " + getName();
+    conservation.description = "Conservation for group " + getName()
+            + " less than " + consPercGaps + "% gaps";
+    // preserve width if already set
+    int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
+            : endRes + 1)
+            : endRes + 1;
+    conservation.annotations = null;
+    conservation.annotations = new Annotation[aWidth]; // should be alignment
+                                                       // width
+    c.completeAnnotations(conservation, null, startRes, endRes + 1);
+  }
+
+  public Hashtable[] consensusData = null;
+
+  private void _updateConsensusRow(Hashtable[] cnsns)
+  {
+    if (consensus == null)
+    {
+      getConsensus();
+    }
+    consensus.label = "Consensus for " + getName();
+    consensus.description = "Percent Identity";
+    consensusData = cnsns;
+    // preserve width if already set
+    int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
+            : endRes + 1)
+            : endRes + 1;
+    consensus.annotations = null;
+    consensus.annotations = new Annotation[aWidth]; // should be alignment width
+
+    AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
+            ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+                                                      // for
+                                                      // ignoreGapsInConsensusCalculation);
+  }
+
   /**
-   * DOCUMENT ME!
-   * 
    * @param s
-   *                DOCUMENT ME!
+   *          sequence to either add or remove from group
    * @param recalc
-   *                DOCUMENT ME!
+   *          flag passed to delete/addSequence to indicate if group properties
+   *          should be recalculated
    */
   public void addOrRemove(SequenceI s, boolean recalc)
   {
@@ -500,9 +592,9 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param recalc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
@@ -538,7 +630,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setStartRes(int i)
   {
@@ -549,7 +641,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setEndRes(int i)
   {
@@ -570,7 +662,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -583,7 +675,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setColourText(boolean state)
   {
@@ -604,7 +696,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDisplayText(boolean state)
   {
@@ -625,7 +717,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDisplayBoxes(boolean state)
   {
@@ -672,7 +764,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setOutlineColour(Color c)
   {
@@ -692,11 +784,13 @@ public class SequenceGroup
   /**
    * 
    * returns the sequences in the group ordered by the ordering given by al.
-   * this used to return an array with null entries regardless, new behaviour is below.
-   * TODO: verify that this does not affect use in applet or application
+   * this used to return an array with null entries regardless, new behaviour is
+   * below. TODO: verify that this does not affect use in applet or application
+   * 
    * @param al
-   *                Alignment
-   * @return SequenceI[] intersection of sequences in group with al, ordered by al, or null if group does not intersect with al
+   *          Alignment
+   * @return SequenceI[] intersection of sequences in group with al, ordered by
+   *         al, or null if group does not intersect with al
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al)
   {
@@ -713,15 +807,15 @@ public class SequenceGroup
         seqs[index++] = al.getSequenceAt(i);
       }
     }
-    if (index==0)
+    if (index == 0)
     {
       return null;
     }
-    if (index<seqs.length)
+    if (index < seqs.length)
     {
       SequenceI[] dummy = seqs;
       seqs = new SequenceI[index];
-      while (--index>=0)
+      while (--index >= 0)
       {
         seqs[index] = dummy[index];
         dummy[index] = null;
@@ -740,7 +834,7 @@ public class SequenceGroup
 
   /**
    * @param idColour
-   *                the idColour to set
+   *          the idColour to set
    */
   public void setIdColour(Color idColour)
   {
@@ -756,14 +850,17 @@ public class SequenceGroup
   }
 
   /**
-   * set the representative sequence for this group.
-   * Note - this affects the interpretation of the Hidereps attribute.
-   * @param seqrep the seqrep to set (null means no sequence representative)
+   * set the representative sequence for this group. Note - this affects the
+   * interpretation of the Hidereps attribute.
+   * 
+   * @param seqrep
+   *          the seqrep to set (null means no sequence representative)
    */
   public void setSeqrep(SequenceI seqrep)
   {
     this.seqrep = seqrep;
   }
+
   /**
    * 
    * @return true if group has a sequence representative
@@ -772,39 +869,48 @@ public class SequenceGroup
   {
     return seqrep != null;
   }
+
   /**
    * visibility of rows or represented rows covered by group
    */
-  private boolean hidereps=false;
+  private boolean hidereps = false;
+
   /**
-   * set visibility of sequences covered by (if no sequence representative is defined) 
-   * or represented by this group.
+   * set visibility of sequences covered by (if no sequence representative is
+   * defined) or represented by this group.
+   * 
    * @param visibility
    */
   public void setHidereps(boolean visibility)
   {
     hidereps = visibility;
   }
+
   /**
    * 
-   * @return true if sequences represented (or covered) by this group should be hidden
+   * @return true if sequences represented (or covered) by this group should be
+   *         hidden
    */
   public boolean isHidereps()
   {
     return hidereps;
   }
+
   /**
    * visibility of columns intersecting this group
    */
-  private boolean hidecols=false;
+  private boolean hidecols = false;
+
   /**
    * set intended visibility of columns covered by this group
+   * 
    * @param visibility
    */
   public void setHideCols(boolean visibility)
   {
     hidecols = visibility;
   }
+
   /**
    * 
    * @return true if columns covered by group should be hidden
@@ -813,33 +919,38 @@ public class SequenceGroup
   {
     return hidecols;
   }
+
   /**
-   * create a new sequence group from the intersection of this group
-   * with an alignment Hashtable of hidden representatives
+   * create a new sequence group from the intersection of this group with an
+   * alignment Hashtable of hidden representatives
    * 
-   * @param alignment (may not be null)
-   * @param hashtable (may be null)
+   * @param alignment
+   *          (may not be null)
+   * @param hashtable
+   *          (may be null)
    * @return new group containing sequences common to this group and alignment
    */
   public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable)
   {
     SequenceGroup sgroup = new SequenceGroup(this);
-    SequenceI[] insect=getSequencesInOrder(alignment);
+    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]))
-              {
-      sgroup.sequences.addElement(insect[s]); }
-    }
-    //Enumeration en =getSequences(hashtable).elements();
-    //while (en.hasMoreElements())
-   // {
-   //   SequenceI elem = (SequenceI) en.nextElement();
-   //   if (alignment.getSequences().contains(elem))
-   //   {
-   //     sgroup.addSequence(elem, false);
-   //   }
-   // }
+    for (int s = 0; insect != null && s < insect.length; s++)
+    {
+      if (hashtable == null || hashtable.containsKey(insect[s]))
+      {
+        sgroup.sequences.addElement(insect[s]);
+      }
+    }
+    // Enumeration en =getSequences(hashtable).elements();
+    // while (en.hasMoreElements())
+    // {
+    // SequenceI elem = (SequenceI) en.nextElement();
+    // if (alignment.getSequences().contains(elem))
+    // {
+    // sgroup.addSequence(elem, false);
+    // }
+    // }
     return sgroup;
   }
 
@@ -852,17 +963,157 @@ public class SequenceGroup
   }
 
   /**
-   * @param showUnconserved the showUnconserved to set
+   * @param showUnconserved
+   *          the showUnconserved to set
    */
   public void setShowunconserved(boolean displayNonconserved)
   {
     this.showUnconserved = displayNonconserved;
   }
 
+  AlignmentAnnotation consensus = null, conservation = null;
+
+  /**
+   * flag indicating if consensus histogram should be rendered
+   */
+  private boolean showConsensusHistogram;
+
+  /**
+   * 
+   * @return automatically calculated consensus row
+   */
   public AlignmentAnnotation getConsensus()
   {
     // TODO get or calculate and get consensus annotation row for this group
-    this.conserve.getConsSequence();
-    return null;
+    int aWidth = this.getWidth();
+    // pointer
+    // possibility
+    // here.
+    if (aWidth < 0)
+    {
+      return null;
+    }
+    if (consensus == null)
+    {
+      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";
+    return consensus;
+  }
+
+  /**
+   * get the conservation annotation row for this group
+   * 
+   * @return autoCalculated annotation row
+   */
+  public AlignmentAnnotation getConservationRow()
+  {
+    if (conservation == null)
+    {
+      conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+              11f, AlignmentAnnotation.BAR_GRAPH);
+    }
+
+    conservation.hasText = true;
+    conservation.autoCalculated = true;
+    conservation.groupRef = this;
+    conservation.label = "Conservation for " + getName();
+    conservation.description = "Conservation for group " + getName()
+            + " less than " + consPercGaps + "% gaps";
+    return conservation;
+  }
+
+  /**
+   * 
+   * @return true if annotation rows have been instantiated for this group
+   */
+  public boolean hasAnnotationRows()
+  {
+    return consensus != null || conservation != null;
+  }
+
+  public SequenceI getConsensusSeq()
+  {
+    getConsensus();
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      if (consensus.annotations[i] != null)
+      {
+        if (consensus.annotations[i].description.charAt(0) == '[')
+        {
+          seqs.append(consensus.annotations[i].description.charAt(1));
+        }
+        else
+        {
+          seqs.append(consensus.annotations[i].displayCharacter);
+        }
+      }
+    }
+
+    SequenceI sq = new Sequence("Group" + getName() + " Consensus", seqs
+            .toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensus) ? " without gaps" : ""));
+    return sq;
+  }
+
+  public void setIgnoreGapsConsensus(boolean state)
+  {
+    if (this.ignoreGapsInConsensus != state && consensus != null)
+    {
+      ignoreGapsInConsensus = state;
+      recalcConservation();
+    }
+    ignoreGapsInConsensus = state;
+  }
+
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensus;
+  }
+
+  /**
+   * @param includeAllConsSymbols
+   *          the includeAllConsSymbols to set
+   */
+  public void setIncludeAllConsSymbols(boolean includeAllConsSymbols)
+  {
+    if (this.showSequenceLogo != includeAllConsSymbols && consensus != null)
+    {
+      this.showSequenceLogo = includeAllConsSymbols;
+      recalcConservation();
+    }
+    this.showSequenceLogo = includeAllConsSymbols;
+  }
+
+  /**
+   * 
+   * @param showConsHist
+   *          flag indicating if the consensus histogram for this group should
+   *          be rendered
+   */
+  public void setShowConsensusHistogram(boolean showConsHist)
+  {
+
+    if (showConsensusHistogram != showConsHist && consensus != null)
+    {
+      this.showConsensusHistogram = showConsHist;
+      recalcConservation();
+    }
+    this.showConsensusHistogram = showConsHist;
+  }
+
+  /**
+   * @return the showConsensusHistogram
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return showConsensusHistogram;
   }
 }