Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index d30482f..e04bbb7 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -26,6 +26,7 @@ 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.Format;
@@ -77,7 +78,7 @@ public class SiftsClient implements SiftsClientI
 {
   private Entry siftsEntry;
 
-  private PDBfile pdb;
+  private StructureFile pdb;
 
   private String pdbId;
 
@@ -147,7 +148,7 @@ public class SiftsClient implements SiftsClientI
    * @param pdbId
    * @throws SiftsException
    */
-  public SiftsClient(PDBfile pdb) throws SiftsException
+  public SiftsClient(StructureFile pdb) throws SiftsException
   {
     this.pdb = pdb;
     this.pdbId = pdb.getId();
@@ -456,7 +457,7 @@ public class SiftsClient implements SiftsClientI
   {
     ArrayList<Integer> omitNonObserved = new ArrayList<Integer>();
     int nonObservedShiftIndex = 0;
-    System.out.println("Generating mappings for : " + entityId);
+    // System.out.println("Generating mappings for : " + entityId);
     Entity entity = null;
     entity = getEntityById(entityId);
     String originalSeq = AlignSeq.extractGaps(
@@ -491,8 +492,8 @@ public class SiftsClient implements SiftsClientI
     for (Segment segment : segments)
     {
       segStartEnd = segment.getStart() + " - " + segment.getEnd();
-      System.out.println("Mappging segments : " + segment.getSegId() + "\\"
-              + segStartEnd);
+      // System.out.println("Mapping segments : " + segment.getSegId() + "\\"
+      // + segStartEnd);
       List<Residue> residues = segment.getListResidue().getResidue();
       for (Residue residue : residues)
       {
@@ -771,8 +772,8 @@ public class SiftsClient implements SiftsClientI
     Arrays.sort(keys);
     int firstIndex = keys[0];
     int lastIndex = keys[keys.length - 1];
-    System.out.println("Min value " + firstIndex);
-    System.out.println("Max value " + lastIndex);
+    // System.out.println("Min value " + firstIndex);
+    // System.out.println("Max value " + lastIndex);
     for (int x = firstIndex; x <= lastIndex; x++)
     {
       if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x))
@@ -861,8 +862,8 @@ public class SiftsClient implements SiftsClientI
       ++count;
     }
     Arrays.sort(sPojo, Collections.reverseOrder());
-    System.out.println("highest matched entity : " + sPojo[0].entityId);
-    System.out.println("highest matched pid : " + sPojo[0].pid);
+    // System.out.println("highest matched entity : " + sPojo[0].entityId);
+    // System.out.println("highest matched pid : " + sPojo[0].pid);
 
     if (sPojo[0].entityId != null)
     {