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

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 8a563fa..dc93cf9 100755 (executable)
--- 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)
     {