Remove redundancy in Eclipse

diff --git a/src/com/stevesoft/pat/Bits.java b/src/com/stevesoft/pat/Bits.java
index 244889f..0c67903 100755 (executable)
--- a/src/com/stevesoft/pat/Bits.java
+++ b/src/com/stevesoft/pat/Bits.java
@@ -7,7 +7,6 @@ package//
 //\r
 com.stevesoft.pat;\r
 \r
-import java.io.*;\r
 \r
 public class Bits {\r
   char[] carray;\r

diff --git a/src/com/stevesoft/pat/DirFileRegex.java b/src/com/stevesoft/pat/DirFileRegex.java
index 731457c..c46762e 100755 (executable)
--- a/src/com/stevesoft/pat/DirFileRegex.java
+++ b/src/com/stevesoft/pat/DirFileRegex.java
@@ -6,7 +6,6 @@
 //    -- Happy Computing!\r
 //\r
 package com.stevesoft.pat;\r
-import java.io.File;\r
 \r
 /** This class is just like FileRegex, except that its accept method\r
  only returns true if the file matching the pattern is a directory.*/\r

diff --git a/src/com/stevesoft/pat/NonDirFileRegex.java b/src/com/stevesoft/pat/NonDirFileRegex.java
index 92f54a3..7ef24a3 100755 (executable)
--- a/src/com/stevesoft/pat/NonDirFileRegex.java
+++ b/src/com/stevesoft/pat/NonDirFileRegex.java
@@ -6,7 +6,6 @@
 //    -- Happy Computing!\r
 //\r
 package com.stevesoft.pat;\r
-import java.io.File;\r
 \r
 /** This class is just like FileRegex, except that its accept method\r
  only returns true if the file matching the pattern is not a directory.*/\r

diff --git a/src/com/stevesoft/pat/OrMark.java b/src/com/stevesoft/pat/OrMark.java
index e9bf0ca..c323a9d 100755 (executable)
--- a/src/com/stevesoft/pat/OrMark.java
+++ b/src/com/stevesoft/pat/OrMark.java
@@ -7,7 +7,6 @@
 //\r
 package com.stevesoft.pat;\r
 import java.util.Hashtable;\r
-import java.util.Vector;\r
 \r
 /** Implements the parenthesis pattern subelement.*/\r
 class OrMark extends Or {\r

diff --git a/src/com/stevesoft/pat/PartialBuffer.java b/src/com/stevesoft/pat/PartialBuffer.java
index 2239545..fd57b27 100755 (executable)
--- a/src/com/stevesoft/pat/PartialBuffer.java
+++ b/src/com/stevesoft/pat/PartialBuffer.java
@@ -7,7 +7,6 @@
 //\r
 package com.stevesoft.pat;\r
 \r
-import java.io.*;\r
 \r
 /** This class allows you to match on a partial string.\r
     If the allowOverRun flag is true, then the\r

diff --git a/src/com/stevesoft/pat/RBuffer.java b/src/com/stevesoft/pat/RBuffer.java
index 08fb920..b9dda64 100755 (executable)
--- a/src/com/stevesoft/pat/RBuffer.java
+++ b/src/com/stevesoft/pat/RBuffer.java
@@ -7,8 +7,6 @@
 //\r
 package com.stevesoft.pat;\r
 \r
-import java.io.*;\r
-import com.stevesoft.pat.wrap.*;\r
 \r
 /** This class is used internally by RegexReader to\r
     store blocks of data. */\r

diff --git a/src/com/stevesoft/pat/RegOpt.java b/src/com/stevesoft/pat/RegOpt.java
index 1033500..bf99e36 100755 (executable)
--- a/src/com/stevesoft/pat/RegOpt.java
+++ b/src/com/stevesoft/pat/RegOpt.java
@@ -7,7 +7,6 @@
 //\r
 package com.stevesoft.pat;\r
 import java.util.*;\r
-import java.io.*;\r
 \r
 /** This class is just like oneChar, but doesn't worry about case. */\r
 class FastChar extends oneChar {\r

diff --git a/src/com/stevesoft/pat/RegRes.java b/src/com/stevesoft/pat/RegRes.java
index f181564..76ff4ea 100755 (executable)
--- a/src/com/stevesoft/pat/RegRes.java
+++ b/src/com/stevesoft/pat/RegRes.java
@@ -6,8 +6,6 @@
 //    -- Happy Computing!\r
 //\r
 package com.stevesoft.pat;\r
-import java.util.*;\r
-\r
 /** \r
         Shareware: package pat\r
    <a href="copyright.html">Copyright 2001, Steven R. Brandt</a>\r

diff --git a/src/com/stevesoft/pat/Regex.java b/src/com/stevesoft/pat/Regex.java
index c7379de..665632e 100755 (executable)
--- a/src/com/stevesoft/pat/Regex.java
+++ b/src/com/stevesoft/pat/Regex.java
@@ -832,7 +832,7 @@ public class Regex extends RegRes implements FilenameFilter {
             while(!sp.match(')'))\r
                 sp.inc();\r
         } else if(sp.dontMatch && sp.c == 'w') {\r
-            Regex r = new Regex();\r
+            //Regex r = new Regex();\r
             //r._compile("[a-zA-Z0-9_]",mk);\r
             //add(new Goop("\\w",r.thePattern));\r
             Bracket b = new Bracket(false);\r
@@ -853,14 +853,14 @@ public class Regex extends RegRes implements FilenameFilter {
             b.addOr(new oneChar((char)13));\r
             add(b);\r
         } else if(sp.dontMatch && sp.c == 'd') {\r
-            Regex r = new Regex();\r
+            //Regex r = new Regex();\r
             //r._compile("[0-9]",mk);\r
             //add(new Goop("\\d",r.thePattern));\r
             Range digit = new Range('0','9');\r
             digit.printBrackets = true;\r
             add(digit);\r
         } else if(sp.dontMatch && sp.c == 'W') {\r
-            Regex r = new Regex();\r
+            //Regex r = new Regex();\r
             //r._compile("[^a-zA-Z0-9_]",mk);\r
             //add(new Goop("\\W",r.thePattern));\r
             Bracket b = new Bracket(true);\r
@@ -1003,7 +1003,7 @@ public class Regex extends RegRes implements FilenameFilter {
         } else if(sp.match('{')) {\r
             boolean bad = false;\r
             StrPos sp2 = new StrPos(sp);\r
-            StringBuffer sb = new StringBuffer();\r
+            //StringBuffer sb = new StringBuffer();\r
             sp.inc();\r
             patInt i1 = sp.getPatInt();\r
             patInt i2 = null;\r

diff --git a/src/com/stevesoft/pat/RegexTokenizer.java b/src/com/stevesoft/pat/RegexTokenizer.java
index 40302a4..bc6fe51 100755 (executable)
--- a/src/com/stevesoft/pat/RegexTokenizer.java
+++ b/src/com/stevesoft/pat/RegexTokenizer.java
@@ -47,14 +47,14 @@ public class RegexTokenizer implements Enumeration {
     public RegexTokenizer(String txt,String ptrn) {\r
         toParse = txt;\r
         r = new Regex(ptrn);\r
-        offset = r.BackRefOffset;\r
+        offset = Regex.BackRefOffset;\r
         getMore();\r
     }\r
     /** Initialize the tokenizer with a Regex object. */\r
     public RegexTokenizer(String txt,Regex r) {\r
         toParse = txt;\r
         this.r = r;\r
-        offset = r.BackRefOffset;\r
+        offset = Regex.BackRefOffset;\r
         getMore();\r
     }\r
     /** This should always be cast to a String, as in StringTokenizer,\r
@@ -94,7 +94,7 @@ public class RegexTokenizer implements Enumeration {
     public boolean hasMoreTokens() { return hasMoreElements(); }\r
     /** Determines the # of remaining tokens */\r
     public int countTokens() {\r
-        int old_pos=pos,_count=count;\r
+        int _count=count;\r
         while(hasMoreTokens())\r
             nextToken();\r
         count=_count;\r

diff --git a/src/com/stevesoft/pat/Replacer.java b/src/com/stevesoft/pat/Replacer.java
index c78a11d..bdeea39 100755 (executable)
--- a/src/com/stevesoft/pat/Replacer.java
+++ b/src/com/stevesoft/pat/Replacer.java
@@ -7,7 +7,6 @@
 //\r
 package com.stevesoft.pat;\r
 \r
-import java.util.*;\r
 import com.stevesoft.pat.wrap.StringWrap;\r
 \r
 /** Internally used class. */\r
@@ -182,7 +181,6 @@ public class Replacer {
             for(int ii=pos;ii<rmf;ii++)\r
               sb.append(src.charAt(ii));\r
 \r
-            Vector v = new Vector();\r
             for(ReplaceRule x=rp;x != null;x=x.next) {\r
                 x.apply(sb,r);\r
                 if(x instanceof SpecialRule) {\r

diff --git a/src/com/stevesoft/pat/Skip.java b/src/com/stevesoft/pat/Skip.java
index 664c712..ca2dbb5 100755 (executable)
--- a/src/com/stevesoft/pat/Skip.java
+++ b/src/com/stevesoft/pat/Skip.java
@@ -21,7 +21,6 @@ public class Skip {
             CaseMgr.toLowerCase(x) |\r
             CaseMgr.toTitleCase(x));\r
     }\r
-    static { int x = Regex.BackRefOffset; }\r
     String src;\r
     int c,mask;\r
     int offset;\r
@@ -99,7 +98,6 @@ public class Skip {
                     p = p.next;\r
                 }\r
                 String st = sb.toString();\r
-                char c0 = st.charAt(0), c1 = st.charAt(1);\r
                 Skip sk=null;\r
                 if(st.length()>2)\r
                     sk = new SkipBMH(st,ignoreCase,offset);\r

diff --git a/src/com/stevesoft/pat/StrPos.java b/src/com/stevesoft/pat/StrPos.java
index 4a9f287..6043625 100755 (executable)
--- a/src/com/stevesoft/pat/StrPos.java
+++ b/src/com/stevesoft/pat/StrPos.java
@@ -99,7 +99,6 @@ public class StrPos {
     }\r
     /** Read in an integer. */\r
     public patInt getPatInt() {\r
-        patInt pi = null;\r
         if(incMatch("inf"))\r
             return new patInf();\r
         int i,cnt=0;\r

diff --git a/src/com/stevesoft/pat/StringBufferLike.java b/src/com/stevesoft/pat/StringBufferLike.java
index 6987eec..18fa994 100755 (executable)
--- a/src/com/stevesoft/pat/StringBufferLike.java
+++ b/src/com/stevesoft/pat/StringBufferLike.java
@@ -7,7 +7,6 @@ package//
 //\r
 com.stevesoft.pat;\r
 \r
-import com.stevesoft.pat.*;\r
 \r
 /** A tool that is used to make the \E, \U, \L, and \Q\r
     elements of a substitution. */\r

diff --git a/src/com/stevesoft/pat/TransPat.java b/src/com/stevesoft/pat/TransPat.java
index 27c1fb2..125a7bd 100755 (executable)
--- a/src/com/stevesoft/pat/TransPat.java
+++ b/src/com/stevesoft/pat/TransPat.java
@@ -7,7 +7,6 @@
 //\r
 package com.stevesoft.pat;\r
 \r
-import java.util.*;\r
 \r
 /** This class is used to implement the Transformer\r
     @see com.stevesoft.pat.Transform\r
@@ -27,7 +26,7 @@ class TransPat extends Pattern {
         for(int i=0;i<ra_len;i++) {\r
             pt.ignoreCase = ra[i].ignoreCase;\r
             pt.mFlag = ra[i].mFlag;\r
-            pt.dotDoesntMatchCR = ra[i].dotDoesntMatchCR;\r
+            pt.dotDoesntMatchCR = Regex.dotDoesntMatchCR;\r
             int r = ra[i].thePattern.matchInternal(pos,pt);\r
             if(r >= 0) {\r
                 pn = i;\r

diff --git a/src/com/stevesoft/pat/Transformer.java b/src/com/stevesoft/pat/Transformer.java
index f65afb4..14f7e38 100755 (executable)
--- a/src/com/stevesoft/pat/Transformer.java
+++ b/src/com/stevesoft/pat/Transformer.java
@@ -7,7 +7,6 @@
 //\r
 package com.stevesoft.pat;\r
 \r
-import java.util.Vector;\r
 import com.stevesoft.pat.wrap.StringWrap;\r
 \r
 /** Replacement rule used by the Transformer.\r

diff --git a/src/ext/vamsas/JpredSoapBindingStub.java b/src/ext/vamsas/JpredSoapBindingStub.java
index 360a522..a42bc49 100755 (executable)
--- a/src/ext/vamsas/JpredSoapBindingStub.java
+++ b/src/ext/vamsas/JpredSoapBindingStub.java
@@ -83,14 +83,14 @@ public class JpredSoapBindingStub extends org.apache.axis.client.Stub implements
             javax.xml.namespace.QName qName;
             java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
             java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
-            java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+            /*java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
             java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
             java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
             java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
             java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
             java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
             java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;*/
             qName = new javax.xml.namespace.QName("http://simple.objects.vamsas", "JpredResult");
             cachedSerQNames.add(qName);
             cls = vamsas.objects.simple.JpredResult.class;

diff --git a/src/ext/vamsas/MuscleWSSoapBindingStub.java b/src/ext/vamsas/MuscleWSSoapBindingStub.java
index 35e2470..c56432d 100755 (executable)
--- a/src/ext/vamsas/MuscleWSSoapBindingStub.java
+++ b/src/ext/vamsas/MuscleWSSoapBindingStub.java
@@ -61,14 +61,14 @@ public class MuscleWSSoapBindingStub extends org.apache.axis.client.Stub
         javax.xml.namespace.QName qName;\r
         java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;\r
         java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;\r
-        java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;\r
-        java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;\r
+        //java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;\r
+        //java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;\r
         java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;\r
         java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;\r
-        java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;\r
-        java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;\r
-        java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;\r
-        java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;\r
+        //java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;\r
+        // java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;\r
+        //java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;\r
+        //java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;\r
         qName = new javax.xml.namespace.QName("simple.objects.vamsas",\r
                 "Sequence");\r
         cachedSerQNames.add(qName);\r

diff --git a/src/ext/vamsas/RegistryServiceSoapBindingStub.java b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
index cf72cb1..6379c0c 100755 (executable)
--- a/src/ext/vamsas/RegistryServiceSoapBindingStub.java
+++ b/src/ext/vamsas/RegistryServiceSoapBindingStub.java
@@ -52,14 +52,14 @@ public class RegistryServiceSoapBindingStub extends org.apache.axis.client.Stub
             javax.xml.namespace.QName qName;
             java.lang.Class beansf = org.apache.axis.encoding.ser.BeanSerializerFactory.class;
             java.lang.Class beandf = org.apache.axis.encoding.ser.BeanDeserializerFactory.class;
-            java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
-            java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
+            //java.lang.Class enumsf = org.apache.axis.encoding.ser.EnumSerializerFactory.class;
+            //java.lang.Class enumdf = org.apache.axis.encoding.ser.EnumDeserializerFactory.class;
             java.lang.Class arraysf = org.apache.axis.encoding.ser.ArraySerializerFactory.class;
             java.lang.Class arraydf = org.apache.axis.encoding.ser.ArrayDeserializerFactory.class;
-            java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
-            java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
-            java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
-            java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
+            //java.lang.Class simplesf = org.apache.axis.encoding.ser.SimpleSerializerFactory.class;
+            //java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
+            //java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
+            //java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
             qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_ServiceHandle");
             cachedSerQNames.add(qName);
             cls = ext.vamsas.ServiceHandle[].class;

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 461b545..ad1fe4e 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -18,8 +18,6 @@
 */\r
 package jalview.analysis;\r
 \r
-import jalview.analysis.*;\r
-\r
 import jalview.datamodel.*;\r
 \r
 import java.util.*;\r

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 71d6737..97b8519 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -251,14 +251,14 @@ public class NJTree
     {\r
         while (noClus > 2)\r
         {\r
-            if (type.equals("NJ"))\r
+           /* if (type.equals("NJ"))\r
             {\r
                 float mind = findMinNJDistance();\r
             }\r
             else\r
             {\r
                 float mind = findMinDistance();\r
-            }\r
+            }*/\r
 \r
             Cluster c = joinClusters(mini, minj);\r
 \r
@@ -273,7 +273,7 @@ public class NJTree
         boolean onefound = false;\r
 \r
         int one = -1;\r
-        int two = -1;\r
+        //int two = -1;\r
 \r
         for (int i = 0; i < noseqs; i++)\r
         {\r
@@ -281,7 +281,7 @@ public class NJTree
             {\r
                 if (onefound == false)\r
                 {\r
-                    two = i;\r
+                    //two = i;\r
                     onefound = true;\r
                 }\r
                 else\r
@@ -291,7 +291,7 @@ public class NJTree
             }\r
         }\r
 \r
-        Cluster c = joinClusters(one, two);\r
+       // Cluster c = joinClusters(one, two);\r
         top = (SequenceNode) (node.elementAt(one));\r
 \r
         reCount(top);\r
@@ -375,11 +375,11 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,\r
         float dist)\r
     {\r
-        float ih = 0;\r
-        float jh = 0;\r
+        //float ih = 0;\r
+       // float jh = 0;\r
 \r
-        SequenceNode sni = tmpi;\r
-        SequenceNode snj = tmpj;\r
+        //SequenceNode sni = tmpi;\r
+        //SequenceNode snj = tmpj;\r
 \r
         tmpi.dist = ((dist + ri) - rj) / 2;\r
         tmpj.dist = (dist - tmpi.dist);\r
@@ -469,8 +469,8 @@ public class NJTree
      */\r
     public void findClusterNJDistance(int i, int j)\r
     {\r
-        int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
-        int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
+        //int noi = ((Cluster) cluster.elementAt(i)).value.length;\r
+        //int noj = ((Cluster) cluster.elementAt(j)).value.length;\r
 \r
         // New distances from cluster to others\r
         float[] newdist = new float[noseqs];\r
@@ -1121,15 +1121,6 @@ public class NJTree
         }\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param node DOCUMENT ME!\r
-     */\r
-    public void setMaxDist(SequenceNode node)\r
-    {\r
-        this.maxdist = maxdist;\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 662322a..bd0f45c 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -115,7 +115,7 @@ public class SeqsetUtils
   {\r
     // Generate a safely named sequence set and a hash to recover the sequence names\r
     Hashtable map = new Hashtable();\r
-    String[] un_names = new String[sequences.length];\r
+    //String[] un_names = new String[sequences.length];\r
 \r
     for (int i = 0; i < sequences.length; i++)\r
     {\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0f275de..e303500 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -55,7 +55,6 @@ public class AlignFrame
       {\r
         try\r
         {\r
-          treeFile = treeFile;\r
           jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
               getCodeBase() + treeFile, "URL");\r
           fin.parse();\r
@@ -771,7 +770,7 @@ public class AlignFrame
 \r
   public void findMenuItem_actionPerformed(ActionEvent e)\r
   {\r
-    Finder finder = new Finder(alignPanel);\r
+    new Finder(alignPanel);\r
   }\r
 \r
   public void font_actionPerformed(ActionEvent e)\r
@@ -1091,7 +1090,7 @@ public class AlignFrame
 \r
   public void userDefinedColour_actionPerformed(ActionEvent e)\r
   {\r
-    UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
+    new UserDefinedColours(alignPanel, null);\r
   }\r
 \r
   public void PIDColour_actionPerformed(ActionEvent e)\r

diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index e424a42..17fe98a 100755 (executable)
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -48,7 +48,6 @@ public class FontChooser
 \r
   void init()\r
     {\r
-    this.ap = ap;\r
     String fonts[] = Toolkit.getDefaultToolkit().getFontList();\r
     for (int i = 0; i < fonts.length; i++)\r
     {\r

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 30560d7..a277adb 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -21,7 +21,6 @@ package jalview.appletgui;
 \r
 import java.awt.*;\r
 \r
-import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 \r
 public class IdCanvas\r

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index c9285dd..d5243e3 100755 (executable)
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -88,7 +88,7 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);\r
     }\r
 \r
-    AlignFrame af = new AlignFrame(new Alignment(seq),\r
+    new AlignFrame(new Alignment(seq),\r
                                    ap.alignFrame.applet,\r
                                    "Pairwise Aligned Sequences");\r
 \r

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 82207a2..5daa320 100755 (executable)
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -97,7 +97,6 @@ public class RotatableCanvas
   {\r
     this.points = points;\r
     this.npoint = npoint;\r
-    this.av = av;\r
     PaintRefresher.Register(this, av.alignment);\r
 \r
     prefsize = getPreferredSize();\r
@@ -348,7 +347,7 @@ public class RotatableCanvas
 \r
   public void drawScene(Graphics g)\r
   {\r
-    boolean darker = false;\r
+    //boolean darker = false;\r
 \r
     int halfwidth = getSize().width / 2;\r
     int halfheight = getSize().height / 2;\r
@@ -564,7 +563,7 @@ public class RotatableCanvas
 \r
   public void rectSelect(int x1, int y1, int x2, int y2)\r
   {\r
-    boolean changedSel = false;\r
+    //boolean changedSel = false;\r
     for (int i = 0; i < npoint; i++)\r
     {\r
       SequencePoint sp = (SequencePoint) points.elementAt(i);\r

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 76569dd..d4202c3 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -295,9 +295,9 @@ public class TreeCanvas
     if (node.left() == null && node.right() == null)\r
     {\r
       float height = node.height;\r
-      float dist = node.dist;\r
+      //float dist = node.dist;\r
 \r
-      int xstart = (int) ( (height - dist) * scale) + offx;\r
+      //int xstart = (int) ( (height - dist) * scale) + offx;\r
       int xend = (int) (height * scale) + offx;\r
 \r
       int ypos = (int) (node.ycount * chunk) + offy;\r

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 3866140..c88c92a 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,7 +22,6 @@ import java.io.*;
 \r
 import java.util.*;\r
 \r
-import java.net.*;\r
 import org.apache.log4j.Logger;\r
 import org.apache.log4j.SimpleLayout;\r
 import org.apache.log4j.Level;\r

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9a85471..910c947 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,8 +20,6 @@ package jalview.bin;
 \r
 import jalview.gui.*;\r
 \r
-import org.apache.log4j.*;\r
-\r
 import javax.swing.*;\r
 \r
 import java.util.Vector;\r

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 3cc6910..89d3971 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -18,15 +18,8 @@
 */\r
 package jalview.datamodel;\r
 \r
-import jalview.analysis.PCA;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
 import jalview.schemes.*;\r
 \r
-import java.awt.*;\r
 \r
 \r
 /**\r

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 824a33b..d30003d 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,8 +18,6 @@
 */\r
 package jalview.datamodel;\r
 \r
-import jalview.analysis.*;\r
-\r
 import java.awt.*;\r
 \r
 import java.util.*;\r

diff --git a/src/jalview/datamodel/SuperGroup.java b/src/jalview/datamodel/SuperGroup.java
index b2993b5..6c0e604 100755 (executable)
--- a/src/jalview/datamodel/SuperGroup.java
+++ b/src/jalview/datamodel/SuperGroup.java
@@ -18,8 +18,6 @@
 */\r
 package jalview.datamodel;\r
 \r
-import jalview.datamodel.*;\r
-\r
 import jalview.schemes.*;\r
 \r
 import java.util.*;\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9243e99..90e911e 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -27,7 +27,6 @@ import java.awt.datatransfer.*;
 import java.awt.event.*;\r
 import java.awt.print.*;\r
 import javax.swing.*;\r
-import javax.swing.event.*;\r
 \r
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
@@ -1280,7 +1279,7 @@ public class AlignFrame
     if (viewport.showSequenceFeatures &&\r
         ! ( (Alignment) viewport.alignment).featuresAdded)\r
     {\r
-      SequenceFeatureFetcher sft = new SequenceFeatureFetcher(viewport.\r
+      new SequenceFeatureFetcher(viewport.\r
           alignment,\r
           alignPanel);\r
       ( (Alignment) viewport.alignment).featuresAdded = true;\r
@@ -1627,8 +1626,6 @@ public class AlignFrame
     conservationMenuItem.setSelected(false);\r
     viewport.setConservationSelected(false);\r
 \r
-    ColourSchemeI cs = viewport.getGlobalColourScheme();\r
-\r
     changeColour(viewport.getGlobalColourScheme());\r
 \r
     modifyPID_actionPerformed(null);\r
@@ -2242,11 +2239,11 @@ public class AlignFrame
    */\r
   public void BuildWebServiceMenu()\r
   {\r
-    if ( (Desktop.discoverer.services != null)\r
-        && (Desktop.discoverer.services.size() > 0))\r
+    if ( (Discoverer.services != null)\r
+        && (Discoverer.services.size() > 0))\r
     {\r
-      Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");\r
-      Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");\r
+      Vector msaws = (Vector) Discoverer.services.get("MsaWS");\r
+      Vector secstrpr = (Vector) Discoverer.services.get("SecStrPred");\r
       Vector wsmenu = new Vector();\r
       if (msaws != null)\r
       {\r
@@ -2262,7 +2259,7 @@ public class AlignFrame
             public void actionPerformed(ActionEvent e)\r
             {\r
               SequenceI[] msa = gatherSequencesForAlignment();\r
-              MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+              new jalview.ws.MsaWSClient(sh, title, msa,\r
                   false, true);\r
 \r
             }\r
@@ -2279,7 +2276,7 @@ public class AlignFrame
               public void actionPerformed(ActionEvent e)\r
               {\r
                 SequenceI[] msa = gatherSequencesForAlignment();\r
-                MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+                new jalview.ws.MsaWSClient(sh, title, msa,\r
                     true, true);\r
 \r
               }\r
@@ -2308,8 +2305,7 @@ public class AlignFrame
               if (msa.length == 1)\r
               {\r
                 // Single Sequence prediction\r
-                jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
-                    title, msa[0]);\r
+                new jalview.ws.JPredClient(sh,title, msa[0]);\r
               }\r
               else\r
               {\r
@@ -2342,4 +2338,30 @@ public class AlignFrame
     // TODO: group services by location as well as function.\r
   }\r
 \r
+  public void vamsasStore_actionPerformed(ActionEvent e)\r
+{\r
+  /* JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+       getProperty("LAST_DIRECTORY"));\r
+\r
+   chooser.setFileView(new JalviewFileView());\r
+   chooser.setDialogTitle("Export to Vamsas file");\r
+   chooser.setToolTipText("Export");\r
+\r
+   int value = chooser.showSaveDialog(this);\r
+   */\r
+  //  if (value == JalviewFileChooser.APPROVE_OPTION)\r
+  {\r
+         jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+    vs.store("C:\\Documents And Settings\\andrew\\Desktop\\vamsas.zip");\r
+   // chooser.getSelectedFile().getAbsolutePath();\r
+  }\r
+}\r
+\r
+public void vamsasLoad_actionPerformed(ActionEvent e)\r
+{\r
+  jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+  vs.load("C:\\Documents And Settings\\andrew\\Desktop\\vamsas.zip");\r
+}\r
+\r
+\r
 }\r

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d1187ac..a9d532c 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -128,6 +128,13 @@ public class AlignmentPanel extends GAlignmentPanel
                     case KeyEvent.VK_DELETE:\r
                       alignFrame.cut_actionPerformed(null);\r
                       break;\r
+\r
+                    case KeyEvent.VK_P:\r
+                      seqPanel.seqCanvas.increaseAARatio();\r
+                      break;\r
+                    case KeyEvent.VK_L:\r
+                      seqPanel.seqCanvas.decreaseAARation();\r
+                      break;\r
                     }\r
 \r
                 }\r
@@ -294,6 +301,7 @@ public class AlignmentPanel extends GAlignmentPanel
         annotationSpaceFillerHolder.setVisible(b);\r
         annotationScroller.setVisible(b);\r
       }\r
+      repaint();\r
     }\r
 \r
     /**\r

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 57dabff..db6fb18 100755 (executable)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -29,7 +29,6 @@ import java.awt.datatransfer.*;
 import java.awt.event.*;\r
 \r
 import javax.swing.*;\r
-import javax.swing.event.InternalFrameEvent;\r
 \r
 \r
 /**\r

diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java
index 78c1f02..5926563 100755 (executable)
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
@@ -50,7 +50,7 @@ public class EPSOptions
        null, new Object[]{this});\r
 \r
     dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options");\r
-    dialog.show();\r
+    dialog.setVisible(true);\r
 \r
   }\r
 \r
@@ -122,13 +122,13 @@ public class EPSOptions
       jalview.bin.Cache.setProperty("EPS_RENDERING", value);\r
     }\r
 \r
-    dialog.hide();\r
+    dialog.setVisible(false);\r
   }\r
 \r
   public void cancel_actionPerformed(ActionEvent e)\r
   {\r
     cancelled = true;\r
-    dialog.hide();\r
+    dialog.setVisible(false);\r
   }\r
 \r
   public String getValue()\r

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 7d283ba..9b1f10d 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.analysis.*;\r
-\r
 import jalview.datamodel.*;\r
 \r
 import java.awt.*;\r

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index a6b1066..32aad84 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.bin.*;\r
-\r
 import jalview.io.*;\r
 \r
 import jalview.jbgui.*;\r

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 303aac6..42c52d3 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -396,6 +396,7 @@ public class SeqCanvas extends JComponent
 \r
         while ((ypos <= canvasHeight) && (startRes < av.alignment.getWidth()))\r
         {\r
+            g.setFont(av.getFont());\r
             g.setColor(Color.black);\r
 \r
             if (av.scaleLeftWrapped)\r
@@ -489,24 +490,84 @@ public class SeqCanvas extends JComponent
      * @param starty DOCUMENT ME!\r
      * @param offset DOCUMENT ME!\r
      */\r
+\r
+    float aaRatio = 2f/3f;\r
+    public void increaseAARatio()\r
+    {\r
+      aaRatio += .025;\r
+      if(aaRatio>1)\r
+        aaRatio = 1;\r
+\r
+      repaint();\r
+    }\r
+\r
+    public void decreaseAARation()\r
+    {\r
+      aaRatio -= .025;\r
+      if(aaRatio<0)\r
+        aaRatio = 0;\r
+\r
+      repaint();\r
+    }\r
+\r
     synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
         int y2, int startx, int starty, int offset)\r
     {\r
         Graphics2D g = (Graphics2D) g1;\r
         g.setFont(av.getFont());\r
 \r
-        SequenceI nextSeq;\r
+\r
+  SequenceI nextSeq;\r
+\r
+  SequenceI dna = null;\r
+\r
+  int aaHeight = (int)(av.getCharHeight()*aaRatio);\r
+  int dnaHeight =(int)(av.getCharHeight() * (1-aaRatio));\r
+\r
+\r
+  java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
+  transform.scale(1f/3f , 1);\r
+  Font dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+                              dnaHeight);\r
+  dnafont = dnafont.deriveFont(transform);\r
+\r
+  Font aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+                              aaHeight);\r
+  transform = new java.awt.geom.AffineTransform();\r
+  transform.scale(1/aaRatio, 1);\r
+  aafont = aafont.deriveFont(transform);\r
 \r
         /// First draw the sequences\r
         /////////////////////////////\r
         for (int i = y1; i < y2; i++)\r
         {\r
             nextSeq = av.alignment.getSequenceAt(i);\r
+            g.setFont(aafont);\r
+/*\r
+            StringBuffer dnasb = new StringBuffer();\r
+            for (int j = 0; j < nextSeq.getLength(); j++)\r
+            {\r
+              java.util.Vector codons = jalview.schemes.ResidueProperties.getCodons(nextSeq.getSequence(j,\r
+                  j + 1));\r
+              if (codons != null && codons.size() > 0)\r
+                dnasb.append(codons.elementAt(0).toString());\r
+            }\r
+\r
+            dna = new Sequence("dna", dnasb.toString());*/\r
+\r
 \r
             sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
-                x1, x2, (x1 - startx) * av.charWidth,\r
-                offset + ((i - starty) * av.charHeight), av.charWidth,\r
-                av.charHeight);\r
+                            x1, x2, (x1 - startx) * av.charWidth,\r
+                            offset + ( (i - starty) * av.charHeight), av.charWidth,\r
+                            aaHeight);\r
+\r
+\r
+         /*   g.setFont(dnafont);\r
+\r
+            sr.drawSequence(g, dna, null,\r
+                            x1, x2 * 3 +2, ( (x1 - startx) * av.charWidth) / 3,\r
+                            offset + ( (i - starty) * av.charHeight) + aaHeight, av.charWidth / 3,\r
+                            dnaHeight);*/\r
 \r
             if (av.showSequenceFeatures)\r
             {\r

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ab5ed30..a68b226 100755 (executable)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.analysis.*;\r
-\r
 import jalview.datamodel.*;\r
 \r
 import jalview.schemes.*;\r

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 81daef7..8e8b066 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -208,6 +208,14 @@ public class SequenceRenderer
         int charOffset = 0;\r
         char s;\r
 \r
+        float fwidth = width + ((float)av.charWidth/(float)width)/width;\r
+\r
+\r
+        if(av.charWidth != (av.charWidth/width)*width)\r
+        {\r
+\r
+        }\r
+\r
         // Need to find the sequence position here.\r
         String sequence = seq.getSequence();\r
 \r
@@ -262,7 +270,7 @@ public class SequenceRenderer
 \r
             charOffset = (width - fm.charWidth(s)) / 2;\r
             graphics.drawString(String.valueOf(s),\r
-                charOffset + x1 + (width * (i - start)), (y1 + height) - pady);\r
+                charOffset + x1 + (int)(fwidth * (i - start)), (y1 + height) - pady);\r
         }\r
     }\r
 \r

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index fea4704..1d197c3 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -38,7 +38,6 @@ import java.util.*;
 \r
 import javax.imageio.*;\r
 \r
-import javax.swing.*;\r
 import java.beans.PropertyChangeEvent;\r
 \r
 \r

diff --git a/src/jalview/io/EBIFetchClient.java b/src/jalview/io/EBIFetchClient.java
index 2c829ff..eebbfc8 100755 (executable)
--- a/src/jalview/io/EBIFetchClient.java
+++ b/src/jalview/io/EBIFetchClient.java
@@ -24,8 +24,6 @@ import org.apache.axis.encoding.XMLType;
 import org.apache.axis.encoding.ser.JAFDataHandlerDeserializerFactory;\r
 import org.apache.axis.encoding.ser.JAFDataHandlerSerializerFactory;\r
 \r
-import java.io.*;\r
-\r
 import javax.activation.DataHandler;\r
 \r
 import javax.xml.namespace.QName;\r

diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 08eacd6..201ff0c 100755 (executable)
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -114,9 +114,6 @@ public class HTMLOutput
     SequenceI seq;\r
     ColourSchemeI cs = null;\r
     AlignmentI alignment = av.getAlignment();\r
-    String r;\r
-    String g;\r
-    String b;\r
 \r
     // draws the top row, the measure rule\r
     out.println("<tr><td colspan=\"6\"></td>");\r

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 5483f94..cadf153 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -26,8 +26,6 @@ package jalview.io;
 \r
 import jalview.datamodel.*;\r
 \r
-import jalview.util.*;\r
-\r
 import java.io.*;\r
 \r
 import java.util.*;\r

diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 33d18a3..2bac0de 100755 (executable)
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -162,7 +162,7 @@ public class JalviewFileChooser
 \r
       if (confirm != JOptionPane.YES_OPTION)\r
       {\r
-        ret = this.CANCEL_OPTION;\r
+        ret = JalviewFileChooser.CANCEL_OPTION;\r
       }\r
     }\r
 \r

diff --git a/src/jalview/io/JalviewFileFilter.java b/src/jalview/io/JalviewFileFilter.java
index cdd868c..3252a98 100755 (executable)
--- a/src/jalview/io/JalviewFileFilter.java
+++ b/src/jalview/io/JalviewFileFilter.java
@@ -26,8 +26,6 @@ import javax.swing.filechooser.FileFilter;
 public class JalviewFileFilter\r
     extends FileFilter\r
 {\r
-  private static String TYPE_UNKNOWN = "Type Unknown";\r
-  private static String HIDDEN_FILE = "Hidden File";\r
   public static Hashtable suffixHash = new Hashtable();\r
   private Hashtable filters = null;\r
   private String description = "no description";\r

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 0475542..8082ee3 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -72,9 +72,6 @@ public class MSFfile extends AlignFile
      */\r
     public void parse()\r
     {\r
-      com.stevesoft.pat.Regex gapre = new com.stevesoft.pat.Regex("\\~",\r
-          "-");\r
-\r
         int i = 0;\r
         boolean seqFlag = false;\r
         String key = new String();\r
@@ -150,7 +147,7 @@ public class MSFfile extends AlignFile
                 String head = headers.elementAt(i).toString();\r
                 String seq = seqhash.get(head).toString();\r
 \r
-                int start = 1;\r
+                int start = -1;\r
                 int end =  -1;\r
 \r
                 if (maxLength < head.length())\r
@@ -179,7 +176,7 @@ public class MSFfile extends AlignFile
 \r
 \r
                 // Replace ~ with a sensible gap character\r
-                seq = gapre.replaceAll(seq);\r
+                seq = seq.replace('~', '-');\r
 \r
                 Sequence newSeq = new Sequence(head, seq, start, end);\r
 \r
@@ -202,22 +199,18 @@ public class MSFfile extends AlignFile
      */\r
     public static int checkSum(String seq)\r
     {\r
-        //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
         int check = 0;\r
         String sequence = seq.toUpperCase();\r
 \r
-        String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
-        index +=       "--------------------------------------------------------------------------------------------------------------------------------";\r
-\r
         for (int i = 0; i < sequence.length(); i++)\r
         {\r
             try\r
             {\r
-                    int pos = index.indexOf(sequence.charAt(i));\r
 \r
-                    if (index.charAt(pos)!='_')\r
+                    int value = sequence.charAt(i);\r
+                    if (value!=-1)\r
                     {\r
-                        check += (((i % 57) + 1) * pos);\r
+                        check += (i % 57 +1) * value;\r
                     }\r
             }\r
             catch (Exception e)\r
@@ -250,10 +243,10 @@ public class MSFfile extends AlignFile
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public static String print(SequenceI[] s, boolean is_NA)\r
+    public static String print(SequenceI[] seqs, boolean is_NA)\r
     {\r
-      com.stevesoft.pat.Regex re2gap = new com.stevesoft.pat.Regex(\r
-          "[" + jalview.util.Comparison.GapChars + "]", "\\~");\r
+\r
+      SequenceI [] s = new SequenceI[seqs.length];\r
 \r
         StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
                 "_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
@@ -261,16 +254,38 @@ public class MSFfile extends AlignFile
         int max = 0;\r
         int maxid = 0;\r
         int i = 0;\r
-        String big = "";\r
 \r
-        while ((i < s.length) && (s[i] != null))\r
+        while ((i < seqs.length) && (seqs[i] != null))\r
         {\r
-            String sq;\r
-            big += (sq = s[i].getSequence());\r
+          // Replace all internal gaps with . and external spaces with ~\r
+          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));\r
+\r
+          StringBuffer sb = new StringBuffer(s[i].getSequence());\r
+          for (int ii = 0; ii < sb.length(); ii++)\r
+          {\r
+            if (sb.charAt(ii) == '.')\r
+            {\r
+              sb.replace(ii, ii + 1, "~");\r
+            }\r
+            else\r
+              break;\r
+          }\r
 \r
-            if (sq.length() > max)\r
+          for (int ii = sb.length() - 1; ii > 0; ii--)\r
+          {\r
+            if (sb.charAt(ii) == '.')\r
             {\r
-                max = sq.length();\r
+              sb.replace(ii, ii + 1, "~");\r
+            }\r
+            else\r
+              break;\r
+          }\r
+\r
+            s[i].setSequence(sb.toString());\r
+\r
+            if (s[i].getSequence().length() > max)\r
+            {\r
+                max = s[i].getSequence().length();\r
             }\r
 \r
             i++;\r
@@ -282,27 +297,33 @@ public class MSFfile extends AlignFile
                 "d");\r
         i = 0;\r
 \r
-        long bigcheck = checkSum(big);\r
+        int bigChecksum = 0;\r
+        int [] checksums = new int[s.length];\r
+        while ( i < s.length )\r
+        {\r
+          checksums[i] = checkSum(s[i].getSequence());\r
+          bigChecksum += checksums[i];\r
+          i++;\r
+        }\r
+\r
         long maxNB = 0;\r
         out.append("   MSF: " + s[0].getSequence().length() + "   Type: " +\r
-            (is_NA ? "N" : "P") + "    Check:  " + bigcheck + "   ..\n\n\n");\r
+            (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum%10000) + "   ..\n\n\n");\r
 \r
         String[] nameBlock = new String[s.length];\r
         String[] idBlock = new String[s.length];\r
 \r
+        i=0;\r
         while ((i < s.length) && (s[i] != null))\r
         {\r
-            String name = s[i].getName() + "/" + s[i].getStart() + "-" +\r
-                s[i].getEnd();\r
-            int check = checkSum(s[i].getSequence());\r
-            nameBlock[i] = new String("  Name: " + name + " ");\r
+            nameBlock[i] = new String("  Name: " + s[i].getName() + " ");\r
             idBlock[i] = new String("Len: " +\r
-                    maxLenpad.form(s[i].getSequence().length()) + "  Check:" +\r
-                    maxChkpad.form(check) + "  Weight: 1.00\n");\r
+                    maxLenpad.form(s[i].getSequence().length()) + "  Check: " +\r
+                    maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");\r
 \r
-            if (name.length() > maxid)\r
+            if (s[i].getName().length() > maxid)\r
             {\r
-                maxid = name.length();\r
+                maxid = s[i].getName().length();\r
             }\r
 \r
             if (nameBlock[i].length() > maxNB)\r
@@ -349,8 +370,7 @@ public class MSFfile extends AlignFile
             while ((j < s.length) && (s[j] != null))\r
             {\r
                 String name = s[j].getName();\r
-                out.append(new Format("%-" + maxid + "s").form(name + "/" +\r
-                        s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+                out.append(new Format("%-" + maxid + "s").form(name)+ " ");\r
 \r
                 for (int k = 0; k < 5; k++)\r
                 {\r
@@ -360,12 +380,11 @@ public class MSFfile extends AlignFile
                     if ((end < s[j].getSequence().length()) &&\r
                             (start < s[j].getSequence().length()))\r
                     {\r
-                        out.append(re2gap.replaceAll(s[j].getSequence()\r
-                                                         .substring(start, end)));\r
+                        out.append(s[j].getSequence().substring(start, end));\r
 \r
                         if (k < 4)\r
                         {\r
-                            // out.append(" ");\r
+                             out.append(" ");\r
                         }\r
                         else\r
                         {\r
@@ -376,8 +395,7 @@ public class MSFfile extends AlignFile
                     {\r
                         if (start < s[j].getSequence().length())\r
                         {\r
-                            out.append(re2gap.replaceAll(\r
-                                    s[j].getSequence().substring(start)));\r
+                            out.append(s[j].getSequence().substring(start));\r
                             out.append("\n");\r
                         }\r
                         else\r

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index c1ef5b6..d696605 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,8 +26,6 @@ import jalview.datamodel.*;
 \r
 import java.io.*;\r
 \r
-import java.util.*;\r
-\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -196,7 +194,7 @@ public class NewickFile extends FileParse
 \r
         int d = -1;\r
         int cp = 0;\r
-        int flen = nf.length();\r
+        //int flen = nf.length();\r
 \r
         String Error = null;\r
         String nodename = null;\r

diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index 0a24601..65890a9 100755 (executable)
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -184,9 +184,4 @@ public class PIRFile
     return out.toString();\r
   }\r
 \r
-  public static void main(String[] args)\r
-  {\r
-    String inStr = ">P1;LCAT_MOUSE_90.35\nMGLPGSPWQRVLLLLGLLLPPATPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNRLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDFNLFLPLGVDCWIDNTRIVYNHSSGRVSNAPGVQIRVPGFGKTESVEYVDDNKLAGY\n\n>LCAT_PAPAN_95.78\nMGPPGSPWQWVPLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQLEAKLDKPDVVNW\nMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGVQIRVPGFGKTYSVEYLDSSKLAGY\nLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEYYHKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLL\n";\r
-    PIRFile fa = new PIRFile(inStr);\r
-  }\r
 }\r

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 728d1c6..87a1652 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -172,33 +172,22 @@ public class PileUpfile
 \r
   public static int checkSum(String seq)\r
   {\r
-    //String chars =  "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz.*~&@";\r
+\r
     int check = 0;\r
 \r
     String sequence = seq.toUpperCase();\r
 \r
-    String index = "--------------------------------------&---*---.-----------------@ABCDEFGHIJKLMNOPQRSTUVWXYZ------ABCDEFGHIJKLMNOPQRSTUVWXYZ----@";\r
-    index += "--------------------------------------------------------------------------------------------------------------------------------";\r
-\r
     for (int i = 0; i < sequence.length(); i++)\r
     {\r
-      try\r
-      {\r
         if (i < sequence.length())\r
         {\r
-          int pos = index.indexOf(sequence.charAt(i));\r
-\r
-          if (index.charAt(pos)!='_')\r
+          int value = sequence.charAt(i);\r
+          if (value != -1)\r
           {\r
-            check += ( ( (i % 57) + 1) * pos);\r
+            check += (i % 57 + 1) * value;\r
           }\r
         }\r
-      }\r
-      catch (Exception e)\r
-      {\r
-        System.err.println("Exception during MSF Checksum calculation");\r
-        e.printStackTrace();\r
-      }\r
+\r
     }\r
 \r
     return check % 10000;\r
@@ -212,29 +201,24 @@ public class PileUpfile
     int maxid = 0;\r
 \r
     int i = 0;\r
-    String big = "";\r
-\r
-    while ( (i < s.length) && (s[i] != null))\r
+    int bigChecksum = 0;\r
+    int[] checksums = new int[s.length];\r
+    while (i < s.length)\r
     {\r
-      big += s[i].getSequence();\r
+      checksums[i] = checkSum(s[i].getSequence());\r
+      bigChecksum += checksums[i];\r
       i++;\r
     }\r
 \r
-    i = 0;\r
-\r
-    int bigcheck = checkSum(big);\r
-\r
     out.append("   MSF: " + s[0].getSequence().length() +\r
-               "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");\r
+               "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");\r
 \r
+    i=0;\r
     while ( (i < s.length) && (s[i] != null))\r
     {\r
       String seq = s[i].getSequence();\r
-      String name = s[i].getName() + "/" + s[i].getStart() + "-" +\r
-          s[i].getEnd();\r
-      int check = checkSum(s[i].getSequence());\r
-      out.append(" Name: " + name + " oo  Len:  " +\r
-                 s[i].getSequence().length() + "  Check:  " + check +\r
+      out.append(" Name: " + s[i].getName() + " oo  Len:  " +\r
+                 s[i].getSequence().length() + "  Check:  " + checksums[i] +\r
                  "  Weight:  1.00\n");\r
 \r
       if (seq.length() > max)\r
@@ -242,9 +226,9 @@ public class PileUpfile
         max = seq.length();\r
       }\r
 \r
-      if (name.length() > maxid)\r
+      if (s[i].getName().length() > maxid)\r
       {\r
-        maxid = name.length();\r
+        maxid = s[i].getName().length();\r
       }\r
 \r
       i++;\r
@@ -274,8 +258,7 @@ public class PileUpfile
       while ( (j < s.length) && (s[j] != null))\r
       {\r
         String name = s[j].getName();\r
-        out.append(new Format("%-" + maxid + "s").form(name + "/" +\r
-            s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+        out.append(new Format("%-" + maxid + "s").form(name) + " ");\r
 \r
         for (int k = 0; k < 5; k++)\r
         {\r

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 0c82f6f..0a7817a 100755 (executable)
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -22,8 +22,6 @@ import jalview.datamodel.*;
 \r
 import jalview.gui.*;\r
 \r
-import jalview.io.*;\r
-\r
 import java.io.*;\r
 \r
 import java.util.*;\r

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 33d6d92..c221d07 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -24,8 +24,6 @@ import jalview.gui.*;
 \r
 import org.apache.axis.client.*;\r
 \r
-import java.awt.*;\r
-\r
 import java.util.*;\r
 \r
 import javax.swing.*;\r

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 872d490..ed03a80 100755 (executable)
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -24,8 +24,6 @@ import javax.swing.*;
 import javax.swing.event.*;\r
 import jalview.io.FormatAdapter;\r
 import jalview.datamodel.SequenceI;\r
-import java.awt.datatransfer.DataFlavor;\r
-import jalview.io.IdentifyFile;\r
 \r
 public class GFinder\r
     extends JPanel\r

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 81d520a..f9abbda 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -804,13 +804,13 @@ public class Matrix
         //symm.print(System.out);\r
         //System.out.println();\r
         // Copy the symmetric matrix for later\r
-        Matrix origsymm = symm.copy();\r
+        //Matrix origsymm = symm.copy();\r
 \r
         // This produces the tridiagonal transformation matrix\r
-        long tstart = System.currentTimeMillis();\r
+        //long tstart = System.currentTimeMillis();\r
         symm.tred();\r
 \r
-        long tend = System.currentTimeMillis();\r
+        //long tend = System.currentTimeMillis();\r
 \r
         //System.out.println("Time take for tred = " + (tend-tstart) + "ms");\r
         //System.out.println(" ---Tridiag transform matrix ---");\r
@@ -823,9 +823,9 @@ public class Matrix
         //symm.printE(System.out);\r
         //System.out.println();\r
         // Now produce the diagonalization matrix\r
-        tstart = System.currentTimeMillis();\r
+        //tstart = System.currentTimeMillis();\r
         symm.tqli();\r
-        tend = System.currentTimeMillis();\r
+        //tend = System.currentTimeMillis();\r
 \r
         //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");\r
         //System.out.println(" --- New diagonalization matrix ---");\r

diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index 4e035eb..d912173 100755 (executable)
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -645,7 +645,6 @@ public class BrowserLauncher
             }\r
             catch (IllegalArgumentException iare)\r
             {\r
-              browser = browser;\r
               errorMessage = iare.getMessage();\r
 \r
               return null;\r

diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index 629fbcf..a78123f 100755 (executable)
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -27,7 +27,6 @@
  */\r
 package jalview.util;\r
 \r
-import java.io.*;\r
 \r
 \r
 /**\r
@@ -67,7 +66,6 @@ public class Format
         left_align = false;\r
         fmt = ' ';\r
 \r
-        int state = 0;\r
         int length = s.length();\r
         int parse_state = 0;\r
 \r
@@ -414,7 +412,7 @@ public class Format
         int i = 0;\r
         int sign = 1;\r
         double r = 0; // integer part\r
-        double f = 0; // fractional part\r
+        //double f = 0; // fractional part\r
         double p = 1; // exponent of fractional part\r
         int state = 0; // 0 = int part, 1 = frac part\r
 \r

diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java
index b30a05f..4921fb7 100755 (executable)
--- a/src/jalview/ws/Discoverer.java
+++ b/src/jalview/ws/Discoverer.java
@@ -33,7 +33,6 @@ package jalview.ws;
 import ext.vamsas.*;
 import java.util.Vector;
 import java.util.Hashtable;
-import java.util.ArrayList;
 import java.util.StringTokenizer;
 
 public class Discoverer
@@ -309,7 +308,7 @@ public class Discoverer
     // so no need to access original discovery thread.
     // Curent decision is to change properties then notify listeners with old and new values.
     Hashtable oldServices = services;
-    Vector oldServicelist = serviceList;
+    //Vector oldServicelist = serviceList;
     services = sscat;
     serviceList = cat;
     firePropertyChange("services", oldServices, services);

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 8f94e97..fdf0cec 100755 (executable)
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -137,7 +137,7 @@ public class JPredClient
                              " Service location failed\nfor URL :" + WsURL +\r
                              "\n" +\r
                              ex.getMessage());\r
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+      wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
 \r
       return false;\r
     }\r
@@ -172,9 +172,8 @@ public class JPredClient
       this.sequence.setSeq(AlignSeq.extractGaps("-. ",\r
                                                 msf[0].getSequence()));\r
 \r
-      jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
       this.msa = new vamsas.objects.simple.Msfalignment();\r
-      msa.setMsf(mwrite.print(msf));\r
+      msa.setMsf(jalview.io.PileUpfile.print(msf));\r
     }\r
 \r
     public void run()\r
@@ -334,7 +333,7 @@ public class JPredClient
 \r
 \r
 \r
-    private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+  /*  private void addFloatAnnotations(Alignment al, int[] gapmap,\r
                                      Vector values, String Symname,\r
                                      String Visname, float min,\r
                                      float max, int winLength)\r
@@ -350,7 +349,7 @@ public class JPredClient
 \r
       al.addAnnotation(new AlignmentAnnotation(Symname, Visname,\r
                                                annotations, min, max, winLength));\r
-    }\r
+    }*/\r
 \r
     void parseResult()\r
     {\r
@@ -518,7 +517,7 @@ public class JPredClient
           i++;\r
         }\r
 \r
-        Hashtable scores = prediction.getScores();\r
+        //Hashtable scores = prediction.getScores();\r
 \r
         /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),\r
                               "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 253dfba..6d46e4b 100755 (executable)
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -125,7 +125,7 @@ public class MsaWSClient
                              " Service location failed\nfor URL :" + WsURL +\r
                              "\n" +\r
                              ex.getMessage());\r
-      wsInfo.setStatus(wsInfo.ERROR);\r
+      wsInfo.setStatus(WebserviceInfo.ERROR);\r
       ex.printStackTrace();\r
 \r
       return false;\r
@@ -395,7 +395,7 @@ public class MsaWSClient
                            e.toString() +\r
                            "\n");\r
         this.allowedServerExceptions = 0;\r
-        wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
         wsInfo.appendProgressText(\r
             "Failed to submit sequences for alignment.\n" +\r
             "It is most likely that there is a problem with the server.\n" +\r

diff --git a/src/org/jibble/epsgraphics/EpsGraphics2D.java b/src/org/jibble/epsgraphics/EpsGraphics2D.java
index 25ad886..7955440 100755 (executable)
--- a/src/org/jibble/epsgraphics/EpsGraphics2D.java
+++ b/src/org/jibble/epsgraphics/EpsGraphics2D.java
@@ -238,7 +238,7 @@ public class EpsGraphics2D extends java.awt.Graphics2D {
 \r
         if (s != null) {\r
 \r
-            Rectangle2D userBounds = s.getBounds2D();\r
+            //Rectangle2D userBounds = s.getBounds2D();\r
             if (!_transform.isIdentity()) {\r
                 s = _transform.createTransformedShape(s);\r
             }\r