From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 10 Jul 2015 05:15:04 +0000 (+0100)
Subject: JAL-1807 explicit imports (jalview.io.*)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=67b3acb8df1438ef37a756c04e14f5a3b8406808;p=jalview.git

JAL-1807 explicit imports (jalview.io.*)
---

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 2fc17d5..6e81464 100644
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -20,9 +20,10 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 
-public class AMSAFile extends jalview.io.FastaFile
+public class AMSAFile extends FastaFile
 {
 
   AlignmentI al;
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 88cb46e..8706ad5 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -34,6 +34,8 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
+import jalview.util.Comparison;
+import jalview.util.Format;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
@@ -278,8 +280,8 @@ public class AnnotationFile
             graphLine.append("\t");
             graphLine.append(row.getThreshold().label);
             graphLine.append("\t");
-            graphLine.append(jalview.util.Format.getHexString(row
-                    .getThreshold().colour));
+            graphLine
+                    .append(Format.getHexString(row.getThreshold().colour));
             graphLine.append(newline);
           }
 
@@ -310,7 +312,7 @@ public class AnnotationFile
                 && j < row.annotations.length; j++)
         {
           if (refSeq != null
-                  && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+                  && Comparison.isGap(refSeq.getCharAt(j)))
           {
             continue;
           }
@@ -377,7 +379,7 @@ public class AnnotationFile
             {
               text.append(comma
                       + "["
-                      + jalview.util.Format
+                      + Format
                               .getHexString(row.annotations[j].colour)
                       + "]");
               comma = ",";
@@ -398,7 +400,7 @@ public class AnnotationFile
           colours.append("COLOUR\t");
           colours.append(row.label);
           colours.append("\t");
-          colours.append(jalview.util.Format.getHexString(color));
+          colours.append(Format.getHexString(color));
           colours.append(newline);
         }
         if (row.scaleColLabel || row.showAllColLabels
@@ -597,7 +599,7 @@ public class AnnotationFile
         }
       }
       text.append("outlineColour=");
-      text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+      text.append(Format.getHexString(sg.getOutlineColour()));
       text.append("\t");
 
       text.append("displayBoxes=");
@@ -615,13 +617,13 @@ public class AnnotationFile
       if (sg.textColour != java.awt.Color.black)
       {
         text.append("textCol1=");
-        text.append(jalview.util.Format.getHexString(sg.textColour));
+        text.append(Format.getHexString(sg.textColour));
         text.append("\t");
       }
       if (sg.textColour2 != java.awt.Color.white)
       {
         text.append("textCol2=");
-        text.append(jalview.util.Format.getHexString(sg.textColour2));
+        text.append(Format.getHexString(sg.textColour2));
         text.append("\t");
       }
       if (sg.thresholdTextColour != 0)
@@ -633,7 +635,7 @@ public class AnnotationFile
       if (sg.idColour != null)
       {
         text.append("idColour=");
-        text.append(jalview.util.Format.getHexString(sg.idColour));
+        text.append(Format.getHexString(sg.idColour));
         text.append("\t");
       }
       if (sg.isHidereps())
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 90400f4..e4c4f3d 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -827,7 +827,7 @@ public class AppletFormatAdapter
     {
       try
       {
-        String idformat = new jalview.io.IdentifyFile().Identify(file,
+        String idformat = new IdentifyFile().Identify(file,
                 protocol);
         if (idformat == null)
         {
diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 73be79f..e8e993b 100644
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -1,10 +1,13 @@
 package jalview.io;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentExportData;
 import jalview.exceptions.NoFileSelectedException;
+import jalview.gui.AlignFrame;
 import jalview.json.binding.v1.BioJSReleasePojo;
 import jalview.json.binding.v1.BioJSRepositoryPojo;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 
 import java.io.BufferedInputStream;
@@ -31,10 +34,10 @@ public class BioJsHTMLOutput
   public static final String DEFAULT_DIR = System.getProperty("user.home")
           + File.separatorChar + ".biojs_templates" + File.separatorChar;
 
-  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+  public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
           .getDefault("biojs_template_directory", DEFAULT_DIR);
 
-  public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
+  public static final String BJS_TEMPLATE_GIT_REPO = Cache
           .getDefault(
                   "biojs_template_git_repo",
                   "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
@@ -53,7 +56,7 @@ public class BioJsHTMLOutput
     {
       String outputFile = getOutputFile();
       // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
-      AlignmentExportData exportData = jalview.gui.AlignFrame
+      AlignmentExportData exportData = AlignFrame
               .getAlignmentForExport(
               JSONFile.FILE_DESC, ap.getAlignViewport());
       if (exportData.getSettings().isCancelled())
@@ -77,7 +80,7 @@ public class BioJsHTMLOutput
       out.print(generatedBioJsWithJalviewAlignmentAsJson);
       out.flush();
       out.close();
-      jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
+      BrowserLauncher.openURL("file:///" + outputFile);
     } catch (NoFileSelectedException ex)
     {
       // do noting if no file was selected
@@ -91,7 +94,7 @@ public class BioJsHTMLOutput
   {
     String selectedFile = null;
     JalviewFileChooser jvFileChooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "html" }, new String[]
             { "HTML files" }, "HTML files");
     jvFileChooser.setFileView(new JalviewFileView());
@@ -104,7 +107,7 @@ public class BioJsHTMLOutput
     int fileChooserOpt = jvFileChooser.showSaveDialog(null);
     if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
     {
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
+      Cache.setProperty("LAST_DIRECTORY", jvFileChooser
               .getSelectedFile().getParent());
       selectedFile = jvFileChooser.getSelectedFile().getPath();
     }
diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 57f6384..f965d23 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -31,6 +31,7 @@ import jalview.schemes.GraduatedColor;
 import jalview.schemes.UserColourScheme;
 import jalview.util.Format;
 import jalview.util.MapList;
+import jalview.util.ParseHtmlBodyAndLinks;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -393,7 +394,7 @@ public class FeaturesFile extends AlignFile
               }
               try
               {
-                colour = new jalview.schemes.GraduatedColor(
+                colour = new GraduatedColor(
                         new UserColourScheme(mincol).findColour('A'),
                         new UserColourScheme(maxcol).findColour('A'), min,
                         max);
@@ -406,9 +407,9 @@ public class FeaturesFile extends AlignFile
               }
               if (colour != null)
               {
-                ((jalview.schemes.GraduatedColor) colour)
+                ((GraduatedColor) colour)
                         .setColourByLabel(labelCol);
-                ((jalview.schemes.GraduatedColor) colour)
+                ((GraduatedColor) colour)
                         .setAutoScaled(abso == null);
                 // add in any additional parameters
                 String ttype = null, tval = null;
@@ -418,17 +419,17 @@ public class FeaturesFile extends AlignFile
                   ttype = gcol.nextToken();
                   if (ttype.toLowerCase().startsWith("below"))
                   {
-                    ((jalview.schemes.GraduatedColor) colour)
+                    ((GraduatedColor) colour)
                             .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
                   }
                   else if (ttype.toLowerCase().startsWith("above"))
                   {
-                    ((jalview.schemes.GraduatedColor) colour)
+                    ((GraduatedColor) colour)
                             .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
                   }
                   else
                   {
-                    ((jalview.schemes.GraduatedColor) colour)
+                    ((GraduatedColor) colour)
                             .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
                     if (!ttype.toLowerCase().startsWith("no"))
                     {
@@ -444,7 +445,7 @@ public class FeaturesFile extends AlignFile
                   {
                     gcol.nextToken();
                     tval = gcol.nextToken();
-                    ((jalview.schemes.GraduatedColor) colour)
+                    ((GraduatedColor) colour)
                             .setThresh(new Float(tval).floatValue());
                   } catch (Exception e)
                   {
@@ -1155,7 +1156,7 @@ public class FeaturesFile extends AlignFile
     {
       return;
     }
-    jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(
+    ParseHtmlBodyAndLinks parsed = new ParseHtmlBodyAndLinks(
             sf.getDescription(), removeHTML, newline);
 
     sf.description = (removeHTML) ? parsed.getNonHtmlContent()
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3aded05..1edf832 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -22,6 +22,7 @@ package jalview.io;
 
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -199,7 +200,7 @@ public class FileLoader implements Runnable
     String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
             : "RECENT_URL";
 
-    String historyItems = jalview.bin.Cache.getProperty(type);
+    String historyItems = Cache.getProperty(type);
 
     StringTokenizer st;
 
@@ -225,11 +226,11 @@ public class FileLoader implements Runnable
       newHistory.append(recent.elementAt(i));
     }
 
-    jalview.bin.Cache.setProperty(type, newHistory.toString());
+    Cache.setProperty(type, newHistory.toString());
 
     if (protocol.equals(FormatAdapter.FILE))
     {
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format);
     }
   }
 
@@ -411,7 +412,7 @@ public class FileLoader implements Runnable
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+              alignFrame.setMaximum(Cache.getDefault(
                       "SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8a563fa..dc93cf9 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -22,6 +22,7 @@ package jalview.io;
 
 import jalview.api.AlignExportSettingI;
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -29,6 +30,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 /**
  * Additional formatting methods used by the application in a number of places.
@@ -58,13 +60,13 @@ public class FormatAdapter extends AppletFormatAdapter
 
   private void init()
   {
-    if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+    if (Cache.getDefault("STRUCT_FROM_PDB", true))
     {
-      annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
+      annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
               true);
-      localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
+      localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
             true);
-    serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+    serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
             true);
     }
     else
@@ -114,14 +116,14 @@ public class FormatAdapter extends AppletFormatAdapter
         if (startEnd != null)
         {
           // get first non-gaped residue start position
-          while (jalview.util.Comparison.isGap(seqs[i]
+          while (Comparison.isGap(seqs[i]
                   .getCharAt(startIndex)) && startIndex < endIndex)
           {
             startIndex++;
           }
 
           // get last non-gaped residue end position
-          while (jalview.util.Comparison.isGap(seqs[i].getCharAt(endIndex))
+          while (Comparison.isGap(seqs[i].getCharAt(endIndex))
                   && endIndex > startIndex)
           {
             endIndex--;
@@ -165,50 +167,50 @@ public class FormatAdapter extends AppletFormatAdapter
       if (format.equalsIgnoreCase("FASTA"))
       {
         afile = new FastaFile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("FASTA_JVSUFFIX",
+        afile.addJVSuffix(Cache.getDefault("FASTA_JVSUFFIX",
                 true));
       }
       else if (format.equalsIgnoreCase("MSF"))
       {
         afile = new MSFfile();
-        afile.addJVSuffix(jalview.bin.Cache
+        afile.addJVSuffix(Cache
                 .getDefault("MSF_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PileUp"))
       {
         afile = new PileUpfile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX",
+        afile.addJVSuffix(Cache.getDefault("PILEUP_JVSUFFIX",
                 true));
       }
       else if (format.equalsIgnoreCase("CLUSTAL"))
       {
         afile = new ClustalFile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX",
+        afile.addJVSuffix(Cache.getDefault("CLUSTAL_JVSUFFIX",
                 true));
       }
       else if (format.equalsIgnoreCase("BLC"))
       {
         afile = new BLCFile();
-        afile.addJVSuffix(jalview.bin.Cache
+        afile.addJVSuffix(Cache
                 .getDefault("BLC_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PIR"))
       {
         afile = new PIRFile();
-        afile.addJVSuffix(jalview.bin.Cache
+        afile.addJVSuffix(Cache
                 .getDefault("PIR_JVSUFFIX", true));
       }
       else if (format.equalsIgnoreCase("PFAM"))
       {
         afile = new PfamFile();
-        afile.addJVSuffix(jalview.bin.Cache.getDefault("PFAM_JVSUFFIX",
+        afile.addJVSuffix(Cache.getDefault("PFAM_JVSUFFIX",
                 true));
       }
       /*
        * amsa is not supported by this function - it requires an alignment
        * rather than a sequence vector else if (format.equalsIgnoreCase("AMSA"))
        * { afile = new AMSAFile(); afile.addJVSuffix(
-       * jalview.bin.Cache.getDefault("AMSA_JVSUFFIX", true)); }
+       * Cache.getDefault("AMSA_JVSUFFIX", true)); }
        */
 
       afile.setSeqs(seqs);
@@ -233,7 +235,7 @@ public class FormatAdapter extends AppletFormatAdapter
   {
     if (isValidFormat(format))
     {
-      return jalview.bin.Cache.getDefault(format.toUpperCase()
+      return Cache.getDefault(format.toUpperCase()
               + "_JVSUFFIX", true);
     }
     return false;
@@ -277,8 +279,7 @@ public class FormatAdapter extends AppletFormatAdapter
 
   public String formatSequences(String format, AlignmentI alignment,
           String[] omitHidden, int[] exportRange, boolean suffix,
-          ColumnSelection colSel,
-          jalview.datamodel.SequenceGroup selgp)
+          ColumnSelection colSel, SequenceGroup selgp)
   {
     if (omitHidden != null)
     {
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
index 3c31b7f..5376fa4 100755
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -20,14 +20,22 @@
  */
 package jalview.io;
 
-import java.io.*;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
+import jalview.util.BrowserLauncher;
+import jalview.util.Comparison;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Font;
+import java.io.PrintWriter;
+
 public class HTMLOutput
 {
   AlignViewport av;
@@ -48,7 +56,7 @@ public class HTMLOutput
     fr.transferSettings(fr1);
 
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "html" }, new String[]
             { "HTML files" }, "HTML files");
 
@@ -61,7 +69,7 @@ public class HTMLOutput
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       try
@@ -102,7 +110,7 @@ public class HTMLOutput
 
         out.println("\n</body>\n</html>");
         out.close();
-        jalview.util.BrowserLauncher.openURL("file:///" + choice);
+        BrowserLauncher.openURL("file:///" + choice);
       } catch (Exception ex)
       {
         ex.printStackTrace();
@@ -143,7 +151,7 @@ public class HTMLOutput
 
       for (int res = 0; res < seq.getLength(); res++)
       {
-        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+        if (!Comparison.isGap(seq.getCharAt(res)))
         {
           color = sr.getResidueBoxColour(seq, res);
 
@@ -156,9 +164,8 @@ public class HTMLOutput
 
         if (color.getRGB() < -1)
         {
-          out.println("<td bgcolor=\"#"
-                  + jalview.util.Format.getHexString(color) + "\">"
-                  + seq.getCharAt(res) + "</td>");
+          out.println("<td bgcolor=\"#" + Format.getHexString(color)
+                  + "\">" + seq.getCharAt(res) + "</td>");
         }
         else
         {
@@ -245,7 +252,7 @@ public class HTMLOutput
 
         for (int res = startRes; res < endRes; res++)
         {
-          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))
+          if (!Comparison.isGap(seq.getCharAt(res)))
           {
             color = sr.getResidueBoxColour(seq, res);
 
@@ -258,9 +265,8 @@ public class HTMLOutput
 
           if (color.getRGB() < -1)
           {
-            out.println("<td bgcolor=\"#"
-                    + jalview.util.Format.getHexString(color) + "\">"
-                    + seq.getCharAt(res) + "</td>");
+            out.println("<td bgcolor=\"#" + Format.getHexString(color)
+                    + "\">" + seq.getCharAt(res) + "</td>");
           }
           else
           {
diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 781eace..6311b9b 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -1,12 +1,13 @@
 package jalview.io;
-
 import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentExportData;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.HTMLOptions;
 import jalview.math.AlignmentDimension;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -48,14 +49,14 @@ public class HtmlSvgOutput
       {
 
       JalviewFileChooser chooser = getHTMLChooser();
-      chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(ap.alignFrame.getTitle());
       chooser.setToolTipText(MessageManager.getString("action.save"));
       int value = chooser.showSaveDialog(ap.alignFrame);
 
-      if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        if (value == JalviewFileChooser.APPROVE_OPTION)
       {
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+        Cache.setProperty("LAST_DIRECTORY", chooser
                 .getSelectedFile().getParent());
         file = chooser.getSelectedFile();
       }
@@ -67,7 +68,7 @@ public class HtmlSvgOutput
       SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
               aDimension.getHeight());
 
-      String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING",
+      String renderStyle = Cache.getDefault("HTML_RENDERING",
               "Prompt each time");
 
       // If we need to prompt, and if the GUI is visible then
@@ -120,7 +121,7 @@ public class HtmlSvgOutput
       if (!(System.getProperty("java.awt.headless") != null && System
               .getProperty("java.awt.headless").equals("true")))
       {
-      jalview.util.BrowserLauncher.openURL("file:///" + file);
+        BrowserLauncher.openURL("file:///" + file);
       }
     } catch (Exception e)
     {
@@ -130,8 +131,8 @@ public class HtmlSvgOutput
   
   static JalviewFileChooser getHTMLChooser()
   {
-    return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+    return new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "html" }, new String[]
             { "Hypertext Markup Language" }, "Hypertext Markup Language");
   }
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index b079a3c..e0da795 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -45,6 +45,7 @@ import jalview.json.binding.v1.SequenceGrpPojo;
 import jalview.json.binding.v1.SequencePojo;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.Format;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 import java.awt.Color;
@@ -328,9 +329,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
                   String.valueOf(seq.hashCode()));
 
-          String featureColour = (fr == null) ? null : jalview.util.Format
-                  .getHexString(fr
-                  .findFeatureColour(Color.white, seq,
+          String featureColour = (fr == null) ? null : Format
+                  .getHexString(fr.findFeatureColour(Color.white, seq,
                           seq.findIndex(sf.getBegin())));
           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 0a6dc33..9ce7588 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -21,6 +21,7 @@
 //////////////////////////////////////////////////////////////////
 package jalview.io;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -263,7 +264,7 @@ public class JalviewFileChooser extends JFileChooser
     public RecentlyOpened()
     {
 
-      String historyItems = jalview.bin.Cache.getProperty("RECENT_FILE");
+      String historyItems = Cache.getProperty("RECENT_FILE");
       StringTokenizer st;
       Vector recent = new Vector();
 
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index cfa733c..ab2c497 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -22,6 +22,7 @@ package jalview.io;
 
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.util.Format;
 
 import java.io.IOException;
@@ -213,7 +214,7 @@ public class MSFfile extends AlignFile
   public String print(SequenceI[] seqs)
   {
 
-    boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+    boolean is_NA = Comparison.isNucleotide(seqs);
 
     SequenceI[] s = new SequenceI[seqs.length];
 
diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 30f46bf..9a3453f 100755
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -20,7 +20,11 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+
+import com.stevesoft.pat.Regex;
 
 public class ModellerDescription
 {
@@ -95,8 +99,7 @@ public class ModellerDescription
   private resCode validResidueCode(String field)
   {
     Integer val = null;
-    com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
-            "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+    Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
 
     if (!r.search(field))
     {
@@ -107,7 +110,7 @@ public class ModellerDescription
     {
       value = r.stringMatched(1);
     }
-    // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
+    // Cache.log.debug("from '" + field + "' matched '" + value +
     // "'");
     try
     {
@@ -162,7 +165,7 @@ public class ModellerDescription
                 }
                 else
                 {
-                  // jalview.bin.Cache.log.debug(
+                  // Cache.log.debug(
                   // "Ignoring non-Modeller description: invalid integer-like
                   // field '" + field + "'");
                   type = -1; /* invalid field! - throw the FieldSet away */
@@ -273,8 +276,7 @@ public class ModellerDescription
       if (seq.getDatasetSequence() != null
               && seq.getDatasetSequence().getDBRef() != null)
       {
-        jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
-                .getDBRef();
+        DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
         int i, j;
         for (i = 0, j = dbr.length; i < j; i++)
         {
@@ -284,8 +286,7 @@ public class ModellerDescription
             // ModellerField
             // JBPNote Need to get info from the user about whether the sequence
             // is the one being modelled, or if it is a template.
-            if (dbr[i].getSource()
-                    .equals(jalview.datamodel.DBRefSource.PDB))
+            if (dbr[i].getSource().equals(DBRefSource.PDB))
             {
               fields.put(Fields[LOCALID], dbr[i].getAccessionId());
               t = 2;
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 92456d5..90f7faf 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,11 +26,16 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.io.*;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
 import java.util.StringTokenizer;
 
-import jalview.datamodel.*;
-import jalview.util.MessageManager;
+import com.stevesoft.pat.Regex;
 
 /**
  * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
@@ -84,13 +89,13 @@ public class NewickFile extends FileParse
 
   boolean printRootInfo = true;
 
-  private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
-  { new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
+  private Regex[] NodeSafeName = new Regex[]
+  { new Regex().perlCode("m/[\\[,:'()]/"), // test for
       // requiring
       // quotes
-      new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
+      new Regex().perlCode("s/'/''/"), // escaping quote
       // characters
-      new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
+      new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
   // transformation
   };
 
@@ -291,7 +296,7 @@ public class NewickFile extends FileParse
     boolean ascending = false; // flag indicating that we are leaving the
     // current node
 
-    com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+    Regex majorsyms = new Regex(
             "[(\\['),;]");
 
     int nextcp = 0;
@@ -353,7 +358,7 @@ public class NewickFile extends FileParse
       // Deal with quoted fields
       case '\'':
 
-        com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
+        Regex qnodename = new Regex(
                 "'([^']|'')+'");
 
         if (qnodename.searchFrom(nf, fcp))
@@ -362,7 +367,7 @@ public class NewickFile extends FileParse
           nodename = new String(qnodename.stringMatched().substring(1,
                   nl - 1));
           // unpack any escaped colons
-          com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
+          Regex xpandquotes = Regex
                   .perlCode("s/''/'/");
           String widernodename = xpandquotes.replaceAll(nodename);
           nodename = widernodename;
@@ -397,7 +402,7 @@ public class NewickFile extends FileParse
            * '"+nf.substring(cp,fcp)+"'"); }
            */
           // verify termination.
-          com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
+          Regex comment = new Regex("]");
           if (comment.searchFrom(nf, fcp))
           {
             // Skip the comment field
@@ -430,11 +435,11 @@ public class NewickFile extends FileParse
                   + fstring.substring(cend + 1);
 
         }
-        com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
+        Regex uqnodename = new Regex(
                 "\\b([^' :;\\](),]+)");
-        com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
+        Regex nbootstrap = new Regex(
                 "\\s*([0-9+]+)\\s*:");
-        com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
+        Regex ndist = new Regex(
                 ":([-0-9Ee.+]+)");
 
         if (!parsednodename
@@ -964,7 +969,7 @@ public class NewickFile extends FileParse
       trf.parse();
       System.out.println("Original file :\n");
 
-      com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+      Regex nonl = new Regex("\n+", "");
       System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
 
       System.out.println("Parsed file.\n");
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index adbf81a..daf8bf0 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -20,10 +20,12 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Vector;
 
 public class PIRFile extends AlignFile
 {
@@ -106,7 +108,7 @@ public class PIRFile extends AlignFile
 
   public String print(SequenceI[] s)
   {
-    boolean is_NA = jalview.util.Comparison.isNucleotide(s);
+    boolean is_NA = Comparison.isNucleotide(s);
     int len = 72;
     StringBuffer out = new StringBuffer();
     int i = 0;
diff --git a/src/jalview/io/RnamlFile.java b/src/jalview/io/RnamlFile.java
index c15bc6c..2aa6d4b 100644
--- a/src/jalview/io/RnamlFile.java
+++ b/src/jalview/io/RnamlFile.java
@@ -25,6 +25,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
@@ -163,7 +164,7 @@ public class RnamlFile extends AlignFile
       for (int k = 0; k < rna.length(); k++)
       {
         ann[k] = new Annotation(annot[k], "",
-                jalview.schemes.ResidueProperties.getRNASecStrucState(
+                ResidueProperties.getRNASecStrucState(
                         annot[k]).charAt(0), 0f);
       }
 
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 7c96d45..3bfccc9 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -24,6 +24,7 @@ package jalview.io;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
 import jalview.util.UrlLink;
 
 import java.util.ArrayList;
@@ -234,7 +235,7 @@ public class SequenceAnnotationReport
     {
 
       // collect matching db-refs
-      DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
+      DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRef(),
               new String[]
               { target });
       // collect id string too
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 6490d28..3edcd75 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -31,7 +31,10 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.DBRefUtils;
 import jalview.util.Format;
+import jalview.util.MapList;
 import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
@@ -156,7 +159,7 @@ public class StockholmFile extends AlignFile
       for (int k = 0; k < rna.length(); k++)
       {
         ann[k] = new Annotation(annot[k], "",
-                jalview.schemes.ResidueProperties.getRNASecStrucState(
+                ResidueProperties.getRNASecStrucState(
                         annot[k]).charAt(0), 0f);
 
       }
@@ -309,7 +312,7 @@ public class StockholmFile extends AlignFile
             {
               String src = dbr.substring(0, dbr.indexOf(";"));
               String acn = dbr.substring(dbr.indexOf(";") + 1);
-              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
+              DBRefUtils.parseToDbRef(seqO, src, "0", acn);
             }
           }
 
@@ -738,14 +741,14 @@ public class StockholmFile extends AlignFile
       {
         // strip of last subdomain
         sdbac = sdbac.substring(0, sdbac.indexOf("."));
-        dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+        dbrf = DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
                 sdbac);
         if (dbrf != null)
         {
           dbrs.add(dbrf);
         }
       }
-      dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+      dbrf = DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
               dbr);
       if (dbr != null)
       {
@@ -760,7 +763,7 @@ public class StockholmFile extends AlignFile
       {
         // strip off last subdomain
         sdbac = sdbac.substring(0, sdbac.indexOf("."));
-        dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
+        dbrf = DBRefUtils.parseToDbRef(seqO, seqdb, dbsource,
                 sdbac);
         if (dbrf != null)
         {
@@ -768,7 +771,7 @@ public class StockholmFile extends AlignFile
         }
       }
 
-      dbrf = jalview.util.DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
+      dbrf = DBRefUtils.parseToDbRef(seqO, dbsource, dbsource,
               dbr);
       if (dbrf != null)
       {
@@ -779,7 +782,7 @@ public class StockholmFile extends AlignFile
     {
       for (DBRefEntry d : dbrs)
       {
-        jalview.util.MapList mp = new jalview.util.MapList(new int[]
+        MapList mp = new MapList(new int[]
         { seqO.getStart(), seqO.getEnd() }, new int[]
         { st, en }, 1, 1);
         jalview.datamodel.Mapping mping = new Mapping(mp);
@@ -830,12 +833,12 @@ public class StockholmFile extends AlignFile
         {
           if (detectbrackets.search(pos))
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
+            ann.secondaryStructure = ResidueProperties
                     .getRNASecStrucState(pos).charAt(0);
           }
           else
           {
-            ann.secondaryStructure = jalview.schemes.ResidueProperties
+            ann.secondaryStructure = ResidueProperties
                     .getDssp3state(pos).charAt(0);
           }
 
diff --git a/src/jalview/io/TCoffeeScoreFile.java b/src/jalview/io/TCoffeeScoreFile.java
index ca8a22a..4f94be9 100644
--- a/src/jalview/io/TCoffeeScoreFile.java
+++ b/src/jalview/io/TCoffeeScoreFile.java
@@ -25,6 +25,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -592,7 +593,7 @@ public class TCoffeeScoreFile extends AlignFile
       for (int j = 0; j < jSize; j++)
       {
         byte val = srow[j];
-        if (s != null && jalview.util.Comparison.isGap(s.getCharAt(j)))
+        if (s != null && Comparison.isGap(s.getCharAt(j)))
         {
           annotations[j] = null;
           if (val > 0)
diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index 7df7cb2..7608e51 100644
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -23,6 +23,7 @@ package jalview.io;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -33,6 +34,7 @@ import jalview.io.vamsas.Datasetsequence;
 import jalview.io.vamsas.DatastoreItem;
 import jalview.io.vamsas.DatastoreRegistry;
 import jalview.io.vamsas.Rangetype;
+import jalview.util.MapList;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -285,8 +287,8 @@ public class VamsasAppDatastore
   {
     try
     {
-      jalview.datamodel.AlignmentI jal = av.getAlignment();
-      jalview.datamodel.AlignmentI jds = jal.getDataset();
+      AlignmentI jal = av.getAlignment();
+      AlignmentI jds = jal.getDataset();
       boolean nw = false;
       VAMSAS root = null; // will be resolved based on Dataset Parent.
       // /////////////////////////////////////////
@@ -538,7 +540,7 @@ public class VamsasAppDatastore
       // SAVE ANNOTATIONS
       if (jal.getAlignmentAnnotation() != null)
       {
-        jalview.datamodel.AlignmentAnnotation[] aa = jal
+        AlignmentAnnotation[] aa = jal
                 .getAlignmentAnnotation();
         java.util.HashMap AlSeqMaps = new HashMap(); // stores int maps from
         // alignment columns to
@@ -667,7 +669,7 @@ public class VamsasAppDatastore
               }
               setAnnotationType(an, aa[i]);
 
-              if (aa[i].graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+              if (aa[i].graph != AlignmentAnnotation.NO_GRAPH)
               {
                 an.setGraph(true);
                 an.setGroup(Integer.toString(aa[i].graphGroup));
@@ -1041,7 +1043,7 @@ public class VamsasAppDatastore
       // of
       // utf8
       // translation
-      if (alan.graph != jalview.datamodel.AlignmentAnnotation.NO_GRAPH)
+      if (alan.graph != AlignmentAnnotation.NO_GRAPH)
       {
         ae.addValue(alan.annotations[a].value);
       }
@@ -1323,7 +1325,7 @@ public class VamsasAppDatastore
               @Override
               public JarInputStream getJarInputStream() throws IOException
               {
-                jalview.bin.Cache.log
+                Cache.log
                         .debug("Returning client input stream for Jalview from Vamsas Document.");
                 return new JarInputStream(cappdata.getClientInputStream());
               }
@@ -1371,7 +1373,7 @@ public class VamsasAppDatastore
             @Override
             public JarInputStream getJarInputStream() throws IOException
             {
-              jalview.bin.Cache.log
+              Cache.log
                       .debug("Returning user input stream for Jalview from Vamsas Document.");
               return new JarInputStream(cappdata.getUserInputStream());
             }
@@ -1532,14 +1534,14 @@ public class VamsasAppDatastore
       } catch (Exception e)
       {
         // TODO raise GUI warning if user requests it.
-        jalview.bin.Cache.log
+        Cache.log
                 .error("Couldn't update jalview client application data. Giving up - local settings probably lost.",
                         e);
       }
     }
     else
     {
-      jalview.bin.Cache.log
+      Cache.log
               .error("Couldn't access client application data for vamsas session. This is probably a vamsas client bug.");
     }
   }
@@ -1668,7 +1670,7 @@ public class VamsasAppDatastore
               // annotations
               if (dsSeq == null)
               {
-                jalview.bin.Cache.log
+                Cache.log
                         .warn("Couldn't resolve jalview sequenceI for dataset object reference "
                                 + ((Vobject) dataset.getDataSetAnnotations(
                                         dsa).getSeqRef(0)).getVorbaId()
@@ -1711,7 +1713,7 @@ public class VamsasAppDatastore
             // TODO check this handles multiple views properly
             AlignmentViewport av = findViewport(alignment);
 
-            jalview.datamodel.AlignmentI jal = null;
+            AlignmentI jal = null;
             if (av != null)
             {
               // TODO check that correct alignment object is retrieved when
@@ -1753,7 +1755,7 @@ public class VamsasAppDatastore
                         .getAlignmentSequenceAnnotation();
                 for (int a = 0; a < vasannot.length; a++)
                 {
-                  jalview.datamodel.AlignmentAnnotation asa = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
+                  AlignmentAnnotation asa = (AlignmentAnnotation) getvObj2jv(vasannot[a]); // TODO:
                   // 1:many
                   // jalview
                   // alignment
@@ -1839,7 +1841,7 @@ public class VamsasAppDatastore
 
               for (int j = 0; j < an.length; j++)
               {
-                jalview.datamodel.AlignmentAnnotation jan = (jalview.datamodel.AlignmentAnnotation) getvObj2jv(an[j]);
+                AlignmentAnnotation jan = (AlignmentAnnotation) getvObj2jv(an[j]);
                 if (jan != null)
                 {
                   // update or stay the same.
@@ -2185,8 +2187,8 @@ public class VamsasAppDatastore
    * @param annotation
    * @return unbound jalview alignment annotation object.
    */
-  private jalview.datamodel.AlignmentAnnotation getjAlignmentAnnotation(
-          jalview.datamodel.AlignmentI jal,
+  private AlignmentAnnotation getjAlignmentAnnotation(
+          AlignmentI jal,
           uk.ac.vamsas.objects.core.RangeAnnotation annotation)
   {
     if (annotation == null)
@@ -2255,7 +2257,7 @@ public class VamsasAppDatastore
         }
       }
     }
-    jalview.datamodel.AlignmentAnnotation jan = null;
+    AlignmentAnnotation jan = null;
     if (a_label == null || a_label.length() == 0)
     {
       a_label = annotation.getType();
@@ -2297,14 +2299,14 @@ public class VamsasAppDatastore
       {
         if (type == 0)
         {
-          type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH; // default
+          type = AlignmentAnnotation.BAR_GRAPH; // default
           // type of
           // value
           // annotation
           if (has[HASHPHOB])
           {
             // no hints - so we ensure HPHOB display is like this.
-            type = jalview.datamodel.AlignmentAnnotation.BAR_GRAPH;
+            type = AlignmentAnnotation.BAR_GRAPH;
           }
         }
         // make bounds and automatic description strings for jalview user's
@@ -2376,7 +2378,7 @@ public class VamsasAppDatastore
             }
           }
         }
-        jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
+        jan = new AlignmentAnnotation(a_label, a_descr,
                 arow, min, max, type);
       }
       else
@@ -2388,7 +2390,7 @@ public class VamsasAppDatastore
           // width - if it is not complete, then mark regions on the annotation
           // row.
         }
-        jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr,
+        jan = new AlignmentAnnotation(a_label, a_descr,
                 arow);
         jan.setThreshold(null);
         jan.annotationId = annotation.getVorbaId().toString(); // keep all the
@@ -2551,17 +2553,17 @@ public class VamsasAppDatastore
    * @param default unit for mapped
    * @return MapList
    */
-  private jalview.util.MapList parsemapType(MapType maprange, int localu,
+  private MapList parsemapType(MapType maprange, int localu,
           int mappedu)
   {
-    jalview.util.MapList ml = null;
+    MapList ml = null;
     int[] localRange = getMapping(maprange.getLocal());
     int[] mappedRange = getMapping(maprange.getMapped());
     long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
             : localu;
     long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
             .getUnit() : mappedu;
-    ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
+    ml = new MapList(localRange, mappedRange, (int) lu,
             (int) mu);
     return ml;
   }
@@ -2590,7 +2592,7 @@ public class VamsasAppDatastore
    * @param ml
    * @param setUnits
    */
-  private void initMapType(MapType maprange, jalview.util.MapList ml,
+  private void initMapType(MapType maprange, MapList ml,
           boolean setUnits)
   {
     maprange.setLocal(new Local());
@@ -2707,7 +2709,7 @@ public class VamsasAppDatastore
     AlignmentViewport av = viewport;
     try
     {
-      jalview.datamodel.AlignmentI jal = av.getAlignment();
+      AlignmentI jal = av.getAlignment();
       // /////////////////////////////////////////
       // SAVE THE DATASET
       DataSet dataset = null;
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index db4acc4..9061aa0 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -20,15 +20,30 @@
  */
 package jalview.io;
 
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Sequence;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
 
-import javax.swing.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
-import uk.ac.ebi.www.*;
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import uk.ac.ebi.www.Data;
+import uk.ac.ebi.www.InputParams;
+import uk.ac.ebi.www.WSFile;
+import uk.ac.ebi.www.WSWUBlast;
+import uk.ac.ebi.www.WSWUBlastService;
+import uk.ac.ebi.www.WSWUBlastServiceLocator;
 
 /**
  * DOCUMENT ME!
@@ -166,9 +181,8 @@ public class WSWUBlastClient
         DBRefEntry[] entries = oldseq.getDBRef();
         if (entries != null)
         {
-          oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
-                  jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
-                          .getAccessionId()));
+          oldseq.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "0",
+                  entries[0].getAccessionId()));
         }
       }
     }
diff --git a/src/jalview/io/packed/DataProvider.java b/src/jalview/io/packed/DataProvider.java
index fecc5ca..c868b85 100644
--- a/src/jalview/io/packed/DataProvider.java
+++ b/src/jalview/io/packed/DataProvider.java
@@ -20,6 +20,8 @@
  */
 package jalview.io.packed;
 
+import jalview.io.FileParse;
+
 /**
  * API for a data provider that can be used with
  * jalview.io.packed.ParsePackedSet
@@ -67,7 +69,7 @@ public interface DataProvider
    * 
    * @return
    */
-  jalview.io.FileParse getDataSource();
+  FileParse getDataSource();
 
   /**
    * association context for data. Either null or a specific sequence.
diff --git a/src/jalview/io/packed/JalviewDataset.java b/src/jalview/io/packed/JalviewDataset.java
index d613796..76c9b18 100644
--- a/src/jalview/io/packed/JalviewDataset.java
+++ b/src/jalview/io/packed/JalviewDataset.java
@@ -20,6 +20,8 @@
  */
 package jalview.io.packed;
 
+import jalview.analysis.NJTree;
+import jalview.analysis.SeqsetUtils;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.NewickFile;
@@ -103,12 +105,12 @@ public class JalviewDataset
   {
     public AlignmentI al;
 
-    public List<jalview.io.NewickFile> trees;
+    public List<NewickFile> trees;
 
     AlignmentSet(AlignmentI a)
     {
       al = a;
-      trees = new ArrayList<jalview.io.NewickFile>();
+      trees = new ArrayList<NewickFile>();
     }
 
     /**
@@ -141,15 +143,13 @@ public class JalviewDataset
       // jalview.analysis.SeqsetUtils.deuniquifyAndMerge(parentDataset,
       // seqDetails, al,true);
 
-      jalview.analysis.SeqsetUtils.deuniquify(seqDetails,
-              al.getSequencesArray(), true);
+      SeqsetUtils.deuniquify(seqDetails, al.getSequencesArray(), true);
       // 2. Update names of associated nodes in any trees
       for (NewickFile nf : trees)
       {
         // the following works because all trees are already had node/SequenceI
         // associations created.
-        jalview.analysis.NJTree njt = new jalview.analysis.NJTree(
-                al.getSequencesArray(), nf);
+        NJTree njt = new NJTree(al.getSequencesArray(), nf);
         // this just updates the displayed leaf name on the tree according to
         // the SequenceIs.
         njt.renameAssociatedNodes();
diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index a4ef77e..fda4faa 100644
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -21,10 +21,13 @@
 package jalview.io.packed;
 
 import jalview.datamodel.AlignmentI;
+import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
 import jalview.io.packed.DataProvider.JvDataType;
 
 import java.io.BufferedReader;
@@ -124,7 +127,7 @@ public class ParsePackedSet
             br = new BufferedReader(src.getReader());
           }
           // TODO: add columnSelection to context
-          if (new jalview.io.AnnotationFile().parseAnnotationFrom(
+          if (new AnnotationFile().parseAnnotationFrom(
                   context.getLastAlignment(), null, br))
           {
             context.updateSetModified(true);
@@ -161,7 +164,7 @@ public class ParsePackedSet
         }
         try
         {
-          jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
+          FeaturesFile ff = new FeaturesFile(src);
           context.updateSetModified(ff.parse(context.getLastAlignment(),
                   context.featureColours, false, context.relaxedIdMatching));
         } catch (Exception e)
@@ -174,7 +177,7 @@ public class ParsePackedSet
       {
         try
         {
-          jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
+          NewickFile nf = new NewickFile(src);
           if (!nf.isValid())
           {
             nf.close();
diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index 9c86557..d170513 100644
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -23,6 +23,7 @@ package jalview.io.vamsas;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
+
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Sequence;
@@ -137,9 +138,8 @@ public class Datasetsequence extends DatastoreItem
 
       for (int sf = 0; sf < sfSize; sf++)
       {
-        modified |= new jalview.io.vamsas.Sequencefeature(datastore,
-                (jalview.datamodel.SequenceFeature) sq
-                        .getSequenceFeatures()[sf], dataset,
+        modified |= new Sequencefeature(datastore,
+                sq.getSequenceFeatures()[sf], dataset,
                 (Sequence) vobj).docWasUpdated();
       }
     }
@@ -181,7 +181,7 @@ public class Datasetsequence extends DatastoreItem
       // jalview.datamodel.DBRefEntry dbentry;
       for (int db = 0; db < entries.length; db++)
       {
-        modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
+        modifiedthedoc |= new Dbref(datastore,
         // dbentry =
                 entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
 
@@ -208,7 +208,7 @@ public class Datasetsequence extends DatastoreItem
       // DbRef dbentry;
       for (int db = 0; db < entries.length; db++)
       {
-        modifiedtheseq |= new jalview.io.vamsas.Dbref(datastore,
+        modifiedtheseq |= new Dbref(datastore,
         // dbentry =
                 entries[db], vsq, sq).jvWasUpdated();
       }
diff --git a/src/jalview/io/vamsas/DatastoreItem.java b/src/jalview/io/vamsas/DatastoreItem.java
index 11c7e91..3b922a9 100644
--- a/src/jalview/io/vamsas/DatastoreItem.java
+++ b/src/jalview/io/vamsas/DatastoreItem.java
@@ -87,10 +87,12 @@ public abstract class DatastoreItem
    * @param vobj
    * @return Jalview datamodel object bound to the vamsas document object
    */
-  protected Object getvObj2jv(uk.ac.vamsas.client.Vobject vobj)
+  protected Object getvObj2jv(Vobject vobj)
   {
     if (vobj2jv == null)
+    {
       return null;
+    }
     VorbaId id = vobj.getVorbaId();
     if (id == null)
     {
@@ -113,7 +115,7 @@ public abstract class DatastoreItem
    * @param jvobj
    * @param vobj
    */
-  protected void bindjvvobj(Object jvobj, uk.ac.vamsas.client.Vobject vobj)
+  protected void bindjvvobj(Object jvobj, Vobject vobj)
   {
     VorbaId id = vobj.getVorbaId();
     if (id == null)
diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index aacdecf..a82d9d4 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -20,25 +20,29 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+
 import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Map;
 import uk.ac.vamsas.objects.core.Sequence;
-import jalview.io.VamsasAppDatastore;
+import uk.ac.vamsas.objects.utils.SymbolDictionary;
 
 public class Dbref extends Rangetype
 {
-  jalview.datamodel.SequenceI sq = null;
+  SequenceI sq = null;
 
   uk.ac.vamsas.objects.core.Sequence sequence = null;
 
   DataSet ds;
 
   public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
-          jalview.datamodel.SequenceI sq2,
-          uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
+          SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2,
+          DataSet dataset)
   {
     super(datastore, dbentry, DbRef.class);
     // initialise object specific attributes
@@ -53,7 +57,7 @@ public class Dbref extends Rangetype
   public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
           SequenceI dsseq)
   {
-    super(datastore, ref, jalview.datamodel.DBRefEntry.class);
+    super(datastore, ref, DBRefEntry.class);
     sequence = vdseq;
     sq = dsseq;
     ds = (DataSet) vdseq.getV_parent();
@@ -70,7 +74,7 @@ public class Dbref extends Rangetype
     if (jvobj.getMap() != null)
     {
       // Record mapping to external database coordinate system.
-      jalview.datamodel.Mapping mp = jvobj.getMap();
+      Mapping mp = jvobj.getMap();
       if (mp.getMap() != null)
       {
         Map vMap = null;
@@ -91,7 +95,7 @@ public class Dbref extends Rangetype
     }
     else
     {
-      jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+      Cache.log.debug("Ignoring mapless DbRef.Map "
               + jvobj.getSrcAccString());
     }
 
@@ -103,7 +107,7 @@ public class Dbref extends Rangetype
    * 
    * @param mp
    */
-  private void updateMapTo(jalview.datamodel.Mapping mp)
+  private void updateMapTo(Mapping mp)
   {
     log.info("Performing updateMapTo remove this message when we know what we're doing.");
     // TODO determine how sequences associated with database mappings are stored
@@ -124,8 +128,8 @@ public class Dbref extends Rangetype
                   mp.getTo(),
                   (mp.getMappedWidth() == mp.getWidth()) ? sequence
                           .getDictionary()
-                          : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
-                                  : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
+                          : ((mp.getMappedWidth() == 3) ? SymbolDictionary.STANDARD_NA
+                                  : SymbolDictionary.STANDARD_AA),
                   ds);
         }
         //
@@ -157,12 +161,11 @@ public class Dbref extends Rangetype
       // TODO: Jalview ignores all the other maps
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
+        Cache.log
                 .debug("Ignoring additional mappings on DbRef: "
                         + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
-      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
-              parsemapType(vobj.getMap(0)));
+      Mapping mp = new Mapping(parsemapType(vobj.getMap(0)));
       if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
       {
         jvobj.setMap(mp);
@@ -174,7 +177,7 @@ public class Dbref extends Rangetype
   {
     DbRef vobj = (DbRef) this.vobj;
     DBRefEntry jvobj = (DBRefEntry) this.jvobj;
-    jalview.bin.Cache.log.debug("Conflict in dbentry update for "
+    Cache.log.debug("Conflict in dbentry update for "
             + vobj.getAccessionId() + vobj.getSource() + " "
             + vobj.getVorbaId());
     // TODO Auto-generated method stub
@@ -186,7 +189,7 @@ public class Dbref extends Rangetype
     DbRef vobj = (DbRef) this.vobj;
     DBRefEntry jvobj = (DBRefEntry) this.jvobj;
     // add new dbref
-    sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(vobj.getSource()
+    sq.addDBRef(jvobj = new DBRefEntry(vobj.getSource()
             .toString(), vobj.getVersion().toString(), vobj
             .getAccessionId().toString()));
     if (vobj.getMapCount() > 0)
@@ -194,11 +197,11 @@ public class Dbref extends Rangetype
       // TODO: Jalview ignores all the other maps
       if (vobj.getMapCount() > 1)
       {
-        jalview.bin.Cache.log
+        Cache.log
                 .debug("Ignoring additional mappings on DbRef: "
                         + jvobj.getSource() + ":" + jvobj.getAccessionId());
       }
-      jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
+      Mapping mp = new Mapping(
               parsemapType(vobj.getMap(0)));
       jvobj.setMap(mp);
     }
@@ -219,7 +222,7 @@ public class Dbref extends Rangetype
     sequence.addDbRef(dbref);
     if (jvobj.getMap() != null)
     {
-      jalview.datamodel.Mapping mp = jvobj.getMap();
+      Mapping mp = jvobj.getMap();
       if (mp.getMap() != null)
       {
         Map vMap = new Map();
@@ -229,7 +232,7 @@ public class Dbref extends Rangetype
       }
       else
       {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+        Cache.log.debug("Ignoring mapless DbRef.Map "
                 + jvobj.getSrcAccString());
       }
     }
diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index 08b1b52..64a07e1 100644
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -20,7 +20,9 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Cache;
 import jalview.io.VamsasAppDatastore;
+import jalview.util.MapList;
 import jalview.util.MessageManager;
 
 import java.util.List;
@@ -246,26 +248,26 @@ public abstract class Rangetype extends DatastoreItem
    * @param default unit for mapped
    * @return MapList
    */
-  protected jalview.util.MapList parsemapType(MapType maprange, int localu,
+  protected MapList parsemapType(MapType maprange, int localu,
           int mappedu)
   {
-    jalview.util.MapList ml = null;
+    MapList ml = null;
     int[] localRange = getIntervals(maprange.getLocal());
     int[] mappedRange = getIntervals(maprange.getMapped());
     long lu = maprange.getLocal().hasUnit() ? maprange.getLocal().getUnit()
             : localu;
     long mu = maprange.getMapped().hasUnit() ? maprange.getMapped()
             .getUnit() : mappedu;
-    ml = new jalview.util.MapList(localRange, mappedRange, (int) lu,
+    ml = new MapList(localRange, mappedRange, (int) lu,
             (int) mu);
     return ml;
   }
 
-  protected jalview.util.MapList parsemapType(MapType map)
+  protected MapList parsemapType(MapType map)
   {
     if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("using default mapping length of 1:1 for map "
                       + (map.isRegistered() ? map.getVorbaId().toString()
                               : ("<no Id registered> " + map.toString())));
@@ -280,7 +282,7 @@ public abstract class Rangetype extends DatastoreItem
    * @param ml
    * @param setUnits
    */
-  protected void initMapType(MapType maprange, jalview.util.MapList ml,
+  protected void initMapType(MapType maprange, MapList ml,
           boolean setUnits)
   {
     initMapType(maprange, ml, setUnits, false);
@@ -294,7 +296,7 @@ public abstract class Rangetype extends DatastoreItem
    * @param reverse
    *          - reverse MapList mapping for Local and Mapped ranges and units
    */
-  protected void initMapType(MapType maprange, jalview.util.MapList ml,
+  protected void initMapType(MapType maprange, MapList ml,
           boolean setUnits, boolean reverse)
   {
     if (ml == null)
diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 4929a06..9bdd6b3 100644
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -20,12 +20,16 @@
  */
 package jalview.io.vamsas;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Desktop;
 import jalview.io.VamsasAppDatastore;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MapList;
 
 import java.util.Vector;
 
@@ -34,14 +38,15 @@ import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.Sequence;
 import uk.ac.vamsas.objects.core.SequenceMapping;
 import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.utils.SymbolDictionary;
 
 /**
  * binds a vamsas sequence mapping object from the vamsas document to a maplist
  * object associated with a mapping in the Jalview model. We use the maplist
  * object because these are referred to both in the Mapping object associated
- * with a jalview.datamodel.DBRefEntry and in the array of
- * jalview.datamodel.AlCodonFrame objects that Jalview uses to propagate
- * sequence mapping position highlighting across the views.
+ * with a DBRefEntry and in the array of jalview.datamodel.AlCodonFrame objects
+ * that Jalview uses to propagate sequence mapping position highlighting across
+ * the views.
  * 
  * @author JimP
  * 
@@ -51,7 +56,7 @@ public class Sequencemapping extends Rangetype
   public Sequencemapping(VamsasAppDatastore datastore,
           SequenceMapping sequenceMapping)
   {
-    super(datastore, sequenceMapping, jalview.util.MapList.class);
+    super(datastore, sequenceMapping, MapList.class);
     doJvUpdate();
   }
 
@@ -71,7 +76,7 @@ public class Sequencemapping extends Rangetype
    * @param ds
    */
   public Sequencemapping(VamsasAppDatastore datastore,
-          jalview.datamodel.Mapping mjvmapping,
+ Mapping mjvmapping,
           uk.ac.vamsas.objects.core.SequenceType from,
           uk.ac.vamsas.objects.core.DataSet ds)
   {
@@ -96,13 +101,13 @@ public class Sequencemapping extends Rangetype
     }
     if (from != null && sequenceMapping.getLoc() != from)
     {
-      jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+      Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
               + " doesn't match the local mapping sequence.");
     }
     if (ds != null && sequenceMapping.is__stored_in_document()
             && sequenceMapping.getV_parent() != ds)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("Probable IMPLEMENTATION ERROR: "
                       + ds
                       + " doesn't match the parent of the bound sequence mapping object.");
@@ -132,7 +137,7 @@ public class Sequencemapping extends Rangetype
 
   public void updateFromDoc()
   {
-    update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
+    update((SequenceMapping) vobj, (Mapping) jvobj);
   }
 
   private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
@@ -152,7 +157,7 @@ public class Sequencemapping extends Rangetype
     SequenceType to = (SequenceType) getjv2vObj(jvto);
     if (to == null)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
       return;
     }
@@ -162,10 +167,10 @@ public class Sequencemapping extends Rangetype
     boolean dnaToProt = false, sense = false;
     // ensure that we create a mapping with the correct sense
     if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals(
-            uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+            SymbolDictionary.STANDARD_NA))
     {
       if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
-              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+              SymbolDictionary.STANDARD_AA))
       {
         dnaToProt = true;
         sense = true;
@@ -174,7 +179,7 @@ public class Sequencemapping extends Rangetype
     else
     {
       if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
-              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+              SymbolDictionary.STANDARD_NA))
       {
         dnaToProt = true;
         sense = false;
@@ -183,7 +188,7 @@ public class Sequencemapping extends Rangetype
 
     if (!dnaToProt)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
       return;
     }
@@ -223,28 +228,28 @@ public class Sequencemapping extends Rangetype
     // mapping
     bindjvvobj(mjvmapping.getMap(), sequenceMapping);
 
-    jalview.bin.Cache.log.debug("Successfully created mapping "
+    Cache.log.debug("Successfully created mapping "
             + sequenceMapping.getVorbaId());
   }
 
-  // private void update(jalview.util.MapList mjvmapping,
+  // private void update(MapList mjvmapping,
   // SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log
+    Cache.log
             .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
   }
 
   private void update(SequenceMapping sequenceMapping,
-          jalview.datamodel.Mapping mjvmapping)
+ Mapping mjvmapping)
   {
-    jalview.bin.Cache.log
+    Cache.log
             .error("Not implemented: Update DBRef Mapping from Jalview");
   }
 
-  private void update(jalview.datamodel.Mapping mjvmapping,
+  private void update(Mapping mjvmapping,
           SequenceMapping sequenceMapping)
   {
-    jalview.bin.Cache.log
+    Cache.log
             .error("Not implemented: Jalview Update Sequence DBRef Mapping");
   }
 
@@ -281,7 +286,7 @@ public class Sequencemapping extends Rangetype
     }
     if (sdloc == null || sdmap == null)
     {
-      jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+      Cache.log.info("Ignoring non sequence-sequence mapping");
       return;
     }
     mobj = this.getvObj2jv(sdloc);
@@ -297,16 +302,16 @@ public class Sequencemapping extends Rangetype
     if (from == null || to == null)
     {
 
-      jalview.bin.Cache.log
+      Cache.log
               .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
       return;
     }
 
     if (sdloc.getDictionary().equals(
-            uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+SymbolDictionary.STANDARD_NA))
     {
       if (sdmap.getDictionary().equals(
-              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+SymbolDictionary.STANDARD_AA))
       {
         dnaToProt = true;
         sense = true;
@@ -318,7 +323,7 @@ public class Sequencemapping extends Rangetype
     else
     {
       if (sdmap.getDictionary().equals(
-              uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+SymbolDictionary.STANDARD_NA))
       {
         dnaToProt = true;
         sense = false;
@@ -340,13 +345,13 @@ public class Sequencemapping extends Rangetype
     }
     // create and add the new mapping to (each) dataset's codonFrame
 
-    jalview.util.MapList mapping = null;
+    MapList mapping = null;
     if (dnaToProt)
     {
       if (!sense)
       {
         mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
-        mapping = new jalview.util.MapList(mapping.getToRanges(),
+        mapping = new MapList(mapping.getToRanges(),
                 mapping.getFromRanges(), mapping.getToRatio(),
                 mapping.getFromRatio());
         acf.addMap(to, from, mapping);
@@ -363,7 +368,7 @@ public class Sequencemapping extends Rangetype
       acf.addMap(from, to, mapping);
     }
     bindjvvobj(mapping, sequenceMapping);
-    jalview.structure.StructureSelectionManager
+    StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance).addMapping(acf);
     // Try to link up any conjugate database references in the two sequences
     // matchConjugateDBRefs(from, to, mapping);
@@ -372,8 +377,8 @@ public class Sequencemapping extends Rangetype
   }
 
   /**
-   * Complete any 'to' references in jalview.datamodel.Mapping objects
-   * associated with conjugate DBRefEntry under given mapping
+   * Complete any 'to' references in Mapping objects associated with conjugate
+   * DBRefEntry under given mapping
    * 
    * @param from
    *          sequence corresponding to from reference for sequence mapping
@@ -383,37 +388,37 @@ public class Sequencemapping extends Rangetype
    *          maplist parsed in same sense as from and to
    */
   private void matchConjugateDBRefs(SequenceI from, SequenceI to,
-          jalview.util.MapList smap)
+          MapList smap)
   {
     if (from.getDBRef() == null && to.getDBRef() == null)
     {
-      if (jalview.bin.Cache.log.isDebugEnabled())
+      if (Cache.log.isDebugEnabled())
       {
-        jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+        Cache.log.debug("Not matching conjugate refs for "
                 + from.getName() + " and " + to.getName());
       }
       return;
     }
-    if (jalview.bin.Cache.log.isDebugEnabled())
+    if (Cache.log.isDebugEnabled())
     {
-      jalview.bin.Cache.log.debug("Matching conjugate refs for "
+      Cache.log.debug("Matching conjugate refs for "
               + from.getName() + " and " + to.getName());
     }
-    jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
-    jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
+    DBRefEntry[] fdb = from.getDBRef();
+    DBRefEntry[] tdb = new DBRefEntry[to
             .getDBRef().length];
     int tdblen = to.getDBRef().length;
     System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
     Vector matched = new Vector();
-    jalview.util.MapList smapI = smap.getInverse();
+    MapList smapI = smap.getInverse();
     for (int f = 0; f < fdb.length; f++)
     {
-      jalview.datamodel.DBRefEntry fe = fdb[f];
-      jalview.datamodel.Mapping fmp = fe.getMap();
+      DBRefEntry fe = fdb[f];
+      Mapping fmp = fe.getMap();
       boolean fmpnnl = fmp != null;
       // if (fmpnnl && fmp.getTo()!=null)
       // {
-      // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+      // Cache.log.debug("Not overwriting existing To reference in
       // "+fe);
       // continue;
       // }
@@ -425,13 +430,13 @@ public class Sequencemapping extends Rangetype
               : false;
       for (int t = 0; t < tdblen; t++)
       {
-        jalview.datamodel.DBRefEntry te = tdb[t];
+        DBRefEntry te = tdb[t];
         if (te != null)
         {
           if (fe.getSource().equals(te.getSource())
                   && fe.getAccessionId().equals(te.getAccessionId()))
           {
-            jalview.datamodel.Mapping tmp = te.getMap();
+            Mapping tmp = te.getMap();
             boolean tmpnnl = tmp != null;
             if (tmpnnl && tmp.getTo() != null)
             {
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index b5ada26..f007463 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -20,12 +20,6 @@
  */
 package jalview.io.vamsas;
 
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.analysis.NJTree;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -35,10 +29,18 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
+import jalview.gui.AlignFrame;
 import jalview.gui.TreePanel;
 import jalview.io.NewickFile;
 import jalview.io.VamsasAppDatastore;
 import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.Entry;
@@ -68,14 +70,12 @@ public class Tree extends DatastoreItem
   private AlignmentView inputData = null;
 
   public static void updateFrom(VamsasAppDatastore datastore,
-          jalview.gui.AlignFrame alignFrame,
-          uk.ac.vamsas.objects.core.Tree vtree)
+          AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree)
   {
     Tree toTree = new Tree(datastore, alignFrame, vtree);
   }
 
-  public Tree(VamsasAppDatastore datastore,
-          jalview.gui.AlignFrame alignFrame,
+  public Tree(VamsasAppDatastore datastore, AlignFrame alignFrame,
           uk.ac.vamsas.objects.core.Tree vtree)
   {
     super(datastore, vtree, TreePanel.class);
@@ -84,7 +84,7 @@ public class Tree extends DatastoreItem
 
   private NewickFile getNtree() throws IOException
   {
-    return new jalview.io.NewickFile(tree.getNewick(0).getContent());
+    return new NewickFile(tree.getNewick(0).getContent());
   }
 
   public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
@@ -290,8 +290,10 @@ public class Tree extends DatastoreItem
       }
     }
     if (alsq.size() < sequences.length)
+    {
       Cache.log
               .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+    }
     return alsq;
   }
 
@@ -305,7 +307,9 @@ public class Tree extends DatastoreItem
   public void UpdateSequenceTreeMap(TreePanel tp)
   {
     if (tp == null || tree == null)
+    {
       return;
+    }
     Vector leaves = new Vector();
     if (tp.getTree() == null)
     {
@@ -473,7 +477,9 @@ public class Tree extends DatastoreItem
         --occurence;
       }
       else
+      {
         bn = null;
+      }
     }
     return bn;
   }
@@ -511,7 +517,7 @@ public class Tree extends DatastoreItem
   public Object[] recoverInputData(Provenance tp)
   {
     AlignmentViewport javport = null;
-    jalview.datamodel.AlignmentI jal = null;
+    AlignmentI jal = null;
     jalview.datamodel.CigarArray view = null;
     for (int pe = 0; pe < tp.getEntryCount(); pe++)
     {