X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=e22042c355e8b27ae7b51d0d48b4a9461ecf2a99;hb=7157dfd20efd2e1db47db1ac12e879eb51c67b92;hp=6de42b9d23e704384ecc0af78a279b1bab9765a7;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6de42b9..e22042c 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -18,14 +18,12 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.*;
-
-import jalview.schemes.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.*;
-
+import jalview.analysis.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -35,468 +33,568 @@ import java.util.*;
  */
 public class SequenceGroup
 {
-    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()
-    {
-        groupName = "Group";
-        this.displayBoxes = true;
-        this.displayText = true;
-        this.colourText = false;
-        cs = null;
-    }
-
-    /**
-     * 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)
+  String groupName;
+  String description;
+  Conservation conserve;
+  Vector aaFrequency;
+  boolean displayBoxes = true;
+  boolean displayText = true;
+  boolean colourText = true;
+  private Vector sequences = new Vector();
+  int width = -1;
+
+  /** DOCUMENT ME!! */
+  public ColourSchemeI cs;
+  int startRes = 0;
+  int endRes = 0;
+  Color outlineColour = Color.black;
+  public int thresholdTextColour = 0;
+  public Color textColour = Color.black;
+  public Color textColour2 = Color.white;
+
+  /**
+   * Creates a new SequenceGroup object.
+   */
+  public SequenceGroup()
+  {
+    groupName = "JGroup:" + this.hashCode();
+  }
+
+  /**
+   * 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)
+  {
+    this.sequences = sequences;
+    this.groupName = groupName;
+    this.displayBoxes = displayBoxes;
+    this.displayText = displayText;
+    this.colourText = colourText;
+    this.cs = scheme;
+    startRes = start;
+    endRes = end;
+    recalcConservation();
+  }
+
+  public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
+  {
+    int iSize = sequences.size();
+    SequenceI[] seqs = new SequenceI[iSize];
+    SequenceI[] inorder = getSequencesInOrder(align);
+
+    for (int i = 0; i < iSize; i++)
     {
-        this.sequences = sequences;
-        this.groupName = groupName;
-        this.displayBoxes = displayBoxes;
-        this.displayText = displayText;
-        this.colourText = colourText;
-        this.cs = scheme;
-        startRes = start;
-        endRes = end;
-        recalcConservation();
-    }
-
-    /**
-     * 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;
-        }
-
-        if (endRes >= col)
-        {
-            endRes = endRes - col;
-
-            if (startRes > endRes)
-            {
-                startRes = 0;
-            }
-        }
-        else
+      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[i].setDatasetSequence(seq.getDatasetSequence());
+      }
+
+      if (seq.getAnnotation() != null)
+      {
+        for (int a = 0; a < seq.getAnnotation().length; a++)
         {
-            // must delete this group!!
-            return false;
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
         }
-
-        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 seqs;
 
-        return true;
-    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-        return groupName;
-    }
+  /**
+   * If sequence ends in gaps, the end residue can
+   * be correctly calculated here
+   * @param seq SequenceI
+   * @return int
+   */
+  public int findEndRes(SequenceI seq)
+  {
+    int eres = 0;
+    char ch;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name)
+    for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
     {
-        groupName = name;
+      ch = seq.getCharAt(j);
+      if (!jalview.util.Comparison.isGap( (ch)))
+      {
+        eres++;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Conservation getConservation()
+    if (eres > 0)
     {
-        return conserve;
+      eres += seq.getStart() - 1;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setConservation(Conservation c)
-    {
-        conserve = c;
-    }
+    return eres;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void addSequence(SequenceI s, boolean recalc)
+  public Vector getSequences(Hashtable hiddenReps)
+  {
+    if (hiddenReps == null)
     {
-        if (!sequences.contains(s))
-        {
-            sequences.addElement(s);
-        }
-
-        if (recalc)
-        {
-            recalcConservation();
-        }
+      return sequences;
     }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void recalcConservation()
+    else
     {
-        if(cs == null)
-          return;
-
-        cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
-
-
-        if (cs instanceof ClustalxColourScheme)
-        {
-            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-        }
-
-
-        if (cs.conservationApplied())
+      Vector allSequences = new Vector();
+      SequenceI seq, seq2;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        seq = (SequenceI) sequences.elementAt(i);
+        allSequences.addElement(seq);
+        if (hiddenReps.containsKey(seq))
         {
-            Conservation c = new Conservation(groupName,
-                    ResidueProperties.propHash, 3, sequences, 0, getWidth());
-            c.calculate();
-            c.verdict(false, 25);
-
-
-            cs.setConservation(c);
-
-            if (cs instanceof ClustalxColourScheme)
+          SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
+          for (int h = 0; h < hsg.getSize(); h++)
+          {
+            seq2 = hsg.getSequenceAt(h);
+            if (seq2 != seq
+                && !allSequences.contains(seq2))
             {
-                ((ClustalxColourScheme) cs).resetClustalX(sequences,
-                    getWidth());
+              allSequences.addElement(seq2);
             }
+          }
         }
-    }
+      }
 
-    /**
-     * 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);
-        }
+      return allSequences;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void deleteSequence(SequenceI s, boolean recalc)
+  public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+  {
+    Vector tmp = getSequences(hiddenReps);
+    if (tmp == null)
     {
-        sequences.removeElement(s);
-
-        if (recalc)
-        {
-            recalcConservation();
-        }
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
+    SequenceI[] result = new SequenceI[tmp.size()];
+    for (int i = 0; i < result.length; i++)
     {
-        return startRes;
+      result[i] = (SequenceI) tmp.elementAt(i);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
+    return result;
+  }
+
+  /**
+   * 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)
     {
-        return endRes;
+      startRes = startRes - col;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void setStartRes(int i)
+    if (endRes >= col)
     {
-        startRes = i;
-    }
+      endRes = endRes - col;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void setEndRes(int i)
-    {
-        endRes = i;
+      if (startRes > endRes)
+      {
+        startRes = 0;
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getSize()
+    else
     {
-        return sequences.size();
+      // must delete this group!!
+      return false;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getSequenceAt(int i)
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param col DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean adjustForRemoveRight(int col)
+  {
+    if (startRes > col)
     {
-        return (SequenceI) sequences.elementAt(i);
+      // delete this group
+      return false;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
+    if (endRes >= col)
     {
-        colourText = state;
+      endRes = col;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return groupName;
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param name DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    groupName = name;
+  }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Conservation getConservation()
+  {
+    return conserve;
+  }
+
+  /**
+   * 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 (s != null && !sequences.contains(s))
     {
-        return colourText;
+      sequences.addElement(s);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setDisplayText(boolean state)
+    if (recalc)
     {
-        displayText = state;
+      recalcConservation();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getDisplayText()
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void recalcConservation()
+  {
+    if (cs == null)
     {
-        return displayText;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setDisplayBoxes(boolean state)
+    try
     {
-        displayBoxes = state;
-    }
+      cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getDisplayBoxes()
-    {
-        return displayBoxes;
-    }
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+      }
 
-    /**
-     * 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();
-        }
+      if (cs.conservationApplied())
+      {
+        Conservation c = new Conservation(groupName,
+                                          ResidueProperties.propHash, 3,
+                                          sequences,
+                                          startRes, endRes + 1);
+        c.calculate();
+        c.verdict(false, 25);
 
-        for (int i = 1; i < sequences.size(); i++)
-        {
-            SequenceI seq = (SequenceI) sequences.elementAt(i);
+        cs.setConservation(c);
 
-            if (seq.getLength() > width)
-            {
-                width = seq.getLength();
-            }
+        if (cs instanceof ClustalxColourScheme)
+        {
+          ( (ClustalxColourScheme) cs).resetClustalX(sequences,
+              getWidth());
         }
-
-        return width;
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setOutlineColour(Color c)
+    catch (java.lang.OutOfMemoryError err)
     {
-        outlineColour = c;
+      System.out.println("Out of memory loading groups: " + err);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getOutlineColour()
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param recalc DOCUMENT ME!
+   */
+  public void addOrRemove(SequenceI s, boolean recalc)
+  {
+    if (sequences.contains(s))
     {
-        return outlineColour;
+      deleteSequence(s, recalc);
     }
-
-    /**
-     *
-     * returns the sequences in the group ordered by the ordering given by al
-     *
-     * @param al Alignment
-     * @return SequenceI[]
-     */
-    public SequenceI[] getSequencesInOrder(AlignmentI al)
+    else
     {
-        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);
-        }
+      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();
+    }
 
-        int index = 0;
+    for (int i = 1; i < sequences.size(); i++)
+    {
+      SequenceI seq = (SequenceI) sequences.elementAt(i);
 
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-            if (orderedSeqs.containsKey(i + ""))
-            {
-                seqs[index++] = (SequenceI) orderedSeqs.get(i + "");
-            }
-        }
+      if (seq.getLength() > width)
+      {
+        width = seq.getLength();
+      }
+    }
 
-        return seqs;
+    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 sSize = sequences.size();
+    int alHeight = al.getHeight();
+
+    SequenceI[] seqs = new SequenceI[sSize];
+
+    int index = 0;
+    for (int i = 0; i < alHeight && index < sSize; i++)
+    {
+      if (sequences.contains(al.getSequenceAt(i)))
+      {
+        seqs[index++] = al.getSequenceAt(i);
+      }
     }
+
+    return seqs;
+  }
 }