sequence is char []

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index ddf05e1..0cb9f02 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -236,15 +236,15 @@ public class PDBChain {
             try {\r
               b = (Bond) bonds.elementAt(i);\r
 \r
-              ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(\r
-                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.\r
-                                         get(b.at1.resName)).intValue()]\r
+            /*  ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(\r
+                  ResidueProperties.codonTranslate(\r
+                      ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)\r
                   );\r
 \r
               b.endCol = cs.findColour(\r
                   ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.\r
                                          get(b.at2.resName)).intValue()]\r
-                  );\r
+                  );*/\r
 \r
             } catch (Exception e)\r
             {\r

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index e2dd6f1..3d91080 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -75,7 +75,7 @@ public static final void calculate(SequenceI[] sequences,
 \r
   int[] values = new int[132];\r
 \r
-  String seq;\r
+  char [] seq;\r
 \r
   for (i = start; i < end; i++)\r
   {\r
@@ -88,9 +88,9 @@ public static final void calculate(SequenceI[] sequences,
     for (j = 0; j < jSize; j++)\r
     {\r
       seq = sequences[j].getSequence();\r
-      if (seq.length() > i)\r
+      if (seq.length > i)\r
       {\r
-        c = seq.charAt(i);\r
+        c = seq[i];\r
 \r
         if(c == '.' || c==' ')\r
           c = '-';\r

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 0af85f1..d0c5869 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -106,7 +106,7 @@ public class AlignSeq
      */\r
     public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
     {\r
-        SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);\r
+        SeqInit(s1, s1.getSequenceAsString(), s2,  s2.getSequenceAsString(), type);\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bf18b70..24f2ddf 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -52,8 +52,8 @@ public class AlignmentSorter
 \r
         for (int i = 0; i < nSeq; i++)\r
         {\r
-            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),\r
-                                       s.getSequence());\r
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),\r
+                                       s.getSequenceAsString());\r
             seqs[i] = align.getSequenceAt(i);\r
         }\r
 \r

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 1342e93..6098465 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -100,7 +100,7 @@ public class Conservation
 
         if ((i > -1) && (i < sSize))
         {
-            sq = sequences[i].getSequence();
+            sq = sequences[i].getSequenceAsString();
 
             if (seqNums.size() <= i)
             {

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 78c4e60..6f89754 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -298,7 +298,7 @@ public class NJTree
                         leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
                     }
                     leaf.setPlaceholder(true);
-                    
+
                 }
             }
         }
@@ -680,8 +680,8 @@ public class NJTree
                         try
                         {
                             score += ResidueProperties.getBLOSUM62(
-                              sequenceString[i].substring(k, k + 1),
-                              sequenceString[j].substring(k, k + 1));
+                              sequenceString[i].charAt(k),
+                              sequenceString[j].charAt(k));
                         }
                         catch (Exception ex)
                         {

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 885305a..00fbad5 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -204,7 +204,10 @@ public class SeqsetUtils
       boolean ungapped[] = new boolean[sequences.length];
       int msflen=0;
       for (int i=0,j=sequences.length; i<j;i++) {
-        String tempseq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequences[i].getSequence());
+        String tempseq = jalview.analysis.AlignSeq.extractGaps(
+            jalview.util.Comparison.GapChars,
+            sequences[i].getSequenceAsString());
+
         if (tempseq.length()==0)
           ungapped[i]=false;
         else {

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d67b0..ad7113a 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -296,7 +296,7 @@ public class AlignViewport
           cons.findQuality();\r
         }\r
 \r
-        String sequence = cons.getConsSequence().getSequence();\r
+        char [] sequence = cons.getConsSequence().getSequence();\r
         float minR;\r
         float minG;\r
         float minB;\r
@@ -331,7 +331,7 @@ public class AlignViewport
         {\r
           float value = 0;\r
 \r
-          c = sequence.charAt(i);\r
+          c = sequence[i];\r
 \r
           if (Character.isDigit(c))\r
             value = (int) (c - '0');\r
@@ -1201,7 +1201,7 @@ public class AlignViewport
       }\r
       else\r
       {\r
-        selection[i] = seqs[i].getSequence(start, end);\r
+        selection[i] = seqs[i].getSequenceAsString(start, end);\r
       }\r
     }\r
 \r

diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index a24525e..47fbb0d 100755 (executable)
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -293,7 +293,7 @@ public class FeatureRenderer
 \r
           for (i = fstart; i <= fend; i++)\r
           {\r
-            s = seq.getSequence().charAt(i);\r
+            s = seq.getCharAt(i);\r
 \r
             if (jalview.util.Comparison.isGap(s))\r
             {\r
@@ -412,10 +412,10 @@ public class FeatureRenderer
   {\r
     void setTransparency(Graphics g, float value)\r
     {\r
-     Graphics2D g2 = (Graphics2D) g;\r
+    /* Graphics2D g2 = (Graphics2D) g;\r
      g2.setComposite(\r
         AlphaComposite.getInstance(\r
-             AlphaComposite.SRC_OVER, value));\r
+             AlphaComposite.SRC_OVER, value));*/\r
     }\r
   }\r
 \r

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 52be802..4c195e8 100755 (executable)
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -191,7 +191,7 @@ public class Finder extends Panel implements ActionListener
         continue;\r
       }\r
 \r
-      item = seq.getSequence();\r
+      item = seq.getSequenceAsString();\r
       if(!caseSensitive.getState())\r
         item = item.toUpperCase();\r
 \r

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index fccc30f..fd85ce7 100755 (executable)
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -143,8 +143,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 \r
             if(omitHidden==null)\r
             {\r
-              seqi = originalSequences[i].getSequence(start, end);\r
-              seqj = originalSequences[j].getSequence(start, end);\r
+              seqi = originalSequences[i].getSequenceAsString(start, end);\r
+              seqj = originalSequences[j].getSequenceAsString(start, end);\r
             }\r
             else\r
             {\r

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 480a506..04defb7 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -76,7 +76,7 @@ public class SequenceRenderer
   {\r
     if (cs != null)\r
     {\r
-      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);\r
     }\r
     else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
     {\r
@@ -293,7 +293,7 @@ public class SequenceRenderer
       {\r
         if (i < seq.getLength())\r
         {\r
-          s = seq.getSequence().charAt(i);\r
+          s = seq.getCharAt(i);\r
         }\r
 \r
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 20f68b4..b9c0950 100755 (executable)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -248,7 +248,7 @@ public class UserDefinedColours
 \r
     try\r
     {\r
-      col = oldColourScheme.findColour(aa, -1);\r
+      col = oldColourScheme.findColour(aa.charAt(0), -1);\r
     }\r
     catch (Exception ex)\r
     {}\r

diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 6c7197a..50472a5 100755 (executable)
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -55,8 +55,8 @@ public class Comparison
    */\r
   public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
   {\r
-    String si = ii.getSequence();\r
-    String sj = jj.getSequence();\r
+    String si = ii.getSequenceAsString();\r
+    String sj = jj.getSequenceAsString();\r
 \r
     int ilen = si.length() - 1;\r
     int jlen = sj.length() - 1;\r