X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=6de42b9d23e704384ecc0af78a279b1bab9765a7;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=a855f6f4b54096abc7f5b96575493149045e4517;hpb=92a3a0f396a86b2bc0a8d1a311680ceda4abec7b;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index a855f6f..6de42b9 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -20,313 +20,483 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 
-import jalview.datamodel.*;
-
 import jalview.schemes.*;
 
 import java.awt.*;
 
-import java.util.Vector;
+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(Vector sequences, String groupName, ColourSchemeI scheme,
-                       boolean displayBoxes, boolean displayText,
-                       boolean colourText,
-                       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;
-  }
-
-  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)
+    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()
     {
-      startRes = startRes - col;
+        groupName = "Group";
+        this.displayBoxes = true;
+        this.displayText = true;
+        this.colourText = false;
+        cs = null;
     }
 
-    if (endRes >= col)
+    /**
+     * 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)
     {
-      endRes = endRes - col;
+        this.sequences = sequences;
+        this.groupName = groupName;
+        this.displayBoxes = displayBoxes;
+        this.displayText = displayText;
+        this.colourText = colourText;
+        this.cs = scheme;
+        startRes = start;
+        endRes = end;
+        recalcConservation();
+    }
 
-      if (startRes > endRes)
-      {
-        startRes = 0;
-      }
+    /**
+     * 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;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param col DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean adjustForRemoveLeft(int col)
     {
-      // must delete this group!!
-      return false;
+        // 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;
     }
 
-    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;
+        }
 
-  public boolean adjustForRemoveRight(int col)
-  {
-    if (startRes > col)
+        return true;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String getName()
+    {
+        return groupName;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
+        groupName = name;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Conservation getConservation()
     {
-      // delete this group
-      return false;
+        return conserve;
     }
 
-    if (endRes >= col)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setConservation(Conservation c)
     {
-      endRes = col;
+        conserve = c;
     }
 
-    return true;
-  }
+    /**
+     * 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);
 
-  public String getName()
-  {
-    return groupName;
-  }
 
-  public void setName(String name)
-  {
-    groupName = name;
-  }
+            cs.setConservation(c);
 
-  public Conservation getConservation()
-  {
-    return conserve;
-  }
+            if (cs instanceof ClustalxColourScheme)
+            {
+                ((ClustalxColourScheme) cs).resetClustalX(sequences,
+                    getWidth());
+            }
+        }
+    }
 
-  public void setConservation(Conservation c)
-  {
-    conserve = c;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void addOrRemove(SequenceI s, boolean recalc)
+    {
+        if (sequences.contains(s))
+        {
+            deleteSequence(s, recalc);
+        }
+        else
+        {
+            addSequence(s, recalc);
+        }
+    }
 
-  public void addSequence(SequenceI s, boolean recalc)
-  {
-    if (!sequences.contains(s))
-      sequences.addElement(s);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param recalc DOCUMENT ME!
+     */
+    public void deleteSequence(SequenceI s, boolean recalc)
+    {
+        sequences.removeElement(s);
 
-    if(recalc)
-      recalcConservation();
-  }
+        if (recalc)
+        {
+            recalcConservation();
+        }
+    }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
+    {
+        return startRes;
+    }
 
-  public void recalcConservation()
-  {
-    if (cs != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
     {
-      cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+        return endRes;
     }
 
-    if ( cs  instanceof ConservationColourScheme)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setStartRes(int i)
     {
-      Conservation c = new Conservation(groupName,
-                                        ResidueProperties.propHash, 3, sequences,
-                                        0, getWidth());
-      c.calculate();
-      c.verdict(false, 25);
-
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
-      ccs.conserve = c;
+        startRes = i;
     }
-  }
 
-  public void addOrRemove(SequenceI s, boolean recalc)
-  {
-    if (sequences.contains(s))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void setEndRes(int i)
     {
-      deleteSequence(s, recalc);
+        endRes = i;
     }
-    else
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getSize()
     {
-      addSequence(s, recalc);
+        return sequences.size();
     }
-  }
-
-  public void deleteSequence(SequenceI s, boolean recalc)
-  {
-    sequences.removeElement(s);
-    if(recalc)
-      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)
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getSequenceAt(int i)
     {
-      width = ( (SequenceI) sequences.elementAt(0)).getLength();
+        return (SequenceI) sequences.elementAt(i);
     }
 
-    for (int i = 1; i < sequences.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setColourText(boolean state)
     {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
+        colourText = state;
+    }
 
-      if (seq.getLength() > width)
-      {
-        width = seq.getLength();
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getColourText()
+    {
+        return colourText;
     }
 
-    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!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayText(boolean state)
     {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-      int index = al.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
+        displayText = state;
     }
 
-    int index = 0;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayText()
+    {
+        return displayText;
+    }
 
-    for (int i = 0; i < sz; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setDisplayBoxes(boolean state)
     {
-      SequenceI seq = null;
+        displayBoxes = state;
+    }
 
-      while (seq == null)
-      {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getDisplayBoxes()
+    {
+        return displayBoxes;
+    }
 
-          break;
+    /**
+     * 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();
         }
-        else
+
+        for (int i = 1; i < sequences.size(); i++)
         {
-          index++;
+            SequenceI seq = (SequenceI) sequences.elementAt(i);
+
+            if (seq.getLength() > width)
+            {
+                width = seq.getLength();
+            }
         }
-      }
 
-      seqs[index] = seq;
+        return width;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     */
+    public void setOutlineColour(Color c)
+    {
+        outlineColour = c;
     }
 
-    return seqs;
-  }
+    /**
+     * 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;
+    }
 }