From 6c4bc68ae8b1c5005e79661bb2d8246515cb787d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 5 Dec 2006 17:56:07 +0000
Subject: [PATCH] sequence is char []

---
 src/MCview/PDBChain.java                      |    8 ++++----
 src/jalview/analysis/AAFrequency.java         |    6 +++---
 src/jalview/analysis/AlignSeq.java            |    2 +-
 src/jalview/analysis/AlignmentSorter.java     |    4 ++--
 src/jalview/analysis/Conservation.java        |    2 +-
 src/jalview/analysis/NJTree.java              |    6 +++---
 src/jalview/analysis/SeqsetUtils.java         |    5 ++++-
 src/jalview/appletgui/AlignViewport.java      |    6 +++---
 src/jalview/appletgui/FeatureRenderer.java    |    6 +++---
 src/jalview/appletgui/Finder.java             |    2 +-
 src/jalview/appletgui/RedundancyPanel.java    |    4 ++--
 src/jalview/appletgui/SequenceRenderer.java   |    4 ++--
 src/jalview/appletgui/UserDefinedColours.java |    2 +-
 src/jalview/util/Comparison.java              |    4 ++--
 14 files changed, 32 insertions(+), 29 deletions(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index ddf05e1..0cb9f02 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -236,15 +236,15 @@ public class PDBChain {
             try {
               b = (Bond) bonds.elementAt(i);
 
-              ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
-                  ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
-                                         get(b.at1.resName)).intValue()]
+            /*  ( (Bond) bonds.elementAt(i)).startCol = cs.findColour(
+                  ResidueProperties.codonTranslate(
+                      ResidueProperties.aa3Hash.get(b.at1.resName).toString().charAt(0)
                   );
 
               b.endCol = cs.findColour(
                   ResidueProperties.aa[ ( (Integer) ResidueProperties.aa3Hash.
                                          get(b.at2.resName)).intValue()]
-                  );
+                  );*/
 
             } catch (Exception e)
             {
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index e2dd6f1..3d91080 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -75,7 +75,7 @@ public static final void calculate(SequenceI[] sequences,
 
   int[] values = new int[132];
 
-  String seq;
+  char [] seq;
 
   for (i = start; i < end; i++)
   {
@@ -88,9 +88,9 @@ public static final void calculate(SequenceI[] sequences,
     for (j = 0; j < jSize; j++)
     {
       seq = sequences[j].getSequence();
-      if (seq.length() > i)
+      if (seq.length > i)
       {
-        c = seq.charAt(i);
+        c = seq[i];
 
         if(c == '.' || c==' ')
           c = '-';
diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 0af85f1..d0c5869 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -106,7 +106,7 @@ public class AlignSeq
      */
     public AlignSeq(SequenceI s1, SequenceI s2, String type)
     {
-        SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);
+        SeqInit(s1, s1.getSequenceAsString(), s2,  s2.getSequenceAsString(), type);
     }
 
     /**
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bf18b70..24f2ddf 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -52,8 +52,8 @@ public class AlignmentSorter
 
         for (int i = 0; i < nSeq; i++)
         {
-            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
-                                       s.getSequence());
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
+                                       s.getSequenceAsString());
             seqs[i] = align.getSequenceAt(i);
         }
 
diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 1342e93..6098465 100755
--- 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
--- 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
--- 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
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -296,7 +296,7 @@ public class AlignViewport
           cons.findQuality();
         }
 
-        String sequence = cons.getConsSequence().getSequence();
+        char [] sequence = cons.getConsSequence().getSequence();
         float minR;
         float minG;
         float minB;
@@ -331,7 +331,7 @@ public class AlignViewport
         {
           float value = 0;
 
-          c = sequence.charAt(i);
+          c = sequence[i];
 
           if (Character.isDigit(c))
             value = (int) (c - '0');
@@ -1201,7 +1201,7 @@ public class AlignViewport
       }
       else
       {
-        selection[i] = seqs[i].getSequence(start, end);
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
     }
 
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index a24525e..47fbb0d 100755
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -293,7 +293,7 @@ public class FeatureRenderer
 
           for (i = fstart; i <= fend; i++)
           {
-            s = seq.getSequence().charAt(i);
+            s = seq.getCharAt(i);
 
             if (jalview.util.Comparison.isGap(s))
             {
@@ -412,10 +412,10 @@ public class FeatureRenderer
   {
     void setTransparency(Graphics g, float value)
     {
-     Graphics2D g2 = (Graphics2D) g;
+    /* Graphics2D g2 = (Graphics2D) g;
      g2.setComposite(
         AlphaComposite.getInstance(
-             AlphaComposite.SRC_OVER, value));
+             AlphaComposite.SRC_OVER, value));*/
     }
   }
 
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 52be802..4c195e8 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -191,7 +191,7 @@ public class Finder extends Panel implements ActionListener
         continue;
       }
 
-      item = seq.getSequence();
+      item = seq.getSequenceAsString();
       if(!caseSensitive.getState())
         item = item.toUpperCase();
 
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index fccc30f..fd85ce7 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -143,8 +143,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
             if(omitHidden==null)
             {
-              seqi = originalSequences[i].getSequence(start, end);
-              seqj = originalSequences[j].getSequence(start, end);
+              seqi = originalSequences[i].getSequenceAsString(start, end);
+              seqj = originalSequences[j].getSequenceAsString(start, end);
             }
             else
             {
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 480a506..04defb7 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -76,7 +76,7 @@ public class SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);
     }
     else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
     {
@@ -293,7 +293,7 @@ public class SequenceRenderer
       {
         if (i < seq.getLength())
         {
-          s = seq.getSequence().charAt(i);
+          s = seq.getCharAt(i);
         }
 
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 20f68b4..b9c0950 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -248,7 +248,7 @@ public class UserDefinedColours
 
     try
     {
-      col = oldColourScheme.findColour(aa, -1);
+      col = oldColourScheme.findColour(aa.charAt(0), -1);
     }
     catch (Exception ex)
     {}
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
index 6c7197a..50472a5 100755
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -55,8 +55,8 @@ public class Comparison
    */
   public static float compare(SequenceI ii, SequenceI jj, int start, int end)
   {
-    String si = ii.getSequence();
-    String sj = jj.getSequence();
+    String si = ii.getSequenceAsString();
+    String sj = jj.getSequenceAsString();
 
     int ilen = si.length() - 1;
     int jlen = sj.length() - 1;
-- 
1.7.10.2