JAL-1807 explicit imports (jalview.bin)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 10aba00..4ed6e1a 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,6 +20,12 @@
  */
 package jalview.bin;
 
+import jalview.gui.UserDefinedColours;
+import jalview.io.PIRFile;
+import jalview.jbgui.GDesktop;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
 
@@ -253,7 +259,7 @@ public class Cache
       // log output
       Logger laxis = Logger.getLogger("org.apache.axis");
       Logger lcastor = Logger.getLogger("org.exolab.castor");
-      jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
+      Cache.log = Logger.getLogger("jalview.bin.Jalview");
 
       laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
               Level.INFO.toString())));
@@ -265,13 +271,13 @@ public class Cache
       // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
       // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
       // Level.INFO.toString())));
-      jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
+      Cache.log.setLevel(Level.toLevel(Cache.getDefault(
               "logs.Jalview.level", Level.INFO.toString())));
       // laxis.addAppender(ap);
       // lcastor.addAppender(ap);
-      // jalview.bin.Cache.log.addAppender(ap);
+      // Cache.log.addAppender(ap);
       // Tell the user that debug is enabled
-      jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
+      Cache.log.debug("Jalview Debugging Output Follows.");
     } catch (Exception ex)
     {
       System.err.println("Problems initializing the log4j system\n");
@@ -470,9 +476,9 @@ public class Cache
     setProperty("VERSION", codeVersion);
 
     // LOAD USERDEFINED COLOURS
-    jalview.gui.UserDefinedColours
+    UserDefinedColours
             .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
-    jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
+    PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
             false);
   }
 
@@ -608,10 +614,10 @@ public class Cache
     {
       try
       {
-        if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
+        if (GDesktop.class.getClassLoader().loadClass(
                 "uk.ac.vamsas.client.VorbaId") != null)
         {
-          jalview.bin.Cache.log
+          Cache.log
                   .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
           vamsasJarsArePresent = 1;
           Logger lvclient = Logger.getLogger("uk.ac.vamsas");
@@ -625,7 +631,7 @@ public class Cache
       } catch (Exception e)
       {
         vamsasJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+        Cache.log.debug("Vamsas Classes are not present");
       }
     }
     return (vamsasJarsArePresent > 0);
@@ -650,7 +656,7 @@ public class Cache
         if (Cache.class.getClassLoader().loadClass(
                 "groovy.lang.GroovyObject") != null)
         {
-          jalview.bin.Cache.log
+          Cache.log
                   .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
           groovyJarsArePresent = 1;
           Logger lgclient = Logger.getLogger("groovy");
@@ -664,11 +670,11 @@ public class Cache
       } catch (Error e)
       {
         groovyJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+        Cache.log.debug("Groovy Classes are not present", e);
       } catch (Exception e)
       {
         groovyJarsArePresent = 0;
-        jalview.bin.Cache.log.debug("Groovy Classes are not present");
+        Cache.log.debug("Groovy Classes are not present");
       }
     }
     return (groovyJarsArePresent > 0);
@@ -723,9 +729,9 @@ public class Cache
                 new Object[]
                 {
                     "Jalview Desktop",
-                    (vrs = jalview.bin.Cache.getProperty("VERSION")
+                    (vrs = Cache.getProperty("VERSION")
                             + "_"
-                            + jalview.bin.Cache.getDefault("BUILD_DATE",
+                            + Cache.getDefault("BUILD_DATE",
                                     "unknown")), "UA-9060947-1" });
         jgoogleanalyticstracker.getMethod("trackAsynchronously",
                 new Class[]
@@ -811,13 +817,12 @@ public class Cache
     {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty
-            .getAWTColorFromName(colprop);
+    Color col = ColourSchemeProperty.getAWTColorFromName(colprop);
     if (col == null)
     {
       try
       {
-        col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+        col = new UserColourScheme(colprop).findColour('A');
       } catch (Exception ex)
       {
         log.warn("Couldn't parse '" + colprop + "' as a colour for "
@@ -836,7 +841,7 @@ public class Cache
    */
   public static void setColourProperty(String property, Color colour)
   {
-    setProperty(property, jalview.util.Format.getHexString(colour));
+    setProperty(property, Format.getHexString(colour));
   }
 
   public static final DateFormat date_format = SimpleDateFormat

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f6d0099..8669a96 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -22,8 +22,17 @@ package jalview.bin;
 
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -231,7 +240,7 @@ public class Jalview
     }
 
     String file = null, protocol = null, format = null, data = null;
-    jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless);
+    FileLoader fileLoader = new FileLoader(!headless);
     Vector getFeatures = null; // vector of das source nicknames to fetch
     // features from
     // loading is done.
@@ -262,13 +271,13 @@ public class Jalview
       {
         try
         {
-          String viprotocol = jalview.io.AppletFormatAdapter
+          String viprotocol = AppletFormatAdapter
                   .checkProtocol(vamsasImport);
-          if (viprotocol == jalview.io.FormatAdapter.FILE)
+          if (viprotocol == FormatAdapter.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
           }
-          else if (viprotocol == jalview.io.FormatAdapter.URL)
+          else if (viprotocol == FormatAdapter.URL)
           {
             inSession = desktop.vamsasImport(new URL(vamsasImport));
           }
@@ -354,9 +363,9 @@ public class Jalview
         }
       }
 
-      protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
+      protocol = AppletFormatAdapter.checkProtocol(file);
 
-      format = new jalview.io.IdentifyFile().Identify(file, protocol);
+      format = new IdentifyFile().Identify(file, protocol);
 
       AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
@@ -372,12 +381,12 @@ public class Jalview
         {
           data.replaceAll("%20", " ");
 
-          jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
+          ColourSchemeI cs = ColourSchemeProperty
                   .getColour(af.getViewport().getAlignment(), data);
 
           if (cs == null)
           {
-            jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+            UserColourScheme ucs = new UserColourScheme(
                     "white");
             ucs.parseAppletParameter(data);
             cs = ucs;
@@ -392,14 +401,14 @@ public class Jalview
         if (data != null)
         {
           af.parseFeaturesFile(data,
-                  jalview.io.AppletFormatAdapter.checkProtocol(data));
+                  AppletFormatAdapter.checkProtocol(data));
           System.out.println("Added " + data);
         }
         data = aparser.getValue("features", true);
         if (data != null)
         {
           af.parseFeaturesFile(data,
-                  jalview.io.AppletFormatAdapter.checkProtocol(data));
+                  AppletFormatAdapter.checkProtocol(data));
           System.out.println("Added " + data);
         }
 
@@ -425,11 +434,11 @@ public class Jalview
         data = aparser.getValue("tree", true);
         if (data != null)
         {
-          jalview.io.NewickFile fin = null;
+          NewickFile fin = null;
           try
           {
-            fin = new jalview.io.NewickFile(data,
-                    jalview.io.AppletFormatAdapter.checkProtocol(data));
+            fin = new NewickFile(data,
+                    AppletFormatAdapter.checkProtocol(data));
             if (fin != null)
             {
               af.getViewport().setCurrentTree(
@@ -470,7 +479,7 @@ public class Jalview
         {
           // Execute the groovy script after we've done all the rendering stuff
           // and before any images or figures are generated.
-          if (jalview.bin.Cache.groovyJarsPresent())
+          if (Cache.groovyJarsPresent())
           {
             System.out.println("Executing script " + groovyscript);
             executeGroovyScript(groovyscript, new Object[]
@@ -553,11 +562,11 @@ public class Jalview
     // ////////////////////
 
     if (!headless && file == null && vamsasImport == null
-            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+            && Cache.getDefault("SHOW_STARTUP_FILE", true))
     {
-      file = jalview.bin.Cache.getDefault(
+      file = Cache.getDefault(
               "STARTUP_FILE",
-              jalview.bin.Cache.getDefault("www.jalview.org",
+              Cache.getDefault("www.jalview.org",
                       "http://www.jalview.org")
                       + "/examples/exampleFile_2_7.jar");
       if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
@@ -565,7 +574,7 @@ public class Jalview
         // hardwire upgrade of the startup file
         file.replace("_2_3.jar", "_2_7.jar");
         // and remove the stale setting
-        jalview.bin.Cache.removeProperty("STARTUP_FILE");
+        Cache.removeProperty("STARTUP_FILE");
       }
 
       protocol = "File";
@@ -581,7 +590,7 @@ public class Jalview
       }
       else
       {
-        format = new jalview.io.IdentifyFile().Identify(file, protocol);
+        format = new IdentifyFile().Identify(file, protocol);
       }
 
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
@@ -603,7 +612,7 @@ public class Jalview
     // Once all other stuff is done, execute any groovy scripts (in order)
     if (groovyscript != null)
     {
-      if (jalview.bin.Cache.groovyJarsPresent())
+      if (Cache.groovyJarsPresent())
       {
         System.out.println("Executing script " + groovyscript);
         executeGroovyScript(groovyscript, new Object[]
@@ -673,7 +682,7 @@ public class Jalview
     /**
      * start a User Config prompt asking if we can log usage statistics.
      */
-    jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
+    PromptUserConfig prompter = new PromptUserConfig(
             desktop.desktop,
             "USAGESTATS",
             "Jalview Usage Statistics",

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index ae5c63f..5d1f0b0 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -20,6 +20,7 @@
  */
 package jalview.bin;
 
+import jalview.analysis.SequenceIdMatcher;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.appletgui.AlignFrame;
 import jalview.appletgui.AlignViewport;
@@ -44,6 +45,11 @@ import jalview.io.NewickFile;
 import jalview.javascript.JSFunctionExec;
 import jalview.javascript.JalviewLiteJsApi;
 import jalview.javascript.JsCallBack;
+import jalview.javascript.JsSelectionSender;
+import jalview.javascript.MouseOverListener;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -178,7 +184,7 @@ public class JalviewLite extends Applet implements
           final String position, final String alignedPosition)
   {
     // TODO: could try to highlight in all alignments if alf==null
-    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+    SequenceIdMatcher matcher = new SequenceIdMatcher(
             alf.viewport.getAlignment().getSequencesArray());
     final SequenceI sq = matcher.findIdMatch(sequenceId);
     if (sq != null)
@@ -284,7 +290,7 @@ public class JalviewLite extends Applet implements
     final SequenceGroup sel = new SequenceGroup();
     final ColumnSelection csel = new ColumnSelection();
     AlignmentI al = alf.viewport.getAlignment();
-    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+    SequenceIdMatcher matcher = new SequenceIdMatcher(
             alf.viewport.getAlignment().getSequencesArray());
     int start = 0, end = al.getWidth(), alw = al.getWidth();
     boolean seqsfound = true;
@@ -598,7 +604,7 @@ public class JalviewLite extends Applet implements
     SequenceI[] sqs = null;
     if (ids != null && ids.length > 0)
     {
-      jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+      SequenceIdMatcher matcher = new SequenceIdMatcher(
               alf.viewport.getAlignment().getSequencesArray());
       int s = 0;
       sqs = new SequenceI[ids.length];
@@ -876,7 +882,7 @@ public class JalviewLite extends Applet implements
     setMouseoverListener(currentAlignFrame, listener);
   }
 
-  private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+  private Vector<JSFunctionExec> javascriptListeners = new Vector<JSFunctionExec>();
 
   /*
    * (non-Javadoc)
@@ -897,7 +903,7 @@ public class JalviewLite extends Applet implements
         return;
       }
     }
-    jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
+    MouseOverListener mol = new MouseOverListener(
             this, af, listener);
     javascriptListeners.addElement(mol);
     StructureSelectionManager.getStructureSelectionManager(this)
@@ -941,8 +947,7 @@ public class JalviewLite extends Applet implements
         return;
       }
     }
-    jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
-            this, af, listener);
+    JsSelectionSender mol = new JsSelectionSender(this, af, listener);
     javascriptListeners.addElement(mol);
     StructureSelectionManager.getStructureSelectionManager(this)
             .addSelectionListener(mol);
@@ -974,7 +979,7 @@ public class JalviewLite extends Applet implements
         return;
       }
     }
-    jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
+    MouseOverStructureListener mol = new MouseOverStructureListener(
             this, listener, separatorListToArray(modelSet));
     javascriptListeners.addElement(mol);
     StructureSelectionManager.getStructureSelectionManager(this)
@@ -1071,8 +1076,7 @@ public class JalviewLite extends Applet implements
     {
       while (javascriptListeners.size() > 0)
       {
-        jalview.javascript.JSFunctionExec mol = javascriptListeners
-                .elementAt(0);
+        JSFunctionExec mol = javascriptListeners.elementAt(0);
         javascriptListeners.removeElement(mol);
         if (mol instanceof SelectionListener)
         {
@@ -1098,7 +1102,7 @@ public class JalviewLite extends Applet implements
     StructureSelectionManager.release(this);
   }
 
-  private jalview.javascript.JSFunctionExec jsFunctionExec;
+  private JSFunctionExec jsFunctionExec;
 
   /*
    * (non-Javadoc)
@@ -1996,8 +2000,8 @@ public class JalviewLite extends Applet implements
       // alignPdbStructures is true)
       Vector pdbs = new Vector();
       // create a lazy matcher if we're asked to
-      jalview.analysis.SequenceIdMatcher matcher = (applet
-              .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+      SequenceIdMatcher matcher = (applet.getDefaultParameter(
+              "relaxedidmatch", false)) ? new SequenceIdMatcher(
               alignFrame.getAlignViewport().getAlignment()
                       .getSequencesArray()) : null;
 
@@ -2853,13 +2857,12 @@ public class JalviewLite extends Applet implements
     {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty
-            .getAWTColorFromName(colprop);
+    Color col = ColourSchemeProperty.getAWTColorFromName(colprop);
     if (col == null)
     {
       try
       {
-        col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+        col = new UserColourScheme(colprop).findColour('A');
       } catch (Exception ex)
       {
         System.err.println("Couldn't parse '" + colprop

diff --git a/src/jalview/bin/JalviewLiteURLRetrieve.java b/src/jalview/bin/JalviewLiteURLRetrieve.java
index 6be1016..f84cd07 100644 (file)
--- a/src/jalview/bin/JalviewLiteURLRetrieve.java
+++ b/src/jalview/bin/JalviewLiteURLRetrieve.java
@@ -23,6 +23,7 @@ package jalview.bin;
 import jalview.datamodel.AlignmentI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
+import jalview.io.IdentifyFile;
 
 import java.applet.Applet;
 import java.io.InputStream;
@@ -113,7 +114,7 @@ public class JalviewLiteURLRetrieve extends Applet
       String format = getParameter("format");
       if (format == null || format.length() == 0)
       {
-        format = new jalview.io.IdentifyFile().Identify(file, protocol);
+        format = new IdentifyFile().Identify(file, protocol);
         System.out.println("Format is " + format);
       }
       else