X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=e22042c355e8b27ae7b51d0d48b4a9461ecf2a99;hb=7157dfd20efd2e1db47db1ac12e879eb51c67b92;hp=b4c21fc10b66ba07238e2170e4b26c7b41e0d8e5;hpb=927ff64eabd7bb06ed31f3a94a7eee6b927d68a1;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index b4c21fc..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
@@ -18,44 +18,64 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import java.util.*;
 
 import java.awt.*;
 
-import java.util.Vector;
+import jalview.analysis.*;
+import jalview.schemes.*;
 
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class SequenceGroup
 {
   String groupName;
+  String description;
   Conservation conserve;
   Vector aaFrequency;
-  boolean displayBoxes;
-  boolean displayText;
-  boolean colourText;
-  public Vector sequences = new Vector();
+  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 = "Group";
-    this.displayBoxes = true;
-    this.displayText = true;
-    this.colourText = false;
-    cs = null;
+    groupName = "JGroup:" + this.hashCode();
   }
 
-  public SequenceGroup(Vector sequences, String groupName, ColourSchemeI scheme,
-                       boolean displayBoxes, boolean displayText,
-                       boolean colourText,
-                       int start, int end)
+  /**
+   * 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;
@@ -68,20 +88,126 @@ public class SequenceGroup
     recalcConservation();
   }
 
-  public SequenceGroup(String groupName, ColourSchemeI scheme,
-                       boolean displayBoxes, boolean displayText,
-                       boolean colourText,
-                       int start, int end)
+  public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
   {
-    this.groupName = groupName;
-    this.displayBoxes = displayBoxes;
-    this.displayText = displayText;
-    this.colourText = colourText;
-    this.cs = scheme;
-    startRes = start;
-    endRes = end;
+    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(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
@@ -108,6 +234,13 @@ public class SequenceGroup
     return true;
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param col DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
   public boolean adjustForRemoveRight(int col)
   {
     if (startRes > col)
@@ -124,56 +257,125 @@ public class SequenceGroup
     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 (!sequences.contains(s))
+    if (s != null && !sequences.contains(s))
+    {
       sequences.addElement(s);
+    }
 
-    if(recalc)
+    if (recalc)
+    {
       recalcConservation();
+    }
   }
 
-
+  /**
+   * DOCUMENT ME!
+   */
   public void recalcConservation()
   {
-    if (cs != null)
+    if (cs == null)
     {
-      cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
+      return;
     }
 
-    if ( cs  instanceof ConservationColourScheme)
+    try
     {
-      Conservation c = new Conservation(groupName,
-                                        ResidueProperties.propHash, 3, sequences,
-                                        0, getWidth());
-      c.calculate();
-      c.verdict(false, 25);
-
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
-      ccs.conserve = c;
+      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))
@@ -186,73 +388,149 @@ public class SequenceGroup
     }
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param s DOCUMENT ME!
+   * @param recalc DOCUMENT ME!
+   */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
     sequences.removeElement(s);
-    if(recalc)
+
+    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
@@ -274,11 +552,21 @@ public class SequenceGroup
     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;
@@ -291,41 +579,20 @@ public class SequenceGroup
    * @param al Alignment
    * @return SequenceI[]
    */
-  public SequenceI[] getSequencesInOrder(Alignment al)
+  public SequenceI[] getSequencesInOrder(AlignmentI al)
   {
-    int sz;
-    java.util.Hashtable orderedSeqs = new java.util.Hashtable();
-    SequenceI[] seqs = new SequenceI[sz = sequences.size()];
+    int sSize = sequences.size();
+    int alHeight = al.getHeight();
 
-    for (int i = 0; i < sz; i++)
-    {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-      int index = al.findIndex(seq);
-      orderedSeqs.put(index + "", seq);
-    }
+    SequenceI[] seqs = new SequenceI[sSize];
 
     int index = 0;
-
-    for (int i = 0; i < sz; i++)
+    for (int i = 0; i < alHeight && index < sSize; i++)
     {
-      SequenceI seq = null;
-
-      while (seq == null)
+      if (sequences.contains(al.getSequenceAt(i)))
       {
-        if (orderedSeqs.containsKey(index + ""))
-        {
-          seq = (SequenceI) orderedSeqs.get(index + "");
-          index++;
-
-          break;
-        }
-        else
-        {
-          index++;
-        }
+        seqs[index++] = al.getSequenceAt(i);
       }
-
-      seqs[index] = seq;
     }
 
     return seqs;