JAL-3628 Changed other calls to renameTo to use BackupFiles.moveFileToFile

diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 93a289e..aaf5e10 100644 (file)
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -767,7 +767,7 @@ public class BackupFiles
     return ret;
   }
 
-  private boolean moveFileToFile(File oldFile, File newFile)
+  public static boolean moveFileToFile(File oldFile, File newFile)
   {
     boolean ret = false;
     Path oldPath = Paths.get(oldFile.getAbsolutePath());

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index b5f9653..9790f79 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -20,28 +20,6 @@
  */
 package jalview.ws.sifts;
 
-import jalview.analysis.AlignSeq;
-import jalview.analysis.scoremodels.ScoreMatrix;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.api.DBRefEntryI;
-import jalview.api.SiftsClientI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.Format;
-import jalview.xml.binding.sifts.Entry;
-import jalview.xml.binding.sifts.Entry.Entity;
-import jalview.xml.binding.sifts.Entry.Entity.Segment;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
-import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
-
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -73,6 +51,28 @@ import javax.xml.stream.XMLStreamReader;
 
 import MCview.Atom;
 import MCview.PDBChain;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.DBRefEntryI;
+import jalview.api.SiftsClientI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceI;
+import jalview.io.BackupFiles;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureMapping;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.Format;
+import jalview.xml.binding.sifts.Entry;
+import jalview.xml.binding.sifts.Entry.Entity;
+import jalview.xml.binding.sifts.Entry.Entity.Segment;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
 
 public class SiftsClient implements SiftsClientI
 {
@@ -123,6 +123,7 @@ public class SiftsClient implements SiftsClientI
   private enum CoordinateSys
   {
     UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
+
     private String name;
 
     private CoordinateSys(String name)
@@ -140,6 +141,7 @@ public class SiftsClient implements SiftsClientI
   {
     NAME_SEC_STRUCTURE("nameSecondaryStructure"),
     CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
+
     private String code;
 
     private ResidueDetailType(String code)
@@ -225,7 +227,7 @@ public class SiftsClient implements SiftsClientI
               SiftsSettings.getCacheThresholdInDays()))
       {
         File oldSiftsFile = new File(siftsFileName + "_old");
-        siftsFile.renameTo(oldSiftsFile);
+        BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
         try
         {
           siftsFile = downloadSiftsFile(pdbId.toLowerCase());
@@ -234,7 +236,7 @@ public class SiftsClient implements SiftsClientI
         } catch (IOException e)
         {
           e.printStackTrace();
-          oldSiftsFile.renameTo(siftsFile);
+          BackupFiles.moveFileToFile(oldSiftsFile, siftsFile);
           return new File(siftsFileName);
         }
       }
@@ -461,7 +463,7 @@ public class SiftsClient implements SiftsClientI
           SequenceI seq, java.io.PrintStream os) throws SiftsException
   {
     List<Integer> omitNonObserved = new ArrayList<>();
-    int nonObservedShiftIndex = 0,pdbeNonObserved=0;
+    int nonObservedShiftIndex = 0, pdbeNonObserved = 0;
     // System.out.println("Generating mappings for : " + entityId);
     Entity entity = null;
     entity = getEntityById(entityId);
@@ -492,7 +494,7 @@ public class SiftsClient implements SiftsClientI
     TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
     List<Segment> segments = entity.getSegment();
     SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
-            omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
+            omitNonObserved, nonObservedShiftIndex, pdbeNonObserved);
     processSegments(segments, shp);
     try
     {
@@ -514,18 +516,20 @@ public class SiftsClient implements SiftsClientI
     {
       throw new SiftsException("SIFTS mapping failed");
     }
-    // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
+    // also construct a mapping object between the seq-coord sys and the PDB
+    // seq's coord sys
 
     Integer[] keys = mapping.keySet().toArray(new Integer[0]);
     Arrays.sort(keys);
     seqStart = keys[0];
     seqEnd = keys[keys.length - 1];
-    List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
-    int[]_cfrom=null,_cto=null;
+    List<int[]> from = new ArrayList<>(), to = new ArrayList<>();
+    int[] _cfrom = null, _cto = null;
     String matchedSeq = originalSeq;
-    if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
+    if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb
+                                // sequence that starts <-1
     {
-      for (int seqps:keys)
+      for (int seqps : keys)
       {
         int pdbpos = mapping.get(seqps)[PDBE_POS];
         if (pdbpos == UNASSIGNED)
@@ -533,19 +537,23 @@ public class SiftsClient implements SiftsClientI
           // not correct - pdbpos might be -1, but leave it for now
           continue;
         }
-        if (_cfrom==null || seqps!=_cfrom[1]+1)
+        if (_cfrom == null || seqps != _cfrom[1] + 1)
         {
-          _cfrom = new int[] { seqps,seqps};
+          _cfrom = new int[] { seqps, seqps };
           from.add(_cfrom);
           _cto = null; // discontinuity
-        } else {
-          _cfrom[1]= seqps;
         }
-        if (_cto==null || pdbpos!=1+_cto[1])
+        else
+        {
+          _cfrom[1] = seqps;
+        }
+        if (_cto == null || pdbpos != 1 + _cto[1])
         {
-          _cto = new int[] { pdbpos,pdbpos};
+          _cto = new int[] { pdbpos, pdbpos };
           to.add(_cto);
-        } else {
+        }
+        else
+        {
           _cto[1] = pdbpos;
         }
       }
@@ -567,8 +575,7 @@ public class SiftsClient implements SiftsClientI
       ;
 
       seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
-              1,
-              1);
+              1, 1);
       pdbStart = mapping.get(seqStart)[PDB_RES_POS];
       pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
       int orignalSeqStart = seq.getStart();
@@ -699,12 +706,12 @@ public class SiftsClient implements SiftsClientI
         }
         // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
         // true
-                                                                         // numbering
-                                                                         // is
-                                                                         // not
-                                                                         // up
-                                                                         // to
-                                                                         // seq.getEnd()
+        // numbering
+        // is
+        // not
+        // up
+        // to
+        // seq.getEnd()
         {
 
           int resNum = (pdbRefDb == null)
@@ -1044,6 +1051,7 @@ public class SiftsClient implements SiftsClientI
     {
       return pdbeNonObserved;
     }
+
     public SequenceI getSeq()
     {
       return seq;