JAL-1807 explicit imports (jalview.datamodel)

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c78ec22..e1f9d00 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -21,6 +21,8 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
@@ -28,6 +30,8 @@ import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
@@ -119,10 +123,9 @@ public class Sequence extends ASequence implements SequenceI
     checkValidRange();
   }
 
-  com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
-          "[/][0-9]{1,}[-][0-9]{1,}$");
+  Regex limitrx = new Regex("[/][0-9]{1,}[-][0-9]{1,}$");
 
-  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
+  Regex endrx = new Regex("[0-9]{1,}$");
 
   void parseId()
   {
@@ -151,7 +154,7 @@ public class Sequence extends ASequence implements SequenceI
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
       {
-        if (!jalview.util.Comparison.isGap(sequence[j]))
+        if (!Comparison.isGap(sequence[j]))
         {
           endRes++;
         }
@@ -643,7 +646,7 @@ public class Sequence extends ASequence implements SequenceI
     // Rely on end being at least as long as the length of the sequence.
     while ((i < sequence.length) && (j <= end) && (j <= pos))
     {
-      if (!jalview.util.Comparison.isGap(sequence[i]))
+      if (!Comparison.isGap(sequence[i]))
       {
         j++;
       }
@@ -669,7 +672,7 @@ public class Sequence extends ASequence implements SequenceI
     int seqlen = sequence.length;
     while ((j < i) && (j < seqlen))
     {
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
         pos++;
       }
@@ -689,15 +692,15 @@ public class Sequence extends ASequence implements SequenceI
    */
   public int[] gapMap()
   {
-    String seq = jalview.analysis.AlignSeq.extractGaps(
-            jalview.util.Comparison.GapChars, new String(sequence));
+    String seq = AlignSeq.extractGaps(
+            Comparison.GapChars, new String(sequence));
     int[] map = new int[seq.length()];
     int j = 0;
     int p = 0;
 
     while (j < sequence.length)
     {
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
         map[p++] = j;
       }
@@ -718,7 +721,7 @@ public class Sequence extends ASequence implements SequenceI
     while ((j < seqlen))
     {
       map[j] = pos;
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
         pos++;
       }
@@ -737,7 +740,7 @@ public class Sequence extends ASequence implements SequenceI
     int seqlen = sequence.length;
     while ((j < seqlen))
     {
-      if (jalview.util.Comparison.isGap(sequence[j]))
+      if (Comparison.isGap(sequence[j]))
       {
         if (lastj == -1)
         {
@@ -781,7 +784,7 @@ public class Sequence extends ASequence implements SequenceI
     boolean ecalc = false, scalc = false;
     for (int s = i; s < j; s++)
     {
-      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      if (ResidueProperties.aaIndex[sequence[s]] != 23)
       {
         if (createNewDs)
         {
@@ -1001,7 +1004,7 @@ public class Sequence extends ASequence implements SequenceI
     }
     for (int i = 0; i < sequence.length; i++)
     {
-      if (jalview.util.Comparison.isGap(sequence[i]))
+      if (Comparison.isGap(sequence[i]))
       {
         return false;
       }
@@ -1030,7 +1033,7 @@ public class Sequence extends ASequence implements SequenceI
         // Create a new, valid dataset sequence
         SequenceI ds = seq;
         ds.setSequence(AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars, new String(sequence)));
+                Comparison.GapChars, new String(sequence)));
         setDatasetSequence(ds);
         ds.setSequenceFeatures(getSequenceFeatures());
         seq = this; // and return this sequence as the derived sequence.
@@ -1049,7 +1052,7 @@ public class Sequence extends ASequence implements SequenceI
     if (datasetSequence == null)
     {
       datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, getSequenceAsString()),
+              Comparison.GapChars, getSequenceAsString()),
               getStart(), getEnd());
       datasetSequence.setSequenceFeatures(getSequenceFeatures());
       datasetSequence.setDescription(getDescription());