X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=bb075aacc819152065b97558424878b47c8eff23;hb=5c212e384ee48b37d899cc88fc3d12c5028cc3b4;hp=bae586312eccc0aced6304388cc1d431958e1734;hpb=3de2a606531d25cfb36e42276c44e75dca32f591;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index bae5863..bb075aa 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
@@ -26,30 +26,52 @@ import jalview.analysis.*;
 import jalview.schemes.*;
 
 /**
- * DOCUMENT ME!
- *
+ * Collects a set contiguous ranges on a set of sequences
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class SequenceGroup
 {
   String groupName;
+
   String description;
+
   Conservation conserve;
+
   Vector aaFrequency;
+
   boolean displayBoxes = true;
+
   boolean displayText = true;
-  boolean colourText = true;
+
+  boolean colourText = false;
+  /**
+   * group members
+   */
   private Vector sequences = new Vector();
+  /**
+   * representative sequence for this group (if any)
+   */
+  private SequenceI seqrep = null;
   int width = -1;
 
-  /** DOCUMENT ME!! */
+  /**
+   * Colourscheme applied to group if any */
   public ColourSchemeI cs;
+
   int startRes = 0;
+
   int endRes = 0;
-  Color outlineColour = Color.black;
+
+  public Color outlineColour = Color.black;
+
+  public Color idColour = null;
+
   public int thresholdTextColour = 0;
+
   public Color textColour = Color.black;
+
   public Color textColour2 = Color.white;
 
   /**
@@ -62,20 +84,21 @@ public class SequenceGroup
 
   /**
    * Creates a new SequenceGroup object.
-   *
-   * @param sequences DOCUMENT ME!
-   * @param groupName DOCUMENT ME!
-   * @param scheme DOCUMENT ME!
-   * @param displayBoxes DOCUMENT ME!
-   * @param displayText DOCUMENT ME!
-   * @param colourText DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
+   * 
+   * @param sequences
+   * @param groupName
+   * @param scheme
+   * @param displayBoxes
+   * @param displayText
+   * @param colourText
+   * @param start
+   *                first column of group
+   * @param end
+   *                last column of group
    */
   public SequenceGroup(Vector sequences, String groupName,
-                       ColourSchemeI scheme, boolean displayBoxes,
-                       boolean displayText,
-                       boolean colourText, int start, int end)
+          ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
+          boolean colourText, int start, int end)
   {
     this.sequences = sequences;
     this.groupName = groupName;
@@ -94,40 +117,73 @@ public class SequenceGroup
     SequenceI[] seqs = new SequenceI[iSize];
     SequenceI[] inorder = getSequencesInOrder(align);
 
-    for (int i = 0; i < iSize; i++)
+    for (int i = 0, ipos = 0; i < inorder.length; i++)
     {
       SequenceI seq = inorder[i];
 
-      seqs[i] = new Sequence(seq.getName(),
-                             seq.getSequence(startRes, endRes + 1),
-                             seq.findPosition(startRes),
-                             findEndRes(seq));
-
-      seqs[i].setDescription(seq.getDescription());
-      seqs[i].setDBRef(seq.getDBRef());
-      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
-      if (seq.getDatasetSequence() != null)
+      seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+      if (seqs[ipos] != null)
       {
-        seqs[i].setDatasetSequence(seq.getDatasetSequence());
-      }
+        seqs[ipos].setDescription(seq.getDescription());
+        seqs[ipos].setDBRef(seq.getDBRef());
+        seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        if (seq.getDatasetSequence() != null)
+        {
+          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+        }
 
-      if (seq.getAnnotation() != null)
-      {
-        for (int a = 0; a < seq.getAnnotation().length; a++)
+        if (seq.getAnnotation() != null)
         {
-          seqs[i].addAlignmentAnnotation(new AlignmentAnnotation(seq.getAnnotation()[a]));
+          AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
+          // Only copy annotation that is either a score or referenced by the
+          // alignment's annotation vector
+          for (int a = 0; a < seq.getAnnotation().length; a++)
+          {
+            AlignmentAnnotation tocopy = seq.getAnnotation()[a];
+            if (alann != null)
+            {
+              boolean found = false;
+              for (int pos = 0; pos < alann.length; pos++)
+              {
+                if (alann[pos] == tocopy)
+                {
+                  found = true;
+                  break;
+                }
+              }
+              if (!found)
+                continue;
+            }
+            AlignmentAnnotation newannot = new AlignmentAnnotation(seq
+                    .getAnnotation()[a]);
+            newannot.restrict(startRes, endRes);
+            newannot.setSequenceRef(seqs[ipos]);
+            newannot.adjustForAlignment();
+            seqs[ipos].addAlignmentAnnotation(newannot);
+          }
         }
+        ipos++;
+      }
+      else
+      {
+        iSize--;
       }
     }
-
+    if (iSize != inorder.length)
+    {
+      SequenceI[] nseqs = new SequenceI[iSize];
+      System.arraycopy(seqs, 0, nseqs, 0, iSize);
+      seqs = nseqs;
+    }
     return seqs;
 
   }
 
   /**
-   * If sequence ends in gaps, the end residue can
-   * be correctly calculated here
-   * @param seq SequenceI
+   * If sequence ends in gaps, the end residue can be correctly calculated here
+   * 
+   * @param seq
+   *                SequenceI
    * @return int
    */
   public int findEndRes(SequenceI seq)
@@ -138,7 +194,7 @@ public class SequenceGroup
     for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
     {
       ch = seq.getCharAt(j);
-      if (!jalview.util.Comparison.isGap( (ch)))
+      if (!jalview.util.Comparison.isGap((ch)))
       {
         eres++;
       }
@@ -172,8 +228,7 @@ public class SequenceGroup
           for (int h = 0; h < hsg.getSize(); h++)
           {
             seq2 = hsg.getSequenceAt(h);
-            if (seq2 != seq
-                && !allSequences.contains(seq2))
+            if (seq2 != seq && !allSequences.contains(seq2))
             {
               allSequences.addElement(seq2);
             }
@@ -203,9 +258,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param col DOCUMENT ME!
-   *
+   * 
+   * @param col
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean adjustForRemoveLeft(int col)
@@ -236,9 +292,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param col DOCUMENT ME!
-   *
+   * 
+   * @param col
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean adjustForRemoveRight(int col)
@@ -259,7 +316,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getName()
@@ -274,8 +331,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param name DOCUMENT ME!
+   * 
+   * @param name
+   *                DOCUMENT ME!
    */
   public void setName(String name)
   {
@@ -289,7 +347,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Conservation getConservation()
@@ -299,8 +357,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
    */
   public void setConservation(Conservation c)
   {
@@ -308,10 +367,12 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * Add s to this sequence group
+   * 
+   * @param s
+   *                alignment sequence to be added
+   * @param recalc
+   *                true means Group's conservation should be recalculated
    */
   public void addSequence(SequenceI s, boolean recalc)
   {
@@ -327,7 +388,7 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
+   * calculate residue conservation for group
    */
   public void recalcConservation()
   {
@@ -338,19 +399,19 @@ public class SequenceGroup
 
     try
     {
-      cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
+      cs.setConsensus(AAFrequency
+              .calculate(sequences, startRes, endRes + 1));
 
       if (cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
       }
 
       if (cs.conservationApplied())
       {
         Conservation c = new Conservation(groupName,
-                                          ResidueProperties.propHash, 3,
-                                          sequences,
-                                          startRes, endRes + 1);
+                ResidueProperties.propHash, 3, sequences, startRes,
+                endRes + 1);
         c.calculate();
         c.verdict(false, 25);
 
@@ -358,13 +419,12 @@ public class SequenceGroup
 
         if (cs instanceof ClustalxColourScheme)
         {
-          ( (ClustalxColourScheme) cs).resetClustalX(sequences,
-              getWidth());
+          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
         }
       }
-    }
-    catch (java.lang.OutOfMemoryError err)
+    } catch (java.lang.OutOfMemoryError err)
     {
+      // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
 
@@ -372,9 +432,11 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param recalc
+   *                DOCUMENT ME!
    */
   public void addOrRemove(SequenceI s, boolean recalc)
   {
@@ -390,9 +452,11 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param recalc
+   *                DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
@@ -406,7 +470,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getStartRes()
@@ -416,7 +480,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getEndRes()
@@ -426,8 +490,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
    */
   public void setStartRes(int i)
   {
@@ -436,8 +501,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
    */
   public void setEndRes(int i)
   {
@@ -446,7 +512,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getSize()
@@ -456,9 +522,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceI getSequenceAt(int i)
@@ -468,8 +535,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setColourText(boolean state)
   {
@@ -478,7 +546,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getColourText()
@@ -488,8 +556,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setDisplayText(boolean state)
   {
@@ -498,7 +567,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getDisplayText()
@@ -508,8 +577,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
    */
   public void setDisplayBoxes(boolean state)
   {
@@ -518,7 +588,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getDisplayBoxes()
@@ -528,7 +598,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getWidth()
@@ -536,7 +606,7 @@ public class SequenceGroup
     // MC This needs to get reset when characters are inserted and deleted
     if (sequences.size() > 0)
     {
-      width = ( (SequenceI) sequences.elementAt(0)).getLength();
+      width = ((SequenceI) sequences.elementAt(0)).getLength();
     }
 
     for (int i = 1; i < sequences.size(); i++)
@@ -554,8 +624,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
    */
   public void setOutlineColour(Color c)
   {
@@ -564,7 +635,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Color getOutlineColour()
@@ -573,10 +644,11 @@ public class SequenceGroup
   }
 
   /**
-   *
+   * 
    * returns the sequences in the group ordered by the ordering given by al
-   *
-   * @param al Alignment
+   * 
+   * @param al
+   *                Alignment
    * @return SequenceI[]
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al)
@@ -597,4 +669,88 @@ public class SequenceGroup
 
     return seqs;
   }
+
+  /**
+   * @return the idColour
+   */
+  public Color getIdColour()
+  {
+    return idColour;
+  }
+
+  /**
+   * @param idColour
+   *                the idColour to set
+   */
+  public void setIdColour(Color idColour)
+  {
+    this.idColour = idColour;
+  }
+
+  /**
+   * @return the representative sequence for this group
+   */
+  public SequenceI getSeqrep()
+  {
+    return seqrep;
+  }
+
+  /**
+   * 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
+   */
+  public boolean hasSeqrep()
+  {
+    return seqrep != null;
+  }
+  /**
+   * visibility of rows or represented rows covered by group
+   */
+  private boolean hidereps=false;
+  /**
+   * 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
+   */
+  public boolean isHidereps()
+  {
+    return hidereps;
+  }
+  /**
+   * visibility of columns intersecting this group
+   */
+  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
+   */
+  public boolean isHideCols()
+  {
+    return hidecols;
+  }
 }