JAL-1807 explicit imports (jalview.commands)

diff --git a/src/jalview/commands/CommandI.java b/src/jalview/commands/CommandI.java
index ea36d34..1679243 100644 (file)
--- a/src/jalview/commands/CommandI.java
+++ b/src/jalview/commands/CommandI.java
@@ -20,11 +20,13 @@
  */
 package jalview.commands;
 
+import jalview.datamodel.AlignmentI;
+
 public interface CommandI
 {
-  public void doCommand(jalview.datamodel.AlignmentI[] views);
+  public void doCommand(AlignmentI[] views);
 
-  public void undoCommand(jalview.datamodel.AlignmentI[] views);
+  public void undoCommand(AlignmentI[] views);
 
   public String getDescription();
 

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 2d3a8d8..e44068d 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -20,12 +20,15 @@
  */
 package jalview.commands;
 
+import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.ReverseListIterator;
 import jalview.util.StringUtils;
 
@@ -641,7 +644,7 @@ public class EditCommand implements CommandI
         tmp.insert(command.position, command.string[i]);
         for (int s = 0; s < command.string[i].length; s++)
         {
-          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
+          if (ResidueProperties.aaIndex[command.string[i][s]] != 23)
           {
             if (!newDSNeeded)
             {
@@ -680,8 +683,8 @@ public class EditCommand implements CommandI
             // make a new DS sequence
             // use new ds mechanism here
             ds = new Sequence(command.seqs[i].getName(),
-                    jalview.analysis.AlignSeq.extractGaps(
-                            jalview.util.Comparison.GapChars,
+                    AlignSeq.extractGaps(
+                            Comparison.GapChars,
                             command.seqs[i].getSequenceAsString()),
                     command.seqs[i].getStart(), command.seqs[i].getEnd());
             ds.setDescription(command.seqs[i].getDescription());
@@ -731,16 +734,16 @@ public class EditCommand implements CommandI
       oldstring = command.seqs[i].getSequenceAsString();
       tmp = new StringBuffer(oldstring.substring(0, start));
       tmp.append(command.string[i]);
-      String nogaprep = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, new String(
+      String nogaprep = AlignSeq.extractGaps(
+              Comparison.GapChars, new String(
                       command.string[i]));
       int ipos = command.seqs[i].findPosition(start)
               - command.seqs[i].getStart();
       tmp.append(oldstring.substring(end));
       command.seqs[i].setSequence(tmp.toString());
       command.string[i] = oldstring.substring(start, end).toCharArray();
-      String nogapold = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, new String(
+      String nogapold = AlignSeq.extractGaps(
+              Comparison.GapChars, new String(
                       command.string[i]));
       if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
       {

diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java
index 490dc4a..3e0023d 100644 (file)
--- a/src/jalview/commands/RemoveGapColCommand.java
+++ b/src/jalview/commands/RemoveGapColCommand.java
@@ -41,6 +41,7 @@ package jalview.commands;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 public class RemoveGapColCommand extends EditCommand
 {
@@ -67,7 +68,7 @@ public class RemoveGapColCommand extends EditCommand
       {
         if (seqs[j].getLength() > i)
         {
-          if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i)))
+          if (!Comparison.isGap(seqs[j].getCharAt(i)))
           {
             if (delete)
             {

diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java
index db1725b..3a485c8 100644 (file)
--- a/src/jalview/commands/RemoveGapsCommand.java
+++ b/src/jalview/commands/RemoveGapsCommand.java
@@ -41,6 +41,7 @@ package jalview.commands;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 public class RemoveGapsCommand extends EditCommand
 {
@@ -92,7 +93,7 @@ public class RemoveGapsCommand extends EditCommand
       {
         delete = true;
 
-        if (!jalview.util.Comparison.isGap(sequence[j]))
+        if (!Comparison.isGap(sequence[j]))
         {
           if (delete)
           {

diff --git a/src/jalview/commands/SlideSequencesCommand.java b/src/jalview/commands/SlideSequencesCommand.java
index 8a27059..c5dd14e 100644 (file)
--- a/src/jalview/commands/SlideSequencesCommand.java
+++ b/src/jalview/commands/SlideSequencesCommand.java
@@ -21,6 +21,7 @@
 package jalview.commands;
 
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 public class SlideSequencesCommand extends EditCommand
 {
@@ -38,7 +39,7 @@ public class SlideSequencesCommand extends EditCommand
     {
       for (j = 0; j < slideSize; j++)
       {
-        if (!jalview.util.Comparison.isGap(seqsLeft[i].getCharAt(j)))
+        if (!Comparison.isGap(seqsLeft[i].getCharAt(j)))
         {
           gapsInsertedBegin = true;
           break;