HiddenSequences now array, not hashtable

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e4bc25e..5f60530 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -146,8 +146,9 @@ public class Alignment implements AlignmentI
           getDataset().addSequence(ds);
         }
       }
-
       sequences.addElement(snew);
+
+      hiddenSequences.adjustHeightSequenceAdded();
     }
 
 
@@ -310,13 +311,7 @@ public class Alignment implements AlignmentI
      */
     public void deleteSequence(SequenceI s)
     {
-        for (int i = 0; i < getHeight(); i++)
-        {
-            if (getSequenceAt(i) == s)
-            {
-                deleteSequence(i);
-            }
-        }
+      deleteSequence(findIndex(s));
     }
 
     /**
@@ -327,6 +322,7 @@ public class Alignment implements AlignmentI
     public void deleteSequence(int i)
     {
         sequences.removeElementAt(i);
+        hiddenSequences.adjustHeightSequenceDeleted(i);
     }
 
 

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index aca108d..71ba3e0 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -107,6 +107,7 @@ public interface AlignmentI
      */
     public void deleteSequence(int i);
 
+
     /**
      * Deletes all residues in every sequence of alignment within given columns.
      *

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 0a588a2..e244dd7 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -23,7 +23,7 @@ import java.util.*;
 \r
 public class HiddenSequences\r
 {\r
-  Hashtable hiddenSequences;\r
+  public SequenceI []  hiddenSequences;\r
   AlignmentI alignment;\r
 \r
   public HiddenSequences(AlignmentI al)\r
@@ -33,31 +33,88 @@ public class HiddenSequences
 \r
   public int getSize()\r
   {\r
-    return hiddenSequences == null ? 0 : hiddenSequences.size();\r
+    if(hiddenSequences==null)\r
+    {\r
+      System.out.println("H is null");\r
+      return 0;\r
+    }\r
+    int count = 0;\r
+    for(int i=0; i<hiddenSequences.length; i++)\r
+      if(hiddenSequences[i] !=null )\r
+        count ++;\r
+\r
+    return count;\r
   }\r
 \r
   public int getWidth()\r
   {\r
-    Enumeration en = hiddenSequences.elements();\r
     int width = 0;\r
-    while(en.hasMoreElements())\r
+    for (int i = 0; i < hiddenSequences.length; i++)\r
+      if (hiddenSequences[i] != null && hiddenSequences[i].getLength()>width)\r
+        width = hiddenSequences[i].getLength();\r
+\r
+    return width;\r
+  }\r
+\r
+  /**\r
+   * Call this method if sequences are removed from the\r
+   * main alignment\r
+   */\r
+  public void adjustHeightSequenceDeleted(int seqIndex)\r
+  {\r
+    if(hiddenSequences==null)\r
     {\r
-      SequenceI seq = (SequenceI)en.nextElement();\r
-      if(seq.getLength()>width)\r
-        width = seq.getLength();\r
+      return;\r
     }\r
-    return width;\r
+\r
+    int alHeight = alignment.getHeight();\r
+\r
+    SequenceI [] tmp = new SequenceI [alHeight + getSize()];\r
+    int deletionIndex = adjustForHiddenSeqs(seqIndex);\r
+\r
+    for (int i = 0; i < hiddenSequences.length; i++)\r
+    {\r
+      if (i > deletionIndex)\r
+        tmp[i-1] = hiddenSequences[i];\r
+      else\r
+        tmp[i] = hiddenSequences[i];\r
+    }\r
+\r
+   hiddenSequences = tmp;\r
+\r
   }\r
 \r
+  /**\r
+   * Call this method if sequences are added to or removed from the\r
+   * main alignment\r
+   */\r
+  public void adjustHeightSequenceAdded()\r
+  {\r
+    if(hiddenSequences==null)\r
+    {\r
+      return;\r
+    }\r
+\r
+    int alHeight = alignment.getHeight();\r
+\r
+    SequenceI [] tmp = new SequenceI [alHeight + getSize()];\r
+    System.arraycopy(hiddenSequences,0,tmp,0,hiddenSequences.length);\r
+    hiddenSequences = tmp;\r
+  }\r
+\r
+\r
   public void hideSequence(SequenceI sequence)\r
   {\r
     if(hiddenSequences==null)\r
-      hiddenSequences = new Hashtable();\r
+      hiddenSequences = new SequenceI[alignment.getHeight()];\r
 \r
     int alignmentIndex = alignment.findIndex(sequence);\r
     alignmentIndex = adjustForHiddenSeqs(alignmentIndex);\r
 \r
-    hiddenSequences.put(new Integer(alignmentIndex), sequence);\r
+    if(hiddenSequences[alignmentIndex]!=null)\r
+    System.out.println("ERROR!!!!!!!!!!!");\r
+\r
+    hiddenSequences[alignmentIndex] = sequence;\r
 \r
     alignment.deleteSequence(sequence);\r
   }\r
@@ -65,11 +122,14 @@ public class HiddenSequences
   public Vector showAll()\r
   {\r
    Vector revealedSeqs = new Vector();\r
-   for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)\r
+   for(int i=0; i<hiddenSequences.length; i++)\r
     {\r
-      Vector tmp = showSequence(i);\r
-      for(int t=0; t<tmp.size(); t++)\r
-        revealedSeqs.addElement(tmp.elementAt(t));\r
+      if(hiddenSequences[i]!=null)\r
+      {\r
+        Vector tmp = showSequence(i);\r
+        for (int t = 0; t < tmp.size(); t++)\r
+          revealedSeqs.addElement(tmp.elementAt(t));\r
+      }\r
     }\r
     return revealedSeqs;\r
   }\r
@@ -89,12 +149,13 @@ public class HiddenSequences
 \r
     int start = adjustForHiddenSeqs(alignmentIndex-1);\r
     int end = adjustForHiddenSeqs(alignmentIndex);\r
+    if(end>=hiddenSequences.length)\r
+      end = hiddenSequences.length-1;\r
 \r
     for(int index = end; index > start; index--)\r
     {\r
-      SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(\r
-          index));\r
-\r
+      SequenceI seq =  hiddenSequences[index];\r
+      hiddenSequences[index] = null;\r
 \r
       if(seq!=null)\r
       {\r
@@ -105,28 +166,27 @@ public class HiddenSequences
           repSequence.showHiddenSequence(seq);\r
         }\r
       }\r
+\r
     }\r
 \r
     return revealedSeqs;\r
   }\r
 \r
-  public Hashtable getHiddenSequences()\r
-  {\r
-    return hiddenSequences;\r
-  }\r
-\r
   public SequenceI getHiddenSequence(int alignmentIndex)\r
   {\r
-    return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));\r
+    return hiddenSequences[alignmentIndex];\r
   }\r
 \r
   public int findIndexWithoutHiddenSeqs(int alignmentIndex)\r
   {\r
     int index = 0;\r
     int hiddenSeqs = 0;\r
+    if(hiddenSequences.length<=alignmentIndex)\r
+      System.out.println(alignmentIndex+" "+hiddenSequences.length);\r
+\r
     while(index <= alignmentIndex)\r
     {\r
-     if(hiddenSequences.containsKey(new Integer(index)))\r
+     if(hiddenSequences[index]!=null)\r
      {\r
        hiddenSeqs ++;\r
      }\r
@@ -139,40 +199,35 @@ public class HiddenSequences
   public int adjustForHiddenSeqs(int alignmentIndex)\r
   {\r
     int index = 0;\r
-    while(index <= alignmentIndex)\r
+    int hSize = hiddenSequences.length;\r
+    while(index <= alignmentIndex && index<hSize)\r
     {\r
-     if(hiddenSequences.containsKey(new Integer(index)))\r
-     {\r
-       alignmentIndex ++;\r
-     }\r
+      if(hiddenSequences[index]!=null)\r
+      {\r
+        alignmentIndex ++;\r
+      }\r
       index ++;\r
     };\r
 \r
     return alignmentIndex ;\r
   }\r
 \r
+\r
   public AlignmentI getFullAlignment()\r
   {\r
-    int isize = alignment.getHeight()+hiddenSequences.size();\r
+    int isize = hiddenSequences.length;\r
     SequenceI [] seq = new Sequence[isize];\r
 \r
-    Enumeration en = hiddenSequences.keys();\r
-    while(en.hasMoreElements())\r
-    {\r
-      Integer key = (Integer)en.nextElement();\r
-      seq[key.intValue()] = (SequenceI)hiddenSequences.get(key);\r
-    }\r
-\r
     int index = 0;\r
-    for(int i=0; i<isize; i++)\r
+    for(int i=0; i<hiddenSequences.length; i++)\r
     {\r
-      if(seq[i]!=null)\r
+      if(hiddenSequences[i]!=null)\r
+        seq[i] = hiddenSequences[i];\r
+      else\r
       {\r
-        continue;\r
+        seq[i] = alignment.getSequenceAt(index);\r
+        index++;\r
       }\r
-\r
-      seq[i] = alignment.getSequenceAt(index);\r
-      index++;\r
     }\r
 \r
     return new Alignment(seq);\r
@@ -180,6 +235,10 @@ public class HiddenSequences
 \r
   public boolean isHidden(SequenceI seq)\r
   {\r
-    return hiddenSequences.contains(seq);\r
+    for(int i=0; i<hiddenSequences.length; i++)\r
+      if(hiddenSequences[i] !=null && hiddenSequences[i]==seq)\r
+        return true;\r
+\r
+    return false;\r
   }\r
 }\r