X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=116e172fd28bdf4ef416c6b99cef1b934829ae4e;hb=2a40019eb6a0beb79dc29263a4173e6adb2909a7;hp=4c6420c0082e69f77863da4fdd68465c9c516c5c;hpb=d75ccc3b6f6e8f3e22b8c5732c0553f15e24d4ef;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 4c6420c..116e172 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,11 +1,33 @@
+/*
+ * 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 jalview.schemes.*;
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
-import java.util.Vector;
+
+import jalview.schemes.*;
+
 import java.awt.*;
 
+import java.util.Vector;
+
 public class SequenceGroup
 {
   String groupName;
@@ -14,7 +36,6 @@ public class SequenceGroup
   boolean displayBoxes;
   boolean displayText;
   boolean colourText;
-  boolean aaFrequencyValid = false;
   public Vector sequences = new Vector();
   int width = -1;
   public ColourSchemeI cs;
@@ -31,13 +52,27 @@ public class SequenceGroup
     cs = null;
   }
 
-  public SequenceGroup(String groupName, ColourSchemeI scheme,
+  public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,
                        boolean displayBoxes, boolean displayText,
                        boolean colourText,
-                       int start,
-                       int end)
+                       int start, int end)
   {
+    this.sequences = sequences;
+    this.groupName = groupName;
+    this.displayBoxes = displayBoxes;
+    this.displayText = displayText;
+    this.colourText = colourText;
+    this.cs = scheme;
+    startRes = start;
+    endRes = end;
+    recalcConservation();
+  }
 
+  public SequenceGroup(String groupName, ColourSchemeI scheme,
+                       boolean displayBoxes, boolean displayText,
+                       boolean colourText,
+                       int start, int end)
+  {
     this.groupName = groupName;
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
@@ -47,6 +82,48 @@ public class SequenceGroup
     endRes = end;
   }
 
+  public boolean adjustForRemoveLeft(int col)
+  {
+    // return value is true if the group still exists
+    if (startRes >= col)
+    {
+      startRes = startRes - col;
+    }
+
+    if (endRes >= col)
+    {
+      endRes = endRes - col;
+
+      if (startRes > endRes)
+      {
+        startRes = 0;
+      }
+    }
+    else
+    {
+      // must delete this group!!
+      return false;
+    }
+
+    return true;
+  }
+
+  public boolean adjustForRemoveRight(int col)
+  {
+    if (startRes > col)
+    {
+      // delete this group
+      return false;
+    }
+
+    if (endRes >= col)
+    {
+      endRes = col;
+    }
+
+    return true;
+  }
+
   public String getName()
   {
     return groupName;
@@ -67,26 +144,67 @@ public class SequenceGroup
     conserve = c;
   }
 
-  public void addSequence(SequenceI s)
+  public void addSequence(SequenceI s, boolean recalc)
   {
-    if(!sequences.contains(s))
+    if (!sequences.contains(s))
       sequences.addElement(s);
+
+    if(recalc)
+      recalcConservation();
   }
 
-  public void addOrRemove(SequenceI s)
+
+  public void recalcConservation()
   {
-    if(sequences.contains(s))
-      deleteSequence(s);
+    System.out.println("sg recalc");
+    if (cs != null)
+    {
+      cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+    }
+
+    if (cs instanceof ClustalxColourScheme)
+    {
+      ( (ClustalxColourScheme) cs).resetClustalX(sequences,getWidth());
+    }
+
+
+    if ( cs  instanceof ConservationColourScheme)
+    {
+      Conservation c = new Conservation(groupName,
+                                        ResidueProperties.propHash, 3, sequences,
+                                        0, getWidth());
+      c.calculate();
+      c.verdict(false, 25);
+
+      ConservationColourScheme ccs = (ConservationColourScheme) cs;
+      ccs.conserve = c;
+      if (ccs.cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) ccs.cs).resetClustalX(sequences, getWidth());
+      }
+
+    }
+  }
+
+  public void addOrRemove(SequenceI s, boolean recalc)
+  {
+    if (sequences.contains(s))
+    {
+      deleteSequence(s, recalc);
+    }
     else
-      addSequence(s);
+    {
+      addSequence(s, recalc);
+    }
   }
 
-  public void deleteSequence(SequenceI s)
+  public void deleteSequence(SequenceI s, boolean recalc)
   {
     sequences.removeElement(s);
+    if(recalc)
+      recalcConservation();
   }
 
-
   public int getStartRes()
   {
     return startRes;
@@ -147,36 +265,81 @@ public class SequenceGroup
     return displayBoxes;
   }
 
-  public Vector getAAFrequency()
+  public int getWidth()
   {
-    if (aaFrequency == null || aaFrequencyValid == false)
+    // MC This needs to get reset when characters are inserted and deleted
+    if (sequences.size() > 0)
     {
-      aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
-      aaFrequencyValid = true;
+      width = ( (SequenceI) sequences.elementAt(0)).getLength();
     }
-    return aaFrequency;
-  }
 
-  public int getWidth()
-  {
-    System.out.println("it is called");
-    // MC This needs to get reset when characters are inserted and deleted
-    for (int i = 0; i < sequences.size(); i++)
+    for (int i = 1; i < sequences.size(); i++)
     {
       SequenceI seq = (SequenceI) sequences.elementAt(i);
+
       if (seq.getLength() > width)
+      {
         width = seq.getLength();
+      }
     }
+
     return width;
   }
 
-
   public void setOutlineColour(Color c)
   {
     outlineColour = c;
   }
+
   public Color getOutlineColour()
   {
     return outlineColour;
   }
+
+  /**
+   *
+   * returns the sequences in the group ordered by the ordering given by al
+   *
+   * @param al Alignment
+   * @return SequenceI[]
+   */
+  public SequenceI[] getSequencesInOrder(Alignment al)
+  {
+    int sz;
+    java.util.Hashtable orderedSeqs = new java.util.Hashtable();
+    SequenceI[] seqs = new SequenceI[sz = sequences.size()];
+
+    for (int i = 0; i < sz; i++)
+    {
+      SequenceI seq = (SequenceI) sequences.elementAt(i);
+      int index = al.findIndex(seq);
+      orderedSeqs.put(index + "", seq);
+    }
+
+    int index = 0;
+
+    for (int i = 0; i < sz; i++)
+    {
+      SequenceI seq = null;
+
+      while (seq == null)
+      {
+        if (orderedSeqs.containsKey(index + ""))
+        {
+          seq = (SequenceI) orderedSeqs.get(index + "");
+          index++;
+
+          break;
+        }
+        else
+        {
+          index++;
+        }
+      }
+
+      seqs[index] = seq;
+    }
+
+    return seqs;
+  }
 }