JAL-1807 explicit imports (jalview.util)

diff --git a/src/jalview/util/BrowserLauncher.java b/src/jalview/util/BrowserLauncher.java
index cd9c969..55343c1 100755 (executable)
--- a/src/jalview/util/BrowserLauncher.java
+++ b/src/jalview/util/BrowserLauncher.java
@@ -20,8 +20,14 @@
  */
 package jalview.util;
 
-import java.io.*;
-import java.lang.reflect.*;
+import jalview.bin.Cache;
+
+import java.io.File;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 
 /**
  * BrowserLauncher is a class that provides one static method, openURL, which
@@ -673,7 +679,7 @@ public class BrowserLauncher
 
     case OTHER:
     default:
-      browser = jalview.bin.Cache.getDefault("DEFAULT_BROWSER", "firefox");
+      browser = Cache.getDefault("DEFAULT_BROWSER", "firefox");
 
       break;
     }

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 123a4e1..0349ff2 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -430,7 +430,7 @@ public class DBRefUtils
          * Check for PFAM style stockhom PDB accession id citation e.g.
          * "1WRI A; 7-80;"
          */
-        Regex r = new com.stevesoft.pat.Regex(
+        Regex r = new Regex(
                 "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
         if (r.search(acn.trim()))
         {

diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index 6665f51..026e289 100644 (file)
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -24,7 +24,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 import java.util.Hashtable;
-import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
 
 public class GroupUrlLink
 {
@@ -150,7 +151,7 @@ public class GroupUrlLink
     }
     ptok[ntoks] = link.length();
     tmtch[ntoks] = "$$$$$$$$$";
-    jalview.util.QuickSort.sortInt(ptok, tmtch);
+    QuickSort.sortInt(ptok, tmtch);
     for (int i = 0; i < ntoks; i++)
     {
       mtch[i] = tmtch[i]; // TODO: check order is ascending
@@ -217,7 +218,7 @@ public class GroupUrlLink
         regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
         try
         {
-          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+          Regex rg = Regex.perlCode("/"
                   + regexReplace[pass] + "/");
           if (rg == null)
           {
@@ -320,10 +321,12 @@ public class GroupUrlLink
   private String _replaceFor(String token)
   {
     for (int i = 0; i < mtch.length; i++)
+    {
       if (segs[i] > -1 && mtch[i].equals(token))
       {
         return regexReplace[i];
       }
+    }
     return null;
   }
 
@@ -499,13 +502,13 @@ public class GroupUrlLink
     // iterate through input, collating segments to be inserted into url
     StringBuffer matched[] = new StringBuffer[idseq.length];
     // and precompile regexes
-    com.stevesoft.pat.Regex[] rgxs = new com.stevesoft.pat.Regex[matched.length];
+    Regex[] rgxs = new Regex[matched.length];
     for (pass = 0; pass < matched.length; pass++)
     {
       matched[pass] = new StringBuffer();
       if (regexReplace[pass] != null)
       {
-        rgxs[pass] = com.stevesoft.pat.Regex.perlCode("/"
+        rgxs[pass] = Regex.perlCode("/"
                 + regexReplace[pass] + "/");
       }
       else
@@ -544,7 +547,7 @@ public class GroupUrlLink
         }
         if (rgxs[pass] != null)
         {
-          com.stevesoft.pat.Regex rg = rgxs[pass];
+          Regex rg = rgxs[pass];
           int rematchat = 0;
           // concatenate all matches of re in the given string!
           while (rg.searchFrom(idseq[pass][sq], rematchat))

diff --git a/src/jalview/util/ImageMaker.java b/src/jalview/util/ImageMaker.java
index 8abe965..e32dfee 100755 (executable)
--- a/src/jalview/util/ImageMaker.java
+++ b/src/jalview/util/ImageMaker.java
@@ -20,10 +20,12 @@
  */
 package jalview.util;
 
+import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.gui.EPSOptions;
 import jalview.gui.SVGOptions;
 import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 
 import java.awt.Component;
 import java.awt.Graphics;
@@ -99,14 +101,14 @@ public class ImageMaker
     {
       JalviewFileChooser chooser;
       chooser = type.getChooser();
-      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(title);
       chooser.setToolTipText(MessageManager.getString("action.save"));
       int value = chooser.showSaveDialog(parent);
 
-      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();
       }
@@ -177,7 +179,7 @@ public class ImageMaker
   {
     boolean accurateText = true;
 
-    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+    String renderStyle = Cache.getDefault("EPS_RENDERING",
             "Prompt each time");
 
     // If we need to prompt, and if the GUI is visible then
@@ -231,7 +233,7 @@ public class ImageMaker
     g2 = new SVGGraphics2D(width, height);
     Graphics2D ig2 = g2;
 
-    String renderStyle = jalview.bin.Cache.getDefault("SVG_RENDERING",
+    String renderStyle = Cache.getDefault("SVG_RENDERING",
             "Prompt each time");
 
     // If we need to prompt, and if the GUI is visible then
@@ -265,7 +267,7 @@ public class ImageMaker
       return null;
     }
     return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "png" }, new String[]
             { "Portable network graphics" }, "Portable network graphics");
   }
@@ -276,8 +278,8 @@ public class ImageMaker
     {
       return null;
     }
-    return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+    return new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "eps" }, new String[]
             { "Encapsulated Postscript" }, "Encapsulated Postscript");
   }
@@ -288,8 +290,8 @@ public class ImageMaker
   {
       return null;
     }
-    return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+    return new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "svg" }, new String[]
             { "Scalable Vector Graphics" }, "Scalable Vector Graphics");
   }

diff --git a/src/jalview/util/UrlLink.java b/src/jalview/util/UrlLink.java
index 3f72ab4..c0cf821 100644 (file)
--- a/src/jalview/util/UrlLink.java
+++ b/src/jalview/util/UrlLink.java
@@ -22,16 +22,17 @@ package jalview.util;
 
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 public class UrlLink
 {
   /**
    * helper class to parse URL Link strings taken from applet parameters or
-   * jalview properties file using the com.stevesoft.pat.Regex implementation.
-   * Jalview 2.4 extension allows regular expressions to be used to parse ID
-   * strings and replace the result in the URL. Regex's operate on the whole ID
-   * string given to the matchURL method, if no regex is supplied, then only
-   * text following the first pipe symbol will be susbstituted. Usage
-   * documentation todo.
+   * jalview properties file using the Regex implementation. Jalview 2.4
+   * extension allows regular expressions to be used to parse ID strings and
+   * replace the result in the URL. Regex's operate on the whole ID string given
+   * to the matchURL method, if no regex is supplied, then only text following
+   * the first pipe symbol will be susbstituted. Usage documentation todo.
    */
   private String url_suffix, url_prefix, target, label, regexReplace;
 
@@ -85,7 +86,7 @@ public class UrlLink
         regexReplace = link.substring(psqid + 14, p);
         try
         {
-          com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
+          Regex rg = Regex.perlCode("/"
                   + regexReplace + "/");
           if (rg == null)
           {
@@ -200,8 +201,7 @@ public class UrlLink
     {
       if (regexReplace != null)
       {
-        com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
-                + regexReplace + "/");
+        Regex rg = Regex.perlCode("/" + regexReplace + "/");
         if (rg.search(idstring))
         {
           int ns = rg.numSubs();