X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=6de42b9d23e704384ecc0af78a279b1bab9765a7;hb=8a18973f7e4521c7dd3705ebd8fabd3ca08cfcaf;hp=d6ea5dd8131d8ee996d840ac693ac74b44eb6f31;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index d6ea5dd..6de42b9 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,287 +1,502 @@
 /*
-* 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
-*/
-
+ * 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.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SequenceGroup
 {
-  String groupName;
-  Conservation conserve;
-  Vector aaFrequency;
-  boolean displayBoxes;
-  boolean displayText;
-  boolean colourText;
-  public Vector sequences = new Vector();
-  int width = -1;
-  public ColourSchemeI cs;
-  int startRes = 0;
-  int endRes = 0;
-  Color outlineColour = Color.black;
-
-  public SequenceGroup()
-  {
-    groupName = "Group";
-    this.displayBoxes = true;
-    this.displayText = true;
-    this.colourText = false;
-    cs = null;
-  }
-
-  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;
-    this.colourText = colourText;
-    this.cs = scheme;
-    startRes = start;
-    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)
+    String groupName;
+    Conservation conserve;
+    Vector aaFrequency;
+    boolean displayBoxes;
+    boolean displayText;
+    boolean colourText;
+
+    /** DOCUMENT ME!! */
+    public Vector sequences = new Vector();
+    int width = -1;
+
+    /** DOCUMENT ME!! */
+    public ColourSchemeI cs;
+    int startRes = 0;
+    int endRes = 0;
+    Color outlineColour = Color.black;
+
+    /**
+     * Creates a new SequenceGroup object.
+     */
+    public SequenceGroup()
     {
-      endRes = endRes - col;
-      if(startRes>endRes)
-        startRes = 0;
+        groupName = "Group";
+        this.displayBoxes = true;
+        this.displayText = true;
+        this.colourText = false;
+        cs = null;
     }
-    else
+
+    /**
+     * 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!
+     */
+    public SequenceGroup(Vector sequences, String groupName,
+        ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
+        boolean colourText, int start, int end)
     {
-        // must delete this group!!
-        return false;
+        this.sequences = sequences;
+        this.groupName = groupName;
+        this.displayBoxes = displayBoxes;
+        this.displayText = displayText;
+        this.colourText = colourText;
+        this.cs = scheme;
+        startRes = start;
+        endRes = end;
+        recalcConservation();
     }
 
-    return true;
-  }
+    /**
+     * Creates a new SequenceGroup object.
+     *
+     * @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!
+     */
+    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;
+        this.colourText = colourText;
+        this.cs = scheme;
+        startRes = start;
+        endRes = end;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean adjustForRemoveLeft(int col)
+    {
+        // return value is true if the group still exists
+        if (startRes >= col)
+        {
+            startRes = startRes - col;
+        }
 
-  public boolean adjustForRemoveRight(int col)
-  {
+        if (endRes >= col)
+        {
+            endRes = endRes - col;
 
-    if(startRes>col)
+            if (startRes > endRes)
+            {
+                startRes = 0;
+            }
+        }
+        else
+        {
+            // must delete this group!!
+            return false;
+        }
+
+        return true;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean adjustForRemoveRight(int col)
+    {
+        if (startRes > col)
+        {
+            // delete this group
+            return false;
+        }
+
+        if (endRes >= col)
+        {
+            endRes = col;
+        }
+
+        return true;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
     {
-      // delete this group
-      return false;
+        return groupName;
     }
 
-    if(endRes>=col)
-      endRes = col;
-
-    return true;
-  }
-
-
-  public String getName()
-  {
-    return groupName;
-  }
-
-  public void setName(String name)
-  {
-    groupName = name;
-  }
-
-  public Conservation getConservation()
-  {
-    return conserve;
-  }
-
-  public void setConservation(Conservation c)
-  {
-    conserve = c;
-  }
-
-  public void addSequence(SequenceI s)
-  {
-    if(!sequences.contains(s))
-      sequences.addElement(s);
-
-
-    if(cs!=null)
-      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
-
-    if(cs instanceof ConservationColourScheme)
-      recalcConservation();
-  }
-
-  void recalcConservation()
-  {
-      Conservation c = new Conservation(groupName,
-                                        ResidueProperties.propHash, 3,
-                                        sequences, 0, getWidth());
-      c.calculate();
-      c.verdict(false, 25);
-      ConservationColourScheme ccs = (ConservationColourScheme)cs;
-      ccs.conserve = c;
-  }
-
-  public void addOrRemove(SequenceI s)
-  {
-    if(sequences.contains(s))
-      deleteSequence(s);
-    else
-      addSequence(s);
-  }
-
-  public void deleteSequence(SequenceI s)
-  {
-    sequences.removeElement(s);
-
-    if(cs!=null)
-      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
-
-    if(cs instanceof ConservationColourScheme)
-      recalcConservation();
-  }
-
-
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  public void setStartRes(int i)
-  {
-    startRes = i;
-  }
-
-  public void setEndRes(int i)
-  {
-    endRes = i;
-  }
-
-  public int getSize()
-  {
-    return sequences.size();
-  }
-
-  public SequenceI getSequenceAt(int i)
-  {
-    return (SequenceI) sequences.elementAt(i);
-  }
-
-  public void setColourText(boolean state)
-  {
-    colourText = state;
-  }
-
-  public boolean getColourText()
-  {
-    return colourText;
-  }
-
-  public void setDisplayText(boolean state)
-  {
-    displayText = state;
-  }
-
-  public boolean getDisplayText()
-  {
-    return displayText;
-  }
-
-  public void setDisplayBoxes(boolean state)
-  {
-    displayBoxes = state;
-  }
-
-  public boolean getDisplayBoxes()
-  {
-    return displayBoxes;
-  }
-
-  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();
-    for (int i = 1; i < sequences.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
     {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-      if (seq.getLength() > width)
-        width = seq.getLength();
+        groupName = name;
     }
-    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++)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Conservation getConservation()
     {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-      int index = al.findIndex(seq);
-      orderedSeqs.put(index+"", seq);
+        return conserve;
     }
 
-    int index=0;
-    for(int i=0; i<sz; i++) {
-      SequenceI seq = null;
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setConservation(Conservation c)
+    {
+        conserve = c;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void addSequence(SequenceI s, boolean recalc)
+    {
+        if (!sequences.contains(s))
+        {
+            sequences.addElement(s);
+        }
+
+        if (recalc)
+        {
+            recalcConservation();
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void recalcConservation()
+    {
+        if(cs == null)
+          return;
+
+        cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        }
+
+
+        if (cs.conservationApplied())
+        {
+            Conservation c = new Conservation(groupName,
+                    ResidueProperties.propHash, 3, sequences, 0, getWidth());
+            c.calculate();
+            c.verdict(false, 25);
+
+
+            cs.setConservation(c);
+
+            if (cs instanceof ClustalxColourScheme)
+            {
+                ((ClustalxColourScheme) cs).resetClustalX(sequences,
+                    getWidth());
+            }
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void addOrRemove(SequenceI s, boolean recalc)
+    {
+        if (sequences.contains(s))
         {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-          break;
+            deleteSequence(s, recalc);
         }
         else
-          index++;
-      }
-      seqs[index] = seq;
+        {
+            addSequence(s, recalc);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void deleteSequence(SequenceI s, boolean recalc)
+    {
+        sequences.removeElement(s);
+
+        if (recalc)
+        {
+            recalcConservation();
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
+    {
+        return startRes;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
+    {
+        return endRes;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setStartRes(int i)
+    {
+        startRes = i;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setEndRes(int i)
+    {
+        endRes = i;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSize()
+    {
+        return sequences.size();
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getSequenceAt(int i)
+    {
+        return (SequenceI) sequences.elementAt(i);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setColourText(boolean state)
+    {
+        colourText = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getColourText()
+    {
+        return colourText;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayText(boolean state)
+    {
+        displayText = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayText()
+    {
+        return displayText;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayBoxes(boolean state)
+    {
+        displayBoxes = state;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayBoxes()
+    {
+        return displayBoxes;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    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();
+        }
+
+        for (int i = 1; i < sequences.size(); i++)
+        {
+            SequenceI seq = (SequenceI) sequences.elementAt(i);
+
+            if (seq.getLength() > width)
+            {
+                width = seq.getLength();
+            }
+        }
+
+        return width;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setOutlineColour(Color c)
+    {
+        outlineColour = c;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    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(AlignmentI al)
+    {
+        int sz = sequences.size();
+        java.util.Hashtable orderedSeqs = new java.util.Hashtable();
+        SequenceI[] seqs = new SequenceI[sz];
+
+        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 < al.getHeight(); i++)
+        {
+            if (orderedSeqs.containsKey(i + ""))
+            {
+                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");
+            }
+        }
+
+        return seqs;
     }
-    return seqs;
-  }
 }