X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=6ded8bd79adac1a57f27893c8d819d0dd496ae19;hb=942de34caf73a7d61104783c8d278c32eaf6b65d;hp=6f6850bc1ecf657d461642b49159e4788ec02178;hpb=ba0bffb2a7cda833ff1dd2691f756294402b48cd;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6f6850b..6ded8bd 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,344 +1,645 @@
-/*
- * 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.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-
-import java.util.Vector;
-
-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;
-    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;
-    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)
-    {
-      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;
-  }
-
-  public void setName(String name)
-  {
-    groupName = name;
-  }
-
-  public Conservation getConservation()
-  {
-    return conserve;
-  }
-
-  public void setConservation(Conservation c)
-  {
-    conserve = c;
-  }
-
-  public void addSequence(SequenceI s, boolean recalc)
-  {
-    if (!sequences.contains(s))
-      sequences.addElement(s);
-
-    if(recalc)
-      recalcConservation();
-  }
-
-
-  public void recalcConservation()
-  {
-    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, recalc);
-    }
-  }
-
-  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)
-    {
-      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;
-  }
-
-  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;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * 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 java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.schemes.*;
+
+/**
+ * Collects a set contiguous ranges on a set of sequences
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceGroup
+{
+  String groupName;
+  String description;
+  Conservation conserve;
+  Vector aaFrequency;
+  boolean displayBoxes = true;
+  boolean displayText = true;
+  boolean colourText = false;
+  private Vector sequences = new Vector();
+  int width = -1;
+
+  /** DOCUMENT ME!! */
+  public ColourSchemeI cs;
+  int startRes = 0;
+  int endRes = 0;
+  public Color outlineColour = Color.black;
+  public Color idColour = null; 
+  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 
+   * @param groupName 
+   * @param scheme 
+   * @param displayBoxes 
+   * @param displayText 
+   * @param colourText 
+   * @param start first column of group
+   * @param end last column of group
+   */
+  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,ipos=0; i < inorder.length; i++)
+    {
+      SequenceI seq = inorder[i];
+
+      seqs[ipos] = seq.getSubSequence(startRes, endRes+1);
+      if (seqs[ipos]!=null)
+      {
+        seqs[ipos].setDescription(seq.getDescription());
+        seqs[ipos].setDBRef(seq.getDBRef());
+        seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        if (seq.getDatasetSequence() != null)
+        {
+          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+        }
+
+        if (seq.getAnnotation() != null)
+        {
+          AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
+          // Only copy annotation that is either a score or referenced by the alignment's annotation vector
+          for (int a = 0; a < seq.getAnnotation().length; a++)
+          {
+            AlignmentAnnotation tocopy = seq.getAnnotation()[a];
+            if (alann!=null)
+            {
+              boolean found=false;
+              for (int pos=0;pos<alann.length; pos++)
+              {
+                if (alann[pos]==tocopy)
+                { 
+                  found=true;
+                  break;
+                }
+              }
+              if (!found)
+                continue;
+            }
+            AlignmentAnnotation newannot = new AlignmentAnnotation(seq
+                    .getAnnotation()[a]);
+            newannot.restrict(startRes, endRes);
+            newannot.setSequenceRef(seqs[ipos]);
+            newannot.adjustForAlignment();
+            seqs[ipos].addAlignmentAnnotation(newannot);
+          }
+        }
+        ipos++;
+      } else {
+        iSize--;
+      }
+    }
+    if (iSize!=inorder.length)
+    {
+      SequenceI[] nseqs = new SequenceI[iSize];
+      System.arraycopy(seqs, 0, nseqs, 0, iSize);
+      seqs = nseqs;
+    }
+    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(Hashtable hiddenReps)
+  {
+    if (hiddenReps == null)
+    {
+      return sequences;
+    }
+    else
+    {
+      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))
+        {
+          SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
+          for (int h = 0; h < hsg.getSize(); h++)
+          {
+            seq2 = hsg.getSequenceAt(h);
+            if (seq2 != seq
+                && !allSequences.contains(seq2))
+            {
+              allSequences.addElement(seq2);
+            }
+          }
+        }
+      }
+
+      return allSequences;
+    }
+  }
+
+  public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+  {
+    Vector tmp = getSequences(hiddenReps);
+    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;
+  }
+
+  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;
+  }
+
+  /**
+   * Add s to this sequence group
+   *
+   * @param s alignment sequence to be added
+   * @param recalc true means Group's conservation should be recalculated
+   */
+  public void addSequence(SequenceI s, boolean recalc)
+  {
+    if (s != null && !sequences.contains(s))
+    {
+      sequences.addElement(s);
+    }
+
+    if (recalc)
+    {
+      recalcConservation();
+    }
+  }
+
+  /**
+   * calculate residue conservation for group
+   */
+  public void recalcConservation()
+  {
+    if (cs == null)
+    {
+      return;
+    }
+
+    try
+    {
+      cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
+
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+      }
+
+      if (cs.conservationApplied())
+      {
+        Conservation c = new Conservation(groupName,
+                                          ResidueProperties.propHash, 3,
+                                          sequences,
+                                          startRes, endRes + 1);
+        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()
+  {
+    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 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;
+  }
+
+  /**
+   * @return the idColour
+   */
+  public Color getIdColour()
+  {
+    return idColour;
+  }
+
+  /**
+   * @param idColour the idColour to set
+   */
+  public void setIdColour(Color idColour)
+  {
+    this.idColour = idColour;
+  }
+}