X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=08754509f72d7a1da743bc20db4f398e6689d48d;hb=d4ede6b61d4abab78200f334d8df07879dfe6741;hp=69b66e01b8e56249d3f0553517a17a007b778dd7;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 69b66e0..0875450 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,7 +1,5 @@
 package jalview.datamodel;
 
-import jalview.jbgui.*;
-import jalview.schemes.*;
 import jalview.analysis.*;
 import jalview.util.*;
 import java.util.*;
@@ -13,8 +11,8 @@ public class Alignment implements AlignmentI
 
   protected Vector      sequences;
   protected Vector      groups = new Vector();
-  public    Hashtable[] cons;
-  protected String      gapCharacter = ".";
+  protected ArrayList   superGroup = new ArrayList();
+  protected char        gapCharacter = '-';
 
   /** Make an alignment from an array of Sequences.
   *
@@ -23,18 +21,8 @@ public class Alignment implements AlignmentI
   public Alignment(SequenceI[] seqs) {
     sequences = new Vector();
 
-    for (int i=0; i < seqs.length; i++) {
+    for (int i=0; i < seqs.length; i++)
       sequences.addElement(seqs[i]);
-    }
-
-    groups.addElement(new SequenceGroup());
-
-    int i = 0;
-
-    while (i < seqs.length) {
-      addToGroup((SequenceGroup)groups.elementAt(0),seqs[i]);
-      i++;
-    }
 
     getWidth();
   }
@@ -125,7 +113,7 @@ public class Alignment implements AlignmentI
         if (current.getLength() > i)
         {
 	    /* MC Should move this to a method somewhere */
-          if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')
+          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
             delete = false;
 
         }
@@ -230,35 +218,34 @@ public class Alignment implements AlignmentI
   public Vector removeRedundancy(float threshold, Vector sel) {
     Vector del = new Vector();
 
-    for (int i=1; i < sel.size(); i++) {
-      for (int j = 0; j < i; j++) {
+    for (int i = 1; i < sel.size(); i++)
+    {
+      for (int j = 0; j < i; j++)
+      {
         // Only do the comparison if either have not been deleted
-        if (!del.contains((SequenceI)sel.elementAt(i)) ||
-            !del.contains((SequenceI)sel.elementAt(j))) {
+        if (!del.contains( (SequenceI) sel.elementAt(i)) ||
+            !del.contains( (SequenceI) sel.elementAt(j)))
+        {
 
-          float pid = Comparison.compare((SequenceI)sel.elementAt(j),
-                                         (SequenceI)sel.elementAt(i));
+          float pid = Comparison.compare( (SequenceI) sel.elementAt(j),
+                                         (SequenceI) sel.elementAt(i));
 
-          if (pid >= threshold) {
+          if (pid >= threshold)
+          {
             // Delete the shortest one
-            if (((SequenceI)sel.elementAt(j)).getSequence().length() >
-                ((SequenceI)sel.elementAt(i)).getSequence().length()) {
+            if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
+                ( (SequenceI) sel.elementAt(i)).getSequence().length())
               del.addElement(sel.elementAt(i));
-              System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());
-            } else {
+            else
               del.addElement(sel.elementAt(i));
-              System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());
-            }
           }
         }
       }
     }
 
     // Now delete the sequences
-    for (int i=0; i < del.size(); i++) {
-      System.out.println("Deleting sequence " + ((SequenceI)del.elementAt(i)).getName());
+    for (int i=0; i < del.size(); i++)
       deleteSequence((SequenceI)del.elementAt(i));
-    }
 
     return del;
   }
@@ -324,13 +311,33 @@ public class Alignment implements AlignmentI
 
   /**    */
   public SequenceGroup findGroup(SequenceI s) {
-    for (int i = 0; i < this.groups.size();i++) {
+    for (int i = 0; i < this.groups.size();i++)
+    {
       SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-      if (sg.sequences.contains(s)) {
+      if (sg.sequences.contains(s))
         return sg;
-      }
+
     }
     return null;
+  }
+
+  public SequenceGroup [] findAllGroups(SequenceI s)
+  {
+
+    ArrayList temp = new ArrayList();
+
+    for (int i = 0; i < this.groups.size();i++)
+    {
+      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
+
+      if (sg.sequences.contains(s))
+       temp.add(sg);
+    }
+
+    SequenceGroup [] ret = new SequenceGroup[temp.size()];
+    temp.toArray( ret );
+
+    return ret;
 
   }
   /**    */
@@ -351,16 +358,45 @@ public class Alignment implements AlignmentI
     }
   }
 
+  public void addSuperGroup(SuperGroup sg)
+  {
+    superGroup.add(sg);
+  }
+
+  public void removeSuperGroup(SuperGroup sg)
+  {
+    superGroup.remove(sg);
+  }
+
+  public SuperGroup     getSuperGroup(SequenceGroup sg)
+  {
+    for (int i = 0; i < this.superGroup.size(); i++)
+    {
+      SuperGroup temp = (SuperGroup) superGroup.get(i);
+      if (temp.sequenceGroups.contains(sg))
+        return temp;
+    }
+    return null;
+  }
+
   /**    */
   public void addGroup(SequenceGroup sg) {
-    groups.addElement(sg);
+    if(!groups.contains(sg))
+      groups.addElement(sg);
   }
 
-  /**    */
-  public SequenceGroup addGroup() {
-    SequenceGroup sg = new SequenceGroup();
-    groups.addElement(sg);
-    return sg;
+  public void deleteAllGroups()
+  {
+    groups.clear();
+    superGroup.clear();
+   int i=0;
+    while (i < sequences.size()) {
+     SequenceI s = getSequenceAt(i);
+     s.setColor(java.awt.Color.white);
+     i++;
+   }
+
+
   }
 
   /**    */
@@ -375,21 +411,36 @@ public class Alignment implements AlignmentI
     int i = 0;
     while (i < sequences.size()) {
       SequenceI s = getSequenceAt(i);
-      if (s.getName().equals(name)) {
+      if (s.getName().equals(name))
         return s;
-      }
+
       i++;
     }
     return null;
   }
 
   /**    */
-  public int findIndex(SequenceI s) {
-    int i=0;
+  public SequenceI findbyDisplayId(String name) {
+    int i = 0;
     while (i < sequences.size()) {
-      if (s == getSequenceAt(i)) {
+      SequenceI s = getSequenceAt(i);
+      if (s.getDisplayId().equals(name))
+        return s;
+
+      i++;
+    }
+    return null;
+  }
+
+  /**    */
+  public int findIndex(SequenceI s)
+  {
+    int i=0;
+    while (i < sequences.size())
+    {
+      if (s == getSequenceAt(i))
         return i;
-      }
+
       i++;
     }
     return -1;
@@ -430,11 +481,18 @@ public class Alignment implements AlignmentI
     return max;
   }
 
-  public void setGapCharacter(String gc) {
+  public void setGapCharacter(char gc)
+  {
+    char old = getGapCharacter();
     gapCharacter = gc;
+    for (int i=0; i < sequences.size(); i++)
+     {
+       Sequence seq = (Sequence)sequences.elementAt(i);
+       seq.sequence = seq.sequence.replace(old, gc);
+     }
   }
 
-  public String getGapCharacter() {
+  public char getGapCharacter() {
     return gapCharacter;
   }