X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=dc22704ffebd62006b2d55be030b5ac20ee2e6d3;hb=56ab3a18f36a613d943efa0edcfcee3cae248343;hp=4d7509d1a647fb18458d850dc4790c6db92d2b01;hpb=3ac9a19998fe3b2f4e4583bed327a13ca80c874b;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 4d7509d..dc22704 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,170 +1,612 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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;
-  boolean aaFrequencyValid = false;
-  public Vector sequences = new Vector();
-  int width = -1;
-  public ColourSchemeI cs;
-  int startRes = 0;
-  int endRes = 0;
-
-  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 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);
-  }
-
-  public void addOrRemove(SequenceI s)
-  {
-    if(sequences.contains(s))
-      deleteSequence(s);
-    else
-      addSequence(s);
-  }
-
-  public void deleteSequence(SequenceI s)
-  {
-    sequences.removeElement(s);
-  }
-
-
-  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 Vector getAAFrequency()
-  {
-    if (aaFrequency == null || aaFrequencyValid == false)
-    {
-      aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
-      aaFrequencyValid = true;
-    }
-    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++)
-    {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-      if (seq.getLength() > width)
-        width = seq.getLength();
-    }
-    return width;
-  }
+    String groupName;
+    Conservation conserve;
+    Vector aaFrequency;
+    boolean displayBoxes;
+    boolean displayText;
+    boolean colourText;
+    private 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)
+    {
+        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;
+    }
+
+    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++)
+    {
+      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++)
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
+      }
+    }
+
+    return seqs;
+
+    }
+
+    /**
+     * 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;
+
+      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
+      {
+        ch = seq.getCharAt(j);
+        if (!jalview.util.Comparison.isGap( (ch)))
+        {
+          eres++;
+        }
+      }
+
+      if (eres > 0)
+      {
+        eres += seq.getStart() - 1;
+      }
+
+      return eres;
+    }
+
+    public Vector getSequences(boolean includeHidden)
+    {
+      if(!includeHidden)
+        return sequences;
+      else
+      {
+        Vector allSequences = new Vector();
+        SequenceI seq;
+        for (int i = 0; i < sequences.size(); i++)
+        {
+          seq = (SequenceI) sequences.elementAt(i);
+          allSequences.addElement(seq);
+          if (seq.getHiddenSequences() != null)
+          {
+            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)
+            {
+              allSequences.addElement(
+                  seq.getHiddenSequences().getSequenceAt(h)
+                  );
+            }
+          }
+        }
+
+        return allSequences;
+      }
+    }
+
+    public SequenceI[] getSequencesAsArray(boolean includeHidden)
+    {
+      Vector tmp = getSequences(includeHidden);
+      if(tmp==null)
+        return null;
+      SequenceI [] result = new SequenceI[tmp.size()];
+      for(int i=0; i<result.length; i++)
+        result[i] = (SequenceI)tmp.elementAt(i);
+
+      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)
+        {
+            startRes = startRes - col;
+        }
+
+        if (endRes >= col)
+        {
+            endRes = endRes - 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()
+    {
+        return groupName;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     */
+    public void setName(String name)
+    {
+        groupName = name;
+    }
+
+    /**
+     * 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))
+        {
+            sequences.addElement(s);
+        }
+
+        if (recalc)
+        {
+            recalcConservation();
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void recalcConservation()
+    {
+        if(cs == null)
+          return;
+
+        try
+        {
+          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());
+            }
+          }
+        }
+        catch (java.lang.OutOfMemoryError err)
+        {
+          System.out.println("Out of memory loading groups: " + err);
+        }
+
+    }
+
+    /**
+     * 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);
+        }
+    }
+
+    /**
+     * 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(boolean includeHidden)
+    {
+      if(!includeHidden)
+        return sequences.size();
+      else
+      {
+        int total = sequences.size();
+        SequenceI seq;
+        for (int i = 0; i < sequences.size(); i++)
+        {
+          seq = (SequenceI) sequences.elementAt(i);
+          if (seq.getHiddenSequences() != null)
+          {
+            total += seq.getHiddenSequences().getSize(false);
+          }
+        }
+        return total;
+      }
+    }
+
+    /**
+     * 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 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;
+    }
 }